# Patent

## Title
Compositions comprising Yersinia pestis antigens

## Abstract

Disclosed are several Y. pestis antigens that are particularly suitable for immunisation purposes, particularly when used in combinations.

## Background
GOVERNMENT SUPPORT
The invention was supported, in whole or in part, by Grant No. 1U01 A156513-01 from the US National Institute of Allergy and Infectious Diseases. The US Government may have certain rights in the invention.


All documents cited herein are incorporated by reference in their entirety.
TECHNICAL FIELD
This invention is in the fields of immunology and vaccinology. In particular, it relates to antigens derived from Yersinia pestis and their use in immunisation.
BACKGROUND ART
There are three recognised forms of plague in man: bubonic, septicaemic and pneumonic. All are caused by the Yersinia pestis bacterium, which has also been known as Pasteurella pestis, Bacterium pestis and Pestisella pestis. Y. pestis is endemic on every continent in the world except Australia [1], and results in around 1700 cases of plague a year. It is a Gram-negative non-motile aerobic bacillus. 
Bubonic plague is the most common form of disease and arises following a bite from a flea which has fed previously on an infected animal. From the initial site of infection the bacteria are disseminated to the draining lymph nodes, which become swollen and tender to form buboes.
Septicaemic plague occurs when there is bacteremia without the development of buboes and is characterised by an elevated temperature, chills, headache, malaise and gastrointestinal disturbances. Because of the generalised nature of these symptoms a diagnosis of plague is often delayed, and even with medical intervention 50% of patients die, probably as a result of the induction of the systemic inflammatory response syndrome.
The most feared form of plague arises when there is colonisation of the alveolar spaces leading to a pneumonia, causing the pneumonic plague. Pneumonic plague is transmitted by airborne droplets containing bacteria, generated by coughing, which can be inhaled by susceptible individuals. The pneumonic form of the disease is feared because of the rapidity with which the disease develops (1-3 days), the high mortality rate in infected individuals (about 100%) and the rapid spread of disease from man to man.
Due to the high infectivity and mortality of pneumonic plague, Y. pestis is considered to be a likely biological threat agent [2].
The only plague vaccine licensed in the United States is the ‘USP vaccine’, a preparation of formaldehyde-killed Y. pestis, but it is no longer produced. This vaccine relies on the F1 capsular protein as the main immunogen. While it has been shown to be effective against subcutaneous challenge, it is not effective against aerosol challenge [3], and unpleasant side effects have been reported. The vaccine also fails to protect against the F1− variants of Y. pestis, which are equally virulent in rodents [4, 5] and which have been isolated from at least one fatal human case [6].
More recent studies have focused on recombinant subunit vaccines. Purified or recombinant F1 antigen may confer protection against both bubonic and pneumonic plague [7], as may the V antigen [8]. The V antigen is found on the cell surface and is involved in induction of IL-10 synthesis, which contributes to the block of macrophage activation necessary for successful Y. pestis virulence [1]. Recombinant V antigen has been shown to confer protection against parenteral and aerosol challenge by both F1+ and F1− strains [8]. A fully-recombinant subunit vaccine containing both the F1 and V antigens has been formulated either with cholera toxin for transcutaneous and intradermal immunisation [9]. Three immunisations with this vaccine protected animals from a low dose injected challenge with virulent Y. pestis. The same F1/V combination has been adjuvanted with aluminium hydroxide, and confers good protection against aerosol challenge in mouse strains of different genetic background [10]. Importantly, protection was achieved after a single dose of this vaccine although the dose required was high and protective antibody titers against the V antigen required more than two months to develop [11]. For safe use in humans, reference 12 suggests that the V antigen should be altered to delete amino acid residues 271 to 300 in order to reduce immune-modulatory properties.
These studies indicate that development of an efficacious subunit vaccine based on recombinant Y. pestis proteins for use in man is feasible.
While the F1 and V antigens are promising candidates for inclusion in a prophylactic vaccine, these are the only known protective antigens against this pathogen and it is unclear if these antigens alone will afford sufficient protection in humans, or whether they would be useful in immunotherapeutic vaccines. Indeed, variability in the response to F1 in humans has been reported [13]. Reference 14 suggests that an optimal vaccine against plague should include essential virulence factors as immunogens in addition to F1. Furthermore, naturally occurring F1− strains appear to be equally virulent and with current technology it is straightforward to engineer such a strain [5], thereby bypassing any F1-based immunity. In addition, substitution of the LcrV gene in Y. pestis with that of Y. pseudotuberculosis or Y. enterocoliticus is a worry, as there is little cross protection between these different species [15]. A bivalent F1/V vaccine is therefore inadequate for use against bioterrorism.
Thus there remains a need to identify alternatives to the F1 and V antigens for use in immunising against Yersinia, and in particular for developing of a broadly-protective multivalent vaccine against all potential variant and engineered strains [2].
DISCLOSURE OF THE INVENTION
The inventors believe that an effective Y. pestis vaccine will require several antigenic components, and that these components may or may not include the F1 or V antigens.
With this in mind, they have identified various surface-exposed Y. pestis antigens that are particularly suitable for immunisation purposes, particularly when used in combinations. Although the existence of these proteins has been postulated, based on the publication of genome sequences in references 16 (virulent strain CO92), 17 (virulent strain KIM) and 18 (avirulent strain 91001), their immunogenic use has not been disclosed. The antigens are exposed on the bacterial surface and have been identified using “surface shaving” techniques or by detecting proteins that were labelled in situ on the cell surface Y. pestis proteins (e.g., by biotinylation).
Thus the invention provides a composition comprising a combination of Y. pestis antigens, said combination comprising two or more (i.e. 2, or all 3) Y. pestis antigens selected from the group consisting of: (1) a YPO0512 antigen; (2) a YPO0563 antigen; and (3) a YPO3489 antigen. These three antigens form the “first antigen group”.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination comprising two or more (i.e. 2, 3, 4 or all 5) Y. pestis antigens selected from the group consisting of: (1) a YPO0512 antigen; (2) a YPO0563 antigen; (3) a YPO3489 antigen; (4) a YPO4003 antigen; and (5) a YPO1604 antigen. These five antigens form the “second antigen group”, which includes the three antigens of the first antigen group.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination comprising one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or all 21) Y. pestis antigens from the group consisting of: (1) a YPO0512 antigen; (2) a YPO0563 antigen; (3) a YPO3489 antigen; (4) a YPO4003 antigen; (5) a YPO1604 antigen; (6) a YPO3061 antigen; (7) a YPO3559 antigen; (8) a YPO3382 antigen; (9) a YPO0860 antigen; (10) a YPO0086 antigen; (11) a YPO3631 antigen; (12) a YPO2881 antigen; (13) a YPO3343 antigen; (14) a YPO3361 antigen; (15) a YPO3430 antigen; (16) a YPO1411 antigen; (17) a YPO3935 antigen; (18) a YPO0809 antigen; (19) a YPO1123 antigen; (20) a YPO3065 antigen; and (21) a YPO1070 antigen. These 21 antigens form the “third antigen group”, which includes the five antigens from the second antigen group.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination comprising one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or all 36) Y. pestis antigens from the group consisting of: (1) a YPO0102 antigen; (2) a YPO0570 antigen; (3) a YPO1053 antigen; (4) a YPO1435 antigen; (5) a YPO2674 antigen; (6) a YPO2292 antigen; (7) a YPO3050 antigen; (8) a YPO2615 antigen; (9) a YPO1507 antigen; (10) a YPO4111 antigen; (11) a YPO0015 antigen; (12) a YPO0195 antigen; (13) a YPO2342 antigen; (14) a YPO0501 antigen; (15) a YPO0502 antigen; (16) a YPO0819 antigen; (17) a YPO3644 antigen; (18) a YPO1746 antigen; (19) a YPO0351 antigen; (20) a YPO0468 antigen; (21) a YPO0203 antigen; (22) a YPO0216 antigen; (23) a YPO3536 antigen; (24) a YPO0233 antigen; (25) a YPO0067 antigen; (26) a YPO3643 antigen; (27) a YPO3375 antigen; (28) a YPO0494 antigen; (29) a YPO1052 antigen; (30) a YPO1906 antigen; (31) a YPO0663 antigen; (32) a YPO1222 antigen; (33) a YPO2905 antigen; (34) a YPO4070 antigen; (35) a YPPCP1.07 antigen; and (36) a YPMT1.42 antigen. These 36 antigens form the “fourth antigen group”, which does not overlap with the first, second or third antigen groups.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination including one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or all 21) Y. pestis antigens selected from the third antigen group (preferably comprising an antigen from the second group, and more preferably from the first antigen group) and one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or all 36) Y. pestis antigens of the fourth antigen group.
The immunogenicity of other Y. pestis antigens of known and unknown biological function may be improved by combination with one or more Y. pestis antigens from either the first antigen group and/or the second and/or the third antigen group and/or the fourth antigen group. Such other Y. pestis antigens of known and unknown biological function include a F1 antigen and/or a V antigen. These two antigens form the “fifth antigen group”.
Thus the invention provides a composition comprising a combination of Y. pestis antigens, said combination including one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or all 21) Y. pestis antigens selected from the third antigen group (preferably comprising an antigen from the second group, and more preferably from the first antigen group) and one or two Y. pestis antigens from the fifth antigen group.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination including one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or all 36) Y. pestis antigens selected from the fourth antigen group and one or two Y. pestis antigens from the fifth antigen group.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination including one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or all 21) Y. pestis antigens selected from the third antigen group (preferably comprising an antigen from the second group, and more preferably from the first antigen group), one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or all 36) Y. pestis antigens selected from the fourth antigen group, and one or two Y. pestis antigens from the fifth antigen group.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination comprising one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Y. pestis antigens from the group consisting of: (1) a YPO0457 antigen; (2) a YPO0514 antigen; (3) a YPO0694 antigen; (4) a YPO0805 antigen; (5) a YPO0982 antigen; (6) a YPO1354 antigen; (7) a YPO1408 antigen; (8) a YPO1792 antigen; (9) a YPO2506 antigen; (10) a YPO2713 antigen; (11) a YPO2950 antigen; (12) a YPO3026 antigen; (13) a YPO3417 antigen; (14) a YPO3551 antigen; (15) a YPO3646 antigen; (16) a YPO3982 antigen; (17) a YPO0065 antigen; (18) a YPO0499 antigen; (19) a YPO0505 antigen; (20) a YPO0500 antigen; (21) a YPO0503 antigen; (22) a YPO0506 antigen; (23) a YPO0508 antigen; (24) a YPO0509 antigen; (25) a YPO3579 antigen and (26) a YPO4040 antigen. These 26 antigens form the “sixth antigen group”, which does not overlap with the first, second, third, fourth or fifth antigen groups.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination including one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21) Y. pestis antigens selected from the third antigen group (preferably comprising an antigen from the second group, and more preferably from the first antigen group) and one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Y. pestis antigens of the sixth antigen group.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination including one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or all 36) Y. pestis antigens of the fourth antigen group and one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Y. pestis antigens of the sixth antigen group.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination including one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Y. pestis antigens selected from the sixth antigen group and one or two Y. pestis antigens from the fifth antigen group.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination including one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or all 21) Y. pestis antigens selected from the third antigen group (preferably comprising an antigen from the second group, and more preferably from the first antigen group), one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or all 36) Y. pestis antigens selected from the fourth antigen group, one or two Y. pestis antigens from the fifth antigen group, and one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Y. pestis antigens selected from the sixth antigen group.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination comprising one or more (i.e. 1, 2, 3, 4 or all 5) Y. pestis antigens from the group consisting of: (1) a YPO0496 antigen; (2) a YPO1224 antigen; (3) a YPO3553 antigen; (4) a YPO3987 antigen; and (5) a YPO2190 antigen. These 5 antigens form the “seventh antigen group”, which does not overlap with the first, second, third, fourth, fifth or sixth antigen groups.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination including one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or all 21) Y. pestis antigens selected from the third antigen group (preferably comprising an antigen from the second group, and more preferably from the first antigen group) and one or more (i.e. 1, 2, 3, 4 or all 5) Y. pestis antigens of the seventh antigen group.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination including one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or all 36) Y. pestis antigens selected from the fourth antigen group and one or more (i.e. 1, 2, 3, 4 or all 5) Y. pestis antigens of the seventh antigen group.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination including one or two Y. pestis antigens selected from the fifth antigen group and one or more (i.e. 1, 2, 3, 4 or all 5) Y. pestis antigens of the seventh antigen group.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination including one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Y. pestis antigens selected from the sixth antigen group and one or more (i.e. 1, 2, 3, 4 or all 5) Y. pestis antigens of the seventh antigen group.
The invention also provides a composition comprising a combination of Y. pestis antigens, said combination including one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or all 21) Y. pestis antigens selected from the third antigen group (preferably comprising an antigen from the second group, and more preferably from the first antigen group), one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or all 36) Y. pestis antigens selected from the fourth antigen group, one or two Y. pestis antigens from the fifth antigen group, one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Y. pestis antigens selected from the sixth antigen group and one or more (i.e. 1, 2, 3, 4 or all 5) Y. pestis antigens of the seventh antigen group. The invention also provides a composition comprising a combination of Y. pestis antigens, said combination comprising a antigens from the third antigen group, b antigens from the fourth antigen group, and c antigens from the fifth antigen group, wherein: a is selected from 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or 21; b is selected from 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36; and c is selected from 0, 1 or 2; provided that a+b+c is at least 2 (e.g. 2, 3, 4, 5, 6, 7, 8, 9, 10, or more). Preferably a is not 0. Preferably c is not 0.
Such a composition may optionally comprise d antigens from the sixth antigen group, wherein d is selected from 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26; provided that a+b+c+d is at least 2 (e.g. 2, 3, 4, 5, 6, 7, 8, 9, 10, or more). Preferably a is not 0. Preferably c is not 0.
Such compositions may optionally comprise e antigens from the seventh antigen group, wherein e is selected from 0, 1, 2, 3, 4 or 5; provided that a+b+c+d+e is at least 2 (e.g. 2, 3, 4, 5, 6, 7, 8, 9, 10, or more). Preferably a is not 0. Preferably c is not 0.
The above compositions may also include further Y. pestis antigens that are not members of any of the first, second, third, fourth, fifth or sixth antigen groups. For example, the compositions may include a pesticin (YPPCP1.05c), a W antigen, a pH 6 antigen (YPO1303), a Fe or Mn superoxide dismutase (Fe YPO2386; Mn YPO4061), a YOP antigen (e.g. YPCD1.34c), an iron regulated membrane protein (e.g. YPO1313), a murine toxin (YPMT1.74), a hemin storage protein (e.g. YPO0281), etc. Preferably, a composition according to the invention may further comprise an OppA antigen (YPO2182) as described in reference 19.
There is an upper limit to the number of Y. pestis antigens which will be found in compositions of the invention. Preferably, the number of Y. pestis antigens in a composition of the invention is less than 20 (e.g. less than 19, less than 18, less than 17, less than 16, less than 15, less than 14, less than 13, less than 12, less than 11, less than 10, less than 9, less than 8, less than 7, less than 6, less than 5, less than 4, or less than 3). In particular, the number of Y. pestis antigens in a composition of the invention is preferably less than 6, less than 5, or less than 4.
Preferred antigens selected from the third antigen group are those in the second antigen group, and preferred antigens selected from the second antigen group are those in the first antigen group.
Preferred compositions according to the invention may comprise one or more (i.e. 1, 2, 3 or all 4) of a YPO0499 antigen, a YPO1604 antigen, a YPO3489 antigen and a YPO4003 antigen.
Further preferred compositions according to the invention may comprise one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or all 31) of a YPO0065 antigen, a YPO0086 antigen, a YPO0496 antigen, a YPO0499 antigen, a YPO0501 antigen, a YPO0502 antigen, a YPO0505 antigen, a YPO0809 antigen, a YPO0860 antigen, a YPO1070 antigen, a YPO1123 antigen, a YPO1224 antigen, a YPO1411 antigen, a YPO1604 antigen, a YPO2506 antigen, a YPO2881 antigen, a YPO3935 antigen, a YPO3061 antigen, a YPO3065 antigen, a YPO3382 antigen, a YPO3489 antigen, a YPO3551 antigen, a YPO3553 antigen, a YPO3579 antigen, a YPO3631 antigen, a YPO3982 antigen, a YPO4003 antigen, a YPO3987 antigen, a YPO1354 antigen, a YPO2190 antigen and a YPO3417 antigen.
Further preferred compositions according to the invention may comprise one or more of a YPO0468 antigen (DnaK), a YPO0351 antigen (GroEL), a YPO0203 antigen (EF-Tu) and a YPO1222 antigen (OmpC). Compositions may also optionally comprise a YPO1792 antigen (FlhE).
First Antigen Group
(1) YPO0512
The ‘YPO0512’ sequence was annotated in reference 16 as ‘putative lipoprotein’ (see GI:16120843). For reference purposes, the amino acid sequence of full-length YPO0512 as found in the Y. pestis CO92 strain is given as SEQ ID NO:1 herein. Furthermore, it is postulated that YPO0512 forms part of a Type Three Secretion System (TTSS).
Preferred YPO0512 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:1; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:1, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0512 proteins include variants of SEQ ID NO:1. Preferred fragments of (b) comprise an epitope from SEQ ID NO:1. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 1. Other fragments omit one or more protein domains.
(2) YPO0563
The ‘YPO0563’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI:16120891). For reference purposes, the amino acid sequence of full-length YPO0563 as found in the Y. pestis CO92 strain is given as SEQ ID NO:3 herein. This protein is postulated herein to be a putative exported protein and furthermore to be a Secretion Monitor Precursor (SecM) protein.
Preferred YPO0563 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:3; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:3, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0563 proteins include variants of SEQ ID NO:3. Preferred fragments of (b) comprise an epitope from SEQ ID NO:3. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:3. Other fragments omit one or more protein domains.
(3) YPO3489
The ‘YPO3489’ sequence was annotated in reference 16 as ‘lipoprotein NlpI’ (see GI:16123635). For reference purposes, the amino acid sequence of full-length YPO3489 as found in the Y. pestis CO92 strain is given as SEQ ID NO:17 herein.
Preferred YPO3489 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:17; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:17, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3489 proteins include variants of SEQ ID NO:17. Preferred fragments of (b) comprise an epitope from SEQ ID NO:17. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:17. Other fragments omit one or more protein domains.
Second Antigen Group
(4) YPO4003
The ‘YPO4003’ sequence was annotated in reference 16 as ‘periplasmic dipeptide transport protein’ (see GI:16124128), also known as dppA. For reference purposes, the amino acid sequence of full-length YPO4003 as found in the Y. pestis CO92 strain is given as SEQ ID NO:21 herein.
Preferred YPO4003 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:21; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:21, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO4003 proteins include variants of SEQ ID NO:21. Preferred fragments of (b) comprise an epitope from SEQ ID NO:21. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:21. Other fragments omit one or more protein domains.
(5) YPO1604
The ‘YPO1604’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI:16121872). For reference purposes, the amino acid sequence of full-length YPO1604 as found in the Y. pestis CO92 strain is given as SEQ ID NO:9 herein. This protein is postulated herein to be a putative exported protein.
Preferred YPO1604 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:9; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:9, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1604 proteins include variants of SEQ ID NO:9. Preferred fragments of (b) comprise an epitope from SEQ ID NO:9. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:9. Other fragments omit one or more protein domains.
Third Antigen Group
(6) YPO3061
The ‘YPO3061’ sequence was annotated in reference 16 as ‘lipoprotein’ (see GI:16123238), also known as nlpB. For reference purposes, the amino acid sequence of full-length YPO3061 as found in the Y. pestis CO92 strain is given as SEQ ID NO:11 herein.
Preferred YPO3061 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:11; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:11, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3061 proteins include variants of SEQ ID NO:11. Preferred fragments of (b) comprise an epitope from SEQ ID NO:11. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:11. Other fragments omit one or more protein domains.
(7) YPO3559
The ‘YPO3559’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI:16123703). For reference purposes, the amino acid sequence of full-length YPO3559 as found in the Y. pestis CO92 strain is given as SEQ ID NO:18 herein.
Preferred YPO3559 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:18; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:18, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3559 proteins include variants of SEQ ID NO:18. Preferred fragments of (b) comprise an epitope from SEQ ID NO:18. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:18. Other fragments omit one or more protein domains.
(8) YPO3382
The ‘YPO3382’ sequence was annotated in reference 16 as ‘global stress requirement protein GsrA’ (see GI:16123531), also known as htrA or degP. For reference purposes, the amino acid sequence of full-length YPO3382 as found in the Y. pestis CO92 strain is given as SEQ ID NO:15 herein.
Preferred YPO3382 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:15; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:15, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3382 proteins include variants of SEQ ID NO:15. Preferred fragments of (b) comprise an epitope from SEQ ID NO:15. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:15. Other fragments omit one or more protein domains.
(9) YPO0860
The ‘YPO0860’ sequence was annotated in reference 16 as ‘sugar-binding periplasmic protein’ (see GI:16121168). For reference purposes, the amino acid sequence of full-length YPO0860 as found in the Y. pestis CO92 strain is given as SEQ ID NO:5 herein.
Preferred YPO0860 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:5; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:5, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0860 proteins include variants of SEQ ID NO:5. Preferred fragments of (b) comprise an epitope from SEQ ID NO:5. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:5. Other fragments omit one or more protein domains.
(10) YPO0086
The ‘YPO0086’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI:16120437). For reference purposes, the amino acid sequence of full-length YPO0086 as found in the Y. pestis CO92 strain is given as SEQ ID NO:2 herein. This protein is postulated herein to be a putative exported protein.
Preferred YPO0086 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:2; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:2, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0086 proteins include variants of SEQ ID NO:2. Preferred fragments of (b) comprise an epitope from SEQ ID NO:2. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:2. Other fragments omit one or more protein domains.
(11) YPO3631
The ‘YPO3631’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI:16123773). For reference purposes, the amino acid sequence of full-length YPO3631 as found in the Y. pestis CO92 strain is given as SEQ ID NO:19 herein. This protein is postulated herein to be a putative exported protein.
Preferred YPO3631 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:19; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:19, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3631 proteins include variants of SEQ ID NO:19. Preferred fragments of (b) comprise an epitope from SEQ ID NO:19. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:19. Other fragments omit one or more protein domains.
(12) YPO2881
The ‘YPO2881’ sequence was annotated in reference 16 as ‘putative fimbrial biogenesis protein’ (see GI:16123073). For reference purposes, the amino acid sequence of full-length YPO2881 as found in the Y. pestis CO92 strain is given as SEQ ID NO:10 herein.
Preferred YPO2881 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:10; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:10, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO2881 proteins include variants of SEQ ID NO:10. Preferred fragments of (b) comprise an epitope from SEQ ID NO:10. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:10. Other fragments omit one or more protein domains.
(13) YPO3343
The ‘YPO3343’ sequence was annotated in reference 16 as ‘probable extracellular solute-binding protein’ (see GI:16123493). For reference purposes, the amino acid sequence of full-length YPO3343 as found in the Y. pestis CO92 strain is given as SEQ ID NO:13 herein.
Preferred YPO3343 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:13; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:13, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3343 proteins include variants of SEQ ID NO: 13. Preferred fragments of (b) comprise an epitope from SEQ ID NO:13. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 13. Other fragments omit one or more protein domains.
(14) YPO3361
The ‘YPO3361’ sequence was annotated in reference 16 as ‘4-diphosphocytidyl-2C-methyl-D-erythritol synthase’ (see GI:16123511). For reference purposes, the amino acid sequence of full-length YPO3361 as found in the Y. pestis CO92 strain is given as SEQ ID NO:14 herein.
Preferred YPO3361 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:14; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:14, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3361 proteins include variants of SEQ ID NO:14. Preferred fragments of (b) comprise an epitope from SEQ ID NO:14. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:14. Other fragments omit one or more protein domains.
(15) YPO3430
The ‘YPO3430’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI:16123579). For reference purposes, the amino acid sequence of full-length YPO3430 as found in the Y. pestis CO92 strain is given as SEQ ID NO:16 herein.
Preferred YPO3430 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:16; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:16, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3430 proteins include variants of SEQ ID NO:16. Preferred fragments of (b) comprise an epitope from SEQ ID NO:16. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:16. Other fragments omit one or more protein domains.
(16) YPO1411
The ‘YPO1411’ sequence was annotated in reference 16 as ‘putative outer membrane porin C protein’ (see GI:16121691). For reference purposes, the amino acid sequence of full-length YPO1411 as found in the Y. pestis CO92 strain is given as SEQ ID NO:8 herein.
Preferred YPO1411 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:8; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:8, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1411 proteins include variants of SEQ ID NO:8. Preferred fragments of (b) comprise an epitope from SEQ ID NO:8. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:8. Other fragments omit one or more protein domains.
(17) YPO3935
The ‘YPO3935’ sequence was annotated in reference 16 as ‘membrane protein’ (see GI:16124063). For reference purposes, the amino acid sequence of full-length YPO3935 as found in the Y. pestis CO92 strain is given as SEQ ID NO:20 herein.
Preferred YPO3935 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:20; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:20, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3935 proteins include variants of SEQ ID NO:20. Preferred fragments of (b) comprise an epitope from SEQ ID NO:20. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:20. Other fragments omit one or more protein domains.
(18) YPO0809
The ‘YPO0809’ sequence was annotated in reference 16 as ‘general secretion pathway protein K’ (see GI:16121121). For reference purposes, the amino acid sequence of full-length YPO0809 as found in the Y. pestis CO92 strain is given as SEQ ID NO:4 herein.
Preferred YPO0809 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:4; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:4, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0809 proteins include variants of SEQ ID NO:4. Preferred fragments of (b) comprise an epitope from SEQ ID NO:4. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:4. Other fragments omit one or more protein domains.
(19) YPO1123
The ‘YPO1123’ sequence was annotated in reference 16 as ‘TolA colicin import membrane protein’ (see GI:16121423). For reference purposes, the amino acid sequence of full-length YPO1123 as found in the Y. pestis CO92 strain is given as SEQ ID NO:7 herein.
Preferred YPO1123 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:7; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:7, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1123 proteins include variants of SEQ ID NO:7. Preferred fragments of (b) comprise an epitope from SEQ ID NO:7. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:7. Other fragments omit one or more protein domains.
(20) YPO3065
The ‘YPO3065’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI:16123242). For reference purposes, the amino acid sequence of full-length YPO3065 as found in the Y. pestis CO92 strain is given as SEQ ID NO:12 herein.
Preferred YPO3065 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:12; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:12, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3065 proteins include variants of SEQ ID NO:12. Preferred fragments of (b) comprise an epitope from SEQ ID NO:12. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:12. Other fragments omit one or more protein domains.
(21) YPO1070
The ‘YPO1070’ sequence was annotated in reference 16 as ‘putative lipoprotein’ (see GI:16121371), also known as rcsF. For reference purposes, the amino acid sequence of full-length YPO1070 as found in the Y. pestis CO92 strain is given as SEQ ID NO:6 herein.
Preferred YPO1070 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:6; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:6, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1070 proteins include variants of SEQ ID NO:6. Preferred fragments of (b) comprise an epitope from SEQ ID NO:6. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:6. Other fragments omit one or more protein domains.
Fourth Antigen Group
(1) YPO0102
The ‘YPO0102’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI:16120449). For reference purposes, the amino acid sequence of full-length YPO0102 as found in the Y. pestis CO92 strain is given as SEQ ID NO:44 herein.
Preferred YPO0102 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:44; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:44, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0102 proteins include variants of SEQ ID NO:44. Preferred fragments of (b) comprise an epitope from SEQ ID NO:44. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:44. Other fragments omit one or more protein domains.
(2) YPO0570
The ‘YPO0570’ sequence was annotated in reference 16 as ‘putative membrane protein’ (see GI:16120899). For reference purposes, the amino acid sequence of full-length YPO0570 as found in the Y. pestis CO92 strain is given as SEQ ID NO:35 herein.
Preferred YPO0570 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:35; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:35, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0570 proteins include variants of SEQ ID NO:35. Preferred fragments of (b) comprise an epitope from SEQ ID NO:35. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:35. Other fragments omit one or more protein domains.
(3) YPO1053
The ‘YPO1053’ sequence was annotated in reference 16 as ‘cationic 19 kDa outer membrane protein precursor’ (see GI:16121353). For reference purposes, the amino acid sequence of full-length YPO1053 as found in the Y. pestis CO92 strain is given as SEQ ID NO:33 herein. This protein is postulated herein to be a member of the OmpH family of proteins.
Preferred YPO1053 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:33; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:33, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1053 proteins include variants of SEQ ID NO:33. Preferred fragments of (b) comprise an epitope from SEQ ID NO:33. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:33. Other fragments omit one or more protein domains.
(4) YPO1435
The ‘YPO1435’ sequence was annotated in reference 16 as ‘putative outer membrane porin A protein’ (see GI:16121713). For reference purposes, the amino acid sequence of full-length YPO1435 as found in the Y. pestis CO92 strain is given as SEQ ID NO:32 herein.
Preferred YPO1435 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:32; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:32, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1435 proteins include variants of SEQ ID NO:32. Preferred fragments of (b) comprise an epitope from SEQ ID NO:32. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:32. Other fragments omit one or more protein domains.
(5) YPO2674
The ‘YPO2674’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI:16122879). For reference purposes, the amino acid sequence of full-length YPO2674 as found in the Y. pestis CO92 strain is given as SEQ ID NO:26 herein.
Preferred YPO2674 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:26; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:26, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO2674 proteins include variants of SEQ ID NO:26. Preferred fragments of (b) comprise an epitope from SEQ ID NO:26. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:26. Other fragments omit one or more protein domains.
(6) YPO2292
The ‘YPO2292’ sequence was annotated in reference 16 as ‘putative lipoprotein’ (see GI:16122516). For reference purposes, the amino acid sequence of full-length YPO2292 as found in the Y. pestis CO92 strain is given as SEQ ID NO:29 herein.
Preferred YPO2292 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:29; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:29, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO2292 proteins include variants of SEQ ID NO:29. Preferred fragments of (b) comprise an epitope from SEQ ID NO:29. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:29. Other fragments omit one or more protein domains.
(7) YPO3050
The ‘YPO3050’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI:16123227). For reference purposes, the amino acid sequence of full-length YPO3050 as found in the Y. pestis CO92 strain is given as SEQ ID NO:25 herein.
Preferred YPO3050 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:25; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:25, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3050 proteins include variants of SEQ ID NO:25. Preferred fragments of (b) comprise an epitope from SEQ ID NO:25. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:25. Other fragments omit one or more protein domains.
(8) YPO2615
The ‘YPO2615’ sequence was annotated in reference 16 as ‘putative amino acid-binding protein precursor’ (see GI:16122828). For reference purposes, the amino acid sequence of full-length YPO2615 as found in the Y. pestis CO92 strain is given as SEQ ID NO:27 herein.
Preferred YPO2615 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:27; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:27, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO2615 proteins include variants of SEQ ID NO:27. Preferred fragments of (b) comprise an epitope from SEQ ID NO:27. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:27. Other fragments omit one or more protein domains.
(9) YPO1507
The ‘YPO1507’ sequence was annotated in reference 16 as ‘galactose-binding protein’ (see GI:16121780). For reference purposes, the amino acid sequence of full-length YPO1507 as found in the Y. pestis CO92 strain is given as SEQ ID NO:31 herein.
Preferred YPO1507 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:31; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:31, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1507 proteins include variants of SEQ ID NO:31. Preferred fragments of (b) comprise an epitope from SEQ ID NO:31. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:31. Other fragments omit one or more protein domains.
(10) YPO4111
The ‘YPO4111’ sequence was annotated in reference 16 as ‘putative periplasmic solute-binding protein’ (see GI:16124219). For reference purposes, the amino acid sequence of full-length YPO4111 as found in the Y. pestis CO92 strain is given as SEQ ID NO:47 herein.
Preferred YPO4111 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:47; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:47, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO4111 proteins include variants of SEQ ID NO:47. Preferred fragments of (b) comprise an epitope from SEQ ID NO:47. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:47. Other fragments omit one or more protein domains.
(11) YPO0015
The ‘YPO0015’ sequence was annotated in reference 16 as ‘secreted thiol:disulfide interchange protein DsbA’ (see GI:16120369). For reference purposes, the amino acid sequence of full-length YPO0015 as found in the Y. pestis CO92 strain is given as SEQ ID NO:46 herein.
Preferred YPO0015 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:46; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:46, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0015 proteins include variants of SEQ ID NO:46. Preferred fragments of (b) comprise an epitope from SEQ ID NO:46. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:46. Other fragments omit one or more protein domains.
(12) YPO0195
The ‘YPO0195’ sequence was annotated in reference 16 as ‘peptidyl-prolyl cis-trans isomerase’ (see GI:16120534). For reference purposes, the amino acid sequence of full-length YPO0195 as found in the Y. pestis CO92 strain is given as SEQ ID NO:43 herein.
Preferred YPO0195 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:43; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:43, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0195 proteins include variants of SEQ ID NO:43. Preferred fragments of (b) comprise an epitope from SEQ ID NO:43. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:43. Other fragments omit one or more protein domains.
(13) YPO2342
The ‘YPO2342’ sequence was annotated in reference 16 as ‘thiol peroxidase’ (see GI:16122566). For reference purposes, the amino acid sequence of full-length YPO2342 as found in the Y. pestis CO92 strain is given as SEQ ID NO:28 herein.
Preferred YPO2342 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:28; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:28, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO2342 proteins include variants of SEQ ID NO:28. Preferred fragments of (b) comprise an epitope from SEQ ID NO:28. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:28. Other fragments omit one or more protein domains.
(14) YPO0501
The ‘YPO0501’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI:16120831). For reference purposes, the amino acid sequence of full-length YPO0501 as found in the Y. pestis CO92 strain is given as SEQ ID NO:37 herein. However, it is postulated herein that YPO0501 forms part of a Type Three Secretion System (TTSS).
Preferred YPO0501 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:37; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:37, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0501 proteins include variants of SEQ ID NO:37. Preferred fragments of (b) comprise an epitope from SEQ ID NO:37. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:37. Other fragments omit one or more protein domains.
(15) YPO0502
The ‘YPO0502’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI:16120832). For reference purposes, the amino acid sequence of full-length YPO0502 as found in the Y. pestis CO92 strain is given as SEQ ID NO:36 herein. However, it is postulated herein that YPO0502 forms part of a Type Three Secretion System (TTSS).
Preferred YPO0502 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:36; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:36, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0502 proteins include variants of SEQ ID NO:36. Preferred fragments of (b) comprise an epitope from SEQ ID NO:36. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:36. Other fragments omit one or more protein domains.
(16) YPO0819
The ‘YPO0819’ sequence was annotated in reference 16 as ‘putative carbonic anhydrase’ (see GI:16121130). For reference purposes, the amino acid sequence of full-length YPO0819 as found in the Y. pestis CO92 strain is given as SEQ ID NO:34 herein.
Preferred YPO0819 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:34; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:34, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0819 proteins include variants of SEQ ID NO:34. Preferred fragments of (b) comprise an epitope from SEQ ID NO:34. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:34. Other fragments omit one or more protein domains.
(17) YPO3644
The ‘YPO3644’ sequence was annotated in reference 16 as ‘major cold shock protein Cspa1’ (see GI:16123786). For reference purposes, the amino acid sequence of full-length YPO3644 as found in the Y. pestis CO92 strain is given as SEQ ID NO:22 herein.
Preferred YPO3644 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:22; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:22, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3644 proteins include variants of SEQ ID NO:22. Preferred fragments of (b) comprise an epitope from SEQ ID NO:22. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:22. Other fragments omit one or more protein domains.
(18) YPO1746
The ‘YPO1746’ sequence was annotated in reference 16 as ‘cold shock protein’ (see GI:16122003). For reference purposes, the amino acid sequence of full-length YPO1746 as found in the Y. pestis CO92 strain is given as SEQ ID NO:30 herein.
Preferred YPO1746 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:30; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:30, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1746 proteins include variants of SEQ ID NO:30. Preferred fragments of (b) comprise an epitope from SEQ ID NO:30. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:30. Other fragments omit one or more protein domains.
(19) YPO0351
The ‘YPO0351’ sequence was annotated in reference 16 as ‘60 kDa chaperonin’ (see GI:16120686). For reference purposes, the amino acid sequence of full-length YPO0351 as found in the Y. pestis CO92 strain is given as SEQ ID NO:39 herein.
Preferred YPO0351 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:39; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:39, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0351 proteins include variants of SEQ ID NO:39. Preferred fragments of (b) comprise an epitope from SEQ ID NO:39. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:39. Other fragments omit one or more protein domains. A YPO0351 antigen has been shown to be an outer membrane protein suitable for use as an antigenic protein in reference 20.
(20) YPO0468
The ‘YPO0468’ sequence was annotated in reference 16 as ‘chaperone protein DnaK’ (see GI:16120797). For reference purposes, the amino acid sequence of full-length YPO0468 as found in the Y. pestis CO92 strain is given as SEQ ID NO:38 herein.
Preferred YPO0468 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:38; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:38, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0468 proteins include variants of SEQ ID NO:38. Preferred fragments of (b) comprise an epitope from SEQ ID NO:38. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:38. Other fragments omit one or more protein domains. A YPO0468 antigen has been shown to be an outer membrane protein suitable for use as an antigenic protein in reference 20.
(21) YPO0203
The ‘YPO0203’ sequence was annotated in reference 16 as ‘elongation factor Tu’ (see GI:16120542). For reference purposes, the amino acid sequence of full-length YPO0203 as found in the Y. pestis CO92 strain is given as SEQ ID NO:42 herein.
Preferred YPO0203 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:42; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:42, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0203 proteins include variants of SEQ ID NO:42. Preferred fragments of (b) comprise an epitope from SEQ ID NO:42. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:42. Other fragments omit one or more protein domains. A YPO0203 antigen has been shown to be an outer membrane protein suitable for use as an antigenic protein in reference 20.
(22) YPO0216
The ‘YPO0216’ sequence was annotated in reference 16 as ‘30S ribosomal protein S3’ (see GI:16120553). For reference purposes, the amino acid sequence of full-length YPO0216 as found in the Y. pestis CO92 strain is given as SEQ ID NO:41 herein.
Preferred YPO0216 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:41; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:41, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0216 proteins include variants of SEQ ID NO:41. Preferred fragments of (b) comprise an epitope from SEQ ID NO:41. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:41. Other fragments omit one or more protein domains.
(23) YPO3536
The ‘YPO3536’ sequence was annotated in reference 16 as ‘50S ribosomal protein L9’ (see GI:16123682). For reference purposes, the amino acid sequence of full-length YPO3536 as found in the Y. pestis CO92 strain is given as SEQ ID NO:24 herein.
Preferred YPO3536 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:24; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:24, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3536 proteins include variants of SEQ ID NO:24. Preferred fragments of (b) comprise an epitope from SEQ ID NO:24. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:24. Other fragments omit one or more protein domains.
(24) YPO0233
The ‘YPO0233’ sequence was annotated in reference 16 as ‘30S ribosomal protein S4’ (see GI:16120571). For reference purposes, the amino acid sequence of full-length YPO0233 as found in the Y. pestis CO92 strain is given as SEQ ID NO:40 herein.
Preferred YPO0233 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:40; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:40, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0233 proteins include variants of SEQ ID NO:40. Preferred fragments of (b) comprise an epitope from SEQ ID NO:40. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:40. Other fragments omit one or more protein domains.
(25) YPO0067
The ‘YPO0067’ sequence was annotated in reference 16 as ‘protein-export protein’ (see GI:16120418). For reference purposes, the amino acid sequence of full-length YPO0067 as found in the Y. pestis CO92 strain is given as SEQ ID NO:45 herein.
Preferred YPO0067 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:45; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:45, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0067 proteins include variants of SEQ ID NO:45. Preferred fragments of (b) comprise an epitope from SEQ ID NO:45. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:45. Other fragments omit one or more protein domains.
(26) YPO03643
The ‘YPO3643’ sequence was annotated in reference 16 as ‘major cold shock protein Cspa2’ (see GI:16123785). For reference purposes, the amino acid sequence of full-length YPO3643 as found in the Y. pestis CO92 strain is given as SEQ ID NO:23 herein.
Preferred YPO3643 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:23; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:23, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3643 proteins include variants of SEQ ID NO:23. Preferred fragments of (b) comprise an epitope from SEQ ID NO:23. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:23. Other fragments omit one or more protein domains.
(27) YPO3375
The ‘YPO3375’ sequence was annotated in reference 16 as ‘superoxide dismutase [Cu—Zn] precursor’ (see GI:16123524). For reference purposes, the amino acid sequence of full-length YPO3375 as found in the Y. pestis CO92 strain is given as SEQ ID NO:58 herein.
Preferred YPO3375 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:58; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:58, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3375 proteins include variants of SEQ ID NO:58. Preferred fragments of (b) comprise an epitope from SEQ ID NO:58. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:58. Other fragments omit one or more protein domains.
(28) YPO0494
The ‘YPO0494’ sequence was annotated in reference 16 as ‘survival protein SurA precursor (peptidyl-prolyl cis-trans isomerase’ (see GI:16120824). For reference purposes, the amino acid sequence of full-length YPO0494 as found in the Y. pestis CO92 strain is given as SEQ ID NO:53 herein.
Preferred YPO0494 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:53; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:53, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0494 proteins include variants of SEQ ID NO:53. Preferred fragments of (b) comprise an epitope from SEQ ID NO:53. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:53. Other fragments omit one or more protein domains.
(29) YPO1052
The ‘YPO1052’ sequence was annotated in reference 16 as ‘putative surface antigen’ (see GI:16121352). For reference purposes, the amino acid sequence of full-length YPO1052 as found in the Y. pestis CO92 strain is given as SEQ ID NO:51 herein.
Preferred YPO1052 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:51; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:51, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1052 proteins include variants of SEQ ID NO:51. Preferred fragments of (b) comprise an epitope from SEQ ID NO:51. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:51. Other fragments omit one or more protein domains.
(30) YPO1906
The ‘YPO1906’ sequence was annotated in reference 16 as ‘pesticin/yersiniabactin receptor protein’ (see GI:16122154). For reference purposes, the amino acid sequence of full-length YPO1906 as found in the Y. pestis CO92 strain is given as SEQ ID NO:56 herein.
Preferred YPO1906 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:56; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:56, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1906 proteins include variants of SEQ ID NO:56. Preferred fragments of (b) comprise an epitope from SEQ ID NO:56. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:56. Other fragments omit one or more protein domains.
(31) YPO0663
The ‘YPO0663’ sequence was annotated in reference 16 as ‘ABC-transporter outer membrane component’ (see GI:16120988). For reference purposes, the amino acid sequence of full-length YPO0663 as found in the Y. pestis CO92 strain is given as SEQ ID NO:54 herein.
Preferred YPO0663 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:54; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:54, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0663 proteins include variants of SEQ ID NO:54. Preferred fragments of (b) comprise an epitope from SEQ ID NO:54. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:54. Other fragments omit one or more protein domains.
(32) YPO1222
The ‘YPO1222’ sequence was annotated in reference 16 as ‘outer membrane protein C, porin’ (see GI:16121511). For reference purposes, the amino acid sequence of full-length YPO1222 as found in the Y. pestis CO92 strain is given as SEQ ID NO:55 herein.
Preferred YPO1222 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:55; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:55, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1222 proteins include variants of SEQ ID NO:55. Preferred fragments of (b) comprise an epitope from SEQ ID NO:55. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:55. Other fragments omit one or more protein domains. A YPO1222 antigen has been shown to be an outer membrane protein suitable for use as an antigenic protein in reference 20.
(33) YPO2905
The ‘YPO2905’ sequence was annotated in reference 16 as ‘attachment invasion locus protein’ (see GI:16123096). For reference purposes, the amino acid sequence of full-length YPO2905 as found in the Y. pestis CO92 strain is given as SEQ ID NO:57 herein.
Preferred YPO2905 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:57; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:57, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO2905 proteins include variants of SEQ ID NO:57. Preferred fragments of (b) comprise an epitope from SEQ ID NO:57. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:57. Other fragments omit one or more protein domains.
(34) YPO4070
The ‘YPO4070’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI:16124183). For reference purposes, the amino acid sequence of full-length YPO4070 as found in the Y. pestis CO92 strain is given as SEQ ID NO:52 herein.
Preferred YPO4070 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:52; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:52, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO4070 proteins include variants of SEQ ID NO:52. Preferred fragments of (b) comprise an epitope from SEQ ID NO:52. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:52. Other fragments omit one or more protein domains.
(35) YPPCP1.07
The ‘YPPCP1.07’ sequence was annotated in reference 16 as ‘plasminogen activator protease precursor’ (see GI:16082686). For reference purposes, the amino acid sequence of full-length YPPCP1.07 as found in the Y. pestis CO92 strain is given as SEQ ID NO:50 herein.
Preferred YPPCP1.07 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:50; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:50, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPPCP1.07 proteins include variants (e.g. allelic variants, polymorphic forms, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO:50. Preferred fragments of (b) comprise an epitope from SEQ ID NO:50. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:50. Other fragments omit one or more protein domains.
(36) YPMT1.42
The ‘YPMT1.42’ sequence was annotated in reference 16 as ‘putative periplasmic protein’ (see GI:16082828). For reference purposes, the amino acid sequence of full-length YPMT1.42 as found in the Y. pestis CO92 strain is given as SEQ ID NO:59 herein.
Preferred YPMT1.42 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:59; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:59, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPMT1.42 proteins include variants (e.g. allelic variants, polymorphic forms, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO:59. Preferred fragments of (b) comprise an epitope from SEQ ID NO:59. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:59. Other fragments omit one or more protein domains.
Fifth Antigen Group
(1) F1 Antigen
The ‘F1’ antigen is the envelope or capsular protein of Y. pestis, and derives its name from fraction 1′. It is also known as ‘caf1’, and is encoded on a plasmid. Cloning and sequencing of the F1 gene was reported in 1990 in reference 21 (GI:115437). In reference 16, the F1 antigen is referred to as ‘YPMT1.84’ (see GI:16082876). For reference purposes, the amino acid sequence of full-length F1 from the Y. pestis CO92 strain is given as SEQ ID NO:48 herein.
Preferred F1 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:48; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:48, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These F1 proteins include variants of SEQ ID NO:48. Preferred fragments of (b) comprise an epitope from SEQ ID NO:48, and reference 21 suggests that the region located between amino acids 100 and 150 contains such epitopes. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:48. Other fragments omit one or more protein domains. For example, reference 103 discloses F1 proteins in which the 21-mer N-terminus signal peptide has been removed.
(2) V Antigen
The V antigen is recognised as a major virulence factor of Y. pestis. In reference 16, the F1 antigen is referred to as ‘YPCD1.31c’, encoding the ‘antihost protein/regulator’ (see GI:5832451). It is also known as ‘lcrV’ for ‘low-calcium-response V’. For reference purposes, the amino acid sequence of full-length V antigen from the Y. pestis CO92 strain is given as SEQ ID NO:49 herein. Reference 22 reports V antigen sequences for 22 diverse strains of Y. pestis, with all but two being identical.
Preferred V antigens for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:49; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:49, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants of SEQ ID NO:49. For example, GI:17380409 reports on sequence variants (K18N, K72R, I135V, C273S, and a mutant where 324SGK326 is replaced by R). Preferred fragments of (b) comprise an epitope from SEQ ID NO:49. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:49. Other fragments omit one or more protein domains.
Sixth Antigen Group
(1) YPO0457
The ‘YPO0457’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16120786). For reference purposes, the amino acid sequence of full-length YPO0457 as found in the Y. pestis CO92 strain is given as SEQ ID NO:61 herein. This protein is postulated herein to be a putative outer membrane protein.
Preferred YPO0457 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:61; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:61, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0457 proteins include variants of SEQ ID NO:61. Preferred fragments of (b) comprise an epitope from SEQ ID NO:61. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:61. Other fragments omit one or more protein domains.
(2) YPO0514
The ‘YPO0514’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16120845). For reference purposes, the amino acid sequence of full-length YPO0514 as found in the Y. pestis CO92 strain is given as SEQ ID NO:62 herein. However, it is postulated herein that YPO0514 forms part of a Type Three Secretion System (TTSS) and is an OmpA-family member protein.
Preferred YPO0514 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:62; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:62, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0514 proteins include variants of SEQ ID NO:62. Preferred fragments of (b) comprise an epitope from SEQ ID NO:62. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:62. Other fragments omit one or more protein domains.
(3) YPO0694
The ‘YPO0694’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16121015). For reference purposes, the amino acid sequence of full-length YPO0694 as found in the Y. pestis CO92 strain is given as SEQ ID NO:63 herein. This protein is postulated herein to be a putative membrane protein and furthermore, a fimbrial component.
Preferred YPO0694 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:63; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:63, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0694 proteins include variants of SEQ ID NO:63. Preferred fragments of (b) comprise an epitope from SEQ ID NO:63. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:63. Other fragments omit one or more protein domains.
(4) YPO0805
The ‘YPO0805’ sequence was annotated in reference 16 as ‘putative lipoprotein’ (see GI: 16121117). For reference purposes, the amino acid sequence of full-length YPO0805 as found in the Y. pestis CO92 strain is given as SEQ ID NO:64 herein. This protein is postulated herein to be a member of a virulence-associated secretion apparatus.
Preferred YPO0805 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:64; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:64, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0805 proteins include variants of SEQ ID NO:64. Preferred fragments of (b) comprise an epitope from SEQ ID NO:64. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:64. Other fragments omit one or more protein domains.
(5) YPO0982
The ‘YPO0982’ sequence was annotated in reference 16 as ‘putative lipoprotein’ (see GI: 16121286). For reference purposes, the amino acid sequence of full-length YPO0982 as found in the Y. pestis CO92 strain is given as SEQ ID NO:65 herein.
Preferred YPO0982 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:65; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:65, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0982 proteins include variants of SEQ ID NO:65. Preferred fragments of (b) comprise an epitope from SEQ ID NO:65. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:65. Other fragments omit one or more protein domains.
(6) YPO1354
The ‘YPO1354’ sequence was annotated in reference 16 as ‘putative lipoprotein’ (see GI: 16121634). For reference purposes, the amino acid sequence of full-length YPO1354 as found in the Y. pestis CO92 strain is given as SEQ ID NO:66 herein.
Preferred YPO1354 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:66; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:66, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1354 proteins include variants of SEQ ID NO:66. Preferred fragments of (b) comprise an epitope from SEQ ID NO:66. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:66. Other fragments omit one or more protein domains.
(7) YPO1408
The ‘YPO1408’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16121688). For reference purposes, the amino acid sequence of full-length YPO1408 as found in the Y. pestis CO92 strain is given as SEQ ID NO:67 herein. This protein is postulated herein to be a putative exported protein and a member of a type IV secretion system.
Preferred YPO1408 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:67; and/or (b) that is a fragment of at least 17 consecutive amino acids of SEQ ID NO:67, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1408 proteins include variants of SEQ ID NO:67. Preferred fragments of (b) comprise an epitope from SEQ ID NO:67. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:67. Other fragments omit one or more protein domains.
(8) YPO1792
The ‘YPO1792’ sequence was annotated in reference 16 as ‘flagellar protein FlhE precursor’ (see GI: 16122046). For reference purposes, the amino acid sequence of full-length YPO1792 as found in the Y. pestis CO92 strain is given as SEQ ID NO:68 herein.
Preferred YPO1792 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:68; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:68, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1792 proteins include variants of SEQ ID NO:68. Preferred fragments of (b) comprise an epitope from SEQ ID NO:68. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:68. Other fragments omit one or more protein domains. A YPO1792 antigen has been shown to be an effective antigen for immunisation against lethal respiratory challenge with Y. pestis [23].
(9) YPO2506
The ‘YPO2506’ sequence was annotated in reference 16 as ‘outer membrane protein X’ (see GI: 16122727). For reference purposes, the amino acid sequence of full-length YPO2506 as found in the Y. pestis CO92 strain is given as SEQ ID NO:69 herein.
Preferred YPO2506 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:69; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:69, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO2506 proteins include variants of SEQ ID NO:69. Preferred fragments of (b) comprise an epitope from SEQ ID NO:69. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:69. Other fragments omit one or more protein domains.
(10) YPO2713
The ‘YPO2713’ sequence was annotated in reference 16 as ‘periplasmic negative regulator of sigmaE’ (see GI: 16122917). For reference purposes, the amino acid sequence of full-length YPO2713 as found in the Y. pestis CO92 strain is given as SEQ ID NO:70 herein.
Preferred YPO2713 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:70; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:70, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO2713 proteins include variants of SEQ ID NO:70. Preferred fragments of (b) comprise an epitope from SEQ ID NO:70. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:70. Other fragments omit one or more protein domains.
(11) YPO2950
The ‘YPO2950’ sequence was annotated in reference 16 as ‘putative fimbrial protein’ (see GI: 16123133). For reference purposes, the amino acid sequence of full-length YPO2950 as found in the Y. pestis CO92 strain is given as SEQ ID NO:71 herein.
Preferred YPO2950 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:71; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:71, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO2950 proteins include variants of SEQ ID NO:71. Preferred fragments of (b) comprise an epitope from SEQ ID NO:71. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:71. Other fragments omit one or more protein domains.
(12) YPO3026
The ‘YPO3026’ sequence was annotated in reference 16 as ‘putative lipoprotein’ (see GI: 16123203). For reference purposes, the amino acid sequence of full-length YPO3026 as found in the Y. pestis CO92 strain is given as SEQ ID NO:72 herein. This protein is postulated herein to be a pilin component.
Preferred YPO3026 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:72; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:72, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3026 proteins include variants of SEQ ID NO:72. Preferred fragments of (b) comprise an epitope from SEQ ID NO:72. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:72. Other fragments omit one or more protein domains.
(13) YPO3417
The ‘YPO3417’ sequence was annotated in reference 16 as ‘dihydrolipoamide dehydrogenase’ (see GI: 16123566). For reference purposes, the amino acid sequence of full-length YPO3417 as found in the Y. pestis CO92 strain is given as SEQ ID NO:73 herein.
Preferred YPO3417 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:73; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:73, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3417 proteins include variants of SEQ ID NO:73. Preferred fragments of (b) comprise an epitope from SEQ ID NO:73. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:73. Other fragments omit one or more protein domains.
(14) YPO3551
The ‘YPO3551’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16123695). For reference purposes, the amino acid sequence of full-length YPO3551 as found in the Y. pestis CO92 strain is given as SEQ ID NO:74 herein. This protein is postulated herein to be a putative exported protein.
Preferred YPO3551 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:74; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:74, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3551 proteins include variants of SEQ ID NO:74. Preferred fragments of (b) comprise an epitope from SEQ ID NO:74. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:74. Other fragments omit one or more protein domains.
(15) YPO3646
The ‘YPO3646’ sequence was annotated in reference 16 as ‘outer membrane lipoprotein’ (see GI: 16123788). For reference purposes, the amino acid sequence of full-length YPO3646 as found in the Y. pestis CO92 strain is given as SEQ ID NO:75 herein. This protein is postulated herein to play a role in membrane integrity.
Preferred YPO3646 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:75; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:75, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3646 proteins include variants of SEQ ID NO:75. Preferred fragments of (b) comprise an epitope from SEQ ID NO:75. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:75. Other fragments omit one or more protein domains.
(16) YPO3982
The ‘YPO3982’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16124109). For reference purposes, the amino acid sequence of full-length YPO3982 as found in the Y. pestis CO92 strain is given as SEQ ID NO:76 herein.
Preferred YPO3982 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:76; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:76, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3982 proteins include variants of SEQ ID NO:76. Preferred fragments of (b) comprise an epitope from SEQ ID NO:76. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:76. Other fragments omit one or more protein domains.
(17) YPO0065
The ‘YPO0065’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16120416). For reference purposes, the amino acid sequence of full-length YPO0065 as found in the Y. pestis CO92 strain is given as SEQ ID NO:77 herein. This protein is postulated herein to be a putative membrane protein.
Preferred YPO0065 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:77; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:77, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0065 proteins include variants of SEQ ID NO:77. Preferred fragments of (b) comprise an epitope from SEQ ID NO:77. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:77. Other fragments omit one or more protein domains.
(18) YPO0499
The ‘YPO0499’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16120829). For reference purposes, the amino acid sequence of full-length YPO0499 as found in the Y. pestis CO92 strain is given as SEQ ID NO:78 herein. However, it is postulated herein that YPO0499 forms part of a Type Three Secretion System (TTSS).
Preferred YPO0499 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:78; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:78, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0499 proteins include variants of SEQ ID NO:78. Preferred fragments of (b) comprise an epitope from SEQ ID NO:78. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:78. Other fragments omit one or more protein domains.
(19) YPO0505
The ‘YPO0505’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16120835). For reference purposes, the amino acid sequence of full-length YPO0505 as found in the Y. pestis CO92 strain is given as SEQ ID NO:79 herein. However, it is postulated herein that YPO0505 forms part of a Type Three Secretion System (TTSS).
Preferred YPO0505 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:79; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:79, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0505 proteins include variants of SEQ ID NO:79. Preferred fragments of (b) comprise an epitope from SEQ ID NO:79. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:79. Other fragments omit one or more protein domains.
(20) YPO0500
The ‘YPO0500’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16120830). For reference purposes, the amino acid sequence of full-length YPO0500 as found in the Y. pestis CO92 strain is given as SEQ ID NO:80 herein. However, it is postulated herein that YPO0500 forms part of a Type Three Secretion System (TTSS).
Preferred YPO0500 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:80; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:80, wherein 77 is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0500 proteins include variants of SEQ ID NO:80. Preferred fragments of (b) comprise an epitope from SEQ ID NO:80. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:80. Other fragments omit one or more protein domains.
(21) YPO0503
The ‘YPO0503’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16120833). For reference purposes, the amino acid sequence of full-length YPO0503 as found in the Y. pestis CO92 strain is given as SEQ ID NO:81 herein. However, it is postulated herein that YPO0503 forms part of a Type Three Secretion System (TTSS).
Preferred YPO0503 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:81; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:81, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0503 proteins include variants of SEQ ID NO:81. Preferred fragments of (b) comprise an epitope from SEQ ID NO:81. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 81. Other fragments omit one or more protein domains.
(22) YPO0506
The ‘YPO0506’ sequence was annotated in reference 16 as ‘putative Clp ATPase’ (see GI: 16120836). For reference purposes, the amino acid sequence of full-length YPO0506 as found in the Y. pestis CO92 strain is given as SEQ ID NO:82 herein. However, it is postulated herein that YPO0506 forms part of a Type Three Secretion System (TTSS).
Preferred YPO0506 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:82; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:82, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0506 proteins include variants of SEQ ID NO:82. Preferred fragments of (b) comprise an epitope from SEQ ID NO:82. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:82. Other fragments omit one or more protein domains.
(23) YPO0508
The ‘YPO0508’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16120838). For reference purposes, the amino acid sequence of full-length YPO0508 as found in the Y. pestis CO92 strain is given as SEQ ID NO:83 herein. However, it is postulated herein that YPO0508 forms part of a Type Three Secretion System (TTSS).
Preferred YPO0508 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:83; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:83, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0508 proteins include variants of SEQ ID NO:83. Preferred fragments of (b) comprise an epitope from SEQ ID NO:83. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:83. Other fragments omit one or more protein domains.
(24) YPO0509
The ‘YPO0509’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16120839). For reference purposes, the amino acid sequence of full-length YPO0509 as found in the Y. pestis CO92 strain is given as SEQ ID NO:84 herein. However, it is postulated herein that YPO0509 forms part of a Type Three Secretion System (TTSS).
Preferred YPO0509 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:84; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:84, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0509 proteins include variants of SEQ ID NO:84. Preferred fragments of (b) comprise an epitope from SEQ ID NO:84. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 84. Other fragments omit one or more protein domains.
(25) YPO3579
The ‘YPO3579’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16123723). For reference purposes, the amino acid sequence of full-length YPO3579 as found in the Y. pestis CO92 strain is given as SEQ ID NO:85 herein. This protein is postulated herein to be a putative exported protein.
Preferred YPO3579 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:85; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:85, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3579 proteins include variants of SEQ ID NO:85. Preferred fragments of (b) comprise an epitope from SEQ ID NO:85. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:85. Other fragments omit one or more protein domains.
(26) YPO4040
The ‘YPO4040’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16124160). For reference purposes, the amino acid sequence of full-length YPO4040 as found in the Y. pestis CO92 strain is given as SEQ ID NO:86 herein. This protein is postulated herein to be a putative exported protein and furthermore to be a fimbrial component.
Preferred YPO4040 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:86; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:86, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO4040 proteins include variants of SEQ ID NO:86. Preferred fragments of (b) comprise an epitope from SEQ ID NO:86. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:86. Other fragments omit one or more protein domains.
Seventh Antigen Group
(1) YPO0496
The ‘YPO0496’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16120826). For reference purposes, the amino acid sequence of full-length YPO0496 as found in the Y. pestis CO92 strain is given as SEQ ID NO: 87 herein.
Preferred YPO0496 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:87; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:87, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO0496 proteins include variants of SEQ ID NO:87. Preferred fragments of (b) comprise an epitope from SEQ ID NO:87. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:87. Other fragments omit one or more protein domains.
(2) YPO1224
The ‘YPO1224’ sequence was annotated in reference 16 as ‘putative penicillin-bindin protein’ (see GI: 16121513). For reference purposes, the amino acid sequence of full-length YPO1224 as found in the Y. pestis CO92 strain is given as SEQ ID NO: 88 herein.
Preferred YPO1224 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:88; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:88, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO1224 proteins include variants of SEQ ID NO:88. Preferred fragments of (b) comprise an epitope from SEQ ID NO:88. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:88. Other fragments omit one or more protein domains.
(3) YPO3553
The ‘YPO3553’ sequence was annotated in reference 16 as ‘enhancing lycopene biosynthesis protein 2’ (see GI: 16123697). For reference purposes, the amino acid sequence of full-length YPO3553 as found in the Y. pestis CO92 strain is given as SEQ ID NO: 89 herein.
Preferred YPO3553 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:89; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:89, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3553 proteins include variants of SEQ ID NO:89. Preferred fragments of (b) comprise an epitope from SEQ ID NO:89. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:89. Other fragments omit one or more protein domains.
(4) YPO3987
The ‘YPO3987’ sequence was annotated in reference 16 as ‘hypothetical protein’ (see GI: 16124114). For reference purposes, the amino acid sequence of full-length YPO3987 as found in the Y. pestis CO92 strain is given as SEQ ID NO: 90 herein. It has been suggested that this protein is an exported protein.
Preferred YPO3987 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:90; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:90, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO3987 proteins include variants of SEQ ID NO:90. Preferred fragments of (b) comprise an epitope from SEQ ID NO:90. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:90. Other fragments omit one or more protein domains.
(5) YPO2190
The ‘YPO2190’ sequence was annotated in reference 16 as ‘attachment invasion locus protein precursor’ (see GI: 16122420). For reference purposes, the amino acid sequence of full-length YPO2190 as found in the Y. pestis CO92 strain is given as SEQ ID NO: 91 herein.
Preferred YPO2190 proteins for use with the invention comprise an amino acid sequence: (a) that has 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO:91; and/or (b) that is a fragment of at least n consecutive amino acids of SEQ ID NO:91, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YPO2190 proteins include variants of SEQ ID NO:91. Preferred fragments of (b) comprise an epitope from SEQ ID NO:91. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO:91. Other fragments omit one or more protein domains.
Type Three Secretion System
The Y. pestis proteins YPO0499, YPO0500, YPO0501, YPO0502, YPO0503, YPO0504, YPO0505, YPO0506, YPO0507, YPO0508, YPO0509, YPO0510, YPO0511, YPO0512, YPO0513, YPO0514, YPO0515 and YPO0516 are postulated herein to form part of a Type Three Secretion System (TTSS). Analysis reveals sequence similarity between these proteins and those of the Icm/Dot secretion system, also known as the IcmF-associated homologous protein (IAHP) gene cluster of Legionella pneumophila [24-28]. Furthermore, YPO0499-YPO0506 have sequence similarity with proteins of the EVP cluster, which forms a secretion system in Edwardsiella tarda [29]. A further Type Three Secretion System has recently been described in Vibrio cholerae. Elements of this Vibrio system share identity with proteins of the system share identity with proteins of the Y. pestis cluster YPO0499-YPO0516.
Of these proteins, YPO0499, YPO0500, YPO0501, YPO0502, YPO0503, YPO0505, YPO0506, YPO0508, YPO0509, YPO0512 and YPO0514 are considered to be surface exposed and therefore useful as immunising antigens.
Thus, particularly preferred compositions of the invention comprise one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or all 11) of YPO0499, YPO0500, YPO0501, YPO0502, YPO0503, YPO0505, YPO0506, YPO0508, YPO0509, YPO0512 and/or YPO0514.
Fusion and Hybrid Polypeptides
The Y. pestis antigens used in the invention may be present in the composition as individual separate polypeptides. Where more than one antigen is used, however, they do not have to be present as separate polypeptides. Instead, at least two (e.g. 2, 3, 4, 5, or more) antigens can be expressed as a single polypeptide chain (a ‘hybrid’ polypeptide). Hybrid polypeptides offer two main advantages: first, a polypeptide that may be unstable or poorly expressed on its own can be assisted by adding a suitable hybrid partner that overcomes the problem; second, commercial manufacture is simplified as only one expression and purification need be employed in order to produce two polypeptides which are both antigenically useful. The F1 and V antigens, for instance, can be expressed as a hybrid [30].
The hybrid polypeptide may comprise two or more polypeptide sequences from the first antigen group. The hybrid polypeptide may comprise one or more polypeptide sequences from the first antigen group and one or more polypeptide sequences from the second antigen group. The hybrid polypeptide may comprise one or more polypeptide sequences from the first antigen group and one or more polypeptide sequences from the third antigen group. The hybrid polypeptide may comprise one or more polypeptide sequences from the second antigen group and one or more polypeptide sequences from the third antigen group. The hybrid polypeptide may comprise one or more polypeptide sequences from the first, second and/or third antigen group and one or more polypeptide sequences from the fourth antigen group. The hybrid polypeptide may comprise one or more polypeptide sequences from the first, second and/or third antigen group and one or more polypeptide sequences from the fifth antigen group. The hybrid polypeptide may comprise one or more polypeptide sequences from the first, second and/or third antigen group and one or more polypeptide sequences from the sixth antigen group. The hybrid polypeptide may comprise one or more polypeptide sequences from the first, second and/or third antigen group and one or more polypeptide sequences from the seventh antigen group.
Hybrids for use in the present invention may also comprise combinations of antigens selected from the second, third, fourth, fifth, sixth and seventh antigen groups.
Hybrids consisting of amino acid sequences from two, three, four, five, six, seven, eight, nine, or ten Y. pestis antigens are preferred. In particular, hybrids consisting of amino acid sequences from two, three, four, or five Y. pestis antigens are preferred. Particularly preferred are hybrids consisting of amino acid sequences from two or three Y. pestis antigens.
Different hybrid polypeptides may be mixed together in a single formulation. Within such combinations, a Y. pestis antigen may be present in more than one hybrid polypeptide and/or as a non-hybrid polypeptide. It is preferred, however, that an antigen is present either as a hybrid or as a non-hybrid, but not as both.
Hybrid polypeptides can be represented by the formula NH2-A-{-X-L-}n-B—COOH, wherein: X is an amino acid sequence of a Y. pestis antigen, as described above; L is an optional linker amino acid sequence; A is an optional N-terminal amino acid sequence; B is an optional C-terminal amino acid sequence; n is an integer of 2 or more (e.g. 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15). Most preferably, n is 2 or 3.
If a —X— moiety has a leader peptide sequence in its wild-type form, this may be included or omitted in the hybrid protein. In some embodiments, the leader peptides will be deleted except for that of the —X— moiety located at the N-terminus of the hybrid protein i.e. the leader peptide of X1 will be retained, but the leader peptides of X2 . . . Xn will be omitted. This is equivalent to deleting all leader peptides and using the leader peptide of X1 as moiety -A-.
For each n instances of {—X-L-}, linker amino acid sequence -L- may be present or absent. For instance, when n=2 the hybrid may be NH2—X1-L1-X2-L2-COOH, NH2—X1—X2—COOH, NH2—X1-L1-X2—COOH, NH2—X1—X2-L2-COOH, etc. Linker amino acid sequence(s) -L- will typically be short (e.g. 20 or fewer amino acids i.e. 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1). Examples comprise short peptide sequences which facilitate cloning, poly-glycine linkers (i.e. comprising Glyn, where n=2, 3, 4, 5, 6, 7, 8, 9, 10 or more), and histidine tags (i.e. Hisn where n=3, 4, 5, 6, 7, 8, 9, 10 or more). Other suitable linker amino acid sequences will be apparent to those skilled in the art. A useful linker is GSGGGG (SEQ ID NO:60), with the Gly-Ser dipeptide being formed from a BamHI restriction site, thus aiding cloning and manipulation, and the (Gly)4 tetrapeptide being a typical poly-glycine linker.
-A- is an optional N-terminal amino acid sequence. This will typically be short (e.g. 40 or fewer amino acids i.e. 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1). Examples include leader sequences to direct protein trafficking, or short peptide sequences which facilitate cloning or purification (e.g. histidine tags i.e. Hisn, where n=3, 4, 5, 6, 7, 8, 9, 10 or more). Other suitable N-terminal amino acid sequences will be apparent to those skilled in the art. If X1 lacks its own N-terminus methionine, -A- is preferably an oligopeptide (e.g. with 1, 2, 3, 4, 5, 6, 7 or 8 amino acids) which provides a N-terminus methionine.
—B— is an optional C-terminal amino acid sequence. This will typically be short (e.g. 40 or fewer amino acids i.e. 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1). Examples include sequences to direct protein trafficking, short peptide sequences which facilitate cloning or purification (e.g. comprising histidine tags i.e. Hisn where n=3, 4, 5, 6, 7, 8, 9, 10 or more), or sequences which enhance protein stability. Other suitable C-terminal amino acid sequences will be apparent to those skilled in the art.
Preferred fusion protein compositions of the invention comprise one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) of 0809_GST, 0809_His, 0499_GST, 0499_His, 1070_GST, 1070_His, 3489_GST, 3489_His, 1354_GST, 1354_His, 3631_GST, 3631_His, 1604_GST, 1604_His, 4003_GST, 4003_His, 0500_His, 0501_His, 0502_His, 0502_GST, 0503_His, 0503_GST, 0505_His, 0505GST, 0506_His, 0508_GST and/or 0509_GST. According to this nomenclature, each antigen may have a N-terminal GST tag or a C-terminal his tag. Therefore, for example, 3489_His is YPO3489 with a C-terminal his tag and 0809_GST is YPO0809 with a N-terminal GST tag.
Particularly preferred combinations comprise (1) 0809_GST and 0499_GST, (2) 1070_GST and 3489_His, (3) 1354_His and 3631_His, and/or (4) 1604_His and 4003_His. Such preferred combinations may be found in an immunogenic composition further comprising alum and/or CpG.
The invention also provides nucleic acid encoding hybrid polypeptides of the invention. The term “nucleic acid” includes DNA and RNA, and also their analogues, such as those containing modified backbones (e.g. phosphorothioates, etc.), and also peptide nucleic acids (PNA), etc.
Polypeptides Used with the Invention
Polypeptides used with the invention can take various forms (e.g. native, fusions, glycosylated, non-glycosylated, lipidated, non-lipidated, phosphorylated, non-phosphorylated, myristoylated, non-myristoylated, monomeric, multimeric, particulate, denatured, etc.). F1, for instance, is known to exist in various forms, including a multimeric glycoprotein form. Lipoproteins are particularly preferred for use as immunogens.
Polypeptides used with the invention can be prepared by various means (e.g. recombinant expression, purification from cell culture, chemical synthesis, etc.). Recombinantly-expressed proteins are preferred, particularly for hybrid polypeptides.
Polypeptides used with the invention are preferably provided in purified or substantially purified form i.e. substantially free from other polypeptides (e.g. free from naturally-occurring polypeptides), particularly from other Yersinia or host cell polypeptides, and are generally at least about 50% pure (by weight), and usually at least about 90% pure i.e. less than about 50%, and more preferably less than about 10% (e.g. 5%) of a composition is made up of other expressed polypeptides. Thus the antigens in the compositions are separated from the whole organism with which the molecule is expressed.
Polypeptides used with the invention are preferably Y. pestis polypeptides.
The term “polypeptide” refers to amino acid polymers of any length. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-amino acids. The terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component. Also included are, for example, polypeptides containing one or more analogs of an amino acid (including, for example, unnatural amino acids, etc.), as well as other modifications known in the art. Polypeptides can occur as single chains or associated chains.
The invention provides polypeptides comprising a sequence —P-Q- or -Q-P—, wherein: —P— is an amino acid sequence as defined above and -Q- is not a sequence as defined above i.e. the invention provides fusion proteins. Fusion proteins of F1 are known, for instance, from reference 103, where a heterologous anchor domain is attached to allow cell-surface display of a protein that would normally be secreted. Where the N-terminus codon of —P— is not ATG, but this codon is not present at the N-terminus of a polypeptide, it will be translated as the standard amino acid for that codon rather than as a Met. Where this codon is at the N-terminus of a polypeptide, however, it will be translated as Met. Polypeptides used with the invention may be prepared as a GST-fusion protein and/or a His-tagged fusion protein.
The invention also provides a process for producing a polypeptide of the invention, comprising the step of culturing a host cell transformed with nucleic acid of the invention under conditions which induce polypeptide expression.
The invention provides a process for producing a polypeptide of the invention, comprising the step of synthesising at least part of the polypeptide by chemical means.
Strains
Polypeptides of the invention may comprise an amino acid sequence found in a Y. pestis of biovar Antiqua, Mediaevalis, Orientalis and/or Microtus, with biovar orientalis being preferred [31].
Polypeptides of the invention may comprise an amino acid sequence found in a Y. pestis of ribotypes A, B, C, Q, R, and/or T.
Preferred polypeptides of the invention comprise an amino acid sequence found in Y. pestis strains CO92 [16], KIM [17], 91001 [18], 685, etc., including the strains listed in references 31 and 100. The sequence may also be found in other Yersinia species, such as a Y. pseudotuberculosis (full genome sequence available as GI: 51587641 [32]) or a Y. enterocolitica. 
Where hybrid polypeptides are used, the individual antigens within the hybrid (i.e. individual —X— moieties) may be from one or more strains. Where n=2, for instance, X2 may be from the same strain as X1 or from a different strain. Where n=3, the strains might be (i) X1═X2═X3 (ii) X1═X2≠X3 (iii) X1≠X2═X3 (iv) X1≠X2≠X3 or (v) X1═X3≠X2, etc.
Heterologous Hosts
Whilst expression of the polypeptides of the invention may take place in Yersinia, the invention preferably utilises a heterologous host. The heterologous host may be prokaryotic (e.g. a bacterium) or eukaryotic. It is preferably E. coli, but other suitable hosts include Bacillus subtilis, Vibrio cholerae, Salmonella typhi, Salmonella typhimurium, Neisseria lactamica, Neisseria cinerea, Mycobacteria (e.g. M. tuberculosis), yeasts, etc.
Immunogenic Compositions and Medicaments
Compositions of the invention are preferably immunogenic compositions, such as vaccine compositions. The pH of the composition is preferably between 6 and 8, preferably about 7. The pH may be maintained by the use of a buffer. A phosphate buffer is typical. The composition may be sterile and/or pyrogen-free. The composition may be gluten-free. The composition may be substantially free from formaldehyde, phenol, beef-heart extract, yeast extract, and/or agar. The composition may be free from Y. pestis DNA. The composition may be isotonic with respect to humans.
Vaccines according to the invention may either be prophylactic (i.e. to prevent infection) or therapeutic (i.e. to treat infection), but will typically be prophylactic. Accordingly, the invention includes a method for the therapeutic or prophylactic treatment of Y. pestis infection in an animal susceptible to Yersinia infection comprising administering to said animal a therapeutic or prophylactic amount of the immunogenic compositions of the invention.
Compositions may include a preservative, particularly if packaged in a multiple dose format.
Compositions may comprise detergent e.g. a Tween (polysorbate), such as Tween 80. Detergents are generally present at low levels e.g. <0.01%.
Compositions may include sodium salts (e.g. sodium chloride) to give tonicity. A concentration of 10±2 mg/ml NaCl is typical.
Compositions may comprise a sugar alcohol (e.g. mannitol) or a disaccharide (e.g. sucrose or trehalose) e.g. at around 15-30 mg/ml (e.g. 25 mg/ml), particularly if they are to be lyophilised or if they include material which has been reconstituted from lyophilised material.
The immunogenic compositions of the invention may also comprise one or more immunoregulatory agents. Preferably, one or more of the immunoregulatory agents include one or more adjuvants. The adjuvants may include a TH1 adjuvant and/or a TH2 adjuvant, further discussed below.
Adjuvants which may be used in compositions of the invention include, but are not limited to:
A. Mineral-containing Compositions
Mineral containing compositions suitable for use as adjuvants in the invention include mineral salts, such as aluminium salts and calcium salts. The invention includes mineral salts such as hydroxides (e.g. oxyhydroxides), phosphates (e.g. hydroxyphosphates, orthophosphates), sulphates, etc. [e.g. see chapters 8 & 9 of ref. 33], or mixtures of different mineral compounds, with the compounds taking any suitable form (e.g. gel, crystalline, amorphous, etc.), and with adsorption being preferred. The mineral containing compositions may also be formulated as a particle of metal salt [34].
Aluminium phosphates are particularly preferred, particularly in compositions which include a H. influenzae saccharide antigen, and a typical adjuvant is amorphous aluminium hydroxyphosphate with PO4/Al molar ratio between 0.84 and 0.92, included at 0.6 mg Al3+/ml. Adsorption with a low dose of aluminium phosphate may be used e.g. between 50 and 100 μg Al3+ per conjugate per dose. Where there is more than one conjugate in a composition, not all conjugates need to be adsorbed.
B. Oil Emulsions
Oil emulsion compositions suitable for use as adjuvants in the invention include squalene-water emulsions, such as MF59 [Chapter 10 of ref. 33; see also ref. 35] (5% Squalene, 0.5% Tween 80, and 0.5% Span 85, formulated into submicron particles using a microfluidizer). Complete Freund's adjuvant (CFA) and incomplete Freund's adjuvant (IFA) may also be used.
C. Saponin Formulations [Chapter 22 of Ref. 33]
Saponin formulations may also be used as adjuvants in the invention. Saponins are a heterologous group of sterol glycosides and triterpenoid glycosides that are found in the bark, leaves, stems, roots and even flowers of a wide range of plant species. Saponin from the bark of the Quillaia saponaria Molina tree have been widely studied as adjuvants. Saponin can also be commercially obtained from Smilax ornata (sarsaprilla), Gypsophilla paniculata (brides veil), and Saponaria officianalis (soap root). Saponin adjuvant formulations include purified formulations, such as QS21, as well as lipid formulations, such as ISCOMs. QS21 is marketed as StimulonTM.
Saponin compositions have been purified using HPLC and RP-HPLC. Specific purified fractions using these techniques have been identified, including QS7, QS17, QS18, QS21, QH-A, QH-B and QH-C. Preferably, the saponin is QS21. A method of production of QS21 is disclosed in ref. 36. Saponin formulations may also comprise a sterol, such as cholesterol [37].
Combinations of saponins and cholesterols can be used to form unique particles called immunostimulating complexs (ISCOMs) [chapter 23 of ref. 33]. ISCOMs typically also include a phospholipid such as phosphatidylethanolamine or phosphatidylcholine. Any known saponin can be used in ISCOMs. Preferably, the ISCOM includes one or more of QuilA, QHA & QHC. ISCOMs are further described in refs. 37-39. Optionally, the ISCOMS may be devoid of additional detergent [40].
A review of the development of saponin based adjuvants can be found in refs. 41 & 42.
D. Virosomes and Virus-like Particles
Virosomes and virus-like particles (VLPs) can also be used as adjuvants in the invention. These structures generally contain one or more proteins from a virus optionally combined or formulated with a phospholipid. They are generally non-pathogenic, non-replicating and generally do not contain any of the native viral genome. The viral proteins may be recombinantly produced or isolated from whole viruses. These viral proteins suitable for use in virosomes or VLPs include proteins derived from influenza virus (such as HA or NA), Hepatitis B virus (such as core or capsid proteins), Hepatitis E virus, measles virus, Sindbis virus, Rotavirus, Foot-and-Mouth Disease virus, Retrovirus, Norwalk virus, human Papilloma virus, HIV, RNA-phages, Qβ-phage (such as coat proteins), GA-phage, fr-phage, AP205 phage, and Ty (such as retrotransposon Ty protein p1). VLPs are discussed further in refs. 43-48. Virosomes are discussed further in, for example, ref. 49
E. Bacterial or Microbial Derivatives
Adjuvants suitable for use in the invention include bacterial or microbial derivatives such as non-toxic derivatives of enterobacterial lipopolysaccharide (LPS), Lipid A derivatives, immunostimulatory oligonucleotides and ADP-ribosylating toxins and detoxified derivatives thereof.
Non-toxic derivatives of LPS include monophosphoryl lipid A (MPL) and 3-O-deacylated MPL (3dMPL). 3dMPL is a mixture of 3 de-O-acylated monophosphoryl lipid A with 4, 5 or 6 acylated chains. A preferred “small particle” form of 3 De-O-acylated monophosphoryl lipid A is disclosed in ref. 50. Such “small particles” of 3dMPL are small enough to be sterile filtered through a 0.22 μm membrane [50]. Other non-toxic LPS derivatives include monophosphoryl lipid A mimics, such as aminoalkyl glucosaminide phosphate derivatives e.g. RC-529 [51,52]. Lipid A derivatives include derivatives of lipid A from Escherichia coli such as OM-174. OM-174 is described for example in refs. 53 & 54.
Immunostimulatory oligonucleotides suitable for use as adjuvants in the invention include nucleotide sequences containing a CpG motif (a dinucleotide sequence containing an unmethylated cytosine linked by a phosphate bond to a guanosine). Double-stranded RNAs and oligonucleotides containing palindromic or poly(dG) sequences have also been shown to be immunostimulatory.
The CpG's can include nucleotide modifications/analogs such as phosphorothioate modifications and can be double-stranded or single-stranded. References 55, 56 and 57 disclose possible analog substitutions e.g. replacement of guanosine with 2′-deoxy-7-deazaguanosine. The adjuvant effect of CpG oligonucleotides is further discussed in refs. 58-63.
The CpG sequence may be directed to TLR9, such as the motif GTCGTT or TTCGTT [64]. The CpG sequence may be specific for inducing a Th1 immune response, such as a CpG-A ODN, or it may be more specific for inducing a B cell response, such a CpG-B ODN. CpG-A and CpG-B ODNs are discussed in refs. 65-67. Preferably, the CpG is a CpG-A ODN.
Preferably, the CpG oligonucleotide is constructed so that the 5′ end is accessible for receptor recognition. Optionally, two CpG oligonucleotide sequences may be attached at their 3′ ends to form “immunomers”. See, for example, refs. 64 & 68-70.
Bacterial ADP-ribosylating toxins and detoxified derivatives thereof may be used as adjuvants in the invention. Preferably, the protein is derived from E. coli (E. coli heat labile enterotoxin “LT”), cholera (“CT”), or pertussis (“PT”). The use of detoxified ADP-ribosylating toxins as mucosal adjuvants is described in ref. 71 and as parenteral adjuvants in ref. 72. The toxin or toxoid is preferably in the form of a holotoxin, comprising both A and B subunits. Preferably, the A subunit contains a detoxifying mutation; preferably the B subunit is not mutated. Preferably, the adjuvant is a detoxified LT mutant such as LT-K63, LT-R72, and LT-G192. The use of ADP-ribosylating toxins and detoxified derivatives thereof, particularly LT-K63 and LT-R72, as adjuvants can be found in refs. 73-80. Numerical reference for amino acid substitutions is preferably based on the alignments of the A and B subunits of ADP-ribosylating toxins set forth in ref. 81, specifically incorporated herein by reference in its entirety.
F. Human Immunomodulators
Human immunomodulators suitable for use as adjuvants in the invention include cytokines, such as interleukins (e.g. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12 [82], etc.) [83], interferons (e.g. interferon-γ), macrophage colony stimulating factor, and tumor necrosis factor. A preferred immunomodulator is IL-12.
G. Bioadhesives and Mucoadhesives
Bioadhesives and mucoadhesives may also be used as adjuvants in the invention. Suitable bioadhesives include esterified hyaluronic acid microspheres [84] or mucoadhesives such as cross-linked derivatives of poly(acrylic acid), polyvinyl alcohol, polyvinyl pyrollidone, polysaccharides and carboxymethylcellulose. Chitosan and derivatives thereof may also be used as adjuvants in the invention [85].
H. Microparticles
Microparticles may also be used as adjuvants in the invention. Microparticles (i.e. a particle of  ̃100 nm to  ̃150 μm in diameter, more preferably  ̃200 nm to  ̃30 μm in diameter, and most preferably  ̃500 nm to  ̃10 μm in diameter) formed from materials that are biodegradable and non-toxic (e.g. a poly(α-hydroxy acid), a polyhydroxybutyric acid, a polyorthoester, a polyanhydride, a polycaprolactone, etc.), with poly(lactide-co-glycolide) are preferred, optionally treated to have a negatively-charged surface (e.g. with SDS) or a positively-charged surface (e.g. with a cationic detergent, such as CTAB).
I. Liposomes (Chapters 13 & 14 of Ref 33)
Examples of liposome formulations suitable for use as adjuvants are described in refs. 86-88.
J. Polyoxyethylene Ether and Polyoxyethylene Ester Formulations
Adjuvants suitable for use in the invention include polyoxyethylene ethers and polyoxyethylene esters [89]. Such formulations further include polyoxyethylene sorbitan ester surfactants in combination with an octoxynol [90] as well as polyoxyethylene allyl ethers or ester surfactants in combination with at least one additional non-ionic surfactant such as an octoxynol [91]. Preferred polyoxyethylene ethers are selected from the following group: polyoxyethylene-9-lauryl ether (laureth 9), polyoxyethylene-9-steoryl ether, polyoxytheylene-8-steoryl ether, polyoxyethylene-4-lauryl ether, polyoxyethylene-35-lauryl ether, and polyoxyethylene-23-lauryl ether.
K. Polyphosphazene (PCPP)
PCPP formulations are described, for example, in refs. 92 and 93.
L. Muramyl Peptides
Examples of muramyl peptides suitable for use as adjuvants in the invention include N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP), and N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine MTP-PE).
M. Imidazoquinolone Compounds.
Examples of imidazoquinolone compounds suitable for use adjuvants in the invention include Imiquamod and its homologues (e.g. “Resiquimod 3M”), described further in refs. 94 and 95.
The invention may also comprise combinations of aspects of one or more of the adjuvants identified above. For example, the following adjuvant compositions may be used in the invention: (1) a saponin and an oil-in-water emulsion [96]; (2) a saponin (e.g. QS21)+a non-toxic LPS derivative (e.g. 3dMPL) [97]; (3) a saponin (e.g. QS21)+a non-toxic LPS derivative (e.g. 3dMPL)+a cholesterol; (4) a saponin (e.g. QS21)+3dMPL+IL-12 (optionally+a sterol) [98]; (5) combinations of 3dMPL with, for example, QS21 and/or oil-in-water emulsions [99]; (6) SAF, containing 10% squalane, 0.4% Tween 80TM, 5% pluronic-block polymer L121, and thr-MDP, either microfluidized into a submicron emulsion or vortexed to generate a larger particle size emulsion. (7) RibiTM adjuvant system (RAS), (Ribi Immunochem) containing 2% squalene, 0.2% Tween 80, and one or more bacterial cell wall components from the group consisting of monophosphorylipid A (MPL), trehalose dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL+CWS (DetoxTM); and (8) one or more mineral salts (such as an aluminum salt)+a non-toxic derivative of LPS (such as 3dMPL).
Other substances that act as immunostimulating agents are disclosed in chapter 7 of ref. 33.
The use of an aluminium hydroxide and/or aluminium phosphate adjuvant is particularly preferred, and antigens are generally adsorbed to these salts. Calcium phosphate is another preferred adjuvant. Other preferred adjuvant combinations include combinations of Th1 and Th2 adjuvants such as CpG & alum or resiquimod & alum.
Use of the combination of a mineral salt, such as an aluminium salt, and an oligonucleotide containing a CpG motif provide for an enhanced immune response. The invention therefore provides a composition comprising an oligonucleotide containing a CpG motif, a mineral salt such as an aluminium salt, and one or more Y. pestis antigens as defined above. The invention also provides a composition comprising an ADP ribosylating toxin (such as a detoxified ADP ribosylating toxin), an oligonucleotide containing a CpG motif, and one or more Y. pestis antigens as defined above.
The compositions of the invention will preferably elicit both a cell mediated immune response as well as a humoral immune response in order to effectively address a Yersinia intracellular infection. This immune response will preferably induce long lasting (e.g. neutralising) antibodies and a cell mediated immunity that can quickly respond upon exposure to Yersinia. 
Two types of T cells, CD4 and CD8 cells, are generally thought necessary to initiate and/or enhance cell mediated immunity and humoral immunity. CD8 T cells can express a CD8 co-receptor and are commonly referred to as Cytotoxic T lymphocytes (CTLs). CD8 T cells are able to recognized or interact with antigens displayed on MHC Class I molecules.
CD4 T cells can express a CD4 co-receptor and are commonly referred to as T helper cells. CD4 T cells are able to recognize antigenic peptides bound to MHC class II molecules. Upon interaction with a MHC class II molecule, the CD4 cells can secrete factors such as cytokines. These secreted cytokines can activate B cells, cytotoxic T cells, macrophages, and other cells that participate in an immune response. Helper T cells or CD4+ cells can be further divided into two functionally distinct subsets: TH1 phenotype and TH2 phenotypes which differ in their cytokine and effector function.
Activated TH1 cells enhance cellular immunity (including an increase in antigen-specific CTL production) and are therefore of particular value in responding to intracellular infections. Activated TH1 cells may secrete one or more of IL-2, IFN-γ, and TNF-β. A TH1 immune response may result in local inflammatory reactions by activating macrophages, NK (natural killer) cells, and CD8 cytotoxic T cells (CTLs). A TH1 immune response may also act to expand the immune response by stimulating growth of B and T cells with IL-12. TH1 stimulated B cells may secrete IgG2a.
Activated TH2 cells enhance antibody production and are therefore of value in responding to extracellular infections. Activated TH2 cells may secrete one or more of IL-4, IL-5, IL-6, and IL-10. A TH2 immune response may result in the production of IgG1, IgE, IgA and memory B cells for future protection.
An enhanced immune response may include one or more of an enhanced TH1 immune response and a TH2 immune response.
A TH1 immune response may include one or more of an increase in CTLs, an increase in one or more of the cytokines associated with a TH1 immune response (such as IL-2, IFN-γ, and TNF-β), an increase in activated macrophages, an increase in NK activity, or an increase in the production of IgG2a. Preferably, the enhanced TH1 immune response will include an increase in IgG2a production.
A TH1 immune response may be elicited using a TH1 adjuvant. A TH1 adjuvant will generally elicit increased levels of IgG2a production relative to immunization of the antigen without adjuvant. TH1 adjuvants suitable for use in the invention may include for example saponin formulations, virosomes and virus like particles, non-toxic derivatives of enterobacterial lipopolysaccharide (LPS), immunostimulatory oligonucleotides. Immunostimulatory oligonucleotides, such as oligonucleotides containing a CpG motif, are preferred TH1 adjuvants for use in the invention.
A TH2 immune response may include one or more of an increase in one or more of the cytokines associated with a TH2 immune response (such as IL-4, IL-5, IL-6 and IL-10), or an increase in the production of IgG1, IgE, IgA and memory B cells. Preferably, the enhanced TH2 immune response will include an increase in IgG1 production.
A TH2 immune response may be elicited using a TH2 adjuvant. A TH2 adjuvant will generally elicit increased levels of IgG1 production relative to immunization of the antigen without adjuvant. TH2 adjuvants suitable for use in the invention include, for example, mineral containing compositions, oil-emulsions, and ADP-ribosylating toxins and detoxified derivatives thereof. Mineral containing compositions, such as aluminium salts are preferred TH2 adjuvants for use in the invention.
Preferably, the invention includes a composition comprising a combination of a TH1 adjuvant and a TH2 adjuvant. Preferably, such a composition elicits an enhanced TH1 and an enhanced TH2 response, i.e., an increase in the production of both IgG1 and IgG2a production relative to immunization without an adjuvant. Still more preferably, the composition comprising a combination of a TH1 and a TH2 adjuvant elicits an increased TH1 and/or an increased TH2 immune response relative to immunization with a single adjuvant (i.e., relative to immunization with a TH1 adjuvant alone or immunization with a TH2 adjuvant alone).
The immune response may be one or both of a TH1 immune response and a TH2 response. Preferably, immune response provides for one or both of an enhanced TH1 response and an enhanced TH2 response.
The enhanced immune response may be one or both of a systemic and a mucosal immune response. Preferably, the immune response provides for one or both of an enhanced systemic and an enhanced mucosal immune response. Preferably the mucosal immune response is a TH2 immune response. Preferably, the mucosal immune response includes an increase in the production of IgA.
Methods of Treatment and Medical Uses
The invention provides one or more of (1) a YPO0512 antigen; (2) a YPO0563 antigen; (3) a YPO3489 antigen; (4) a YPO4003 antigen; (5) a YPO1604 antigen; (6) a YPO3061 antigen; (7) a YPO3559 antigen; (8) a YPO3382 antigen; (9) a YPO0860 antigen; (10) a YPO0086 antigen; (11) a YPO3631 antigen; (12) a YPO2881 antigen; (13) a YPO3343 antigen; (14) a YPO3361 antigen; (15) a YPO3430 antigen; (16) a YPO1411 antigen; (17) a YPO3935 antigen; (18) a YPO0809 antigen; (19) a YPO1123 antigen; (20) a YPO3065 antigen; and/or (21) a YPO1070 antigen, for use (i) as an immunogen, (ii) in therapy, and/or (iii) in the manufacture of a medicament for raising an immune response in a mammal.
The invention also provides the use of one or more of (1) a YPO0512 antigen; (2) a YPO0563 antigen; (3) a YPO3489 antigen; (4) a YPO4003 antigen; (5) a YPO1604 antigen; (6) a YPO3061 antigen; (7) a YPO3559 antigen; (8) a YPO3382 antigen; (9) a YPO0860 antigen; (10) a YPO0086 antigen; (11) a YPO3631 antigen; (12) a YPO2881 antigen; (13) a YPO3343 antigen; (14) a YPO3361 antigen; (15) a YPO3430 antigen; (16) a YPO1411 antigen; (17) a YPO3935 antigen; (18) a YPO0809 antigen; (19) a YPO1123 antigen; (20) a YPO3065 antigen; and/or (21) a YPO1070 antigen, in the manufacture of a medicament for raising an immune response in a mammal.
The invention provides one or more of (1) a YPO0102 antigen; (2) a YPO0570 antigen; (3) a YPO1053 antigen; (4) a YPO1435 antigen; (5) a YPO2674 antigen; (6) a YPO2292 antigen; (7) a YPO3050 antigen; (8) a YPO2615 antigen; (9) a YPO1507 antigen; (10) a YPO4111 antigen; (11) a YPO0015 antigen; (12) a YPO0195 antigen; (13) a YPO2342 antigen; (14) a YPO0501 antigen; (15) a YPO0502 antigen; (16) a YPO0819 antigen; (17) a YPO3644 antigen; (18) a YPO1746 antigen; (19) a YPO0351 antigen; (20) a YPO0468 antigen; (21) a YPO0203 antigen; (22) a YPO0216 antigen; (23) a YPO3536 antigen; (24) a YPO0233 antigen; (25) a YPO0067 antigen; (26) a YPO3643 antigen; (27) a YPO3375 antigen; (28) a YPO0494 antigen; (29) a YPO1052 antigen; (30) a YPO1906 antigen; (31) a YPO0663 antigen; (32) a YPO1222 antigen; (33) a YPO2905 antigen; (34) a YPO4070 antigen; (35) a YPPCP1.07 antigen; and/or (36) a YPMT1.42 antigen, for use (i) as an immunogen, (ii) in therapy, and/or (iii) in the manufacture of a medicament for raising an immune response in a mammal.
The invention also provides the use of one or more of (1) a YPO0102 antigen; (2) a YPO0570 antigen; (3) a YPO1053 antigen; (4) a YPO1435 antigen; (5) a YPO2674 antigen; (6) a YPO2292 antigen; (7) a YPO3050 antigen; (8) a YPO2615 antigen; (9) a YPO1507 antigen; (10) a YPO4111 antigen; (11) a YPO0015 antigen; (12) a YPO0195 antigen; (13) a YPO2342 antigen; (14) a YPO0501 antigen; (15) a YPO0502 antigen; (16) a YPO0819 antigen; (17) a YPO3644 antigen; (18) a YPO1746 antigen; (19) a YPO0351 antigen; (20) a YPO0468 antigen; (21) a YPO0203 antigen; (22) a YPO0216 antigen; (23) a YPO3536 antigen; (24) a YPO0233 antigen; (25) a YPO0067 antigen; (26) a YPO3643 antigen; (27) a YPO3375 antigen; (28) a YPO0494 antigen; (29) a YPO1052 antigen; (30) a YPO1906 antigen; (31) a YPO0663 antigen; (32) a YPO1222 antigen; (33) a YPO2905 antigen; (34) a YPO4070 antigen; (35) a YPPCP1.07 antigen; and/or (36) a YPMT1.42 antigen, in the manufacture of a medicament for raising an immune response in a mammal.
The invention provides one or more of (1) a YPO0457 antigen; (2) a YPO0514 antigen; (3) a YPO0694 antigen; (4) a YPO0805 antigen; (5) a YPO0982 antigen; (6) a YPO1354 antigen; (7) a YPO1408 antigen; (8) a YPO1792 antigen; (9) a YPO2506 antigen; (10) a YPO2713 antigen; (11) a YPO2950 antigen; (12) a YPO3026 antigen; (13) a YPO3417 antigen; (14) a YPO3551 antigen; (15) a YPO3646 antigen; (16) a YPO3982 antigen; (17) a YPO0065 antigen; (18) a YPO0499 antigen; (19) a YPO0505 antigen, (20) a YPO0500 antigen; (21) a YPO0503 antigen; (22) a YPO0506 antigen; (23) a YPO0508 antigen; (24) a YPO0509 antigen; (25) a YPO3579 antigen and/or (26) a YPO4040 antigen, for use (i) as an immunogen, (ii) in therapy, and/or (iii) in the manufacture of a medicament for raising an immune response in a mammal.
The invention provides the use of one or more of (1) a YPO0457 antigen; (2) a YPO0514 antigen; (3) a YPO0694 antigen; (4) a YPO0805 antigen; (5) a YPO0982 antigen; (6) a YPO1354 antigen; (7) a YPO1408 antigen; (8) a YPO1792 antigen; (9) a YPO2506 antigen; (10) a YPO2713 antigen; (11) a YPO2950 antigen; (12) a YPO3026 antigen; (13) a YPO3417 antigen; (14) a YPO3551 antigen; (15) a YPO3646 antigen; (16) a YPO3982 antigen; (17) a YPO0065 antigen; (18) a YPO0499 antigen; (19) a YPO0505 antigen, (20) a YPO0500 antigen; (21) a YPO0503 antigen; (22) a YPO0506 antigen; (23) a YPO0508 antigen; (24) a YPO0509 antigen; (25) a YPO3579 antigen and/or (26) a YPO4040 antigen in the manufacture of a medicament for raising an immune response in a mammal.
The invention provides one or more of (1) a YPO0496 antigen; (2) a YPO1224 antigen; (3) a YPO3553 antigen; (4) a YPO3987 antigen and/or (5) a YPO2190 antigen, for use (i) as an immunogen, (ii) in therapy, and/or (iii) in the manufacture of a medicament for raising an immune response in a mammal.
The invention provides the use of one or more of (1) a YPO0496 antigen; (2) a YPO1224 antigen; (3) a YPO3553 antigen; (4) a YPO3987 antigen and/or (5) a YPO2190 antigen in the manufacture of a medicament for raising an immune response in a mammal.
These medicaments are preferably vaccines.
The invention also provides a method for raising an immune response in a mammal comprising the step of administering an effective amount of a composition of the invention. The immune response is preferably protective and preferably involves antibodies and/or cell-mediated immunity. The method may raise a booster response.
By raising an immune response in the mammal by these uses and methods, the mammal can be protected against Y. pestis infection. More particularly, the mammal may be protected against a plague, including bubonic plague, septicemic plague and/or pneumonic plague. Other related diseases include cellulocutaneous plague and plague meningitis. The medicament is preferably for protecting a mammal against pneumonic plague.
Compositions of the invention can preferably protect against Y. pestis ribotypes [100,101] including one or more of A, B, C, Q, R, and/or T.
Compositions of the invention can preferably protect against Y. pestis biovars including one or more of antiqua, mediaevalis, orientalis and/or microtus [102].
The invention also provides a kit comprising a first component and a second component wherein neither the first component nor the second component is a composition of the invention as described above, but wherein the first component and the second component can be combined to provide a composition of the invention as described above. The kit may further include a third component comprising one or more of the following: instructions, syringe or other delivery device, adjuvant, or pharmaceutically acceptable formulating solution.
The invention also provides a delivery device pre-filled with an immunogenic composition of the invention.
The mammal is preferably a human. Where the vaccine is for prophylactic use, the human is preferably a child (e.g. a toddler or infant) or a teenager; where the vaccine is for therapeutic use, the human is preferably a teenager or an adult. A vaccine intended for children may also be administered to adults e.g. to assess safety, dosage, immunogenicity, etc.
One way of checking efficacy of therapeutic treatment involves monitoring Y. pestis infection after administration of the compositions of the invention. One way of checking efficacy of prophylactic treatment involves monitoring immune responses, systemically (such as monitoring the level of IgG1 and IgG2a production) and/or mucosally (such as monitoring the level of IgA production), against the Y. pestis antigens in the compositions of the invention after administration of the composition. Typically, serum Yersinia specific antibody responses are determined post-immunisation but pre-challenge whereas mucosal Yersinia specific antibody body responses are determined post-immunisation and post-challenge. The protective effect of a composition can be tested in standard animal models, including the murine aerosol challenge model of reference 8.
Another way of assessing the immunogenicity of the compositions of the present invention is to express the proteins recombinantly for screening patient sera or mucosal secretions by immunoblot and/or microarrays. A positive reaction between the protein and the patient sample indicates that the patient has mounted an immune response to the protein in question. This method may also be used to identify immunodominant antigens and/or epitopes within antigens.
The vaccine compositions of the present invention can be evaluated in in vitro and in vivo animal models prior to host, e.g., human, administration. For example, in vitro neutralization is suitable for testing vaccine compositions directed toward Y. pestis. 
The efficacy of vaccine compositions can also be determined in vivo by challenging animal models of Y. pestis infection, e.g., guinea pigs or mice, with the vaccine compositions. For example, reference 103 describes the immunisation of mice against Y. pestis and then challenging with F1 antigen. The administered compositions may or may not be derived from the same strains as the challenge strains. Preferably the compositions are derived from the same strains as the challenge strains. In vivo efficacy models include but are not limited to: (i) murine infection models using Y. pestis strains that are infectious to humans; (ii) murine disease models which use mouse-adapted Y. pestis strains, such as strains which are particularly virulent in mice; and (iii) primate models using human strains.
Compositions of the invention will generally be administered directly to a patient. Direct delivery may be accomplished by parenteral injection (e.g. subcutaneously, intraperitoneally, intravenously, intramuscularly, or to the interstitial space of a tissue), or mucosally, such as by rectal, oral (e.g. tablet, spray), vaginal, topical, transdermal (see e.g. reference 104) or transcutaneous (see e.g. references 9, 105 and 106), intranasal (see e.g. reference 107), ocular, aural, pulmonary or other mucosal administration.
The invention may be used to elicit systemic and/or mucosal immunity, preferably to elicit an enhanced systemic and/or mucosal immunity.
Preferably the enhanced systemic and/or mucosal immunity is reflected in an enhanced TH1 and/or TH2 immune response. Preferably, the enhanced immune response includes an increase in the production of IgG1 and/or IgG2a and/or IgA.
Dosage treatment can be a single dose schedule or a multiple dose schedule. Multiple doses may be used in a primary immunisation schedule and/or in a booster immunisation schedule. In a multiple dose schedule the various doses may be given by the same or different routes e.g. a parenteral prime and mucosal boost, a mucosal prime and parenteral boost, etc.
Yersinia infections affect various areas of the body and so the compositions of the invention may be prepared in various forms. For example, the compositions may be prepared as injectables, either as liquid solutions or suspensions. Solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection can also be prepared (e.g. a lyophilised composition or a spray-freeze dried composition). The composition may be prepared for topical administration e.g. as an ointment, cream or powder. The composition may be prepared for oral administration e.g. as a tablet or capsule, as a spray, or as a syrup (optionally flavoured). The composition may be prepared for pulmonary administration e.g. as an inhaler, using a fine powder or a spray. The composition may be prepared as a suppository or pessary. The composition may be prepared for nasal, aural or ocular administration e.g. as drops. The composition may be in kit form, designed such that a combined composition is reconstituted just prior to administration to a patient. Such kits may comprise one or more antigens in liquid form and one or more lyophilised antigens.
Where a composition is to be prepared extemporaneously prior to use (e.g. where a component is presented in lyophilised form) and is presented as a kit, the kit may comprise two vials, or it may comprise one ready-filled syringe and one vial, with the contents of the syringe being used to reactivate the contents of the vial prior to injection.
Immunogenic compositions used as vaccines comprise an immunologically effective amount of antigen(s), as well as any other components, as needed. By ‘immunologically effective amount’, it is meant that the administration of that amount to an individual, either in a single dose or as part of a series, is effective for treatment or prevention. This amount varies depending upon the health and physical condition of the individual to be treated, age, the taxonomic group of individual to be treated (e.g. non-human primate, primate, etc.), the capacity of the individual's immune system to synthesise antibodies, the degree of protection desired, the formulation of the vaccine, the treating doctor's assessment of the medical situation, and other relevant factors. It is expected that the amount will fall in a relatively broad range that can be determined through routine trials.
Further Components of the Composition
Yersinia antigens of the invention can be combined with pharmaceutically acceptable carriers. Such carriers include any carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition. Such carriers are well known to those of ordinary skill in the art. The compositions may also contain diluents, such as water, saline, glycerol, etc. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present. Sterile pyrogen-free, phosphate-buffered physiologic saline is a typical carrier. A thorough discussion of pharmaceutically acceptable excipients is available in reference 108.
The invention further provides a method for preparing a pharmaceutical product, comprising the steps of: (a) preparing Yersinia antigens as described above; (b) mixing the antigens with one or more pharmaceutically acceptable carriers; and (c) packaging the antigen/carrier mixture into a container, such as a vial or a syringe, to give a pharmaceutical product. Insertion into a syringe may be performed in a factory or in a surgery.
The compositions can also include non-Yersinia immunogens. Thus the compositions may include one or more of: an immunogen from Bacillus anthracis for protecting against anthrax infection (e.g. a PA antigen [109], a spore antigen, etc.); an immunogen from a bacterium in the Francisella genus, such as F. tularensis for protecting against tularemia; an immunogen from a bacterium in the Pasteurella genus; an immunogen from a bacterium in the Brucella genus for protecting against brucellosis, such as B. abortus, B. melitensis, or B. suis; an immunogen from a bacterium in the Burkholderia genus, such as B. mallei for protecting against glanders or B. pseudomallei for protecting against melioidosis; an immunogen from a bacterium in the Chlamydia genus, such as Chlamydia psittaci for protecting against psittacosis; an immunogen from a bacterium in the Clostridium genus, such as C. botulinum for protecting against botulism or C. perfringens for protecting against Epsilon toxin); an immunogen from a bacterium in the Francisella genus, such as F. tularensis for protecting against tularemia; an immunogen from a Vibrio cholerae bacterium for protecting against cholera; an immunogen from a Coxiella burnetii bacterium for protecting against Q fever; an immunogen from an Ebola virus and/or a Marburg virus and/or a Lassa virus and/or a Machupo virus, for protecting against hemorrhagic fever; an immunogen from a bacterium in the Rickettsia genus, such as R. prowazekii bacterium for protecting against typhus fever, or from R. rickettsii; an immunogen from a fungus in the Coccidioides genus, such as C. immitis or C. posadasii; etc.
Chromosomal Antigens and Epitopes for Use in Immunisation
As mentioned above, the F1 and V antigens have been used for immunisation. These two antigens are encoded by Y. pestis plasmids. Thus, more generally, the invention provides an immunogenic composition comprising one or more chromosomal Y. pestis proteins. It also provides a chromosomal Y. pestis protein for use as an immunogen. It also provides the use of a chromosomal Y. pestis protein in the manufacture of a medicament, as described above.
The chromosomal protein may be, for example, a ribosomal protein, such as a 50S or 30S ribosomal protein. The chromosomal protein may be a lipoprotein. The chromosomal protein may be a periplasmic protein. The chromosomal protein may be a membrane protein. The chromosomal protein may be a heat-shock or cold-shock protein. The chromosomal protein may be an enzyme. The chromosomal protein may be a chaperone or chaperonin.
The composition may include the chromosomal protein in the form of a full-length protein as encoded by the chromosome, a hybrid protein (as described above), or a fragment of the chromosomal protein (as described above).
Nucleic Acid Immunisation
The immunogenic compositions described above include polypeptide antigens from Y. pestis. In all cases, however, the polypeptide antigens can be replaced by nucleic acids (typically DNA) encoding those polypeptides, to give compositions, methods and uses based on nucleic acid immunisation. Nucleic acid immunisation is now a developed field (e.g. see references 103 and 110 to 117 etc.), and has been applied to Y. pestis vaccines [118-123].
The nucleic acid encoding the immunogen is expressed in vivo after delivery to a patient and the expressed immunogen then stimulates the immune system. The active ingredient will typically take the form of a nucleic acid vector comprising: (i) a promoter; (ii) a sequence encoding the immunogen, operably linked to the promoter; and optionally (iii) a selectable marker. Preferred vectors may further comprise (iv) an origin of replication; and (v) a transcription terminator downstream of and operably linked to (ii). In general, (i) & (v) will be eukaryotic and (iii) & (iv) will be prokaryotic.
Preferred promoters are viral promoters e.g. from cytomegalovirus (CMV). The vector may also include transcriptional regulatory sequences (e.g. enhancers) in addition to the promoter and which interact functionally with the promoter. Preferred vectors include the immediate-early CMV enhancer/promoter, and more preferred vectors also include CMV intron A. The promoter is operably linked to a downstream sequence encoding an immunogen, such that expression of the immunogen-encoding sequence is under the promoter's control.
Where a marker is used, it preferably functions in a microbial host (e.g. in a prokaryote, in a bacteria, in a yeast). The marker is preferably a prokaryotic selectable marker (e.g. transcribed under the control of a prokaryotic promoter). For convenience, typical markers are antibiotic resistance genes.
The vector of the invention is preferably an autonomously replicating episomal or extrachromosomal vector, such as a plasmid.
The vector of the invention preferably comprises an origin of replication. It is preferred that the origin of replication is active in prokaryotes but not in eukaryotes.
Preferred vectors thus include a prokaryotic marker for selection of the vector, a prokaryotic origin of replication, but a eukaryotic promoter for driving transcription of the immunogen-encoding sequence. The vectors will therefore (a) be amplified and selected in prokaryotic hosts without polypeptide expression, but (b) be expressed in eukaryotic hosts without being amplified. This arrangement is ideal for nucleic acid immunization vectors.
The vector of the invention may comprise a eukaryotic transcriptional terminator sequence downstream of the coding sequence. This can enhance transcription levels. Where the coding sequence does not have its own, the vector of the invention preferably comprises a polyadenylation sequence. A preferred polyadenylation sequence is from bovine growth hormone.
The vector of the invention may comprise a multiple cloning site
In addition to sequences encoding the immunogen and a marker, the vector may comprise a second eukaryotic coding sequence. The vector may also comprise an IRES upstream of said second sequence in order to permit translation of a second eukaryotic polypeptide from the same transcript as the immunogen. Alternatively, the immunogen-coding sequence may be downstream of an IRES.
The vector of the invention may comprise unmethylated CpG motifs e.g. unmethylated DNA sequences which have in common a cytosine preceding a guanosine, flanked by two 5′ purines and two 3′ pyrimidines. In their unmethylated form these DNA motifs have been demonstrated to be potent stimulators of several types of immune cell.
Vectors may be delivered in a targeted way. Receptor-mediated DNA delivery techniques are described in, for example, references 124 to 129. Therapeutic compositions containing a nucleic acid are administered in a range of about 100 ng to about 200 mg of DNA for local administration in a gene therapy protocol. Concentration ranges of about 500 ng to about 50 mg, about 1 μg to about 2 mg, about 5 μg to about 500 μg, and about 20 μg to about 100 μg of DNA can also be used during a gene therapy protocol. Factors such as method of action (e.g. for enhancing or inhibiting levels of the encoded gene product) and efficacy of transformation and expression are considerations which will affect the dosage required for ultimate efficacy. Where greater expression is desired over a larger area of tissue, larger amounts of vector or the same amounts re-administered in a successive protocol of administrations, or several administrations to different adjacent or close tissue portions may be required to effect a positive therapeutic outcome. In all cases, routine experimentation in clinical trials will determine specific ranges for optimal therapeutic effect.
Vectors can be delivered using gene delivery vehicles. The gene delivery vehicle can be of viral or non-viral origin (see generally references 130 to 133).
Viral-based vectors for delivery of a desired nucleic acid and expression in a desired cell are well known in the art. Exemplary viral-based vehicles include, but are not limited to, recombinant retroviruses (e.g. references 134 to 144), alphavirus-based vectors (e.g. Sindbis virus vectors, Semliki forest virus (ATCC VR-67; ATCC VR-1247), Ross River virus (ATCC VR-373; ATCC VR-1246) and Venezuelan equine encephalitis virus (ATCC VR-923; ATCC VR-1250; ATCC VR 1249; ATCC VR-532); hybrids or chimeras of these viruses may also be used), poxvirus vectors (e.g. vaccinia, fowlpox, canarypox, modified vaccinia Ankara, etc.), adenovirus vectors, and adeno-associated virus (AAV) vectors (e.g. see refs. 145 to 150). Administration of DNA linked to killed adenovirus [151] can also be employed.
Non-viral delivery vehicles and methods can also be employed, including, but not limited to, polycationic condensed DNA linked or unlinked to killed adenovirus alone [e.g. 151], ligand-linked DNA [152], eukaryotic cell delivery vehicles cells [e.g. refs. 153 to 157] and nucleic charge neutralization or fusion with cell membranes. Naked DNA can also be employed. Exemplary naked DNA introduction methods are described in refs. 158 and 159. Liposomes (e.g. immunoliposomes) that can act as gene delivery vehicles are described in refs. 160 to 164. Additional approaches are described in references 165 & 166.
Further non-viral delivery suitable for use includes mechanical delivery systems such as the approach described in ref. 166. Moreover, the coding sequence and the product of expression of such can be delivered through deposition of photopolymerized hydrogel materials or use of ionizing radiation [e.g. refs. 167 & 168]. Other conventional methods for gene delivery that can be used for delivery of the coding sequence include, for example, use of hand-held gene transfer particle gun [169] or use of ionizing radiation for activating transferred genes [167 & 170].
Delivery DNA using PLG {poly(lactide-co-glycolide)} microparticles is a particularly preferred method e.g. by adsorption to the microparticles, which are optionally treated to have a negatively-charged surface (e.g. treated with SDS) or a positively-charged surface (e.g. treated with a cationic detergent, such as CTAB).
Antibodies
Antibodies against Y. pestis antigens can be used for passive immunisation [171]. Thus the invention provides an antibody that is specific for an antigen in the first, second, third or fourth antigen groups. The invention also provides the use of such antibodies in therapy. The invention also provides the use of such antibodies in the manufacture of a medicament. The invention also provides a method for treating a mammal comprising the step of administering an effective amount of a antibody of the invention. As described above for immunogenic compositions, these methods and uses allow a mammal to be protected against Y. pestis infection.
The term “antibody” includes intact immunoglobulin molecules, as well as fragments thereof which are capable of binding an antigen. These include hybrid (chimeric) antibody molecules [172, 173]; F(ab′)2 and F(ab) fragments and Fv molecules; non-covalent heterodimers [174, 175]; single-chain Fv molecules (sFv) [176]; dimeric and trimeric antibody fragment constructs; minibodies [177, 178]; humanized antibody molecules [179-181]; and any functional fragments obtained from such molecules, as well as antibodies obtained through non-conventional processes such as phage display. Preferably, the antibodies are monoclonal antibodies. Methods of obtaining monoclonal antibodies are well known in the art.
Humanised or fully-human antibodies are preferred.
Knockout Mutants
The invention also provides a Yersinia bacterium in which expression of one or more of the genes encoding an antigen in the third or fourth antigen groups has been knocked out.
The bacterium may be any Yersinia species, including Y. pestis, Y. pseudotuberculosis or Y. enterocoliticus. Preferably, however, it is Y. pestis. The homologous non-pestis genes that correspond to the genes encoding the pestis antigens of the third and fourth antigen groups can readily be identified based on sequence similarity and/or chromosomal location.
Techniques for gene knockout in bacteria are well known, and Yersinia knockout mutants have been reported previously (e.g. refs. 182-186, etc.).
The knockout is preferably achieved using isogenic deletion of the coding region, but any other suitable technique may be used e.g. deletion or mutation of the promoter, deletion or mutation of the start codon, antisense inhibition, inhibitory RNA, etc. In the resulting bacterium, however, mRNA encoding the antigen of interest will be absent and/or its translation will be inhibited (e.g. to less than 1% of wild-type levels).
The bacterium may contain a marker gene in place of the knocked out gene e.g. an antibiotic resistance marker.
As well as knocking out the Yersinia antigens of the third and fourth groups, knockout of YPO1025 is also possible, as is knockout of YPO0154, and knockout of one or more genes in the operon including YPO1121, YPO1122, YPO1123, YPO1124 and YPO1125. Again, the homologous genes in Y. pseudotuberculosis or Y. enterocoliticus can readily be identified.
The invention also provides a protein vesicle obtainable from said knockout bacteria. These vesicles may be spontaneously released into culture medium during bacterial growth. The vesicles contain lipids and proteins, and are useful as immunogens. A composition containing the vesicles preferably does not comprise any living and/or whole bacteria.
The vesicles preferably include (e.g. in a surface-exposed form) an antigen from the third antigen group and/or the fourth antigen group and/or the fifth antigen group.
Animal Model
For preliminary screening of antigens for protective efficacy, a simple animal model is useful. For example, reference 8 discloses a murine aerosol challenge model. The invention provides a new animal model that is useful for quickly assessing the protective efficacy of an antigen, or of a new formulation (e.g. new adjuvant, or new combination) of an antigen.
The invention provides a method for assessing the protective efficacy of a composition that comprises a Y. pestis antigen (e.g. a composition of the invention), wherein the method comprises the steps of: immunising an animal with the composition; collecting antiserum from the animal; incubating the antiserum with a Y. pseudotuberculosis or Y. enterocolitica bacterium in the presence of complement; and assessing bacterial growth.
The invention also provides a method for assessing the protective efficacy of a composition that comprises a Y. pestis antigen (e.g. a composition of the invention), wherein the method comprises the steps of: incubating an antiserum with a Yersinia bacterium, other than Y. pestis, in the presence of complement, wherein the antiserum has been taken from an animal that was immunised with the composition; and assessing bacterial growth.
The animal is preferably a rodent, such as a mouse, and preferably an inbred laboratory mouse strain.
The Yersinia bacterium is preferably Y. pseudotuberculosis or Y. enterocolitica. 
The complement is preferably rabbit complement.
In the assessment of bacterial growth, there will usually be a comparison with a negative control or reference sample in which bacteria are grown either in the absence of any antiserum or in the presence of a negative control antiserum. The degree of inhibition of growth (or of bacterial killing) relative to the negative control indicates the degree of protective efficacy of the composition. Similarly, there may be a comparison with a positive control or reference sample in which bacteria are grown either in the presence of an agent (e.g. an antiserum) that is known to be protective.
The control growths may be performed in parallel with the method of the invention, or may be performed separately.
Antisera may be tested at different dilutions, and the result of the assay may be given as the dilution at which growth inhibition does not occur. The degree of dilution required before loss of bactericidal activity indicates the degree of protective efficacy of the composition.
The bacterial growth step may occur at below 37° C. e.g. between 25-32° C., or about 28° C.
General
Antigens are defined above by reference to “YPO” (or, in one case, “YPPCP”) nomenclature. This nomenclature refers to the numbering used in reference 16 for unique identification of open reading frames in the CO92 strain of Y. pestis. The basic reference sequence for any “YPO” or “YPPCP” number can easily be found in public gene databases. For instance, accession number NC—003143 (GI:16120353) is the complete CO92 genome sequence (4,653,728 bp), and the individual YPO sequences are given as “locus_tag” entries in the genome sequence's “features” section. Similarly, NC—003132 (GI:16082679) is the complete sequence of the pPCP1 plasmid, and the “locus_tag” field gives the YPPCP number. Thus the nucleotide and amino acid sequences for any given YPO or YPPCP number can be established unambiguously.
“GI” numbering is also used above. A GI number, or “GenInfo Identifier”, is a series of digits assigned consecutively to each sequence record processed by NCBI when sequences are added to its databases. The GI number bears no resemblance to the Accession number of the sequence record. When a sequence is updated (e.g. for correction, or to add more annotation or information) then it receives a new GI number. Thus the sequence associated with a given GI number is never changed.
Where the invention concerns an “epitope”, this epitope may be a B-cell epitope and/or a T-cell epitope. Such epitopes can be identified empirically (e.g. using PEPSCAN [187,188] or similar methods), or they can be predicted (e.g. using the Jameson-Wolf antigenic index [189], matrix-based approaches [190], TEPITOPE [191,192], neural networks [193], OptiMer & EpiMer [194, 195], ADEPT [196], Tsites [197], hydrophilicity [198], antigenic index [199] or the methods disclosed in reference 200, etc.). Epitopes are the parts of an antigen that are recognised by and bind to the antigen binding sites of antibodies or T-cell receptors, and they may also be referred to as “antigenic determinants”.
Variants of SEQ ID NOs include allelic variants, polymorphic forms, homologs, orthologs, paralogs, mutants, etc.
Polypeptides of the invention may, compared to the CO92 reference sequence, include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, etc.) conservative amino acid replacements i.e. replacements of one amino acid with another which has a related side chain. Genetically-encoded amino acids are generally divided into four families: (1) acidic i.e. aspartate, glutamate; (2) basic i.e. lysine, arginine, histidine; (3) non-polar i.e. alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan; and (4) uncharged polar i.e. glycine, asparagine, glutamine, cystine, serine, threonine, tyrosine. Phenylalanine, tryptophan, and tyrosine are sometimes classified jointly as aromatic amino acids. In general, substitution of single amino acids within these families does not have a major effect on the biological activity. The polypeptides may also include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, etc.) single amino acid deletions relative to the CO92 sequences. The polypeptides may also include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, etc.) insertions (e.g. each of 1, 2, 3, 4 or 5 amino acids) relative to the CO92 sequences.
Where an antigen “domain” is omitted, this may involve omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, of an extracellular domain, etc.
The term “comprising” encompasses “including” as well as “consisting” e.g. a composition “comprising” X may consist exclusively of X or may include something additional e.g. X+Y.
The term “about” in relation to a numerical value x means, for example, x±10%.
If desired, antigens can be conjugated to a carrier protein in order to enhance immunogenicity.
References to a percentage sequence identity between two amino acid sequences means that, when aligned, that percentage of amino acids are the same in comparing the two sequences. This alignment and the percent homology or sequence identity can be determined using software programs known in the art, for example those described in section 7.7.18 of ref. 201. A preferred alignment is determined by the Smith-Waterman homology search algorithm using an affine gap search with a gap open penalty of 12 and a gap extension penalty of 2, BLOSUM matrix of 62. The Smith-Waterman homology search algorithm is disclosed in ref. 202.



BRIEF DESCRIPTION OF DRAWINGS
FIGS. 1 and 2 show the results of opsonophagocytosis assays. Two bars are shown for each assay: the left is with active complement and the right is with inactive complement. The Y-axis shows the fold increase in phagocytosis, and the X-axis shows the antigen used to elicit the antiserum.
FIGS. 3 to 5 show the results of bactericidal assays. Bacterial killing is indicated at the difference between colony forming units (cfu) at time zero and at time 3 hours. In FIG. 5, black bars are data on pLCR- strains and grey bars are data on pgm-pst- strains.
FIG. 6 shows serum bactericidal assay with human blood. Y. pestis CO92 pLCR- Bacteria were re-inoculated from ON cultures grown at 37° C. in BHI and incubated at 37° C. for about 4 h, until OD600=0.4. Bacteria were opsonized for 30′ at 37° C. with mouse antisera (10 μl) specific for Y. pestis antigens (reported in the table) and subsequently incubated with blood (80 μl) of 5 different healthy donors at 37° C. 6% CO2. Colony counting was performed at time 0 and after 3 h incubation with blood. All samples were in duplicates. Bacterial killing was evaluated by determining the difference between the colony forming units (cfu), expressed as log10, at time 0 and at 3 h.
FIG. 7 shows a Western blot indicating the secretion of YPO0502. A: Serum anti-YPO0502 (19 KDa), B: Serum anti-YPO0503 (17 KDa) and C: Serum anti-YPO0213 (30 KDa). Lanes 1-13 are as follows: (1) Bacteria extract, 28° C.; (2) Cells lysate, 28° C.; (3) Bacteria extract, switch 28-37° C.; (4) Cells lysate, switch 28-37° C.; (5) Bacteria extract, 37° C.; (6) Cells lysate, 37° C.; (7) Supernatant bacteria, 28° C.; (8) Supernatant cells, 28° C.; (9) Supernatant bacteria, switch 28-37° C.; (10) Supernatant cells, switch 28-37° C.; (11) Supernatant bacteria, 28° C.; (12) Supernatant cells, 28° C.; and (13) Supernatant cells.
FIG. 8 shows the binding of 0502_His (A) and 2634_His (B) with J774 cells. Cells were incubated for 1 h with 0 μg/ml, 5 μg/ml or 12 μg/ml recombinant 0502_His or 2634_His as negative control. Binding and internalisation was quantified by direct immunofluorescence using anti-mouse sera raised against each respective protein.
FIG. 9 shows the ability of sera raised against 0499_GST to induce bacterial killing.
FIG. 10 shows serum bactericidal assay with human blood. (same protocol as FIG. 6)
FIG. 11 shows the opsophagocytosis assay with the human pro-myelomonocytic Monomac 6 cell line. Monomac 6 cells were sub-cultured in RPMI-10% FCS at 37° C., 6% CO2, stimulated for two days with 50 U/ml IFN-γ and distributed in 96 w plates (4×105 cells/well). For the infection, bacteria grown at 37° C. in BHI until OD600=0.4. Bacteria were opsonized with specific (at 1:30 dilution) for 30′ at 37° C. and added to the cells at a Molteplicity of Infection (MOI) of one bacterium per cell. Non opsonized bacteria and bacteria opsonized with Pre-Immune sera and sera against Antisera against E. coli contaminant proteins obtained from IMAC-purification were included as negative controls of the assay. After 1 h incubation at 37° C., non adhering bacteria were removed by extensive washing and externot determinedly associated bacteria were killed by 1 h incubation with 200 ug/ml gentamycin. Intracellular bacteria were measured after cell lysis with 1% saponin by viable counting. All samples were in triplicates. For each samples % phagocytosis was evaluated as compared to non-opsonized bacteria.
FIG. 12 shows serum bactericidal assay with human blood. (same protocol as FIG. 6)



MODES FOR CARRYING OUT THE INVENTION
Antigen Identification
The Y. pestis genome includes more than 4000 open reading frames, and its annotation includes little information useful for the identification of useful immunogens. To identify useful immunogens from within these 4000 possibilities, four approaches were utilised. Firstly, computational analysis of the genome was used to identify useful immunogens. Second, transcriptional profiling was used to identify highly-expressed genes under in vitro and in vivo growth conditions, and in particular after a temperature shift from 28° C. to 37° C., which mimics the natural host change from flea to mammal. Third, comparative genomic hybridization (CGH) was used to identify genes that are conserved in a variety of Y. pestis clinical isolates representative of major biovars [203]. Fourth, surface shaving and labelling were used to identify surface-exposed proteins (cf. reference 204).
The first three approaches eliminated about 90% of the ORFs. The remaining  ̃400 ORFs were selected for cloning, purification and immunisation tests, together with (a) screening in in vitro and in vivo models in order to identify antigens that can induce a bactericidal immune response, and (b) FACS analysis and western blots to confirm cellular localization. Antigens were typically expressed in E. coli as N-terminal GST fusions, or as C-terminal or N-terminal hex-His fusions, and the amplified coding sequences usually omitted signal peptides, to give intracellular expression. Expression without GST or His fusion partners is also possible, though. 360 ORFs were successfully cloned and expressed in at least one of the two fusion forms. Each recombinant protein was used to immunize groups of 4 CD1 mice.
FACS
Sera from the mice were recovered two weeks after the final immunization and were tested by immunoblot analysis on both purified recombinant proteins and Y. pestis total extracts. In general, all sera specifically recognized the corresponding recombinant protein used for immunization and a protein species with the expected molecular weight in the total cell extract. Having confirmed the specificity of the polyclonal antibodies, the sera were used for flow cytometry analysis (FACS) on whole bacteria to define which of the 360 expressed antigens were sufficiently accessible to interact with their specific antibodies. As CO92 pLCR- strain carries the pMT1 plasmid and expresses the F1 capsular antigen, anti-F1 antigen antibodies were used as positive control in each experiment. Antisera raised against bulk E. coli contaminants of the GST-tagged proteins and His-tagged proteins were obtained and used to define the experimental cut-off of the FACS positive antigens.
Approximately 150 of the 360 sera analyzed gave fluorescence value higher than negative control sera, indicating that the corresponding antigens are exposed on the Y. pestis surface. These 150 antigens were further analyzed for protective activities against Y. pestis. 
Proteolysis of the Yersinia Surface and Analysis of Resultant Peptides.
Infectious forms of Y. pestis were grown in cell cultures and purified by gradient centrifugation as described in the literature. Approximately, 107 IFU in transport buffer were digested (“shaved”) with trypsin. Limited digestion was carried out with 20 μg trypsin (Promega, Madison, Wis., USA) for 30 min at 37° C.
The digestion mixture was centrifuged in an Expender centrifuge at 14,000 g for 30 min at 4° C., in order to separate the Yersinia cells from the peptides released by the surface proteolysis. The supernatant, containing the peptides released by trypsin digestion, was filtered from residual cells by centrifugation at 4° C. in Centric on tubes. The filtrate was treated with formic acid (0.1% formic acid final concentration) and submitted to proteomic analysis for the identification of the released peptides and consequent identification of the proteins which were exposed on the Yersinia surface.
Two different experimental platforms were used for the chromatographic separation of peptides and further identification was performed by tandem mass spectrometry (MS/MS).
In the first platform, prior to analysis salts were removed by off-line HPLC, with a 7-min gradient of 2-80% acetonitrile (ACN) in 0.1% formic acid. Peptide fractions were concentrated with a Speed-van centrifuge (Savant, Holbrook, N. Y.), and kept at −20° C. until further analysis. Peptides were separated by two-dimensional (2-D) nana-liquid chromatography (Dionne, Amsterdam, The Netherlands). In the first dimension, peptides were loaded on a strong cation exchange (SCX) column (10 cm×320 μm i.d.) and eluted by 5 salt concentrations (0.01, 0.05, 0.1, 0.5 and 1 M NaCl). In the second dimension, peptides were separated by a reversed phase C18 analytical column (15 cm×75 μm i.d., C18 PepMap 100TM, 3 μm, 100 Å) via a C18 trap column (PepMapTM C18 μl-precolumn, 300 μm i.d.×1 mm, Dionne). Peptides were eluted with a 45-min gradient from 5 to 50% of 80% ACN in 0.1% formic acid. The flow rate was 300 nl/min. Eluates were continuously spotted onto an Anchor-ChipTM MALDI target, prepared with a thin layer of a saturated solution of α-cyano-4-hydroxycynnamic acid in acetone, every 60 s using a Proteineer FC robot. After fraction collection, spots were recrystallyzed with 0.6 μl of ethanol/acetone/0.1% trifluoroacetic acid (6:3:1). Mass spectrometry analysis was performed automatically with an Ultraflex MALDI TOF-TOF instrument, under the control of the WARP LC software.
In the second platform, peptides were separated by nana-LC on a CapLC HPLC system connected to a Q-ToF Micro ESI mass spectrometer equipped with a nanospray source. Samples were loaded onto an Atlantis C18 NanoEase column (100 μm i.d.×100 mm), via a C18 trap column (300 μm i.d.×5 mm). Peptides were eluted with a 50-min gradient from 2% to 60% of 95% ACN, 0.1% formic acid at a flow of 400 nl/min. The eluted peptides were subjected to an automated data-dependent acquisition program, using the MassLynx software. For both platforms, searching and identification of peptides were performed in batch mode with a licensed version of MASCOT, in a local database.
Shaving identified the following antigens: YPO1507, YPO2674, YPO4111, YPO1435, YPO0015, YPO2292, YPO3375, YPO3050 and YPO0494. In addition, YPO0501 and YPO0502 were identified as surface components which lack a canonical signal peptide and so could not be predicted using in silico analysis.
Biotinylation of Bacterial Surface
Surface proteins were obtained by biotinylating the bacterial surface, fragmenting the bacteria and then isolating the biotinylated proteins. These proteins were then separated on a gel excised, and exposed to tryptic digestion. Peptide mass fingerprinting was then used to identify the protein fragments. This technique identified the following antigens: YPO1052, YPO1906, YPO0663, YPO1435, YPO1222, YPO1411, YPO2905, YPO4905, YPO4070 and YPPCP1.07.
ORFs Selected for Immunogenic Use
These various analyses led to the identification of YPO0015, YPO0067, YPO0086, YPO0102, YPO0195, YPO0203, YPO0216, YPO0233, YPO0351, YPO0468, YPO0501, YPO0502, YPO0512, YPO0563, YPO0570, YPO0809, YPO0819, YPO0860, YPO1053, YPO1070, YPO1123, YPO1411, YPO1435, YPO1507, YPO1604, YPO1746, YPO2292, YPO2342, YPO2615, YPO2674, YPO2881, YPO3050, YPO3061, YPO3065, YPO3343, YPO3361, YPO3382, YPO3430, YPO3489, YPO3536, YPO3559, YPO3631, YPO3643, YPO3644, YPO3935, YPO4003, and YPO4111. These 47 antigens were further characterised using a variety of techniques.
Functional Studies
Various antigens were tested in an opsonophagocytosis assay using human monocytes against CO92 pLCR- cells. The assay was performed using both active complement and inactive complement. It measures the capacity of antibodies to increase Y. pestis phagocytosis by IFNγ-activated monocytes. The rationale of using this assay is that antisera against the V antigen have been shown to promote bacterial phagocytosis by macrophages [205,206]. Thus opsonophagocytosis appears to be an important mechanism of protection against Y. pestis infection.
According to the assay, Y. pestis pLCR- bacteria were incubated with each of the sera raised against the test proteins and subsequently incubated with the Monomac 6 cell line (previously stimulated for two days with 50 U/ml IFN-γ). After 1 h incubation, bacteria adhering to the surface of monocytes were killed by antibiotic treatment and the number of internalized bacteria was determined by colony counting after cell lysis with 1% saponin.
Briefly, the protocol for this assay is as follows: mix bacteria with different sera in 96 well plate (160 μl bacteria with 5.5 μl undiluted serum) and incubate in agitation (120 rpm) at 37° C. for 30 minutes; after opsonization, bacteria are added directly to cells (i.e. without washing step); add 20 μl of each sample to the plate containing the monocytes (resuspended in 60 μl medium); add 20 μl complement; incubate for 1 hour at 37° C. and 20 hours at 37° C. in the incubator with 5% CO2; evaluate total bacteria by adding 100 μl of 2% saponin (diluted in RPMI without kan) and leave 15 minutes at 37° C., then plate at 10−2 and 10−3; evaluate internalisation by transferring entire volume (100 μl) in 96 well plate with “u-bottom”, resuspend pellets with 100 μl gentamycin 200 μg/ml and incubate for 1 hour at 37° C., 1 wash with 20 μl medium per well, add 100 μl of 1% saponin (diluted in RPMI without kan) and leave 10-15 minutes at 37° C., then mix.
When Y. pestis pLCR- bacteria were opsonized with sera against whole bacteria and F1 protein (positive controls) a 40-fold and 100-fold increase of the Monomac 6 cell line phagocytic capacity with respect to pre-immune sera was observed, respectively. Thus the OPA assay was used to screen antisera specific for FACS-positive antigens, in search for sera able to increase bacterial uptake by phagocytic cells.
Results from a first set of experiments, with 3 hours of growth at 37° C., are shown in FIG. 1, expressed as phagocytosis (fold increase) against antiserum used. Results from a second set of experiments, with overnight growth at 37° C., are shown in FIG. 2. Many of the antigens were able to induce a serum response that led to increased phagocytosis. Antisera raised against the following 21 antigens gave the best results: YPO4003, YPO3061, YPO3559, YPO3382, YPO0860, YPO0086, YPO3631, YPO0512, YPO3489, YPO2881, YPO3343, YPO3361, YPO0563, YPO3430, YPO1411, YPO3935, YPO0809, YPMT1.84, YPO1123, YPO3065, and YPO1070. The inclusion of YPMT1.84 in this group (i.e. the F1 antigen) is a useful confirmatory positive control.
Phagocytosis-positive sera were tested for their ability to induce bacterial killing by blood cells, using blood from three donors against pLCR− strain CO92. In this assay bacterial cells were incubated with antigen-specific antisera for 30 minutes and subsequently exposed to human blood from four different healthy donors (age ranging from 26 to 65 years). The capacity of sera to induce bacterial killing was evaluated at 37° C. at different time points over a 3 hour period. Under these experimental conditions, while incubation with pre-immune sera did not prevent bacteria from growing in blood, incubation with anti-F1 protein serum caused over 1 log 10 reduction of viable bacteria after a 3 hour incubation in 3 out of the 4 blood samples.
Briefly, the protocol for this assay is as follows: incubate 10 μl (approximately 1000 CFU) Y. pestis CO92 LCR− pgm− bacteria with 10 μl sera (decomplemented for 30 min at 56° C.) for 30 min 37° C. (the ‘no sera’ control sample used 10 μl RPMI, 10% FCS, no antibiotic); add 80 μl blood with heparin (200 μl heparin “liquemil”/10 ml blood); in a microtitre plate at time zero, dilute 20 μl in 20 μl RPMI-10% FCS-gln-no antibiotic (1:2) and plate (20 μl) 100, 10−1, 10−2, 10−3 dilutions; on a 37° C. rocking platform, mix after 1 hour by pipette; remove 20 μl for plating, and incubation on the rocking platform continued; after 2 hrs, mix again and continue incubation on the rocking platform; plate after 1 hr and 3 hrs; dilute as before (1:2) and plate 100, 10−1 dilutions (20 μl)
Results are shown in FIGS. 3 (1 hour assay) and 4 (3 hour assay) as the percentage of killed bacteria relative to pre-immune sera. The best results were seen with YPO4003, YPO1604, YPO0512, YPO0563 and YPO3489.
Killing was compared between CO92 pgm− and pLCR− strains with human blood. Results are shown in FIG. 5. The best results were seen with YPO0512, YPO0563 and YPO3489. Sera raised against these antigens promoted bacterial killing in all three blood samples at levels comparable to that observed with the anti-F1 antiserum. In particular, sera against proteins YPO0512 and YPO0563 killed Y. pestis in all four blood samples tested, thus performing even better then the F1 antigen. Remarkably, these two sera were also capable of killing the less attenuated CO92 pgm− pst− strain (a CO92-derived mutant lacking the 102 kb pigmentation locus) when tested in the blood of one of the human donors.
In conclusion, these functional studies revealed a number of antigens, in addition to F1, that are able to elicit antibodies that promote phagocytosis in vitro. Considering that the sera against two known protective antigens (the V [206] and F1 antigens) also have phagocytic properties, the identified antigens are very attractive candidates for inclusion in anti-Y. pestis vaccines. Moreover, five antigens (in particular YPO4003, YPO1604 and YPO3489) elicit sera that, in addition to stimulating phagocytosis, also promote substantial bacterial killing in the presence of human blood.
Further studies revealed a 55-fold and 70-fold increase of the Monomac 6 cell line phgocytic capacity with respect to pre-immune sera, when Y. pestis pLCR-bacteria were opsonised with sera against whole bacteria and F1 protein (positive controls), respectively.
Further experiments revealed that the following 23 antigens induced a particularly good serum response that led to increased phagocytosis: YPO4003, YPO1604, YPO3061, YPO0065, YPO3382, YPO0860, YPO0086, YPO1123, YPO1224, YPO3631, YPO3579, YPO3551, YPO3553, YPO0496, YPO3489, YPO2881, YPO3065, YPO1070, YPO2506, YPO1411, YPO3982, YPO0809 and YPO3935 (see FIG. 11). As mentioned above, the inclusion of YPMT1.84 (the F1 antigen) is as a confirmatory positive control.
FACS-positive sera were tested for their ability to induce bacterial killing. Bacterial cells were incubated with antigen specific sera and then exposed to human blood from five different healthy donors. While incubation with pre-immune sera did not prevent bacteria from growing in blood, incubation with anti-F1 protein serum caused over 1 log 10 reduction of viable bacteria in three of the five blood samples tested. The results are shown in FIGS. 12, 6 and 10 as the percentage of killed bacteria relative to pre-immune sera (protocol as described above). The best results were seen with YPO4003, YPO1604 and YPO3489.
Further Studies
To confirm the specificity of an antigen's in vitro protective activity, the gene coding for that antigen is deleted from a Y. pestis strain and the opsonophagocytic and/or killing assays are repeated on the knockout strains. It is expected that the knockout strains will be insensitive to the opsonophagocytic/killing activity of the sera. Y. pestis mutants will be generated essentially as previously described [186]. Briefly, Y. pestis CO92 pLCR- attenuated strain is transformed with a plasmid carrying the λ phageRed recombinase [207] under the control of the ara inducible promoter, and the trimethoprim (tp) resistance cassette. The plasmid-carrying derivative, which has an increased recombination frequency due to the presence of the arabinose-inducible Red recombinase, is used as recipient of gene mutants. For mutant construction, the 500 bp upstream and downstream regions of the gene to be deleted are amplified from Y. pestis CO92 genomic DNA and fused on either side of a kanamycin resistance cassette by PCR. The resulting PCR product is used to transform tp-resistant Y. pestis competent cells and positive clones are identified on BHI plates containing km and tp. Gene deletions are confirmed by PCR on the genomic DNA of resulting tpr-kmr clones. Finally mutants are cured of the plasmid encoding the λ phageRed recombinase by repeated passages on BHI plates in the absence of Tp. The absence of expression of the proteins corresponding to the deleted genes is confirmed by Western blot and/or by FACS analysis.
The knockout mutants are also useful for elucidating the biological role of the knocked out genes.
In addition to the analysis of their in vitro functional activity, antigens are tested for their protective activity in vivo using the mouse model of aerosol challenge in a BL4 facility.
Immunisation Studies
Antigens are selected for combining to give a composition of the invention. BALB/c mice are divided into nine groups and immunized as follows:












Group
Immunizing Composition
Route of Delivery







1
Mixture of antigens
Intra-peritoneal or intra-



(10-20 μg protein/each) +
nasal or subcutaneous



CFA (Complete Freund's Adjuvant)


2
Mixture of antigens (5 μg/each) +
Intra-peritoneal or intra-



Al-hydroxide (200 μg)
nasal or subcutaneous


3
Mixture of antigens
Intra-peritoneal or intra-



(10-20 μg protein/each) +
nasal or subcutaneous



CpG (10 ug)


4
Mixture of antigens
Intra-peritoneal or intra-



(10-20 μg protein/each) +
nasal or subcutaneous



Al-hydroxide



(200 μg) + CpG (10 μg)


5
CFA
Intra-peritoneal or intra-




nasal or subcutaneous


6
Mixture of antigens
Intra-peritoneal or Intra-



(10-20 μg protein/each) +
nasal or subcutaneous



LTK63 (5 μg)


7
Al-hydroxide (200 μg) +
Intra-peritoneal or intra-



CpG (10 μg)
nasal or subcutaneous


8
CpG (10 μg)
Intra-peritoneal or intra-




nasal or subcutaneous


9
LTK63 (5 μg)
Intra-peritoneal or intra-




nasal or subcutaneous









Mice are immunized at two week intervals. Two to three weeks after the last immunization, all mice are challenged with the appropriate Y. pestis strain. When mucosal immunization (e.g. intranasal) is used, the animal model is also challenged mucosally to test the protective effect of the mucosal immunogen. Immediately prior to challenge, mice are bled to determine antibody titre to the antigens that were administered.
Total IgG and IgG1/IgG2A subtypes can be measured in mouse sera resulting from the different immunization regimens by using an ELISA assay on whole bacteria and on purified recombinant proteins. Furthermore, assessment of antigen-specific CD4+ and CD8+Th-cells in spleen cells and/or PBMC isolated from immunized mice can be carried out by multi-parametric FACS analysis, to evaluate the cytokine expression profiles of antigen-specific T-cells. In particular production of IFN-γ and IL-5 can be measured after in vitro stimulation of T cells with purified antigens and/or whole Y. pestis cells. In addition, splenocytes and/or PBMC from mice immunized with each antigen/vaccine formulation may be collected 10-12 days after the last immunization dose and stimulated with whole Y. pestis bacteria. After 4 hours of stimulation, Brefeldin A is added to the cells for the following 12 hours, to block cytokines secretion. Afterwards cells are fixed and stained with antibodies to detect Y. pestis-specific T cells expressing IFN-γ and IL-5.
For the mouse challenge, virulent bacteria will be grown at 30° C. in heart infusion broth (HIB) containing 0.2% xylose. Bacteria are harvested by centrifugation, re-suspended, and serially diluted in HIB for the challenge inoculum. BALD/c mice are challenged using a 1 μm-generating Collision nebulizer contained within a Class III biocabinet. Mice are exposed in a temperature- and humidity-controlled whole-body exposure chamber. The aerosol is continuously sampled by an all glass impinger (AGI) containing HIB. The inhaled dose is determined from serial dilution and culture of AGI samples according to the formula determined by Guyton [208]. Mice are observed daily for 30 days post-exposure. For these initial studies, the virulent strain CO92 at a dose of 100 LD50 units is used for challenges.
Outer Membrane Vesicles
Outer membrane vesicles are produced by a wide variety of gram-negative bacteria during growth in liquid cultures. Although the mechanism by which OMVs are generated has not been fully elucidated, they appear to represent spontaneous release of bacterial membranes which tend to form vesicles. In general the amount of OMVs released is very low. However, defects in proteins involved in membrane and cell wall assembling have been reported to favour OMVs production. In particular, in E. coli mutations of the major lipoprotein (Lpp) and any of the five proteins of the Tol-Pal system promote accumulation of OMVs in the culture supernatant. In Salmonella enterica, DNA adenine methylase (Dam) mutants present a reduction in the amount of Pal, TolB, OmpA and Lpp and, as a result of the absence of Dam methylation, release OMVs into the culture medium. Deletion of the N. meningitidis gna33 gene, which encodes a lytic transglycosylase homologous to E. coli mltA, produces large amounts of vesicles. Vesicles derived from the Δgna33 N. meningitidis mutant elicit a strong antibody-mediated protective activity.
In line with this meningococcal work, the Y. pestis genes encoding the Tol-Pal system homolog (the YPO1121-1125 operon), the DNA adenine methylase homolog (YPO0154), and the GNA33 homolog (YPO01025) are knocked out, and the mutants are tested for their capacity to release vesicles. The vesicles are then tested for their capacity to protect mice against Y. pestis infection.
Type Three Secretion System
It is postulated herein that the Y. pestis gene cluster YPO0499-YPO0516 are part of a Type Three Secretion System due to homology with similar systems in other organisms. A number of these proteins are also surface exposed and therefore useful for raising immune responses.
With the exception of YPO0510 and YPO0514, all of the genes in this cluster have been cloned and purified. Antisera have also been raised against most of these proteins. The antisera produced were tested by Western blot on total protein extract of Y. pestis grown overnight (O/N) at 28° C., O/N at 37° C. and O/N at 28° C. followed by 2 h at 37° C. Western blot analysis was also carried out in the presence or absence of the human J774.1 macrophage cell line to evaluate whether interaction with human cells influence the protein expression level. As shown in Table 1, in agreement with microarray data (see Table 2), in general the proteins showed highest expression at 28° C. rather than 37° C. In some cases the protein was highly expressed at both temperatures (YPO0499, YPO0502, YPO0505, YPO0508 and YPO0509).
Western blot analysis was then carried out to verify whether the interaction of Y. pestis CO92 with a murine macrophage cell line can induce secretion of a component of the cluster. Bacteria grown over night at 28° C. or 37° C. in BHI medium were diluted 1:20 the day after and grown at the same temperature or switched from 28° C. to 37° C. until an O.D.600=0.4 (=logarithmic phase) was reached. Bacteria were harvested by centrifugation at 3,500 g for 10 min, washed once in DMEM high glucose+2% FCS and resuspended in the same cell medium. Bacteria were then added to the murine macrophages cell line J774.1 plated at a density of 1×106 cells/well, with a M.O.I. of 10:1 (bacteria:cells), in 6 wells plates. Bacteria incubated in plates not containing cells were also prepared in parallel. The plates, after a centrifugation of 5 min at 250 g, were incubated for 30 min at 37° C., 5% CO2. Bacteria were harvested by centrifugation and lysed in LSB1X; the supernatant separated from bacteria were TCA precipitated. Cells monolayers were lysed in PBS+0.1% triton X. Samples were tested in western blot with the anti-sera against 7 proteins belonging to the cluster (=YPO0499-0500-0501-0502-0503-0505-0506) and a negative lysis control (=YPO0213, ribosomal protein). The only protein detected in the supernatant was YPO0502 (see FIG. 7).
According to the structure prediction of YPO0502, it was hypothesized that the protein could have a role in altering the permeability of host cells. The fact that the protein is secreted in the bacterial supernatant reinforces this hypothesis. In order to confirm this, the ability of the protein to interact with eukaryotic cells was evaluated. To this purpose, the purified recombinant protein was incubated in the presence of J774.1 cells at different concentrations. The ability of YPO0502 to bind J774.1 surface was evaluated by intracellular staining using the specific antisera. As negative control, an irrelevant protein was included in the assay (2634_His). The following method was used. J774 cells were seeded into 12 well plates at a concentration of 2×106 cells/well and incubated at 37° C. 5% CO2. After 24 hrs incubation purified preparations of recombinant 0502_His and 2634_His were added to the cells at a final concentration of 0, 5 or 12 μg/ml and incubated for a further hour. As a control for 0 μg/ml 0502_His, cells were incubated with 12 μg/ml 2634_His (and inversely the 0 μg/ml 2634_His cells incubated with 12 μg/ml 0502_His). The cells were then washed with PBS, and fixed with 2% paraformaldehyde (15 min at room temperature). The cells were then permeabilized (20 min at room temperature) with permeabilizing solution (PS; PBS containing 1% bovine serum albumin and 0.5% saponin). After permeabilization the cells were washed with PS and incubated for 10 min at room temperature with 20% rabbit serum in PS followed by 30 min at room temperature with anti-mouse sera raised against either 0502_His or 2634_His (1:200) in PS. The cells were then washed in PS, followed by incubation with second antibody (1:300) R-Phycoerthythrin-conjugated AffiniPure F(ab′)2 Fragment Goat Anti-Mouse IgG (Jackson ImmunoResearch Laboratories, Inc. #115-116-072) for 30 min at room temperature. After a washing with PBS containing 1% BSA, the samples were analyzed using a FACSCanto machine (Becton Dickinson). This analysis revealed that YPO0502 is able to bind J774.1 cells (see FIG. 8).
Various proteins of the cluster were tested for their antigenic abilities. Antisera specific for the different antigens of the cluster were tested using the in vitro bactericidal assay with human blood. This analysis revealed that YPO0499 natiserum was capable of killing Y. pestis in the presence of blood from different donors (see FIG. 9). Furthermore, YPO0505, YPO0502 and YPO0501 were also able to induce functional antibodies (data not shown).
It will be understood that the invention has been described by way of example only and modifications may be made whilst remaining within the scope and spirit of the invention.
BRIEF DESCRIPTION OF SEQUENCE LISTING












SEQ ID NO:
Name
GI

















1
YPO0512
16120843


2
YPO0086
16120437


3
YPO0563
16120891


4
YPO0809
16121121


5
YPO0860
16121168


6
YPO1070
16121371


7
YPO1123
16121423


8
YPO1411
16121691


9
YPO1604
16121872


10
YPO2881
16123073


11
YPO3061
16123238


12
YPO3065
16123242


13
YPO3343
16123493


14
YPO3361
16123511


15
YPO3382
16123531


16
YPO3430
16123579


17
YPO3489
16123635


18
YPO3559
16123703


19
YPO3631
16123773


20
YPO3935
16124063


21
YPO4003
16124128


22
YPO3644
16123786


23
YPO3643
16123785


24
YPO3536
16123682


25
YPO3050
16123227


26
YPO2674
16122879


27
YPO2615
16122828


28
YPO2342
16122566


29
YPO2292
16122516


30
YPO1746
16122003


31
YPO1507
16121780


32
YPO1435
16121713


33
YPO1053
16121353


34
YPO0819
16121130


35
YPO0570
16120899


36
YPO0502
16120832


37
YPO0501
16120831


38
YPO0468
16120797


39
YPO0351
16120686


40
YPO0233
16120571


41
YPO0216
16120553


42
YPO0203
16120542


43
YPO0195
16120534


44
YPO1002
16120449


45
YPO0067
16120418


46
YPO0015
16120369


47
YPO4111
16124219


48
YPMT1.84
16082876


49
YPCD1.31c
 5832451


50
YPPCP1.07
16082686


51
YPO1052
16121352


52
YPO4070
16124183


53
YPO0494
16120824


54
YPO0663
16120988


55
YPO1222
16121511


56
YPO1906
16122154


57
YPO2905
16123096


58
YPO3375
16123524


59
YPMT1.42
16082828


60
Linker
—


61
YPO0457
16120786


62
YPO0514
16120845


63
YPO0694
16121015


64
YPO0805
16121117


65
YPO0982
16121286


66
YPO1354
16121634


67
YPO1408
16121688


68
YPO1792
16122046


69
YPO2506
16122727


70
YPO2713
16122917


71
YPO2950
16123133


72
YPO3026
16123203


73
YPO3417
16123566


74
YPO3551
16123695


75
YPO3646
16123788


76
YPO3982
16124109


77
YPO0065
16120416


78
YPO0499
16120829


79
YPO0505
16120835


80
YPO0500
16120830


81
YPO0503
16120833


82
YPO0506
16120836


83
YPO0508
16120838


84
YPO0509
16120839


85
YPO3579
16123723


86
YPO4040
16124160


87
YPO0496
16120826


88
YPO1224
16121513


89
YPO3553
16123697


90
YPO3987
16124114


91
YPO2190
16122420
















TABLE 1







The surface expression of various proteins following growth overnight at 37° C., growth


overnight at 28° C. or growth overnight at 28° C. followed by 2 h at 37° C.












Growth 28° C. overnight




Growth 37° C. overnight
followed by 37° C. for 2 hrs
Growth 28° C. overnight

















Fluorescence

Fluorescence

Fluorescence



Fusion
ΔMean
immune/
ΔMean
immune/
ΔMean
immune/


Protein
type
valuea
preimmune
valuea
preimmune
valuea
preimmune

















YPO0499
HISb
6.6
1.7
18.8
4.8
19.0
4.1


YPO0499
GST
62.0
6.5
42.0
6.2
52.3
5.9


YPO0500
HISb
4.6
1.4
23.8
3.7
26.1
3.7


YPO0501
HISb
3.9
1.3
25.8
4.3
25.4
3.6


YPO0502
HISb
1.0
1.0
26.1
3.7
30.6
4.2


YPO0502
GST
50.2
11.4
42.4
6.3
51.0
5.8


YPO0503
HISb
−3.7
0.8
11.8
1.7
10.9
1.5


YPO0503
GSTb
23.1
6.5
29.0
6.9
39.5
6.7


YPO0505
HISb
24.6
2.7
38.8
3.4
31.4
2.4


YPO0505
GSTb
65.2
12.3
65.6
11.3
118.7
12.7


YPO0506
HISb
12.1
1.6
29.1
2.7
28.1
2.3


YPO508
GST
131.2
8.4
50.1
11.4
58.2
9.3


YPO509
GSTb
31.8
6.8
35.7
7.3
51.1
6.5


GSTc
—
13.1
2.5
10.4
3.3
24.4
4.1





aΔmean value is the difference between the immune and preimmune sera;


bSera raised against an insoluble preparation of the purified protein; and


cGST was used as a negative control for the soluble GST fusions.













TABLE 2







The results of microarray experiments to determine the expression


profile of various proteins at different temperatures.










Gene
pval
ratio 28° C. vs 37° C.
Annotation













YPO0495
4.01E−05
2.10
YPO0495, organic solvent tolerance protein precursor


YPO0498
2.06E−09
39.20
YPO0498, hYPothetical protein


YPO0499
2.04E−07
39.26
YPO0499, hYPothetical protein


YPO0500
1.08E−06
27.68
YPO0500, conserved hYPothetical protein


YPO0501
2.37E−07
30.97
YPO0501, conserved hYPothetical protein


YPO0502
3.01E−07
32.73
YPO0502, conserved hYPothetical protein


YPO0503
1.86E−07
36.30
YPO0503, conserved hYPothetical protein


YPO0504
7.88E−07
46.94
YPO0504, conserved hYPothetical protein


YPO0505
2.40E−06
40.05
YPO0505, conserved hYPothetical protein


YPO0506
1.87E−07
21.88
YPO0506, putative Clp ATPase


YPO0507
1.43E−07
24.88
YPO0507, conserved hYPothetical protein


YPO0508
1.20E−07
28.36
YPO0508, hYPothetical protein


YPO0510
6.32E−05
3.12
YPO0510, hYPothetical protein


YPO0511
5.45E−07
3.20
YPO0511, hYPothetical protein


YPO0511a
2.03E−04
6.98
YPO0511a, hYPothetical protein


YPO0513
7.06E−04
15.09
YPO0513, conserved hYPothetical protein


YPO0513_2
5.71E−05
3.41


YPO0514
7.31E−05
2.65
YPO0514, putative OmpA-family membrane protein









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## Claims

1. An immunogenic composition comprising a combination of isolated Y. pestis (YP) antigens, said combination comprising two or more isolated antigens selected form the group consisting of: a YPO4003 antigen set forth as SEQ ID NO: 21, a YPO1604 antigen set forth as SEQ ID NO: 9, a YPO3489 antigen set forth as SEQ ID NO: 17 and a YPO0499 antigen set forth as SEQ ID NO: 78.

2. The immunogenic composition of claim 1, wherein at least one of the antigens is a fusion protein.

3. The immunogenic composition of claim 1, wherein at least two of the antigens are expressed as a single chain.

4. The immunogenic composition of claim 1, wherein the composition includes one or more immunoregulatory elements.

5. A method for raising an immune response in a mammal comprising the step of administering an effective amount of a composition of claim 1.