# Patent

## Title
La1—the genome of a lactobacillus strain

## Abstract

The present invention pertains to the use of the DNA sequence of a Lactobacillus johnsonii strain, in particular to its genomic sequence for elucidating interactions of micro-organism with hosts they colonize, and moreover for elucidating the basis of probiotic properties exhibited by such strain. In addition, the present invention also relates to methods of detecting nucleic acids or polypeptides of Lactobacilli and related species, respectively. A data carrier is provided comprising nucleotide sequences and/or polypeptide sequences of La1.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a divisional of patent application Ser. No. 10/961,644, filed Oct. 8, 2004, now abandoned which is a continuation of International application PCT/EP03/02882 filed Mar. 19, 2003, the entire content of patent application Ser. No. 10/961,644 and PCT/EP03/02882 are expressly incorporated herein by reference.


BACKGROUND
The present invention pertains to the use of the DNA sequence of a Lactobacillus johnsonii strain, in particular to its genomic sequence for elucidating interactions of micro-organism with hosts they colonize, and moreover for elucidating the basis of probiotic properties exhibited by such strain. In addition, the present invention also relates to methods of detecting nucleic acids or polypeptides of Lactobacilli and related species, respectively. A data carrier is provided comprising nucleotide sequences and/or polypeptide sequences of La1.
Lactic acid bacteria, i.e. micro-organisms that produce lactic acid during their (fermentative) activity, are known for a long time and comprise e.g. the genera Lactococcus, Lactobacillus, Streptococcus, Bifidobacterium and Pediococcus. These bacteria are usually prominent in milk and also in milk processing factories, respectively, living or decaying plants and represent a constituent of the intestinal micro-flora in mankind and animals.
Lactic acid bacteria have been utilized as agents for the preservation of food taking benefit of a lowering of the pH and the action of products generated during the fermentative activity thereof to e.g. inhibit the growth of spoilage bacteria. In addition, lactic acid bacteria have also been used for preparing a variety of different foodstuff such as cheese, yoghurt and other fermented dairy products from milk.
Lately, lactic acid bacteria have attracted a great deal of attention in that some strains have been found to exhibit valuable properties to man and animals upon ingestion. In particular, specific strains of the genus Lactobacillus and Bifidobacterium have been found to pass the gastro-intestinal tract in a viable and live form without getting destroyed in the upper part thereof, especially by the impact of the low pH prevailing in the stomach. Moreover, they were found to be able to colonize the intestinal mucosa, with their temporary or sustained presence in the gut being postulated to bring about numerous positive effects on the health of the living beings. These strains are generically termed probiotics.
EP 0 768 375 discloses such a specific strain of the genus Bifidobacterium, that is capable to become implanted in the intestinal flora. This Bifidobacterium strain is reported to assist in immuno-modulation, being capable to competitively exclude adhesion of pathogenic bacteria to intestinal cells, thus supporting the maintenance of the individual's health.
Apart from Bifidobacteria, also some strains of Lactobacilli have been found to exert favorable properties to humans, such as preventing colonization of the gut by pathogenic bacteria or obstructing rotaviral infection. In particular, PCT/EP02/00958 discloses such a strain having both of said properties.
In the last few years the food industry has applied such strains in products, such as milk drinks or fermented acidified milk products. Clinical studies performed with these products and/or the bacterial strains confirmed the notion that these kind of bacteria account for health promoting traits in vivo and may even be utilized for contending diseases, such as ulcers. In particular, a strain of the genus Lactobacillus johnsonii has proven to be capable to combat Helicobacter, an acknowledged cause of ulcer in man.
In view of these valuable properties particular strains of lactic acid bacteria may provide, there is a strong desire in the art for elucidating the molecular basics of these health promoting properties. In particular it would be of great interest to determine the substance or substances responsible for these effect(s). To this end, tools are required to study these micro-organisms in more detail, so as to clarify the molecular principles underlying the probiotic properties, such as interaction with the hosts, the phenomena of passing (survive in) different environmental conditions in the gut as well as having the capability to adhere to the intestine's mucosa and eventually the involvement in the enhancement of the immune system and defense against pathogens, which information will allow a better understanding of these mechanisms.
Consequently, there is a need for the provision of substantial data about bacterial strains that exhibit properties beneficial for man and/or animals. This is now provided by the present invention.
SUMMARY OF THE INVENTION
The above problem has been solved by providing the DNA sequence making up the probiotic strain Lactobacillus johnsonii La1.
In one aspect the present invention relates to the use of a nucleotide sequence of the lactic acid bacterium Lactobacillus johnsonii La1 genome having the sequence SEQ. ID. NO. 1, parts thereof or sequences homologous thereto for elucidating interactions between bacteria and a host, preferably lactic acid bacteria and a host, more preferably lactobacilli and a host, in particular for determining factors accounting for the probiotic properties of such strains.
In the context of this application the terms genome or genomic sequence shall be understood to mean the sequence of the chromosome of Lactobacillus johnsonii. The terms nucleotide sequence, polynucleotide or nucleic acid shall designate a double-stranded DNA, a single-stranded DNA or transcriptional products of the said DNAs of various length including oligo-nucleotides of about 5 to 200, preferably 10 to 100 nucleotides in length.


DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
According to the present invention a homologous nucleotide sequence is understood to mean a nucleotide sequence having a percentual identity with the sequence of SEQ ID. No. 1 (or selected parts thereof) of at least 90%, preferably at least 95%, more preferably 96% and even more preferably at least 98%. The said homologous may comprise, e.g., sequences corresponding to the genomic sequence or to the sequences of fragments thereof belonging to the species Lactobacillus, more preferably to the species Lactobacillus johnsonii, as well as the sequences corresponding to the genomic sequence or to the sequences of its representative fragments of a bacterium belonging to related species. In the present invention, the terms species and genus are mutually interchangeable.
These homologous sequences may thus correspond to variations linked to mutations within the same species or between species and may correspond in particular to truncations, substitutions, deletions and/or additions of at least one nucleotide. The said homologous sequences may also correspond to variations linked to the degeneracy of the genetic code or to a bias in the genetic code which is specific to the family, to the species or to the variant and which are likely to be present in Lactobacillus. 
Protein and/or nucleic acid sequence homologies may be evaluated using any of the variety of sequence comparison algorithms and programs known in the art. Such algorithms and programs include, but are by no means limited to, TBLASTN, BLASTP, FASTA, TFASTA, and CLUSTALW (see e.g. Pearson and Lipman, 1988, Proc. Natl. Acad. Sci. USA 85 (8): 2444-2448; Altschul et al., 1990, J. Mol. Biol. 215 (3): 403-410; Thompson et al., 1994, Nucleic Acids Res. 22 (2): 4673-4680; Higgins et al., 1996, Methods Enzymol. 266: 383-402; Altschul et al., 1990, J. Mol. Biol. 215 (3): 403-410; Altschul et al., 1993, Nature Genetics 3: 266-272).
In a particularly preferred embodiment, protein and nucleic acid sequence homologies are evaluated using the Basic Local Alignment Search Tool (“BLAST”) which is well known in the art (supra). In particular, four specific BLAST programs have been used to perform the following task:

    (1) BLASTP: Compares an amino acid query sequence against a protein sequence database
    (2) BLASTN: Compares a nucleotide query sequence against a nucleotide sequence database
    (3) BLASTX: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database
    (4) TBLASTN: Compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames


Among these representative fragments, those capable of hybridizing under stringent conditions with a nucleotide sequence disclosed in the present invention are preferred. Hybridization under stringent conditions means that the temperature and ionic strength conditions are chosen such that they allow hybridization to be maintained between two complementary DNA fragments. Such conditions of high stringency may e.g. be achieved by carrying out the hybridisation at a preferred temperature of 65° C. in the presence of SSC buffer, e.g. 1×SSC corresponding to 0.15 M NaCl and 0.05 M Na-citrate. The washing steps may be, for example, the following: 2×SSC, 0.1% SDS at room temperature followed by three washes with 1×SSC, 0.1% SDS; 0.5×SSC, 0.1% SDS; 0.1×SSC, 0.1% SDS at 68 C for 15 minutes.
The nucleotide sequences SEQ. ID. NO. 1 has been obtained by sequencing the genome of Lactobacillus johnsonii La1 by the method of directed sequencing after fluorescent automated sequencing of the inserts of clones and assembling of these sequences of nucleotide fragments (inserts) by means of software. To this end, fragments of the genome were created, ligated into suitable vectors for amplification and propagation and the corresponding fragments were sequenced. Overlaps and the final arrangement of the fragments, the nucleotide sequence thereof, were assessed by the aid of appropriate softwares.
Clones for sequencing also included 10'000 bp plus fragments as BAC clones that were used to provide a larger scale framework to the assembly. Due to the presence of several repeated regions a correct assembly proved extremely difficult. These included especially the repeated regions such as IS elements, the ribosomal operons and specifically the genes for two large cell surface proteins that contain between 100 and 200 almost perfect 10 amino acid repeats. In this case the exact sequence of these regions could not be determined due to the inability of current DNA sequencing techniques to cover the region in one run. Internal sequencing primers are excluded as they prime at multiple sites within the gene. Also, the relative orientation of these two genes, their long and very high sequence similarity makes them potential targets for host recombination. While the topology presented here has been confirmed by PCR with appropriate primers, the genome is very probably a product of such a recombination event as implied by the relative positions of the origin and termination of replication. A second problem encountered with the ribosomal operon repeats is that the presence of 6 operons at only 4 loci had been identified, and the exact location of their positions of the extra loci was only difficult to achieve. Finally, two of the IS elements are present in multiple copies, and depending on their replative orientations, they may be targets for host recombination. Such an event has been identified by studying the sequences flanking the IS element, and specifically the chromosomal target sequence that is duplicated on transposition, and hence each IS element should be flanked by identical direct repeats. We have identified two IS elements where the direct repeats have been switched due to host recombination within the IS elements. This produces an approximately 600'000 bp inversion that has been confirmed by PCR with specific primers. This IS element specific recombination may be a dynamic event that is taking place within a growing culture, leading to a major species plus a small presence of the recombined genome (seen as a faint PCR band). Finally we have the case of the prophage L771 (approximately 40'000 bp) that is constantly being excised by a site-specific recombinase. We have developed a quantitative PCR technique to detect the presence and measure the relative abundance of each variant. No pure cultures have been prepared to date.
Particularly preferred fragments of the nucleic acid sequence as identified by SEQ. ID. No. 1 are from 1-54596, from 56070-77430, from 81302-308537, from 309588-342757, from 378458-389217, from 389779-404510, from 405561-501116, from 503873-558194, from 563262-696518, from 697569-721736, from 722787-756845, from 761682-860446, from 860723-865550, from 867260-867490, from 868541-1448288, from 1463851-1526077, from 1527278-1552024, from 1563147-1809115, from 1810166-1858190, from 1863258-1872871, from 1877939-1930430, from 1932063-1983043, based on the numbering of SEQ ID. No. 1, each.
The present invention may also be utilized for producing polypeptides by using the knowledge of open reading frames (ORFs) as derived from SEQ. ID. NO. 1 and expressing the polypeptide desired according to well known techniques. In this respect, a nucleic acid corresponding to an open reading frame may be selected and inserted into an expression vector. The vector may then be introduced into a host, that enables transcription and translation of the open reading frame into the polypeptide under suitable conditions.
Nucleic acid molecules derived from the genomic sequence as identified by SEQ. ID. NO. 1 may easily be obtained, by e.g. specific amplification of the corresponding sequence using the polymerase chain reaction. Due to the sequence information provided herein the skilled person may design and synthesize any suitable primer nucleotide and amplify a fragment of interest using the polymerase chain reaction. Therefore, the present invention also comprises nucleotide sequences selected from sequence SEQ. ID. NO. 1 which can be used as a primer for the amplification of nucleic acid sequences. Other techniques for amplifying the target nucleic acid may of course also be used, such as e.g. the TAS (Transcription-based Amplification System) technique, the 3SR (Self-Sustained Sequence Replication) technique, the NASBA (Nucleic Acid Sequence Based Amplification) technique, the SDA (Strand Displacement Amplification) technique or the TMA (Transcription Mediated Amplification) technique etc.
The (poly)nucleotides may be used as probes and techniques for amplifying or modifying a nucleic acid serving as a probe, such as e.g. the LCR (Ligase Chain Reaction) technique, the RCR (Repair Chain Reaction) technique, the CPR (Cycling Probe Reaction) technique or the Q-beta-replicase amplification technique may well be applied.
The present invention, therefore, envisages both hybridization (detection) probes and primers for detecting a nucleotide sequence (target nucleotide) of the present invention. In the case of the target being a RNA molecule, e.g. a mRNA, said mRNA may be directly detected or transformed to a cDNA prior to detection.
Alternatively, in order to obtain fragments of the nucleic acid represented by SEQ. ID. NO. 1 the Lactobacillus johnsonii genomic DNA may be subjected to digestion with selected restriction enzymes, with the fragments being separated by e.g. electrophoresis or another suitable separation technique. Such techniques are well known in the art and are inter alia disclosed in Sambrook et al. A Laboratory Manual, Cold Spring Harbor, 1992. Such fragments may easily be obtained by isolating the genomic DNA of Lactobacillus johnsonii La1 and performing the necessary steps.
In an alternative form the nucleic acids may also be obtained by chemical synthesis when they are not too large in size according to methods well known to a person skilled in the art.
Modified nucleotide sequences shall be understood to mean any nucleotide sequence obtained by mutagenesis according to techniques well known to a skilled person and exhibiting modifications in relation to the normal sequences, for example mutations in the regulatory and/or promoter sequences for the expression of a polypeptide, in particular leading to a modification of the level of expression of the said polypeptide or to a modulation of the replicative cycle. Modified nucleotide sequence will also be understood to mean any nucleotide sequence encoding a modified polypeptide as defined herein.
During the study of the Lactobacillus johnsonii genome the following open reading frames could be determined with an annotation of the function of the resulting polypeptide being possible on the basis of homology to known proteins.












TABLE I









%



Gene
Start
Stop
Complement*
ID
Function




















LJ_0008 (78 aa*)
9756
9992

84.8
Ribosomal protein S18


LJ_0043 (384 aa)
52848
54002
complement
76.4
INOSINE-5′-MONOPHOSPHATE DEHYDROGENASE







(EC 1.1.1.205)


LJ_0045 (337 aa)
54728
55741
complement
96.7
D-lactate dehydrogenase (EC 1.1.1.28)


LJ_0054 (304 aa)
75671
76585

93
Prolinase prolyl aminopeptidase (EC 3.4.11.5)


LJ_0056 (316 aa)
77465
78415
complement
99
Conjugated bile salt hydrolase (EC 3.5.1.24)


LJ_0057 (451 aa)
78431
79786
complement
88
Putative bile salt transporter


LJ_0058 (452 aa)
79810
81168
complement
81.4
Putative bile salt transporter


LJ_0065 (235 aa)
87816
88523

74.6
Response regulator


LJ_0124 (149 aa)
146032
146481
complement
80.4
Nucleoside deoxyribosyltransferase-II (EC 2.4.2.6)


LJ_0178 (436 aa)
211269
212579
complement
71.1
Aminopeptidase G (EC 3.4.22.-)


LJ_0182 (482 aa)
214451
215899
complement
98.7
6-PHOSPHO-BETA-GLUCOSIDASE (EC 3.2.1.86)


LJ_0215 (367 aa)
248929
250032

70.2
Multiple sugar-binding transport ATP-binding protein msmK.







(EC 2.7.1.69)


LJ_0229 (517 aa)
264155
265708

75.2
GMP synthase [glutamine-hydrolyzing] (EC 6.3.5.2)


LJ_0258 (471 aa)
287474
288889
complement
85.9
Dipeptidase A (EC 3.4.*.*)


LJ_0260 (653 aa)
290018
291979

75
Raffinose carrier protein (RAFFINOSE PERMEASE)


LJ_0262 (480 aa)
294170
295612

71.6
sucrose phosphorylase (EC 2.4.1.7)


LJ_0274 (323 aa)
307454
308425
complement
84.4
L-lactate dehydrogenase (EC 1.1.1.27)


LJ_0295 (249 aa)
332973
333722

79.7
ORF 169a (prophage protein)


LJ_0307 (284 aa)
343364
344218

100
terminase small subunit (prophage protein)


LJ_0308 (424 aa)
344205
345479

100
orf345; terminase large subunit (prophage protein)


LJ_0309 (499 aa)
345495
346994

99.7
orf500; putative portal protein (prophage protein)


LJ_0311 (360 aa)
347218
348300

100
orf360; putative minor head protein (prophage protein)


LJ_0312 (214 aa)
348455
349099

100
orf214; scaffold protein (prophage protein)


LJ_0313 (121 aa)
349112
349477

100
Orf121 (prophage protein)


LJ_0314 (349 aa)
349498
350547

100
orf349; major head protein (prophage protein)


LJ_0315 (105 aa)
350557
350874

99
Orf105 (prophage protein)


LJ_0316 (117 aa)
350871
351224

100
Orf117 (prophage protein)


LJ_0317 (182 aa)
351217
351765

99
Orf106 (prophage protein)


LJ_0318 (122 aa)
351766
352134

100
Orf122 (prophage protein)


LJ_0319 (159 aa)
352137
352616

100
orf159; putative major tail protein (prophage protein)


LJ_0320 (136 aa)
352694
353104

93.3
Orf136 (prophage protein)


LJ_0321 (97 aa)
353197
353490

100
Orf109 (prophage protein)


LJ_0322 (2021 aa)
353490
359555

92.6
orf1434; putative minor tail protein (prophage protein)


LJ_0323 (118 aa)
359573
359929

99
Orf109a (prophage protein)


LJ_0324 (1624 aa)
359943
364817

100
Orf977 (prophage protein)


LJ_0325 (86 aa)
364949
365209

100
Orf86 (prophage protein)


LJ_0326 (135 aa)
365209
365616

100
Orf135 (prophage protein)


LJ_0327 (85 aa)
365626
365883

88.2
Orf85 (prophage protein)


LJ_0328 (115 aa)
365876
366223

100
orf115; putative holin (prophage protein)


LJ_0329 (310 aa)
366216
367148

99.6
orf376; lysin (prophage protein)


LJ_0332 (1209 aa)
370820
374449

70.9
rpoB; RNA polymerase (beta subunit) (EC 2.7.7.6)


LJ_0333 (1224 aa)
374470
378144

70
rpoC; RNA polymerase (beta subunit) (EC 2.7.7.6)


LJ_0335 (135 aa)
379054
379461

85.8
RS12; ribosomal protein S12


LJ_0336 (156 aa)
379485
379955

76.7
RS7; 30S ribosomal protein S7


LJ_0337 (698 aa)
379985
382081

70.7
translation elongation factor G, EF-G


LJ_0339 (209 aa)
382686
383315

73.4
rplC; 50S ribosomal protein L3


LJ_0342 (278 aa)
384263
385099

75.1
rplB; 50S ribosomal protein L2


LJ_0343 (95 aa)
385121
385408

81.1
rpsS; 30S ribosomal protein S19


LJ_0344 (117 aa)
385429
385782

75.4
rplV; ribosomal protein L22


LJ_0345 (222 aa)
385800
386468

70
30S ribosomal protein S3


LJ_0346 (145 aa)
386468
386905

84.8
ribosomal protein L16


LJ_0347 (88 aa)
387118
387384

72
30S RIBOSOMAL PROTEIN S17


LJ_0348 (122 aa)
387415
387783

72.9
rplN; ribosomal protein L14


LJ_0350 (180 aa)
388058
388600

79.7
RL5; ribosomal protein L5 (BL6)


LJ_0351 (132 aa)
388825
389223

70.4
rpsH; 30S Ribosomal protein S8


LJ_0352 (176 aa)
389248
389778

98.2
lecLA2-20; lectin-like protein LA2-20


LJ_0353 (119 aa)
389806
390165

72.2
rplR; 50S ribosomal protein L18


LJ_0358 (73 aa)
393402
393623

84.5
Translation initiation factor IF-1


LJ_0359 (115 aa)
393788
394135

73.6
rpsM; ribosomal protein S13


LJ_0360 (129 aa)
394160
394549

73
rpsK; 30S Ribosomal protein S11


LJ_0362 (127 aa)
395560
395943

73.2
rplQ; 50S Ribosomal protein L17


LJ_0368 (131 aa)
399970
400365

70
30S RIBOSOMAL PROTEIN S9


LJ_0395 (449 aa)
441168
442517
complement
81.5
Aminopeptidase C (EC 3.4.22.40)


LJ_0399 (499 aa)
445878
447377

73.5
Glutamyl-tRNA synthetase (EC 6.1.1.17)


LJ_0410
458506
458931

77
50S ribosomal protein L11


LJ_0441 (330 aa)
483735
484727
complement
70.6
GMP reductase (EC 1.6.6.8)


LJ_0460 (94 aa)
501772
502056

99
GroES chaperone


LJ_0461 (543 aa)
502087
503718

99
GroEL chaperone


LJ_0490 (368 aa)
543751
544857
complement
75.2
pepQ; Xaa-Pro dipeptidase (EC 3.4.13.9)


LJ_0493 (465 aa)
548984
550381
complement
71.6
pepV; Xaa-His dipeptidase (EC 3.4.13.3)


LJ_0505 (309 aa)
565393
566322

73.1
Mannose-specific phosphotransferase system comp. IID







(EC 2.7.1.69)


LJ_0521 (536 aa)
583645
585255

79
Putative ABC transporter


LJ_0563 (228 aa)
623532
624218

83.7
putative response regulator


LJ_0631 (158 aa)
705767
706243
complement
74
Autoinducer protein luxS


LJ_0677 (402 aa)
762315
763523

70
metK; S-adenosylmethionine synthetase (EC 2.5.1.6)


LJ_0764 (435 aa)
859739
861046

100
putative sensor histidine kinase


LJ_0767 (719 aa)
863354
865513

77.9
Sequence from patent


LJ_0768 (197 aa)
865524
866117

91.4
Lacticin F transporter accesory protein


LJ_0769 (75 aa)
866244
866471

98.6
Bacteriocin lactacin F, subunit lafA precursor


LJ_770 (62 aa)
866485
866671

100
Bacteriocin lacticin F, subunit lafX precursor


LJ_0771 (124 aa)
866757
867131

90.3
Bacteriocin lacticin F immunity protein, lafI


LJ_0775 (719 na)
869095
871254

77.9
Sequence from patent


LJ_0776 (197 aa)
871265
871858

77.1
Hypothetical protein


LJ_0817 (88 aa)
910392
910658

79.5
Phosphocarrier protein HPr


LJ_0827 (591 aa)
918499
920274

71
Sequence from patent


LJ_0840 (360 aa)
932899
933981

72
recA; Recombinase A


LJ_0846 (181 aa)
939718
940263

80.1
Hypothetical protein


LJ_0847 (799 aa)
940421
942820

81.9
preprotein translocase SecA subunit


LJ_0848 (332 aa)
943020
944018

72.5
peptide chain release factor 2


LJ_0853 (311 aa)
947228
948163

71.8
trxB; THIOREDOXIN REDUCTASE (EC 1.6.4.5)


LJ_0855 (317 aa)
949277
950230
complement
71
lacM; Beta-galactosidase small subunit (EC 3.2.1.23)


LJ_0856 (626 na)
950211
952091
complement
75.2
lacL; Beta-galactosidase large subunit (EC 3.2.1.23)


LJ_0860 (389 aa)
957611
958780

76.8
galK; Galactokinase (EC 2.7.1.6) (Galactose kinase)


LJ_0861 (495 aa)
958799
960286

74.7
galT; Galactose-1-phosphate uridylyltransferase (EC 2.7.7.10)


LJ_0864 (671 aa)
963226
965241

76.9
uvrB; EXCINUCLEASE ABC SUBUNIT B


LJ_0870 (195 aa)
971745
972332
complement
70
clpP, ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92)


LJ_0873 (338 aa)
975442
976458

87.8
gapdh; Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12)


LJ_0874 (403 aa)
976565
977776

84.3
pgk; Phosphoglycerate kinase (EC 2.7.2.3)


LJ_0875 (251 aa)
977795
978550

84.8
tim; Triosephosphate isomerase (EC 5.3.1.1)


LJ_0876
978600
979898

71
Enolase (EC 4.2.1.11) (2-phosphoglycerate dehydratase)


LJ_0925 (447 aa)
1023089
1024432

72.5
Glucose-6-phosphate isomerase (EC 5.3.1.9)


LJ_0934 (203 aa)
1032968
1033579

73.7
uracil phosphoribosyltransferase (EC 2.4.2.9)


LJ_0936 (70 aa)
1034425
1034637

73.9
atpE; F1F0-ATPase subunit c (EC 3.6.1.34)


LJ_0937 (166 aa)
1034690
1035190

70
atpF, F1F0-ATPase subunit b (EC 3.6.1.34)


LJ_0939 (503 aa)
1035750
1037261

84.8
atpA; F1F0-ATPase subunit alpha (EC 3.6.1.34)


LJ_0941 (480 aa)
1038258
1039700

84.7
atpD; F1F0-ATPase subunit beta (EC 3.6.1.34)


LJ_0954 (384 aa)
1049212
1050366

70.8
nifS; pyridoxal-phosphate dependent aminotransferase (EC 4.4.1.-)


LJ_0976 (458 aa)
1074934
1076310

73
CELL DIVISION PROTEIN FTSZ


LJ_0996 (618 aa)
1093985
1095841

70
elongation factor Tu family protein


LJ_1007 (89 aa)
1103999
1104268

71.9
rpsO; 30S ribosomal protein S15


LJ_1010 (396 aa)
1107239
1108429

74
EF-Tu; Elongation factor Tu


LJ_1033 (372 aa)
1129276
1130394

85.8
Sequence from patent


LJ_1079 (319 aa)
1181384
1182343

76.1
K6PF; 6-phosphofructokinase (EC 2.7.1.11)


LJ_1080 (589 aa)
1182378
1184147

83
pyk; Pyruvate kinase (EC 2.7.1.40)


LJ_1092 (91 aa)
1193710
1193985

77.5
hu; DNA-binding protein II


LJ_1111 (174 aa)
1215382
1215906

83.9
hslU; heat shock induced protein HtpI


LJ_1112 (464 aa)
1215917
1217311

76.1
HSLU; ATP-dependent hsl protease ATP-binding subunit hslU.


LJ_1138 264 aa)
1255582
1256376

70
ABC transporter ATP-binding protein


LJ_1170 (661 aa)
1287817
1289802

71
topoisomerase IV B subunit (EC 5.99.1.*)


LJ_1200 (432 aa)
1324275
1325573
complement
83.5
asnA1; Asparaginyl-tRNA synthetase (EC 6.1.1.22)


LJ_1207 (357 aa)
1338065
1339138

70.1
pmk; phosphomevalonate kinase (EC 2.7.1.36)


LJ_1298 (75 aa)
1425244
1425471

71.8
tpnA; transposase, fragment only


LJ_1303 (415 aa)
1428575
1429822
complement
85.4
pepT, PEPTIDASE T (EC 3.4.11.-) (aminotripeptidase)







(tripeptidase)


LJ_1304 (265 aa)
1429834
1430631
complement
81.1
Hypothetical protein


LJ_1317 (372 aa)
1441016
1442134
complement
81.4
rpoD; RNA polymerase sigma factor rpoD (Sigma-42)


LJ_1320 (305 aa)
1446050
1446967
complement
70.4
glyQ; Glycyl-tRNA synthetase alpha chain (EC 6.1.1.14)


LJ_1389 (142 aa)
1457128
1457556
complement
71.7
Peptide methionine sulfoxide reductase (EC 1.8.4.6)


LJ_1356 (326 aa)
1484903
1485883
complement
99
conjugated bile salt hydrolase bile (EC 3.5.1.24)


LJ_1384 (470 aa)
1510322
1511734
complement
100
orf338; putative portal protein (prophage protein)


LJ_1385 (422 aa)
1511746
1513014
complement
100
orf42; terminase large subunit (prophage protein)


LJ_1386 (151 aa)
1513007
1513462
complement
100
orf155; terminase small subunit (prophage protein)


LJ_1387 (218 aa)
1513519
1514175
complement
100
Orf221 (prophage protein)


LJ_1388 (174 aa)
1514357
1514881
complement
90.5
Orf174 (prophage protein)


LJ_1389 (146 aa)
1515925
1516365
complement
100
Orf154 (prophage protein)


LJ_1390 (73 aa)
1516454
1516675
complement
100
Orf85 (prophage protein)


LJ_1391 (184 aa)
1516695
1517249
complement
93.4
Orf197 (prophage protein)


LJ_1392 (132 aa)
1517251
1517649
complement
82.6
Orf79 (prophage protein)


LJ_1393 (71 aa)
1517650
1517865
complement
96.5
Orf78a (prophage protein)


LJ_1394 (296 aa)
1518025
1518915
complement
98.1
Orf212 (prophage protein)


LJ_1395 (261 aa)
1518928
1519713
complement
93.9
Orf223 (prophage protein)


LJ_1396 (297 aa)
1519715
1520608
complement
100
Orf309 (prophage protein)


LJ_1397 (71 aa)
1521285
1521500
complement
100
Orf73 (prophage protein)


LJ_1415 (318 aa)
1534064
1535020
complement
71.4
thyA; thymidylate synthase (EC 2.1.1.45)


LJ_1423 (624 aa)
1545410
1547284
complement
85.3
dnaK; heat shock protein DnaK


LJ_1431 (880 aa)
1553796
1556438
complement
70.3
IF2; Translation initiation factor IF-2.


LJ_1442 (241 aa)
1568288
1569013
complement
70.5
pyrH; UMP-kinase (EC 2.7.4.-)


LJ_1444 (261 aa)
1570186
1570971
complement
75.6
RS2; 30S ribosomal protein S2.


LJ_1446 (125 aa)
1581060
1581437
complement
76.1
RL19; 50S ribosomal protein L19.


LJ_1447 (84 aa)
1605746
1606000

80
RL28; 50S ribosomal protein L28.


LJ_1429 (794 aa)
1656725
1659109

71.5
pepX; Xaa-Pro dipeptidyl-peptidase (EC 3.4.14.11)


LJ_1537 (301 aa)
1666162
1667067
complement
71.2
galU; UDP-glucose pyrophosphorylase, (EC 2.7.7.9)


LJ_1558 (445 aa)
1686863
1688200
complement
72.8
Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase)


LJ_1584 (118 aa)
1713330
1713686
complement
70.7
RL20; 50S ribosomal protein L20


LJ_1681 (128 aa)
1826901
1827287

72.6
tagD; Glycerol-3-phosphate cytidylyltransferase (EC 2.7.7.39)


LJ_1741 (215 aa)
1902945
1903592
complement
72.5
Pyrrolidone-carboxylate peptidase (EC 3.4.19.3)


LJ_1767 (215 aa)
1930610
1931257

100
deoxyadenosine kinase (EC 2.7.1.76)


LJ_1768 (224 aa)
1931279
1931953

99.1
deoxyguanosine kinase (EC 2.7.1.113)





*complement = on the reverse strand


*aa = amino acids






The ORFs corresponding to various polypeptides are shown in table 1, supra, and are represented by their position in the genomic sequence as identified by SEQ. ID. NO. 1.
The open reading frames have been identified via homology analyses as well as via analyses of potential ORF start sites. It is to be understood that each identified ORF comprises a nucleotide sequence that spans the contiguous nucleotide sequence from the codon immediately 3′ to the stop codon of the preceding ORF and through the 5′ codon to the next stop codon of SEQ. ID. NO. 1 in frame to the ORF nucleotide sequence.
Table 1 also depicts the results of homology searches that compared the sequences of the polypeptides encoded by each of the ORFs to sequences present in databases.
The sequence information disclosed in the present application may be utilized for selecting a polynucleotide of interest, i.e. a nucleic acid containing an open reading frame encoding a known or an unknown, putative polypeptide and transforming micro-organisms with the selected polynucleotide. As transformation vehicles the well known plasmids, phage vectors (transfection) or F-vectors (conjugation) may be utilized. The nucleic acid introduced into the micro-organism selected may be expressed and its biological function may be either utilized as such, if known, or elucidated, in case a so far unknown polypeptide is expressed. The micro-organism selected may be a Lactobacillus itself or other well known micro-organisms, such as bacteria, e.g. E. coli, Streptococci or yeast, insect cells or even animal and plant cells.
It will be understood that the polypeptides may be expressed as such or as a fusion polypeptide. The skilled person is well aquatinted with techniques performing such a ligation and expressing the corresponding fusion-polypeptide in an appropriate cell.
In view of the present invention also new recombinant vectors for the cloning and/or the expression of a nucleotide sequence according to the present invention may be devised. The vectors comprise elements necessary to enable expression and/or secretion of the nucleotide sequences in a given host cell, such as a promoter, signals for initiation and for termination of translation, as well as appropriate regions for regulation of transcription. For example, expression of a protein or peptide may be controlled by any promoter/enhancer element known in the art. Exemplary promotors are the CMV promoter, the SV40 early promoter region, the promoter contained in the 3′ long terminal repeat of the rous sarcoma virus, the herpes thymidine kinase promoter, the regulatory sequences of the metallothionein gene, or, for prokaryotic expression systems, the β-lactamase promoter, the tac promoter or the T7 promoter.
The vector should be capable of being stably maintained in the host cell and may optionally possess particular signals specifying the secretion of the translated protein. These different elements are chosen according to the host cell utilized. To this effect the nucleotide sequences according to the invention may be inserted into autonomously-replicating vectors within the chosen host, or integrative vectors in the chosen host, such as e.g. yeast artificial chromosomes, plasmids or viral vectors.
Any of the standard methods known to those skilled in the art for inserting DNA fragments into a vector may be used to construct expression vectors containing a chimeric gene consisting of appropriate transcriptional/translational control signals and the protein coding sequences. These methods may include in vitro recombinant DNA and synthetic techniques and in vivo recombinants (genetic recombination).
The vector may be used for transcription and/or translation of a nucleic acid comprised in SEQ. ID. NO. 1, to produce RNA or antisense RNA, respectively. Such a vector can remain episomal or become chromosomally integrated, as long as it can be transcribed to produce the desired transcript.
The antisense nucleic acids of the invention comprise a sequence complementary to at least a portion of a RNA transcript of a polynucleotide sequence in SEQ. ID. NO. 1, designating a sequence having sufficient complementarity to be able to hybridize with the RNA, forming a stable duplex. In the case of double-stranded antisense nucleic acid sequence, a single strand of the duplex DNA may thus be tested, or triplex formation may be assayed.
In knowledge of the present invention also host cells may be obtained transformed with a nucleic acid or a vector according described herein. These cells may be attained by introducing into an appropriate cell a nucleotide sequence or a vector as defined above, and then culturing the said cell under conditions allowing the replication and/or the expression of the transformed/transfected nucleotide sequence.
The host cell may be chosen from eukaryotic or prokaryotic system, such as for example bacterial cells, yeast cells, animal cells as well as plant cells. In the context of this invention a cell shall be understood to comprise higher biological systems. Such as animals, whole plants or parts thereof.
Furthermore, a host cell strain may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired.
A preferred host cell for the expression of the proteins of the invention consists of prokaryotic cells, such as gram negative or gram positive bacteria. A further preferred host cell according to the invention is a bacterium belonging to the Lactobacillus family, more preferably belonging to the species Lactobacillus johnsonii or chosen from a microorganism associated with the species Lactobacillus. 
The transformed/transfected cells according to the invention may advantageously serve as a model and may be used in methods for studying, identifying and/or selecting compounds capable of being responsible for any of the beneficial effects brought about by the present Lactobacillus strain.
The invention further enables the synthesis of polypeptides encoded by the Lactobacillus johnsonii ORFs, in particular those listed in table 1. In the present description, the terms polypeptide, peptide and protein are used interchangeably. Furthermore the present invention also enables to carry out method for preparing such polypeptides by recombinant means comprising the steps of (a) culturing a host cell according to the present invention under conditions suitable to produce the polypeptide encoded by the polynucleotide; and (b) recovering the polypeptide from the culture.
It will be appreciated that the above polypeptides may also be obtained using combinatory chemistry, wherein the polypeptide is modified at some locations before testing them in model systems, so as to select the compounds which are the most active or which exhibit the desired properties.
In this context, chemical synthesis has the advantage of being able to use non-natural amino acids or non-peptide bonds. Accordingly, in order to e.g. extend the life of the polypeptides according to the invention, it may be advantageous to use such non-natural amino acids, for example in the D form, or alternatively amino acid analogues, preferably sulphur-containing forms.
Finally, the structure of the polypeptides according to the invention, its homologous or modified forms, as well as the corresponding fragments may be integrated into chemical structures of the polypeptide type and the like. Accordingly, in order to preserve the polypeptide in an in vivo environment it will be preferred to provide at the N- and C-terminal ends compounds which convey a resistance to degradation to proteases.
It will also be appreciated that the different polypeptides according to the present invention and produced by the above method may represent antigens to the immune system of a host animal, so that antibodies may be produced directed against said polypeptides. These antibodies may be used for the detection of a polypeptide of interest in a mixture or generically of a strain of Lactobacillus in a sample. In addition they may be used as research tools by e.g. producing antibodies against cellular surface epitopes and determining the effect of blocking certain polypeptides on the bacterial cell wall.
According to another aspect the present invention also provides a method for the detection and/or identification of Lactobacilli, preferably Lactobacillus johnsonii in a biological sample. This method may comprise several techniques known in the art, such as PCR or simply hybridization with a suitable probe. Alternatively, an antibody raised against a cell wall epitope of Lactobacillus, preferably Lactobacillus johnsonii may be used for said purpose. It will be appreciated that the above method may also be reversed and the presence of antibodies against Lactobacillus may be determined by contacting the sample to be tested with a polypeptide of Lactobacillus under conditions to allow formation of immune complexes.
The polypeptides and antibodies obtainable in knowledge of the present invention and the nucleotide sequences described herein may be used in in vitro and/or in vivo methods for the detection and/or the identification of bacteria belonging to the species Lactobacillus in a biological sample (biological tissue or fluid) which is likely to contain them. These methods, depending on the specificity of the polypeptides, of the antibodies and of the nucleotide sequences described herein, which will be used, may detect and/or identify the bacterial variants belonging to the species Lactobacillus as well as associated microorganisms capable of being detected by the polypeptides, the antibodies and the nucleotide sequences according to the invention which will be chosen. It may, for example, be advantageous to choose a polypeptide, an antibody or a nucleotide sequence according to the invention, which is capable of detecting any bacterium of the Lactobacillus family by choosing a polypeptide, an antibody and/or a nucleotide sequence according to the invention which is specific to the family.
The sequences referred to herein SEQ ID. NO. 1 is listed in the attached sequence listings which is to be considered as part of the specification.
The invention also comprises the nucleotide sequences or polypeptides according to the invention covalently or non-covalently immobilized on a solid support. In the first case such a support may serve to capture, through specific hybridization, the target nucleic acid obtained from a biological sample to be tested. If necessary, the solid support is separated from the sample and the hybridization complex formed between the capture probe and the target nucleic acid is then detected by means of a second probe, called detection probe, labeled with an easily detectable element.
Such support may take the form of so-called DNA array or DNA chips, a multitude of molecular probes precisely organized or arrayed on a solid support, which will allow sequencing genes, studies of mutations contained therein and the expression of genes, and which are currently of interest given their very small size and their high capacity in terms of number of analyses.
The function of these arrays/chips is based on molecular probes, mainly oligonucleotides which are attached to a carrier having a size of generally a few square centimetres or more as desired. For an analysis the carrier (DNA array/chip) is coated with probes that are arranged at a predetermined location of the carrier. A sample containing fragments of a target nucleic acid to be analyzed, for example DNA or RNA or cDNA, that has been labeled beforehand, is subsequently contacted with the DNA array/chip leading to the formation, through hybridization, of a duplex. After a washing step, analysis of the surface of the chip allows the effective hybridization to be located by means of the signals emitted by the labels tagging the target. A hybridization fingerprint results from this analysis which, by appropriate computer processing, allows to retrieve information such as the expression of genes, the presence of specific fragments in the sample, the determination of sequences and the presence of mutations.
The hybridization between the probes of the invention, deposited or synthesized in situ on the DNA chips, and the sample to be analyzed, may, e.g. be determined by means of fluorescence, radioactivity or by electronic detection.
The nucleotide sequences according to the invention may be used in DNA arrays/chips to carry out analyses of the expression of the Lactobacillus genes. This analysis is based on DNA arrays/chips on which probes, chosen for their specificity to characterize a given gene, are present. The target sequences to be analyzed are labeled before being hybridized onto the chip. After washing the labeled compounds are detected and quantified, with the hybridization being carried out at least in duplicate. Comparative analyses of the signal intensities obtained with respect to the same probe for different samples and/or for different probes with the same sample, determine a differential transcription of RNA derived from the sample.
The DNA arrays/chips according to the present invention may also contain nucleotide probes specific for other microorganisms, which will enable a serial testing allowing rapid identification of the presence of a microorganism in a sample.
The principle of the DNA chip, as detailed above may also be used to produce protein chips on which the support has been coated with a polypeptide or an antibody according to the invention, or arrays thereof, in place of the DNA. These protein chips make it possible to analyze the biomolecular interactions (BIA) induced by the affinity capture of target analytes onto a support coated e.g. with proteins, by surface plasma resonance (SPR). The polypeptides or antibodies according to the invention, capable of specifically binding antibodies or polypeptides derived from the sample to be analyzed, may thus be used in protein chips for the detection and/or the identification of proteins in samples.
The present invention also relates to a computer readable medium having recorded thereon one or more nucleotide and/or a polypeptide sequences according to the invention. This medium may also comprise additional information extracted from the present invention, such as e.g. analogies with already known sequences and/or information relating to the nucleotide and/or polypeptide sequences of other microorganisms so as to facilitate the comparative analysis and the exploitation of the results obtained. Preferred media are e.g. magnetic, optical, electrical and hybrid media such as, for example, floppy disks, CD-ROMs or recording cassettes.
The invention also relates to kits or sets for the detection and/or the identification of bacteria belonging to the species Lactobacillus johnsonii or to associated microorganisms, which comprises, a polypeptide according to the invention, where appropriate, the reagents for constituting the medium appropriate for the immunological or specific reaction, the reagents allowing the detection of the antigen-antibody complexes produced by the immunological reaction between the polypeptide (s) of the invention and the antibodies which may be present in the biological sample, it being possible for these reagents also to carry a label, or to be capable of being recognized in turn by a labeled reagent, more particularly in the case where the polypeptide according to the invention is not labeled, a reference biological sample (negative control) free of antibodies recognized by a polypeptide according to the invention, a reference biological sample (positive control) containing a predetermined quantity of antibodies recognized by a polypeptide according to the invention.
The invention also relates to a kit or set for the detection and/or the identification of bacteria belonging to the species Lactobacillus johnsonii or to an associated microorganism, or for the detection and/or the identification of a microorganism, wherein the kit comprises a protein chip according to the invention.

## Claims

1. A method for elucidating a biological function of a protein involved in an interaction between a host and a bacteria, said method comprising:
introducing a nucleotide sequence comprising an entire open reading frame that codes for the protein into the bacteria;
expressing the protein in the bacteria;
contacting the host with the bacteria; and
determining the interaction between the host and the bacteria,
wherein the interaction between the host and the bacteria elucidates the function of the protein and wherein the nucleotide sequence that comprises an entire open reading frame coding for the protein is SEQ ID NO: 1 or a fragment thereof.

2. The method according to claim 1, wherein the protein functions as a probiotic, anti-pathogenic or anti-viral.

3. The method according to claim 1, wherein the protein functions as a probiotic for stimulating the immune system.

4. The method according to claim 1, wherein the fragment of SEQ ID. No. 1 is selected from the group consisting of: nucleotides 1-54596, 56070-77430; 81302-308537, 309588-342757, 378458-389217, 389779-404510, 405561-501116, 503873-558194, 563262-696518, 697569-721736, 722787-756845, 761682-860446, 860723-865550, 867260-867490, 868541-1448288, 1463851-1526077, 1527278-1552024, 1563147-1809115, 1810166-1858190, 1863258-1872871, 1877939-1930430, and 1932063-1983043, based on the numbering of SEQ ID. No. 1.