Abstract:
The invention provides a complex inducible promoter system from a phage of a lactic acid bacterium, especially one having the DNA sequence of SEQ. ID. No: 3 given in FIG. 2, or a DNA sequence essentially corresponding to those sequences, and a modification of (an essential part of) such promoter system in which the mitomycin C induction system is replaced by a good-grade system, e.g. a temperature-initiated induction system or a salt-initiated induction system. Also is provided a recombinant vector and a transformed lactic acid bacterium comprising (an essential part of) such promoter system. Further a process for producing a desired protein by such transformed bacterium is provided, comprising expressing a gene encoding said desired protein or a precursor thereof under control of such promoter system or an essential part thereof. Preferably, the transformed lactic acid bacterium is made food-grade due to using food-grade DNA sequences and/or removing non-food-grade DNA sequences. When required, the desired protein can be secreted by the lactic acid bacterium if a DNA sequence fused to the gene encoding the desired protein is present which effects secretion of the desired protein or its precursor. The process can be used in a fermentation process, in which the desired protein causes lysis of the bacterial cells so that the contents of the cells can be released, or in which the desired protein is an enzyme involved in flavour formation, or in which the desired protein has a function in a cheese production process, such as chymosin or a precursor thereof, or an enzyme involved in flavour formation.

Description:
This application is the national phase of international application PCT/NL95/00172, filed May 12, 1995 which designated the U.S. 
    
    
     BACKGROUND OF THE INVENTION 
     1. Field of the Invention 
     The present invention relates to a complex inducible promoter system derivable from a phage of a lactic acid bacterium. 
     2. Background of the Invention and Prior Art 
     Although complex inducible promoter systems are known in Gram-negative bacteria like E. coli and in the Gram-positive bacterium Bacillus subtilis, no such promoter system has been described for lactic acid bacteria or their phages. 
     The invention is directed to an inducible strong promoter for lactic acid bacteria, which preferably can be induced in a food-grade manner. Although various constitutive, weak and strong, promoters for lactic acid bacteria are known, there is still a need for an inducible promoter effective in lactic acid bacteria. 
     BRIEF SUMMARY OF THE INVENTION 
     The invention provides a complex inducible promoter system derivable-from a phage of a lactic acid bacterium, in particular a complex inducible promoter system comprising the DNA sequence given in FIG. 2 and SEQ. ID. NOS: 3-6 or a functionally equivalent DNA sequence. A suitable embodiment is formed by a DNA sequence essentially corresponding to the DNA sequence of sequence id no 3. Other alternative embodiments comprise at least an essential part of such a complex inducible promoter system such as the DNA sequence given in FIG. 3 (which is the part of FIG. 2 or sequence id. no. 3 lacking ORF 29 and its ribosome binding site RBS). The promoter system can be modified by replacing the mitomycin C induction system by a food-grade system, such as a temperature-initiated induction system or a salt-initiated induction system by mutation techniques known per se. 
     &#34;A functional equivalent promoter system to that of sequence id no 3&#34; is understood as to include variants and mutants that have a different nucleic acid sequence but form a functional inducible complex promoter which is capable of regulating expression of a gene operatively linked to it under inducing circumstances or after having undergone induction to a degree comparable to the specifically disclosed sequences forming a complex inducible promoter system according to the invention. 
     For example the nucleic acid sequences linking and flanking certain essential elements of the complex promoter system required for it to function as an inducible promoter can be different to those in the disclosed nucleic acid sequence id no 3. Preferably the length of such linking and flanking sequences will be the same as in the disclosed sequences in order to maintain a similar structure to that of the disclosed sequences of sequence id no 3. The spacing and orientation of the elements should be preferably be the same as of the nucleic acid sequences in sequence id no. 3. The essential elements are a combination of operator sequences 1 and 2, the repressor gene (ORF 27), the topological equivalent of cro gene (ORF 28) and the ribosomal binding sites of the corresponding genes, the SD sequence and the promoters of the genes. 
     A number of variations or mutations that can be considered to be obvious to a person skilled in the art in comparison to the illustrated nucleic acid sequences whilst still retaining the functionality of the complex inducible promoter and thus being considered functionally equivalent will now be presented. Any variations or mutations of the complex inducible promoter system encoded by the nucleic acid sequence not impairing the expression capacity of the promoter system or the foodgrade status is considered to fall within the scope of the invention. With regard to the expression products of ORF 27, ORF 28 and ORF 29 it is obvious that various nucleic acid sequences encode the same amino acid sequences of these expression products other than the nucleic acid sequence of sequence id no 3 or segments 880-1654, 390-350, 336-1 of Sequence id no 3. Simply by substituting one or more codons encoding the same amino acid a nucleic acid sequence different to that of Sequence id no 3 can be obtained which will be functionally equivalent to the complex inducible promoter system formed by Sequence id no 3. These functionally equivalent nucleic acid sequences naturally fall within the definition of functional equivalent and any nucleic acid sequence differing from the specifically illustrated nucleic acid sequences merely in this aspect fall within the scope of the invention. 
     Also the complex inducible promoter system will retain its functionality if mutations are incorporated in any of the aforementioned polypeptide encoding parts (ORF 27, ORF 28 or ORF 29), which do not affect the functionality of the resulting polypeptide. In general nucleic acid sequences encoding polypeptides can vary quite substantially without affecting the functionality of the expression product. Amino acid sequences with an overall homology of more than 50% are already considered to be likely to exhibit the same function. Using computer programmes it is quite simple to predict whether a particular sequence is sufficiently homologous to be a functional equivalent, so a person skilled in the art will be able to ascertain what modifications of these particular portions of the nucleic acid sequence forming the complex inducible promoter system will lead to expression products that are functionally equivalent to those encoded by ORF 27, 28 and 29 of Sequence id no 3 and thus also can form essential elements of a functionally equivalent promoter system, such a mutant promoter system thereby falling within the scope of the invention. Functionally equivalent elements of ORF 27, ORF 28 and ORF 29 are generally nucleic acid sequences having the same length as the respective ORF&#39;s of sequence id no 3 and exhibiting more than 50% homolgy, preferably more than 60%, more preferably more than 70% with most preference for 80-100% homology at amino acid level with the respective expression products of the respective ORF&#39;s. 
     Functionally equivalent elements of ORF 27, ORF 28 and ORF 29 are generally also nucleic acid sequences having the same length as the respective ORF&#39;s of sequence id no 3 and exhibiting hybridisation with the respective ORF&#39;s under normal to stringent hybridisation conditions. In general if a nucleic acid sequence can hybridize under normal to stringent conditions to an ORF 27, 28 or 29 and the expression product functions in an analogous manner to the non mutated expression product it can be used as a functional equivalent of that element in a complex inducible promoter system according to the invention. 
     Mutations of one to 5 amino acids mostly do not affect the functionality of the polypeptide expression product and thus nucleic acid sequences encoding a polypeptide differing from a polypeptide encoded by ORF 27, ORF 28 or ORF 29 merely by one to 5 amino acids can be considered as functionally equivalent elements of ORF 27, ORF 28 or ORF 29 for a complex inducible promoter system according to the invention. A complex inducible promoter system comprising one or more of such mutants as elements therefore falls within the scope of the invention. 
     Certainly now the bacteriophage repressor gene (ORF 29) and tec gene (ORF 28) have been sequenced a person skilled in the art will quite readily be able to either synthesize an equivalent sequence to replace the natural sequence illustrated in the ORFs 27, 28 and 29 or to search the genomes of other bacteriophages derivable from lactic acid bacteria for functionally equivalent sequences forming part of a natural complex inducible promoter system of a type according to the invention. This can be done by using the knowledge of nucleic acid sequences and/or amino acid sequences to screen known sequences for similar structures or to use probes or primers designed on the basis of the information now provided to screen genomic libraries for corresponding sequences and subsequently following the methodology of the subject invention to finally obtain the desired promoter system. DNA nucleotide and amino acid sequences obtained can be analyzed for example with the PC/GENE (version 6.7) sequence analysis program (IntelliGenetics, Inc., Geneva, Switzerland). Protein homology searches can be carried out with the data bases SWISSPROT (release 27) and the ATLAS of protein and genomic sequences (March, 1994) by means of the FASTA program (12). The technologies to be applied are well known to a person skilled in the art and can be carried out without requiring inventive skill, merely standard experimentation. 
     Apart from the computer programmes and the hybridisation tests it is also possible to carry out activity assays on the expression products to ascertain whether the function of the polypeptide is maintained. Thus a person skilled in the art can readily ascertain whether a particular nucleic acid sequence falls within the scope of being a functional equivalent of an element ORF 27, ORF 28 or ORF 29 or of a complex promoter system according to the invention using standard techniques. Naturally combinations of the above mentioned groups of variations and mutations can also be considered to fall within the scope of the invention. 
     Examples of complex inducible promoter systems falling within the scope of the invention are now illustrated. 
     A complex inducible promoter system derivable from a phage of a lactic acid bacterium, in particular comprising the DNA sequence of FIG. 2 or Sequence id no 3 or a functional equivalent thereof is claimed. A suitable embodiment of a functional equivalent complex inducible promoter system according to the invention as disclosed above comprises at least the following elements: a gene encoding a repressor equivalent to the repressor encoded by ORF 27, the corresponding RBS of ORF 27, the -35 and -10 promoter sequences of P2, operator sequence 01, operator sequence 02, the -35 and -10 promoter sequences of P1, a gene encoding a protein equivalent to tec encoded by ORF 28, the corresponding SD sequence of said gene, the RBS of ORF 29 and the nucleic acid sequence encoding an amino acid sequence equivalent to the amino acid sequence encoded by ORF 29, the elements being linked by intervening sequences and optionally flanked by flanking sequences, said intervening sequences and optionally said flanking sequences having the same length as in the sequence of FIG. 2 or Sequence id no 3 but not necessarily the same composition and the elements having the same order and direction of operation as in FIG. 2 or Sequence id. no 3. In particular an embodiment of the invention is formed by a complex inducible promoter system as disclosed above comprising at least the following elements: the nucleic acid sequence ORF 27, the corresponding RBS of ORF 27, the -35 and -10 promoter sequences of P2, operator sequence 01, operator sequence 02, the -35 and -10 promoter sequences of P1, the nucleic acid sequence ORF 28, the corresponding SD sequence of ORF 28, the RBS of ORF 29 and the nucleic acid sequence ORF 29, the elements being linked by intervening sequences and optionally flanked by flanking sequences, said intervening sequences and optionally said flanking sequences having the same length as in the sequence of FIG. 2 or Sequence id no 3 but not necessarily the same composition and the elements having the same order and direction of operation as in FIG. 2 or Sequence id. no 3. Preferably the flanking sequences and intervening sequences will be the same as in sequence id no 3 as this mimics the natural situation. 
     The presence of the sequence OBF 29 is optional. It has been found however that this sequence provides a suitable precursor sequence to the gene the complex inducible promoter system is to control. The length of this ORF 29 and the corresponding RBS are suitable for operatively linking the complex inducible promoter system to the gene to be controlled. A person skilled in the art will realize that variations of this region are possible without eliminating the inducible character or the ability of a complex promoter according to the invention to control expression of a gene placed 5&#39; of ORF 28. 
     A suitable embodiment of the invention can thus also be formed by a complex inducible promoter system derivable from a phage of a lactic acid bacterium, which comprises the DNA sequence id no 3 (equal to the part of the DNA sequence given in FIG. 2 or Sequence id no 3 3&#39; downstream from the codon encoding the terminal Ser of tec in ORF 28) or a functional equivalent thereof. Such a functional equivalent comprises the following elements: a gene encoding a repressor equivalent to the repressor encoded by ORF 27, the corresponding RBS of ORF 27, the -35 and -10 promoter sequences of P2, operator sequence 01, operator sequence 02, the -35 and -10 promoter sequences of P1, a gene encoding a protein equivalent to tec encoded by ORF 28, the corresponding SD sequence of said gene, the RBS of ORF 29 and the nucleic acid sequence encoding an amino acid sequence equivalent to the amino acid sequence encoded by ORF 29, the elements being linked by intervening sequences and optionally flanked by flanking sequences, said intervening sequences and optionally said flanking sequences having the same length as in the sequence of FIG. 2 or Sequence id no 3 but not necessarily the same composition and the elements having the same order and direction of operation as in FIG. 2 or Sequence id. no 3. In particular such a functional variant embodiment of the invention comprises at least the following elements: the nucleic acid sequence ORF 27, the corresponding RBS of ORF 27, the -35 and -10 promoter sequences of P2, operator sequence 01, operator sequence 02, the -35 and -10 promoter sequences of P1, the nucleic acid sequence ORF 28, the corresponding SD sequence of ORP 28, the RBS of ORF 29 and the nucleic acid sequence ORF 29, the elements being linked by intervening sequences and optionally flanked by flanking sequences, said intervening sequences and optionally said flanking sequences having the same length as in the sequence of FIG. 2 or Sequence id no 3 but not necessarily the same composition and the elements having the same order and direction of operation as in FIG. 2 or Sequence id. no 3. Preferably the flanking sequences and intervening sequences will be the same as in sequence id no 3 as this mimics the natural situation. 
     There is a possibility that operator sequence 03 of sequence id no 3 is not an essential element, however it is preferred that in a complex promoter system according to the invention the amino acid sequence and more preferably also the nucleic acid sequence of 03 is present as further essential element at the terminal part of ORF 28 or at the terminal part of the functional equivalent of ORF 28 as this will mimic the naturally operating promoter system more closely. 
     Hybrid sequences containing a complex inducible promoter system or essential part thereof according to the invention coupled to other homologous or heterologous DNA sequences including regulatory regions also fall within the scope of the invention. 
     As stated above the modification of such a complex promoter system also falls within the scope of the invention, the practical use of such a promoter system can be greatly improved by a modification of a complex inducible promoter system or an essential part thereof as disclosed above in various embodiments, such that under inducing circumstances or after being subjected to inducing circumstances the expression product of the repressor gene can no longer repress the promoter system, said inducing circumstances occurring via a food grade induction mechanism. Such a modification can arise for example when the gene encoding the repressor is mutated such that the expression product thereof is made incapable of repression via a food grade induction mechanism under inducing circumstances or after having been subjected to inducing circumstances. This can occur at the level of the operator binding sites or at the level of the repressor. A particular embodiment of a modification comprises a modification of a complex inducible promoter system of any of the above disclosed types which is located within the repressor gene. A suitable embodiment of a desirable modification comprises a modification of a complex inducible promoter system of any of the above disclosed types, wherein the modification renders the repressor incapable of binding to the complex promoter system via a food grade induction mechanism under inducing circumstances or after having been subjected to inducing circumstances. In particular a suitable modification of this type is one in which the food-grade system is a temperature-initiated induction system. We illustrate such a modified complex inducible promoter system, wherein the modification is located in the repressor gene as comprised on plasmid pIR14 and deposited as Lactococcus lactis subsp. cremoris LL302(pIR14) at Centraal Bureau voor Schimmelcultures in Baarn, The Netherlands in accordance with the Budapest Treaty on May 11, 1995 with accession number CBS 327.95. Such a modified inducible complex promoter is a foodgrade strong promoter suitable for expression of a desired gene in lactic acid bacterium. 
     The invention also provides a recombinant vector and a transformed lactic acid bacterium each comprising such complex inducible promoter system or an essential part thereof, which lactic acid bacterium is either the natural host of the phage from which the complex inducible promoter system is derivable, or a different lactic acid bacterium. In particular such a transformed lactic acid bacterium, obtainable through transformation with a recombinant vector according to the invention, said transformed lactic acid bacterium comprising a complex inducible promoter system or an essential part thereof as disclosed in any of the embodiments above free of the bacteriophage sequences normally associated with the promoter system when incorporated in it&#39;s native bacteriophage is covered by the scope of the invention. A recombinant vector or transformed lactic acid bacterium will preferably further comprise a desired gene that is to be expressed upon induction, said desired gene being operatively linked to a complex inducible promoter system according to the invention in any of the modified or non modified embodiments disclosed. 
     Further the invention provides a process for the production of a desired expression product like a protein by a transformed lactic acid bacterium, which comprises the expression of a gene encoding said desired protein or a precursor thereof under control of a complex inducible promoter system or an essential part thereof according to the invention. Preferably the transformed lactic acid bacterium is food-grade due to the presence of food-grade DNA sequences and/or absence of non-food-grade DNA sequences. For some embodiments it is desirable that the desired protein is secreted by the lactic acid bacterium due to the presence of a DNA sequence fused to the gene encoding the desired expression product and effecting secretion of the desired expression product, said expression product for example being a protein or a precursor thereof. For ease of production the sequences closest to that of a complex inducible promoter system in its natural setting will be used as this is preferred for quickly being able to commercially produce recombinant expression products that can be consumed by humans with the minimum of legislative problems. 
     A process in which the complex inducible promoter system can be used in a manner known per se for promoters is a fermentation process. In particular a fermentation process for producing a product for consumption or being applied to humans is a suitable process, most particularly when a food grade induction mechanism can be applied to regulate the expression of a product controlled by a complex inducible promoter according to the invention. 
     Very elegantly other inventions disclosed in two copending patent applications (EP-94201354.1 and EP94201353.3) filed on May 12, 1994 directed at processes of production using foodgrade organisms can be combined with the current invention. The processes and recombinant vectors disclosed in these applications can be applied in concert with the subject invention. For example the desired expression product to be expressed, i.e. the expression product encoded by the nucleic acid sequence operatively linked to the complex inducible promoter system of the subject invention can be a lysis protein and/or a holin causing lysis of the bacterial cells so that the contents of the cells can be released. The embodiments of vectors and processes can be considered to be incorporated by reference in the subject patent application in combination with the presence of a complex inducible promoter system according to the subject invention. Alternatively the desired expression product can be an enzyme involved in flavour formation, or in a fermentation process, in which the desired expression product is a protein having a function in a cheese production process, such as chymosin or a precursor thereof, or an enzyme involved in flavour formation. 
     The invention is illustrated below on the basis of a draft publication. 
     Inducible Gene Expression Mediated by a Repressor-operator System Isolated from Lactococcus lactis subsp. cremoris Bacteriophage R1-t 
     SUMMARY 
     A regulatory region of the temperate small isometric-headed Lactococcus lactis subsp. cremoris bacteriophage R1-t chromosome has been cloned and characterized. Sequence analysis revealed the presence of two divergently oriented Open Reading Frames (ORFs), each preceded by a sequence identical to the consensus promoter used by the vegetative form of RNA polymerase. The region contained three 21-bp direct repeats with internal dyad symmetry which could act as operators. Two of these repeats were separated by only 2 base pairs and partially overlapped the two potential promoter sequences. The third repeat was located at a distance of 380 bp from the other two at the end of one of the ORFs. To study possible transcriptional regulation of the region, a lacZ translational fusion with an ORF following one of the identified ORFs was constructed. Under conditions that favour the lysogenic life cycle of R1-t, β-galactosidase activity was very low. However, the expression of the lacZ fusion could be induced by the addition of mitomycin C, which promotes the switch to the lytic life cycle. This resulted in a 70-fold increase in the production of β-galactosidase as compared to the non-induced situation. In non-induced cells promoter activity was assumed to be repressed by the rro gene product, because a frameshift mutation in the rro gene resulted in constitutive expression of the lacZ gene fusion. 
     INTRODUCTION 
     Gram-positive lactic acid bacteria (LAB) are used in a variety of industrial food and dairy fermentations as part of a starter culture, inoculated in order to drive the primary fermentation. A major problem is bacteriophage contamination of the culture which can result in the failure of the fermentation process (10). A better understanding of the bacteriophage life cycle would possibly allow the development of strategies to prevent phage infections. In addition, the study of lysogeny could offer powerful tools for the design of regulatory gene expression systems. 
     Until recently characterization of lactococcal bacteriophages was mainly limited to phage morphology, protein composition, and DNA homology-determinations, on the basis of which the bacteriophages have been grouped into different classes (9). Although many reports on lysogeny among Lactococci have been published, little is known about the molecular basis for control and maintenance of the lysogenic relationship in LAB hosts. A putative regulator gene, bpi (for BK5-T promoter inhibitor), of the temperate L. lactis subsp. cremoris phage BK5-T has been cloned (11). The bpi gene product inhibited the activity of some identified BK5-T promoters. The mechanism by which the bpi gene product operates is unknown. 
     In the context of the ultimate aim to develop a gene expression system, which can be turned on by temperature, we report here the characterization of a regulatory region of the chromosome of the temperate small isometric-headed Lactococcus lactis subsp. cremoris bacteriophage R1-t. The data presented show that a specific DNA fragment of bacteriophage R1-t contains an ORF (rro) that specifies a protein capable of repressing gene expression, presumably from an overlapping promotor-operator region (P 1 ) encompassed by the same fragment. With the use of a lacZ reporter gene, it is shown that this regulatory region can be exploited for the construction of inducible gene expression systems in L. lactis. 
    
    
     BRIEF DESCRIPTION OF THE DRAWINGS 
     FIG. 1A depicts the 1428 bp PVUII.sup.(2) /XbaI.sup.(1) fragment of pHD subcloned into pUC18 restricted with SmaI and XbaI, resulting in plasmid pPXR1. The production of pIR12 from pPXR1, in which ORF 29 was fused in frame to the lacz gene of E. coli by cloning the 482-bp XbaI fragment of pHD into the unique XbaI site of pIR11, is presented as a flow chart. The three 21 bp direct repeats are symbolized by open boxes. The ORFs that were subcloned are shaded. EM R  (erythromycin resistance marker), Amp R  (ampicillin resistance marker) and T (transcription terminator) are shown were indicated. 
     FIG. 1B shows the nucleic acid sequence (SEQ ID NO: 1) and corresponding deduced amino acid sequence (SEQ ID NO: 2) at the fusion site between ORF 29 and the lacZ gene in plasmid pIR12. 
     FIG. 2 (comprising FIGS. 2A, 2B and 2C) depict the double strand nucleotide sequence of the 1888 bp HindIII.sup.(1) /Pvu.sup.(2) fragment (SEQ ID NO: 3). The -10 and -35 sequences of the two divergent putative promoters, P 1  and P 2 , are underlined. The 21-bp direct repeats with dyad symmetry O 1 , O 2  and O 3  are shaded. The deduced amino acid sequences of the ORFs are indicated and relevant restriction enzyme sites are in bold-face type. Stop codons are indicated by asterisks. The putative ribosomal binding sites (RBS) of ORF 27 and ORF 28 are indicated in italic, and the putative alpha-helix-turn-alpha helix in the deduced amino acid sequences of ORF 27 and ORF 28 are doubly underlined. 
     FIG. 3 shows the alignment of the deduced amino acid sequence of ORF 27 (SEQ ID NO: 6), Bacillus subtilus DinR protein (SEQ ID NO.: 8) and the cI repressor of the E. coli bacteriophage 434 (SEQ ID NO: 7). Identical amino acid residues are indicated by asterisks and conservative changes are indicated by dots. 
     FIG. 4 shows an alignment of the putative helix-turn-helix motifs in rro and tec with the transcriptional control proteins of three E. coli bacteriophages (λCII, SEQ ID NO: 10; φ80 gp30, SEQ ID NO: 9; and P22 C2, SEQ ID NO 11). The sequences were taken from Dodd et al. (4). Segments of the ORF 27 (SEQ ID NO: 6) and ORF 28 (SEQ ID NO: 5) sequences having a strong likelihood for adopting the same helix-turn-helix conformation are shown, and strongly conserved amino acids in the motif (Ala or Gly in position 5, Gly in position 9, and Ile or Val in position 15) are underlined. 
     FIGS. 5A and 5B show the putative operator sites contained within the 1888-bp HindII/PvuII fragment (SEQ ID NO: 3). The double strand sequences of the putative operator sites O 1 , O 2  and O 3  are shown in FIG. 5A. The central base pair, the axis of symmetry, is shown in bold-face type. Alignment of the six half-sites enabled the designation of an 11 base pair long consensus half-site, shown in FIG. 5B. 
     FIG. 6 shows the effect of mitomycin C on β-galactosidase activity in L. lactics subsp. cremoris strain LL302 cells carrying plasmid pIR12 (dark circles) as a function of time. The time point at which 1 μg/ml mitomycin C was added is denoted by t 0 . The β-galactosidase activities measured in cells carrying pIR12 and pIR13 in the absence of mitomycin C are represented by open circles and open squares, respectively. Time scale is in hours before and after t 0 . 
     FIG. 7 shows the restriction enzyme sites NcoI and EclXI for primers rrol and rro2 in plasmid pIR12. 
     FIG. 8 is the nucleic acid and corresponding deduced amino acid sequence of rro sequence (bases 820-1654 of SEQ ID NO: 3). The NcoI and EclXL restriction enzyme sites within rro are indicated in bold. 
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     Materials and Methods 
     Bacterial Strains, Phage, Plasmids, and Media 
     The bacterial strains, phage and plasmids used in this study are listed in Table 1. Escherichia coli was grown in TY broth (22) or on TY broth solidified with 1.5% agar. L. lactis was grown in glucose M17 broth (25), or on glucose M17 agar. Erythromycin was used at 100 μg/ml and 5 μg/ml for E. coli and L. lactis, respectively. The chromogenic substrate 5-bromo-4-chloro-3-indolyl β-D-galactopyranoside (X-gal) (Sigma Chemical Co., St.Louis, Mo.) was added to plates at a final concentration of 40 μg/ml. 
     DNA Techniques 
     Plasmid DNA was isolated essentially by the method of Birnboim and Doly (1). Restriction enzymes, Klenow enzyme, and T4 DNA ligase were obtained from Boehringer GmbH (Mannheim, Germany) and used according to the instructions of the supplier. All plasmids were constructed in E. coli, which was transformed by the method of Mandel and Higa (15). Plasmids were introduced in L. lactis subsp. cremoris LL302 by means of electroporation (31). DNA and protein sequences were analysed using the programs developed by Staden (24). Helix-turn-helix motif predictions were performed according to Brennan (2) 
     
                                           TABLE 1__________________________________________________________________________Bacterial strains, plasmids and bacteriophage.   relevant features        reference__________________________________________________________________________Bacterial strainsL. lactis  subsp. cremoris  LL302 MG1363 carrying the pWV01 repA gene on the CBS 327.95   chromosome  E. coli  MC1000 araD139, Δlacx74, Δ(ara, leu)7697, galU, galK, strA                            3PlasmidspUC18   Ap.sup.R                 33  pHD Ap.sup.R ; pUC18 derivative, containing a 2.2-kb HindIII- This work   fragment of phage R1-t  pPXR1 Ap.sup.R ; carrying a 1428-bp PvuII/XbaI fragment of pHD This                            work  pMG57 Em.sup.R ; lacZ fusion vector, replicates in E. coli and 29                              L. lactis  pIR11 Em.sup.R ; pMG57 derivative, carrying a 1450-bp EcoRI/AccI This                            work   fragment of pPXR1  pIR12 Em.sup.R ; pIR11 derivative, carrying a 482-bp XbaI This work                              fragment of pHD  pIR13 Em.sup.R ; pIR12 derivative, carrying a frameshift This work                              mutation in rroBacteriophageR1-t    type P335, small isometric lactococcal phage, isolated                             9.14   from L. lactis subsp. cremoris R1__________________________________________________________________________ Em.sup.R, Ap.sup.R represent resistances to erythromycin and ampicillin, respectively. 
    
     Mitomycin C Induction 
     Overnight cultures were diluted hundred-fold in fresh glucose M17 medium and grown until the culture reached an OD600 of 0.3 at which point mitomycin C (Sigma) was added to a final concentration of 1 μg/ml. 
     Assay of β-galactosidase Activity 
     Cells from 5 ml of cultures were collected by centrifugation and resuspended in 1 ml of cold Z-buffer (16). Glass beads (0.1 mm in diameter) were added and the cells were disrupted at 4° C. for 15 minutes using a &#34;Shake it, Baby&#34; cell disrupter (Biospec Products, Bartleville, Okla.). Cells debris was removed by centrifugation for 5 min in an Eppendorf centrifuge. Equal amounts of supernatant (0.5 ml) and cold Z-buffer were mixed and specific β-galactosidase activity per OD600 was determined essentially as described by Miller (16). 
     Plasmid Constructions 
     A 2.2-kb R1-t HindIII fragment containing a putative genetic switch involved in control of lysogeny of bacteriophage R1-t (32), was subcloned in the unique HindIII site of pUC18 resulting in the plasmid pHD. The 1428-bp PvuII.sup.(2) /XbaI.sup.(1) fragment of pHD was subcloned into pUC18 restricted with SmaI and XbaI (FIG. 1A). The resulting plasmid, pPXR1, was restricted with AccI and the 5&#39;-protruding ends were flushed with Klenow enzyme. The linearized vector was subsequently digested with EcoRI and the fragment carrying ORF 27 and the partial ORF 28 was ligated into EcoRI-SmaI-digested pMG57, resulting in plasmid pIR11. To restore ORF 28 and to fuse ORF 29 in frame to the lacZ gene of E. coli, the 482-bp XbaI fragment of pHD was cloned into the unique XbaI site of pIR11 resulting in plasmid pIR12. The amino acid sequence at the fusion site between ORF 29 and the lacZ gene is shown in FIG. 1B. 
     pIR13 was constructed as follows. To introduce a frameshift mutation in ORF 27 pIR12 was restricted with NcoI and the resulting 5&#39;-sticky ends were filled in with Klenow enzyme. After selfligation an NsiI restriction site was created in the resulting plasmid pIR13, as was verified by digestion with this enzyme, thus confirming that a frameshift mutation had been introduced in ORF 27. 
     RESULTS 
     Analysis of the Nucleotide Sequence of the Bacteriophage R1-t Regulatory Region 
     We recently determined the complete nucleotide sequence of the temperate L. lactis subsp. cremoris bacteriophage R1-t (32). All of the identified ORFs had the same orientation, except for a cluster of three consecutive ORFs, the first of which is ORF 27, that had an orientation opposite to that of the two other ORFs (28 and 29). The non-coding region between the oppositely directed ORF 27 and ORF 28 contained two divergently oriented sequences identical to the consensus promoter sequence used by the vegetative form of RNA polymerase of L. lactis (30). FIG. 2 represents the nucleotide sequence of the 18889-bp HindIII.sup.(2) /PvuII.sup.(2) fragment, containing the two divergent putative promoters (designated P 1  and P 2 ) and the ORFs on this DNA fragment, which will be discussed below (see SEQ. ID. NO: 3). 
     The deduced amino acid sequence of ORF 27 (see SEQ. ID. NO: 6) shows significant similarity with the Bacillus subtilis DinR protein, the repressor of a set of damage inducible genes, corresponding to the LexA repressor of E. coli (21) and the c1 repressor of the E. coli bacteriophage 434 (17). These similarities are shown in FIG. 3 and suggest that ORF 27, designated hereafter as rro, might specify the bacteriophage R1-t repressor protein (see SEQ. ID. NOS: 6, 8 and 7). A putative ribosomal binding site could be identified upstream of rro with a ΔG of -11.8 kcal/mole according to Tinoco et al. (26). If the methionine immediately downstream of the putative ribosomal binding site would serve as the translational start of rro, the gene product would consist of 258 amino acids with an estimated molecular weight of 28,940 Da. 
     Since most bacteriophage-specific repressor proteins contain a so-called α-helix-turn-α-helix motif involved in binding of the protein to its DNA target, we compared the deduced amino acid sequence of rro with a &#34;master set&#34; of pre-aligned sequences taken from proteins known to contain a helix-turn-helix motif (2). The results of the alignment are shown in FIG. 4. By using an amino acid versus position score matrix (weight matrix) derived from amino acid conservations in the master set, an AAC (average amino acid change per codon)-score of 0.75 was obtained for a stretch of 20-amino acids, suggesting that this sequence is a strong candidate for adopting a helix-turn-helix conformation involved in binding to a specific DNA target (see SEQ. ID. NO: 6, 5, 10, 9 and 11). ORF 28 can specify a protein of 80 amino acids with a calculated molecular mass of 9,081 Da. Upstream of ORF 28 a potential ribosome binding site is present showing strong complementarity to the L. lactis 3&#39; 16S rRNA sequence (ΔG=-19.4 kcal/mole) and a window of 8 bp. In addition to the topological similarity with the lambda cro gene, the ORF 28 amino acid sequence contains a stretch of amino acids with the characteristics of a putative helix-turn-helix motif (FIG. 4). ORF 28 therefore is designated hereafter as tee (topological equivalent of cro). 
     The intergenic region between rro and tec contains two almost perfectly matching 21-bp direct repeats with internal dyad symmetry, O 1  and O 2  (FIG. 2). They are separated by two nucleotides, overlap the -35 sequences of the two putative promoters in this region, and may function as operator binding sites for the R1-t repressor. Careful inspection of the entire 1889-bp HindIII/PvuII fragment revealed a third putative operator site, O 3 , situated within the coding region of ORF 28 at a distance of 380 basepairs upstream of O 1 . The double strand sequences of the putative operator sites are shown in FIG. 5A. Alignment of the six half-sites enabled the designation of an 11 base pair long consensus half-site (FIG. 5B), see FIG. 2. 
     The Expression of ORF 29 is Subject to Repression by the rro Gene Product 
     Analogous to the situation in the regulatory regions of several other temperate bacteriophages, the non-coding area between the divergently oriented ORFs could function as the regulatory region involved in lysogeny of the phage. In this scheme P 1  might function as the transcriptional start signal for the lytic genes, whereas P 2  might be responsible for the establishment of the lysogenic state. 
     To examine whether transcription of ORF 29 was regulated by upstream sequences, a lacZ-ORF 29 translational fusion was constructed in plasmid pIR12 (FIG. 1). In L. lactis subsp. cremoris LL302 cells carrying pIR12 very little β-galactosidase activity 
     (17 U) was observed (FIG. 6). To determine whether lacZ expression could be induced under conditions which induce the lytic state, the effect of mitomycin C on β-galactosidase activity was examined. After the addition of 1 μg/ml of mitomycin C to a culture carrying pIR12, the β-galactosidase activity increased considerably. Two and a half hours after the addition of mitomycin C β-galactosidase activity had increased approximately 70-fold, indicating that ORF 29 was transcriptionally regulated, presumably by promoter P 1 , because the region between ORF 28 and ORF 29 does not provide space for a promoter and because no promoter-like sequence could be discerned in the 3&#39; region of ORF 28. 
     In order to examine whether the low lacZ expression in non-induced cells carrying plasmid pIR12 was established through repression of promoter activity by the rro gene product, pIR13 was constructed. Filling-in the NcoI restriction site of pIR12 resulted in a frameshift mutation and the introduction of two stop codons in the rro gene. Cells containing pIR13 are not expected to produce a functional rro gene product. As can be seen from FIG. 6, such cells constitutively expressed lacZ at a high level. From these results we infer that the rro gene is required for the repression of ORF 29 transcription under conditions that favour the lysogenic state of the bacteriophage R1-t. Apparently inactivation of the rro gene by the introduction of a frameshift led to derepression of promoter activity required for ORF 29 transcription. 
     DISCUSSION 
     We recently determined the complete nucleotide sequence of the temperate L. lactis subsp. cremoris bacteriophage R1-t. All identified ORFs were oriented in one direction, except for a cluster of three consecutive ORFs, the first of which is ORF 27. The non-coding region between the oppositely directed ORF 27 and ORF 28 contains two divergently oriented sequences, designated P 1  and P 2 , identical to the consensus promoter sequence used by the vegetative form of RNA polymerase of L. lactis (30). On the basis of significant similarity of the deduced amino acid sequence with various repressor proteins we assumed that ORF 27, designated rro, specifies the bacteriophage R1-t repressor protein. The deduced rro gene product is a protein of 258 amino acids with an estimated molecular weight of 28,940 Da. 
     To study possible transcriptional regulation of the region by the rro gene product, a lacZ translational fusion with ORF 29, which is located downstream of ORF 28, was constructed. It was shown that under conditions that favour the lysogenic life cycle of R1-t, β-galactosidase activity was very low. Expression of the lacZ fusion could be induced by the addition of mitomycin C, which promotes the switch to the lytic life cycle. In non-induced cells promoter activity is likely to be repressed by the rro gene product, because a frameshift mutation in the rro gene resulted in constitutive expression of the LacZ gene fusion. These results indicate that ORF 29 is transcriptionally regulated, presumably by promoter P 1 . It is likely that, analogous to several lambdoid phages, prophage induction is the result of cleavage of the phage repressor via a RecA-mediated pathway. DNA damage activates RecA, which presumably catalyzes self-cleavage of Rro at a site that seems to be conserved in proteins that undergo RecA-mediated cleavage (13). 
     The rro gene is directly preceded by the P2 promoter. The identity of the putative -10 and -35 sequences of P2 to the vegetative L. lactis promoter sequences is therefore consistant with the idea that the lysogenic response to infection by a temperate phage requires the synthesis of a phage-encoded repressor (20). The repressor gene therefore is probably one of the first phage genes to be expressed after infection and, consequently, its expression should rely entirely upon phage-specific transcription initiation sequences recognized by the host RNA-polymerase. A putative DNA-binding motif is present in the deduced Rro amino acid sequence. Like most of the bacteriophage-specified repressor proteins, Rro contains a so-called α-helix-turn-α-helix motif, suggesting that this stretch of amino acids is involved in binding to a specific DNA target, the so-called operator (19). The intergenic region between rro and tec contains two almost perfectly matching 21-bp direct repeats with internal dyad symmetry, designated O 1  and O 2 . These sequences are separated by two nucleotides, overlap both -35 sequences of the two putative promoters in this region, and may function as operator binding sites for the R1-t repressor. Careful inspection of the entire 1889-bp HindIII/PvuII fragment revealed a third putative operator site, O 3 , situated within the coding region of ORF 28 at a distance of 380 basepairs upstream of O 1 . Of the 11 bp that constitute the operator half-site, 7 bp are invariable. 
     Most of the operators described hitherto consist of imperfect symmetrical binding sites. In the case of phage lambda operators, on which detailed structural information concerning protein-DNA complex formation is available, this 2-fold rotational symmetry reflects the two binding sites for each of the two subunits of the repressor dimer (18). The subtle structural variation in the individual binding sites of the operators form the basis for their differential relative affinities towards the c1 and cro products (20). With respect to the localization of the putative operators, however, there is an obvious difference in the organization of the R1-t immunity region compared to that of the studied E. coli phages. In contrast to the situation in lambda where the three operators are clustered in the non-coding area between the two divergent promoters, enabling co-operative binding, the third operator site (O 3 ) of R1-t is located 380 bp upstream of O 1 , within the ORF 28 coding region. Such organization is not unique, since similar arrangements of multiple operator sites have been demonstrated in several E. coli operons, such as gal (7, 8), araBAD (5), deo (27) and Lac (6). In all these cases there is now accumulating evidence for a regulatory mechanism that involves cooperative binding of the repressor to the separated sites through protein-protein contacts holding together a loop of intervening DNA (23). 
     A similar situation has also been demonstrated for the B.subtilis phage φ105 (28). The third operator of φ105, designated O R  3, is located approximately 250 bp downstream from P R , within the ORF 3 coding region of the proximal gene of the P R  transcription unit. Although the three φ105 O R  sites are required for maximal gene control during phage development, it was shown that repression of P R  could be observed in the absence of the O R  3 copy. Preliminary results indicated that deletion of the O 3  -containing 482-bp XbaI-fragment of pIR12, resulting in an in frame fusion of ORF 28 to the lacZ gene, had only a minor effect on the repression of expression of the fusion protein, suggesting that a similar situation exists in the case of R1-t. However, since the deletion of the XbaI-fragment also results in the inactivation of tec, further experiments have to reveal the exact role of O 3  in the control of lysogeny. 
     On the basis of the results obtained, it would appear that the general strategy employed by R1-t to control lysogeny is similar to that used by the lambdoid phages of E. coli. In this concept P 1  functions as the transcriptional start signal of the lytic genes and P2 is the equivalent initiator for the genes expressed during the lysogenic state, including rro which specifies the phage repressor. Although ORF 28, designated tec, is the topological equivalent of the lambda cro gene and the deduced amino acid sequence contains a putative DNA-binding α-helix-turn-α-helix motif, it has to be clarified whether the tec gene product is actually playing a role in the control of lysogeny and if so, whether it is the functional equivalent of cro. 
     Inducible gene expression in E. coli based on the temperature-sensitive C1 repressor C1857, has been extremely helpful as a simple means to overexpress (heterologous) genes in this organism. By analogy, to dispose of such a system in Lactococci would be valuable to modulate gene expression. Experiments were carried out to develop such a thermo-inducible gene expression system. 
     Construction of a Thermo-inducible Gene Expression System for Lactococcus lactis 
     Inducible gene expression in Escherichia coli based on the temperature-sensitive CI repressor CI857, has been extremely helpful as a simple means to overexpress (heterologous) genes in this organism. By analogy, to dispose of such a system in Lactococci would be valuable to modulate gene expression. We developed such a thermoinducible gene expression system for Lactococcus lactis on the basis of the regulatory region of the lactococcal temperate bacteriophage R1-t. 
     A regulatory region of the lactococcal temperate bacteriophage R1-t encompassing rro, encoding the phage repressor, and tec (the topological equivalent of phage lambda cro) was subcloned in such a way that the ORF immediately downstream of tee was translationally fused with lacZ in plasmid pIR12 34  (Nauta et al., 1994). Expression of the fused lacZ could be induced by the addition of 1 μg/ml mitomycin C to pIR12 containing cells. 
     In order to construct a thermo-inducible gene expression system, part of the rro gene (corresponding to the segment of Rro in which a mutation could result in a heat-labile repressor mutant 33 , M. Lieb, 1991), was mutagenized using PCR and dITP 35  (J. J. Spee et al., 1993). The two synthetic primers used for amplification (Table 1) both encompassed a restriction enzyme site that was located within rro and unique in pIR12: NcoI and EclXI for primers rro1 and rro2 respectively (FIG. 7). After restriction of the PCR products with both enzymes, the NcoI/EclXI fragment of pIR12 could therefore be replaced by the mutagenized fragment. 
     Mutagenesis of rro 
     Random mutagenization of rro was performed by PCR essentially as described by Spee et al. (1993). A 372-basepair rro fragment was amplified with Supertaq polymerase (HT Biotechnology, Cambridge, England). The following conditions were used. Approximately 10 ng of pIR12 DNA was used as a template for PCR in a total volume of 50 μl, containing 1 unit of Supertaq polymerase, 10 mM Tris-HCl 2  pH 9.0, 5 mM MgCl 2 , 50 mM KCl, 0.01% (w/v) gelatin, 0.1% Triton X-100, and 200 μM dNTP&#39;s. PCR reactions were performed in the presence of 200 μM dITP using 10 pmol of the primers rro1 and rro2 (Table 1). The concentration of the limiting dNTP was 14 μM. PCR fragments were purified by fenol/chloroform extraction, digested with NcoI and EclXI and subcloned in NcoI/EclXI digested pIR12. The ligation mixture was used to transform Lactococcus lactis LL302. 
     Screening for Temperature-sensitive Rro Mutants 
     Screening for mutations in Rro that resulted in a loss of DNA-binding activity at elevated temperatures was performed by using a plate assay. After transformation, cells were plated on GSM17 agar plates supplemented with 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal) and incubated overnight at 30° C. By this procedure, the strain Lactococcus lactis subsp. cremoris LL302 (pIR14) was obtained. Colonies of this strain are white at 30° C. and blue at 37° C. The β-galactosidase activities at both temperatures were measured. The strain was grown to an OD600 of 0.3 at 30° C. after which time point the culture was divided in two parts. One half of the culture was grown at 30° C., the other part at 37° C. AFter two hours, the β-galactosidase activity of both cultures was determined. The β-galactosidase activity at 30° C. was slightly higher than that observed in the Lactococcus lactis subsp. cremoris LL302 strain carrying pIR12 (wild type Rro) due to some lacZ expression at this temperature (this leakage could be diminished by growing cells at lower temperatures). The lacZ expression in strain lactococcus lactis subsp. cremoris LL302 (pIR14) could be induced by a shift in temperature. In cells that were grown at 37° C., the lacZ expression had increased considerably. The mutation within rro is present on plasmid pIR14 deposited at CBS Baarn under accession nr. CBS 327.195. 
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     3 Casadaban, M. J., and S. N. Cohen. (1980). Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J. Mol. Biol. 138: 179-207. 
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     6 Eismann, E., von Wilcken-Bergmann, B., and Muller-Hill, B. (1987). Specific destruction of the second Lac operator decreases repression of the lac operon in Escherichia coli fivefold. J. Mol. Biol. 195: 949-952. 
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     12 Pearson W. R. and D. J. Lipman 1988. Improved tools for biological sequence comparison Proc. Natl. Sci USA 85:2444-2448. 
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                       TABLE 2______________________________________Primers used to amplify part of rro                             basepair    position    within rro  Primer 5&#39;-3&#39; nucleotide sequence (FIG. 2)______________________________________rro1  GAA GTC CCA TGG TTG AAG ATT TTG                         128-151  rro2 CAA GAG GAA GTC CGG CCG CTA TCC  476-499______________________________________ * The Ncol and EclXI restriction enzyme sites are underlined 
    
     
         __________________________________________________________________________#             SEQUENCE LISTING   - -  - - (1) GENERAL INFORMATION:   - -    (iii) NUMBER OF SEQUENCES: 11   - -  - - (2) INFORMATION FOR SEQ ID NO: 1:   - -      (i) SEQUENCE CHARACTERISTICS:       (A) LENGTH: 93 base - #pairs       (B) TYPE: nucleic acid       (C) STRANDEDNESS: double       (D) TOPOLOGY: linear   - -     (ii) MOLECULE TYPE: DNA (genomic)   - -     (vi) ORIGINAL SOURCE:       (A) ORGANISM: Lactococcus - #lactis phage R1-t       (C) INDIVIDUAL ISOLATE: - #Fig.1B cds ORF 29 and E.coli lacZ  - -     (ix) FEATURE:      (A) NAME/KEY: CDS      (B) LOCATION: 1..93  - -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #1:  - - ACA ATC CGA AGC ACG GAG TAC ATG ACG GAT GC - #G AAG CTT GCA TGC CTG 48 Thr Ile Arg Ser Thr Glu Tyr Met Thr Asp Al - #a Lys Leu Ala Cys Leu   1               5 - #                 10 - #                 15  - - CAG GTC GAC TCT AGA GTC GGG GCC GTC GTT TT - #A CAA CGT CGT GAC - #93 Gln Val Asp Ser Arg Val Gly Ala Val Val Le - #u Gln Arg Arg Asp         20     - #             25     - #             30  - -  - - (2) INFORMATION FOR SEQ ID NO: 2:  - -      (i) SEQUENCE CHARACTERISTICS:      (A) LENGTH: 31 amino - #acids      (B) TYPE: amino acid      (D) TOPOLOGY: linear  - -     (ii) MOLECULE TYPE: protein  - -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #2:  - - Thr Ile Arg Ser Thr Glu Tyr Met Thr Asp Al - #a Lys Leu Ala Cys Leu   1               5 - #                 10 - #                 15  - - Gln Val Asp Ser Arg Val Gly Ala Val Val Le - #u Gln Arg Arg Asp         20     - #             25     - #             30  - -  - - (2) INFORMATION FOR SEQ ID NO: 3:  - -      (i) SEQUENCE CHARACTERISTICS:      (A) LENGTH: 1888 base - #pairs      (B) TYPE: nucleic acid      (C) STRANDEDNESS: double      (D) TOPOLOGY: linear  - -     (ii) MOLECULE TYPE: DNA (genomic)  - -     (vi) ORIGINAL SOURCE:      (A) ORGANISM: Lactococcus - #lactis phage R1-t      (C) INDIVIDUAL ISOLATE: - #Fig.2 cds ORF27, ORF 28 and ORF29  - -     (ix) FEATURE:      (A) NAME/KEY: CDS      (B) LOCATION: complement - #(1..336)  - -     (ix) FEATURE:      (A) NAME/KEY: CDS      (B) LOCATION: complement - #(350..590)  - -     (ix) FEATURE:      (A) NAME/KEY: CDS      (B) LOCATION: 880..1654  - -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #3:  - - AAGCTTCGCA TCCGTCATGT ACTCCGTGCT TCGGATTGTT GGGAGGACTT CT -#TCATATAC     60   - - CCAATCCTGA AATGGCTCAG CACTTGGCAA TTTACTTTCG CCAGCTAATT GA -#TAAAGACC    120   - - AGGTTCTGAA ATTACTGTGA CACTTTGTAC TCCTGAGGGG GTCGTGATTC GC -#GACTCCCT    180   - - CTTATATTTG TCTTTTACAT GAGATTTCAA AGCATCCCTG AAATTCTTGT AA -#CCAATAGC    240   - - AATTGCTACA TCTTTTCCGA CAAACCAAGG TTCATCATTG ATAAGTACTG TT -#CGTACTGG    300   - - TAAGTTATTA AAATTAAAAT TTTGTAATTC TTTCATGTTT TGCCTTTCTA AC -#TAGCCAAT    360   - - TTGTCAAGTT TTTGATTAAA ATTTTTCAGC ACAAAAATAA CATCGGTTAA AT -#CTACTCCA    420   - - ATAACCTCTG CAATGTTCGC TGCTGAAACA GCATCTATTC TAGATGGGTT GA -#TACGCCAC    480   - - TTATAAAATG TTGTATAGGG AACGTTAATT TTTTTTGCGA TAACTTTATA CT -#TCATTCCT    540   - - GAAGAGTCTA ATAACTCATC TAGTGGCTCA TAAGTTTTTT TCTCTGCCAT AC -#TGGCTCCT    600   - - TTCTGCCCCT CTGGGGCTTT TTATTTGCCA AACTTGCTAC TTACATCGCG GT -#GGATACGT    660   - - CGTGTACCGT CATTTGAGCC TGTTCCGTCC GCCGTACTGA ATGCTCCATG AT -#TGTTCGCT    720   - - TGTTTGACTT TATGAATTAA TTATAACCTT AACTATCCAA TTTGTCAAGT TA -#AAACTTTC    780   - - CAAATTGACA AGTTTTGTTG TTTGTGCTAT AATTAGTGTA TGAAAAAAAT AC -#GACTACCT    840   - - GAAATGATAG ATTATTTCAG AAAAGAGAAT GGTTGGACG ATG AAA GAG - # TTT GGC 894              - #                  - #       Met Lys Glu Phe Gly              - #                  - #         1         - #      5  - - GAA AAG CTA GGA AAA TCT GAG TCA GCT ATT TC - #G AAA TGG ATA AAA GGG942 Glu Lys Leu Gly Lys Ser Glu Ser Ala Ile Se - #r Lys Trp Ile Lys Gly             10 - #                 15 - #                 20  - - GTT AGA AGT CCC ATG GTT GAA GAT TTT GAT AA - #A ATG GTC AAT CTA TTC990 Val Arg Ser Pro Met Val Glu Asp Phe Asp Ly - #s Met Val Asn Leu Phe         25     - #             30     - #             35  - - AAT ACT GAT CCT GAG ACA TTA ATG TAT GGT GC - #T TCT GAC CTT TCT ACA    1038 Asn Thr Asp Pro Glu Thr Leu Met Tyr Gly Al - #a Ser Asp Leu Ser Thr     40         - #         45         - #         50  - - ACT CTA TCC GAA ATA AAT AAA ATC AGT TCA CA - #A CTC GAA GAA CCA CGT    1086 Thr Leu Ser Glu Ile Asn Lys Ile Ser Ser Gl - #n Leu Glu Glu Pro Arg 55             - #     60             - #     65  - - CAG AAA GTT GTT TTA AAT ACT GCA AAT AAT CA - #G TTA GAT GAG CAA AAC    1134 Gln Lys Val Val Leu Asn Thr Ala Asn Asn Gl - #n Leu Asp Glu Gln Asn  70                 - # 75                 - # 80                 - # 85  - - CAA GAA AAG AAA AAG GAA TCT AAA GTG ATT CC - #A ATT AAT AAA ATA CCT    1182 Gln Glu Lys Lys Lys Glu Ser Lys Val Ile Pr - #o Ile Asn Lys Ile Pro             90 - #                 95 - #                100  - - GAC GAT TTA CCA CCA TAT ATA AGT AGA AAG AT - #T TTA GAG AAT TTC GTT    1230 Asp Asp Leu Pro Pro Tyr Ile Ser Arg Lys Il - #e Leu Glu Asn Phe Val        105      - #           110      - #           115  - - ATG CCT ACA AAC ACT ATG GAA TAT GAG GCT GA - #T GAA GAT ATG GTA GAT    1278 Met Pro Thr Asn Thr Met Glu Tyr Glu Ala As - #p Glu Asp Met Val Asp    120          - #       125          - #       130  - - GTT CCT ATT CTT GGT AGG ATA GCG GCC GGA CT - #T CCT CTT GAT GCA GTA    1326 Val Pro Ile Leu Gly Arg Ile Ala Ala Gly Le - #u Pro Leu Asp Ala Val135              - #   140              - #   145  - - GAA AAC TTC GAC GGT ACA AGA CCA GTA CCT GC - #G CAC TTC TTA TCT TCT    1374 Glu Asn Phe Asp Gly Thr Arg Pro Val Pro Al - #a His Phe Leu Ser Ser 150                 1 - #55                 1 - #60                 1 -#65   - - GCT CGT GAT TAC TAT TGG TTA ATG GTT GAT GG - #G CAT AGC ATG GAACCG     1422  Ala Arg Asp Tyr Tyr Trp Leu Met Val Asp Gl - #y His Ser Met Glu Pro            170  - #               175  - #               180  - - AAA ATT CCA TAT GGA GCT TAT GTT TTA ATT GA - #A GCT GTT CCT GAT GTG    1470 Lys Ile Pro Tyr Gly Ala Tyr Val Leu Ile Gl - #u Ala Val Pro Asp Val        185      - #           190      - #           195  - - AGC GAC GGT ACT ATT GGA GCT GTT CTT TTC CA - #T GAT GAT TGT CAG GCA    1518 Ser Asp Gly Thr Ile Gly Ala Val Leu Phe Hi - #s Asp Asp Cys Gln Ala    200          - #       205          - #       210  - - ACA TTA AAA AAA GTT TAT CAT GAA ATA GAT TG - #C TTG AGA CTT GTG TCA    1566 Thr Leu Lys Lys Val Tyr His Glu Ile Asp Cy - #s Leu Arg Leu Val Ser215              - #   220              - #   225  - - ATC AAC AAA GAA TTT AAA GAC CAA TTT GCT AC - #A CAA GAC AAT CCA GCA    1614 Ile Asn Lys Glu Phe Lys Asp Gln Phe Ala Th - #r Gln Asp Asn Pro Ala 230                 2 - #35                 2 - #40                 2 -#45   - - GCT GTG ATT GGG CAA GCT GTC AAA GTA GAA AT - #T GAT TTATAATTAA1660 Ala Val Ile Gly Gln Ala Val Lys Val Glu Il - #e Asp Leu            250  - #               255  - - ATATACGAGC AATGTCTTGA TTCTCGTTAA AAGCTAGGTT AGGAAATATA AA -#CATTATGA   1720   - - AAAATGGAAA AACTCCTAAA GCTAAAAAAC CAATTTATAA AAGAATATGG TT -#TTGGATTG   1780   - - TTGTAGTAAT CGTAGTAGCG GTTATTGGTA GCGCACTTGG AGGAGGAGGC AA -#AGGCAAAA   1840   - - GTGGAACATC AACTTCTACA TCCTCAAGTT CTAAAATTAA AACAGCTG  - #    1888  - -  - - (2) INFORMATION FOR SEQ ID NO: 4:  - -      (i) SEQUENCE CHARACTERISTICS:      (A) LENGTH: 112 amino - #acids      (B) TYPE: amino acid      (D) TOPOLOGY: linear  - -     (ii) MOLECULE TYPE: protein  - -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #4:  - - Met Lys Glu Leu Gln Asn Phe Asn Phe Asn As - #n Leu Pro Val Arg Thr   1               5 - #                 10 - #                 15  - - Val Leu Ile Asn Asp Glu Pro Trp Phe Val Gl - #y Lys Asp Val Ala Ile         20     - #             25     - #             30  - - Ala Ile Gly Tyr Lys Asn Phe Arg Asp Ala Le - #u Lys Ser His Val Lys     35         - #         40         - #         45  - - Asp Lys Tyr Lys Arg Glu Ser Arg Ile Thr Th - #r Pro Ser Gly Val Gln 50             - #     55             - #     60  - - Ser Val Thr Val Ile Ser Glu Pro Gly Leu Ty - #r Gln Leu Ala Gly Glu  65                 - # 70                 - # 75                 - # 80  - - Ser Lys Leu Pro Ser Ala Glu Pro Phe Gln As - #p Trp Val Tyr Glu Glu             85 - #                 90 - #                 95  - - Val Leu Pro Thr Ile Arg Ser Thr Glu Tyr Me - #t Thr Asp Ala Lys Leu        100      - #           105      - #           110  - -  - - (2) INFORMATION FOR SEQ ID NO: 5:  - -      (i) SEQUENCE CHARACTERISTICS:      (A) LENGTH: 80 amino - #acids      (B) TYPE: amino acid      (D) TOPOLOGY: linear  - -     (ii) MOLECULE TYPE: protein  - -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #5:  - - Met Ala Glu Lys Lys Thr Tyr Glu Pro Leu As - #p Glu Leu Leu Asp Ser   1               5 - #                 10 - #                 15  - - Ser Gly Met Lys Tyr Lys Val Ile Ala Lys Ly - #s Ile Asn Val Pro Tyr         20     - #             25     - #             30  - - Thr Thr Phe Tyr Lys Trp Arg Ile Asn Pro Se - #r Arg Ile Asp Ala Val     35         - #         40         - #         45  - - Ser Ala Ala Asn Ile Ala Glu Val Ile Gly Va - #l Asp Leu Thr Asp Val 50             - #     55             - #     60  - - Ile Phe Val Leu Lys Asn Phe Asn Gln Lys Le - #u Asp Lys Leu Ala Ser  65                 - # 70                 - # 75                 - # 80  - -  - - (2) INFORMATION FOR SEQ ID NO: 6:  - -      (i) SEQUENCE CHARACTERISTICS:      (A) LENGTH: 258 amino - #acids      (B) TYPE: amino acid      (D) TOPOLOGY: linear  - -     (ii) MOLECULE TYPE: protein  - -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #6:  - - Met Lys Glu Phe Gly Glu Lys Leu Gly Lys Se - #r Glu Ser Ala Ile Ser   1               5 - #                 10 - #                 15  - - Lys Trp Ile Lys Gly Val Arg Ser Pro Met Va - #l Glu Asp Phe Asp Lys         20     - #             25     - #             30  - - Met Val Asn Leu Phe Asn Thr Asp Pro Glu Th - #r Leu Met Tyr Gly Ala     35         - #         40         - #         45  - - Ser Asp Leu Ser Thr Thr Leu Ser Glu Ile As - #n Lys Ile Ser Ser Gln 50             - #     55             - #     60  - - Leu Glu Glu Pro Arg Gln Lys Val Val Leu As - #n Thr Ala Asn Asn Gln  65                 - # 70                 - # 75                 - # 80  - - Leu Asp Glu Gln Asn Gln Glu Lys Lys Lys Gl - #u Ser Lys Val Ile Pro             85 - #                 90 - #                 95  - - Ile Asn Lys Ile Pro Asp Asp Leu Pro Pro Ty - #r Ile Ser Arg Lys Ile        100      - #           105      - #           110  - - Leu Glu Asn Phe Val Met Pro Thr Asn Thr Me - #t Glu Tyr Glu Ala Asp    115          - #       120          - #       125  - - Glu Asp Met Val Asp Val Pro Ile Leu Gly Ar - #g Ile Ala Ala Gly Leu130              - #   135              - #   140  - - Pro Leu Asp Ala Val Glu Asn Phe Asp Gly Th - #r Arg Pro Val Pro Ala 145                 1 - #50                 1 - #55                 1 -#60   - - His Phe Leu Ser Ser Ala Arg Asp Tyr Tyr Tr - #p Leu Met Val AspGly             165  - #               170  - #               175  - - His Ser Met Glu Pro Lys Ile Pro Tyr Gly Al - #a Tyr Val Leu Ile Glu        180      - #           185      - #           190  - - Ala Val Pro Asp Val Ser Asp Gly Thr Ile Gl - #y Ala Val Leu Phe His    195          - #       200          - #       205  - - Asp Asp Cys Gln Ala Thr Leu Lys Lys Val Ty - #r His Glu Ile Asp Cys210              - #   215              - #   220  - - Leu Arg Leu Val Ser Ile Asn Lys Glu Phe Ly - #s Asp Gln Phe Ala Thr 225                 2 - #30                 2 - #35                 2 -#40   - - Gln Asp Asn Pro Ala Ala Val Ile Gly Gln Al - #a Val Lys Val GluIle             245  - #               250  - #               255  - - Asp Leu  - -  - - (2) INFORMATION FOR SEQ ID NO: 7:  - -      (i) SEQUENCE CHARACTERISTICS:      (A) LENGTH: 210 amino - #acids      (B) TYPE: amino acid      (D) TOPOLOGY: linear  - -     (ii) MOLECULE TYPE: protein  - -     (vi) ORIGINAL SOURCE:      (A) ORGANISM: Escherichia - #coli phage 434      (B) STRAIN: CI represso - #r protein      (C) INDIVIDUAL ISOLATE: - #Fig.3 CI434 a.a. sequence  - -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #7:  - - Met Ser Ile Ser Ser Arg Val Lys Ser Lys Ar - #g Ile Gln Leu Gly Leu 1               5   - #                10  - #                15  - - Asn Gln Ala Glu Leu Ala Gln Lys Val Gly Th - #r Thr Gln Gln Ser Ile        20      - #            25      - #            30  - - Glu Gln Leu Glu Asn Gly Lys Thr Lys Arg Pr - #o Arg Phe Leu Pro Glu    35          - #        40          - #        45  - - Leu Ala Ser Ala Leu Gly Val Ser Val Asp Tr - #p Leu Leu Asn Gly Thr50              - #    55              - #    60  - - Ser Asp Ser Asn Val Arg Phe Val Gly His Va - #l Glu Pro Lys Gly Lys 65                  - #70                  - #75                  - #80  - - Tyr Pro Leu Ile Ser Met Val Arg Ala Gly Se - #r Trp Cys Glu Ala Cys            85  - #                90  - #                95  - - Glu Pro Tyr Asp Ile Lys Asp Ile Asp Glu Tr - #p Tyr Asp Ser Asp Val        100      - #           105      - #           110  - - Asn Leu Leu Gly Asn Gly Phe Trp Leu Lys Va - #l Glu Gly Asp Ser Met    115          - #       120          - #       125  - - Thr Ser Pro Val Gly Gln Ser Ile Pro Glu Gl - #y His Met Val Leu Val130              - #   135              - #   140  - - Asp Thr Gly Arg Glu Pro Val Asn Gly Ser Le - #u Val Val Ala Lys Leu 145                 1 - #50                 1 - #55                 1 -#60   - - Thr Asp Ala Asn Glu Arg Thr Phe Lys Lys Le - #u Val Ile Asp GlyGly             165  - #               170  - #               175  - - Gln Lys Tyr Leu Lys Gly Leu Asn Pro Ser Tr - #p Pro Met Thr Pro Ile        180      - #           185      - #           190  - - Asn Gly Asn Cys Lys Ile Ile Gly Val Val Va - #l Glu Ala Arg Val Lys    195          - #       200          - #       205  - - Phe Val210  - -  - - (2) INFORMATION FOR SEQ ID NO: 8:  - -      (i) SEQUENCE CHARACTERISTICS:      (A) LENGTH: 205 amino - #acids      (B) TYPE: amino acid      (D) TOPOLOGY: linear  - -     (ii) MOLECULE TYPE: protein  - -     (vi) ORIGINAL SOURCE:      (A) ORGANISM: Bacillus - #subtilis      (B) STRAIN: DinR protei - #n      (C) INDIVIDUAL ISOLATE: - #Fig.3 DinR a.a. sequence  - -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #8:  - - Met Thr Lys Leu Ser Lys Arg Gln Leu Asp Il - #e Leu Arg Phe Ile Lys 1               5   - #                10  - #                15  - - Ala Glu Val Lys Ser Lys Gly Tyr Pro Pro Se - #r Val Arg Glu Ile Gly        20      - #            25      - #            30  - - Glu Ala Val Gly Leu Ala Ser Ser Ser Thr Va - #l His Gly His Leu Ala    35          - #        40          - #        45  - - Arg Leu Glu Thr Lys Gly Leu Ile Arg Arg As - #p Pro Thr Lys Pro Arg50              - #    55              - #    60  - - Ala Ile Glu Ile Leu Asp Glu Glu Val Asp Il - #e Pro Gln Ser Gln Val 65                  - #70                  - #75                  - #80  - - Val Asn Val Pro Val Ile Gly Lys Val Thr Al - #a Gly Ser Pro Ile Thr            85  - #                90  - #                95  - - Ala Val Glu Asn Ile Glu Glu Tyr Phe Pro Le - #u Pro Asp Arg Met Val        100      - #           105      - #           110  - - Pro Pro Asp Glu His Val Phe Met Leu Glu Il - #e Met Gly Asp Ser Met    115          - #       120          - #       125  - - Ile Asp Ala Gly Ile Leu Asp Lys Asp Tyr Va - #l Ile Val Lys Gln Gln130              - #   135              - #   140  - - Asn Thr Ala Asn Asn Gly Glu Ile Val Val Al - #a Met Thr Glu Asp Asp 145                 1 - #50                 1 - #55                 1 -#60   - - Glu Ala Thr Val Lys Arg Phe Tyr Lys Glu As - #p Thr His Ile ArgLeu             165  - #               170  - #               175  - - Gln Pro Glu Asn Pro Thr Met Glu Pro Ile Il - #e Leu Gln Asn Val Ser        180      - #           185      - #           190  - - Ile Leu Gly Lys Val Ile Gly Val Phe Arg Th - #r Val His    195          - #       200          - #       205  - -  - - (2) INFORMATION FOR SEQ ID NO: 9:  - -      (i) SEQUENCE CHARACTERISTICS:      (A) LENGTH: 20 amino - #acids      (B) TYPE: amino acid      (D) TOPOLOGY: linear  - -     (ii) MOLECULE TYPE: protein  - -     (vi) ORIGINAL SOURCE:      (A) ORGANISM: Escherichia - #coli phage phi80      (C) INDIVIDUAL ISOLATE: - #Fig.4 phi80 gp30 partial a.a.           sequence  - -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #9:  - - His Lys Val Leu Ala Glu Lys Val Gly Val Th - #r Pro Gln Gln Ala Ile 1               5   - #                10  - #                15  - - Asn Met Leu Lys        20  - -  - - (2) INFORMATION FOR SEQ ID NO: 10:  - -      (i) SEQUENCE CHARACTERISTICS:      (A) LENGTH: 20 amino - #acids      (B) TYPE: amino acid      (D) TOPOLOGY: linear  - -     (ii) MOLECULE TYPE: protein  - -     (vi) ORIGINAL SOURCE:      (A) ORGANISM: Escherichia - #coli phage lambda CII      (C) INDIVIDUAL ISOLATE: - #Fig.4 lambda CII partial a.a.           sequence  - -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #10:  - - Thr Glu Lys Thr Ala Glu Ala Val Gly Val As - #p Lys Ser Gln Ile Ser 1               5   - #                10  - #                15  - - Arg Trp Lys Arg        20  - -  - - (2) INFORMATION FOR SEQ ID NO: 11:  - -      (i) SEQUENCE CHARACTERISTICS:      (A) LENGTH: 20 amino - #acids      (B) TYPE: amino acid      (D) TOPOLOGY: linear  - -     (ii) MOLECULE TYPE: protein  - -     (vi) ORIGINAL SOURCE:      (A) ORGANISM: Escherichia - #coli phage P22      (C) INDIVIDUAL ISOLATE: - #Fig.4 P22 C2 partial a.a. sequence  - -     (xi) SEQUENCE DESCRIPTION: SEQ ID NO: - #11:  - - Gln Ala Ala Leu Gly Lys Met Val Gly Val Se - #r Asn Val Ala Ile Ser 1               5   - #                10  - #                15  - - Gln Trp Glu Arg        20__________________________________________________________________________