Isolated DNA encoding enzyme for phage resistance

Abstract

An isolated DNA of a Lactococcus lactis showing a SEQ ID NO: 1 encoding a restriction and twp modification enzymes (R/M SEQ ID NO: 2, 3 and 4). The isolated DNA is used to transform sensitive dairy cultures, such as Lactococcus lactis and Streptococcus thermophilus, to provide phage resistance. Escherichia coli can be used to produce endonucleases.

Description

BACKGROUND OF THE INVENTION

(1) Field of the Invention

The present invention relates to transformed dairy cultures with a natural 7.8-kb plasmid pSRQ700 which was isolated from Lactococcus lactis subsp. cremoris DCH-4, a known strain. pSRQ700 encodes a restriction/modification system named LlaII. When introduced into a phage-sensitive dairy culture, such as L. lactis, pSRQ700 confers strong phage resistance against the three most common lactococcal phage species: 936, c2 and P335 found in dairy product fermentations. The LlaII endonuclease was purified and found to cleave the palindromic sequence 5'/GATC-3'. The low copy plasmid pSRQ700 was mapped and the genetic organization of LlaII localized. Cloning and sequencing of the entire LlaII system allowed the identification of three open reading frames. The three genes (LlaIIA, LlaIIB, and LlaIIC) overlapped and are under one promoter. A terminator was found at the end of LlaIIC. The genes LlaIIA and LlaIIB coded for m.sup.6 A-methyltransferases and LlaIIC for an endonuclease. The native LlaII R/M system from Lactococcus lactis is also expressed by and conferred strong phage resistance to various industrial S. thermophilus strains. Resistance was observed against phages isolated from yogurt and Mozzarella wheys. This is the first demonstration of increased phage resistance in S. thermophilus.

(2) Description Of Related Art

Lactococcus lactis and Streptococcus salivarius subsp. thermophilus cultures are used extensively worldwide in the manufacture of fermented dairy products. The cultures are normally inoculated into pasteurized or heat-treated milk to quickly start and control the fermentation. In this non-sterile milk environment, the added cells come into contact with the wild bacteriophage population that has survived pasteurization. Although natural phage concentration is low, their population increases very rapidly if phage-sensitive cells are present in the starter culture. The consequent lysis of a large number of sensitive cells retards the fermentation process. To cope with this natural phenomenon, the dairy industry has developed a series of solutions including the use of phage resistant Lactococcus lactis strains (Hill, C., FEMS Microbiol. Rev. 12: 87-108 (1993)).

Lactococcus lactis:

In the last decade, extensive research was conducted on interactions between lactococcal phage and their hosts. Lactococcus lactis was found to possess many plasmids coding for natural defense mechanisms against bacteriophages. Over 40 plasmids with phage defense barriers have been identified. Phage resistance systems are classified into three groups based on their mode of action: blocking of phage adsorption, restriction/modification and abortive infection. Phage-resistant Lactococcus lactis strains have been constructed by introducing these natural plasmids into phage-sensitive strains (Sanders, M. E., et al., Appl. Environ. Microbiol. 40: 500-506 (1980)). The conjugative abilities of some of these plasmids was exploited to construct such resistant strains (Harrington, A., et al., Appl. Environ. Microbiol. 57: 3405-3409 (1991); Jarvis, A. W., et al., Appl. Environ. Microbiol. 55: 1537-1543 (1988); Sanders, M. E., et al., Appl. Environ. Microbiol. 52: 1001-1007 (1986); and Ward, A. C., et al., J. Dairy Sci. 75: 683-691 (1992)). However, after considerable industrial use of these strains, new phages capable of overcoming the introduced defense mechanism have emerged (Alatossava, T., et al., Appl. Environ. Microbiol. 57: 1346-1353 (1991); Hill, C., et al., J. Bacteriol. 173: 4363-4370 (1991); and Moineau, S., et al., Appl. Environ. Microbiol. 59: 197-202 (1993)). Thus, the search for different natural phage barriers is still an ongoing objective for dairy product starter culture manufacturers.

Over the years several studies have established the heterologous nature of the lactococcal phage population (Jarvis, A. W., et al., Intervirology 32: 2-9 (1991)). Based on electron microscopy and DNA hybridization studies, the Lactococcal and Streptococcal Phage Study Group, which is part of the International Committee on Taxonomy of Viruses, reported the existence of 12 different lactococcal phage species. Recently, this number has been reduced to 10 due to the reclassification of the 1483 and T187 species into the P335 species. Strong DNA homology is observed among members of the same species but no homology is found between species (Braun, V., et al., J. Gen. Microbiol. 135: 2551-2560 (1989); Jarvis, A. W., et al., Intervirology, 32: 2-9 (1991); Moineau, S., et al., Can. J. Microbiol. 38: 875-882 (1992); Powell, I. A., et al., Can. J. Microbiol. 35: 860-866 (1989); and Prevots, F., et al., Appl. Environ. Microbiol. 56: 2180-2185 (1990)). Although many species have been isolated, only three appear to be the most problem for the dairy industry. The species 936 (small isometric head) and c2 (prolate head) have been, by far, the most disturbing lactococcal phage species worldwide. Interestingly, phages from the P335 species (small isometric head) are now being isolated with increasing frequency from North American dairy plants (Moineau, S., et al., Appl. Environ. Microbiol. 59: 197-202 (1993)). Two recent surveys revealed that 100% of the 45 lactococcal phages isolated from Canadian cheese plants and U.S. buttermilk plants were classified within one of these three species: 22 phages belonged to the 936 species, 18 to the c2 species and 5 to the P335 species (Moineau, S., et al., J. Dairy Sci. 77: 18 suppl. 1 (1994); and Moineau, S., et al., Can. J. Microbiol. 38: 875-882 (1992)). Therefore from a practical point of view, industrial Lactococcus lactis strains should at least be resistant to the three most common phage species: 936, c2 and P335. Due to the diversity of lactococcal phages, the need for phage defense mechanisms with broad activity (attacking many species) is becoming more meaningful. Because of the characteristics of phages, restriction/modification (R/M) systems have the potential to fulfill this objective.

The phenomenon of R/M was first reported more than 40 years ago (Luria, S. E., et al., J. Bacteriol. 64: 557-569 (1952)) and received a molecular explanation ten (10) years later (Bickle, T. A., et al., Microbiol. Rev. 57: 434-450 (1993); and Dussoix, D., et al., J. Mol. Biol. 5: 37-49 (1962)). The main biological activity of R/M is believed to be in preventing the entrance of foreign DNA (including phage DNA) into the cell. These gatekeepers are roughly the prokaryotic equivalent of the immune system (Wilson, G. G., Nucleic Acids Res. 19: 2539-2566 (1991)). There are currently more than 2400 known restriction enzymes and over 100 have been cloned and sequenced (Raschke, E., GATA 10: 49-60 (1993); and Roberts, R. J., et al., Nucleic Acid Res. 21: 3125-3137 (1993)). There are several kinds of R/M systems and they appear to have equivalent biological activities but achieved in different ways. At least four types of R/M systems have been identified: I, II, IIs, and IIII (Bickle, T. A., et al., Microbiol. Rev. 57: 434-450 (1993); Wilson, G. G., Nucleic Acids Res. 19: 2539-2566 (1991); and Wilson, G. G., et al., Annu. Rev. Genet. 25: 585-627 (1991)). Of these, type II is the simplest and the most common. Illustrative patents are European Patent Application 0 316 677, European Patent Application 0 452 224, U.S. Pat. Nos. 4,530,904 to Hershberger, et al, 4,883,756 to Klaenhammer et al, 4,931,396 to Klaenhammer et al and 5,019,506 to Daly et al.

Many R/M systems have been characterized at the protein level. Restriction enzymes are very dissimilar, suggesting an independent evolution and not from a common ancestor (Bickle, T. A., et al., Microbiol. Rev. 57: 434-450 (1993); Wilson, G. G., Nucleic Acids Res. 19: 2539-2566 (1991); and Wilson, G. G., et al., Annu. Rev. Genet. 25: 585-627 (1991)). In contrast, extensive similarities occur among the methyltransferases (Bickle, T. A., et al., Microbiol. Rev. 57: 434-450 (1993); Klimasauskas, S., et al., Nucleic Acids Res. 17: 9823-9832 (1989); Lauster, R., J. Mol. Biol. 206: 313-321 (1989); McClelland, M., et al., Nucleic Acids Res. 20: 2145-2157 (1992); Wilson, G. G., Nucleic Acids Res. 19: 2539-2566 (1991); and Wilson, G. G., et al., Annu. Rev. Genet. 25: 585-627 (1991)). They can be grouped into three classes corresponding to the modification types: m.sup.4 C, m.sup.5 C and m.sup.6 A (Wilson, G. G., Nucleic Acids Res. 19: 2539-2566 (1991); and Wilson, G. G., et al., Annu. Rev. Genet. 25: 585-627 (1991)). m.sup.4 C and m.sup.6 A can be further divided in two (.alpha. and .beta.) and three (.alpha., .beta., and .gamma.) subclasses respectively, based on their amino acid sequences (Klimasauskas, S., et al., Nucleic Acids Res. 17: 9823-9832 (1989); and Lauster, R., J. Mol. Biol. 206: 313-321 (1989)).

A number of plasmids encoding for R/M have been identified in Lactococcus (Hill, C., FEMS Microbiol. Rev. 12: 87-108 (1993)). Surprisingly, only a handful have been partially characterized. The LlaI R/M system encoded on the conjugative plasmid pTR2030, isolated from Lactococcus lactis subsp. lactis ME2, was the first analyzed at the sequence level (Hill, C., et al., J. Bacteriol. 173: 4363-4370 (1991)). The methylase gene of pTR2030 system has been sequenced and the deduced protein was found to share similarities with the type-IIs methyltransferase (m.sup.6 A), M. FokI (Hill, C. L., et al., J. Bacteriol. 173: 4363-4370 (1991)). The endonuclease genes have also been sequenced and four open reading frames were identified (O'Sullivan, D. J., et al., FEMS Microbiol. Rev. 12: P100 (1993)). Recent data have provided evidence for a new class of multisubunit endonucleases (O'Sullivan, D. J., et al., FEMS Microbiol. Rev. 12: P100 (1993)). The restriction complex, however, has yet to be purified and its recognition sequence is unknown.

ScrFI was the first classical type II restriction enzyme isolated from Lactococcus lactis and is the only one commercially available (Fitzgerald, G. F., et al., Nucleic Acid Research. 10: 8171-8179 (1982)). ScrFI recognizes the sequence 5'-CCNGG-3' where N is any nucleotide. Two methylase genes from the Lactococcus lactis subsp. lactis UC503 chromosome have been cloned and sequenced (Davis, R., et al., Appl. Environ. Microbiol. 59: 777-785 (1993); and Twomey, D. P., et al., Gene 136: 205-209 (1993)). They both coded for a m.sup.5 C MTase. The endonuclease gene has yet to be identified. Mayo et al (Mayo, B., et al., FEMS Microbiol. Lett. 79: 195-198 (1991) isolated a type II endonuclease (also named Llal) from L. lactis subsp. lactis NCD0497 which recognized the sequence 5'-CCWGG-3 (W is A or T) but the R/M genes have not been cloned.

Recently Nyengaard, N., et al, Gene 136, 371-372 (1993) described LlaI and LlaBI, which are type II restriction endonucleases from Lactococcus lactis subsp. cremoris W9 and W56. These endonucleases recognize DNA sequences 5'/GATC-3 and 5'-C/TRYAG3', respectively. The plasmids from these strains were transformed into a plasmid free and endonuclease negative Lactococcus lactis subsp. lactis by electroporation to produce a transformed strain which resisted phage attack. The DNA was not isolated and sequenced and the natural plasmid was used for the transformation. Further, the authors did not indicate if the plasmids encoded methyl transferase. Strains W9 and W56 were not tested.

Streptococcus thermophilus:

Similar information on phage and phage resistance is still very limited for Streptococcus thermophilus despite sustained phage infections in the yogurt and Mozzarella cheese industry (Mercenier et al, Genetic engineering of lactobacilli, leuconostocs and Streptococcus thermophilus, In M. J. Gasson and W. M. DeVos (ed.), Genetics and biotechnology of lactic acid bacteria. Blackie Acad. Prof. Glaskow, UK p. 253-293 (1994)). Fortunately, S. thermophilus phages are much more closely related to each other than the L. lactis phages. It appears that there is only one S. thermophilus phage species (Mercenier et al Genetic engineering of lactobacilli, leuconostocs and Streptococcus thermophilus, In M. J. Gasson and W. M. DeVos (ed.), Genetics and biotechnology of lactic acid bacteria. Blackie Acad. Prof. Glaskow, UK p. 253-293 (1994)). Only very few phage defense mechanisms have been reported for S. thermophilus. Four chromosomally-encoded type II R/M systems have been identified in S. thermophilus. Solaiman and Somkuti (Solaiman, D. K. Y., et al., FEMS Microbiol. Lett. 67: 261-266 (1990); and Solaiman, D. K. Y., et al., FEMS Microbiol. Lett. 80: 75-80 (1991)) have isolated the endonuclease Sth134I and Sth117I which are isoschizomers of HpaII and EcoRII, respectively. Benbadis et al (Benbadis, L., et al., Appl. Environ. Microbiol. 57: 3677-3678 (1991)) and Guimont et al (Guimont, C., et al., Appl. Microbiol. Biotechnol. 39: 216-220 (1993)) have isolated the endonucleases sslI and Sth455I, respectively. Both are also isoschizomers of EcoRII. In addition, S. thermophilus might possess abortive-like phage defense mechanisms (Larbi et al. J. Dairy Res. 59: 349-357 (1992)), although definitive proof has yet to be demonstrated. None of the R/M systems so far identified in S. thermophilus have been cloned, sequenced, or used in commercial strains for improvement of phage resistance. There is believed to be no report on improvement of phage resistance of S. thermophilus strains.

OBJECTS

It is therefore an object of the present invention to provide an isolated DNA encoding only restriction and modification enzymes to impart phage resistance. Further, it is an object of the present invention to provide transformation vectors and transformed bacteria incorporating the DNA which are particularly useful in the dairy industry. These and other objects will become increasingly apparent by reference to the following description and the drawings.

BRIEF DESCRIPTION OF DRAWINGS

FIG. 1 is an electrophoresis gel showing a plasmid analysis of Lactococcus lactis strains wherein Lane 1 is supercoiled DNA ladder (GIBCO/BRL); Lane 2 is Lactococcus lactis DCH-4; Lane 3 is Lactococcus lactis SMQ-17 (pSA3 and pSRQ700); Lane 4 is Lactococcus lactis SMQ-16 (pSA3).

FIG. 2 is an endonuclease restriction map of lactococcal plasmid pSRQ700. Site positions are indicated in kb.

FIG. 3 is a map showing cloning of LlaII from pSRQ700 into pSA3. Clones were electroporated into LM0230. Transformants were tested for phage resistance against .O slashed.p2.

FIGS. 4A to 4C are a nucleotide sequence of the 3-kb Nrul-EcoRV fragment from pSRQ700. The deduced amino acid sequence of the 3 ORFs is presented. The putatives promoter, terminator and ribosome binding site are underlined. The first codon of each ORF is in bold. The amino acids are in single letter code.

FIGS. 5A to 5C are charts showing a comparison of the amino acids between A) M.M. LlaIIA (SEQ ID NO. 2), M. DpnII (SEQ ID NO. 5), M.MboA (SEQ ID NO. 6) and E. coli Dam (SEQ ID NO. 7) methylases; B) M.LlaIIB (SEQ ID NO. 3), DpnA (SEQ ID NO. 8), M.MboC (SEQ ID NO. 9) and M.HinfI (SEQ ID NO. 10); C) R.LlaII (SEQ ID NO. 4), R.DpnII (SEQ ID NO. 11) and R.MboI (SEQ ID NO. 12). The asterisk (*) indicates conserved amino acids. Bars show gaps in the aligned sequences.

FIG. 6 is an electrophoresis gel showing restriction patterns of .O slashed.Q1, .O slashed.Q3 and .O slashed.Q5. Lane 1 and 5, 1-kb ladder (Bethesda Research Laboratories); Lane 2, .O slashed.Q1 DNA cut with EcoRV, Lane 3, .O slashed.Q2 cut with EcoRV; Lane 4, .O slashed.Q5 cut with EcoRV; Lane 6, .O slashed.Q1 cut with Mbol; Lane 7, .O slashed.Q7 cut with Mbol; Lane 8, .O slashed.Q5 cut with Mbol.

FIG. 7 is a schematic flow sheet showing the construction of the plasmids used in this study.

DESCRIPTION OF PREFERRED EMBODIMENTS

The present invention relates to an isolated DNA encoding only an enzyme which is sufficiently duplicative of a member selected from the group consisting of LlaIIA, LlaIIB and LlaIIC and mixtures thereof to restrict or modify a phage. Further the present invention relates to an isolated DNA having a nucleotide sequence essentially as set forth in SEQ ID NO. 1 selected from the group consisting of ORF1 (positions 97 to 948), ORF2 (positions 941 to 1747) and ORF3 (positions 1740 to 2651) and combinations thereof.

The present invention also relates to a recombinant plasmid containing DNA encoding an enzyme sufficiently duplicative of a member selected from the group consisting of LlaIIA, LlaIIB and LlaIIC and mixtures thereof to restrict or modify a phage.

Further the present invention relates to a bacterium harboring a recombinant plasmid containing DNA encoding for an enzyme sufficiently duplicative of a member selected from the group consisting of LlaIIA, LlaIIB and LlaIIC and mixtures thereof to restrict or modify a phage.

Further still, the present invention relates to a recombinantly produced purified protein which is an enzyme containing a sequence of amino acids sufficiently duplicative of that set forth in a member selected from the group consisting of ORF 1, ORF 2 and ORF 3 and combinations thereof in SEQ ID NO. 2, 3 or 4 such that restriction or modification of a phage can be performed with the enzyme, wherein the protein has been produced from isolated DNA of the SEQ ID NO: 1. The protein can be used for assays as described hereinafter.

Further, the present invention relates to a method of imparting phage resistance to a bacterium which is sensitive to the phage which comprises incorporating recombinant DNA encoding an enzyme sufficiently duplicative of a member selected from the group consisting of LlaIIA, LlaIIB and LlaIIC and mixtures thereof into the bacterium to impart the phage resistance, wherein the DNA encoding the member is contained in strain Lactococcus lactis SMQ-17 deposited as NRRL-B-21337. Preferably the bacterium is a dairy culture. In particular, the present invention relates to a bacterium, preferably isolated and purified, selected from the group consisting of Streptococcus salivarius subsp. thermophilus and Lactococcus lactis naturally lacking in phage resistance which bacterium contains recombinant DNA encoding for an enzyme sufficiently duplicate of a member selected from the group consisting of LlaIIA, LlaIIB and LlaIIC and having a sequence of the DNA for the member is essentially as set forth in SEQ ID NO: 1 to impart phage resistance.

Finally, the present invention relates to a method for fermenting a dairy product, the improvement which comprises using a dairy culture selected from the group consisting of Lactococcus lactis and Streptococcus salivarius subsp. thermophilus incorporating recombinant DNA encoding for an enzyme sufficiently duplicative of a member selected from the group consisting of LlaIIA, LlaIIB and LlaIIC to impart phage resistance, wherein the DNA for the member is contained in strain Lactococcus lactis SMQ-17 deposited as NRRL-B-21337. The DNA is generally transformed into the dairy culture.

The DNA of SEQ ID NO: 1 and FIGS. 4A to 4C (Appendix I) is contained in Lactococcus lactis SMQ-17 deposited under the Budapest Treaty on Sep. 29, 1994 as NRRL-B-21337. The strain is available upon request by name and deposit number. The isolated DNA is obtained by means of EcoRV or Nrul-TcoRV digestion of pSRQ700 as described hereinafter.

The art of DNA isolation and cloning is well known to those skilled in the art. Further, the terminology of this art is well developed, see for instance EP 0316677 A2. As used herein, the term "transformed" means to transfer DNA from one bacterium to another in related bacterium. The term "recombinant" as used herein means DNA in a form not existing in nature. In general the recombinant DNA contains DNA encoding only one or more of the sequence of amino acids for LlaIIA, LlaIIB and LlaIIC as set forth in SEQ ID NO: 1. The recombinant enzymes encoded are like the natural enzymes except that the physical configurations are different and they are thus different. They retain the ability to restrict or modify (methylate) the phage DNA.

Various shuttle vectors can be used. pSA3 from Dao, M., et al., Applied Environ. Microb. 49: 115-119 (1985) was used.

The recombinant bacterium can be for instance Escherichia coli, a Lactococcus sp. or a Streptococcus sp. used in dairy fermentations. The E. coli are used to produce the enzymes of SEQ ID NO: 2, 3 and/or 4 which can be used to produce a DNA or RNA probe in a known manner or can be used to produce antibodies to the enzymes in a well known manner for use in assays for the enzymes. Purification of the enzymes is achieved using affinity chromatography and/or molecular filtration.

The DNA of SEQ ID NO: 1 can have modifications in sequence and still be homologous and still encode enzymes which have the necessary phage resistance properties. Generally within 75-100% homology is sufficient.

The preferred use of the transformed cultures containing the recombinant DNA of SEQ ID NO: 1 is in dairy product fermentations. Such fermentations are well known to those skilled in the art. The preferred strains are transformed Lactococcus lactis and Streptococcus salivarius sp. thermophilus which are used in the dairy product fermentations.

EXAMPLE 1

Bacterial Strains, Plasmids, and Media

The strains and plasmids and enzymes used in this invention are listed in Tables 1 and 2.

TABLE 1______________________________________Bacterial strains, plasmids and bacteriophages.Bacteria,plasmids,and phages Relevant characteristics Source______________________________________L. lactis subsp.cremorisDCH-4 Industrial strain, multiple Invention plasmids, Lac.sup.+UL8 Industrial strain, host for Moineau, S., et al., P335 phages, Lac.sup.+ Can J. Microbiol. 38: 875-882 (1992)SMQ-87 UL8 (pSRQ701), Lac.sup.+, Em.sup.r InventionL. lactis subsp.lactisLMO230 Plasmid free, host for 936 McKay, L. L., et al, and c2 phages, Lac.sup.- Appl. Environ. Microbiol. 23:1090-1096 (1972)SMQ-16 LM0230 (pSA3), Lac.sup.-, Em.sup.r. InventionSMQ-17 LM0230 (pSA3, pSRQ700), Invention Lac.sup.-, Em.sup.rSMQ-39 LM0230 (pSRQ701), Lac.sup.-, Invention Em.sup.rSMQ-40 LM0230 (pSRQ702), Lac.sup.-, Invention Em.sup.rSMQ-50 LM0230 (pSRQ703), Lac.sup.-, Invention Em.sup.rSMQ-117 LM0230 (pSRQ704), Lac.sup.-, Invention Em.sup.rSMQ-140 LM0230 (pSRQ706), Lac.sup.-, Invention Em.sup.rE. coliDH5.alpha. Transformation host GIBCO/BRL (Grand Island, NY)DMQ-149 DH5.alpha. (pSRQ708), Ap.sup.r InventionPages.O slashed.p2 Small isometric headed, 936 L. L. McKay species, 30.5 kb.O slashed.sk1 Small isometric headed, 936 L. L. McKay species, 28.1 kb.O slashed.jj50 Small isometric headed, 936 J. Josephsen, et al., species, 30.5 kb FEMS Microbiol. Lett. 59:161-166 (1989).O slashed.c2 Prolate headed, c2 species, Sanders, M. E., et al., 20.7 kb Appl. Environ. Microbiol. 40:500-506 (1980).O slashed.m13 Prolate headed, c2 species, W. E. Sandine 20.2 kb.O slashed.eb1 Prolate headed, c2 species, L. L. McKay 19.6 kb.O slashed.u136 Small isometric headed, P335 Moineau, S., et al., species, 28.8 kb Can J. Microbiol. 38: 875-882 (1992).O slashed.Q30 Small isometric headed, P335 Moineau, S., et al., species, 37.0 kb J. Dairy Sci. 77:18 Suppl. 1 (1994).O slashed.Q33 Small isometric headed, P335 Moineau, S., et al., species, 29.6 kb J. Dairy Sci. 77:18 Suppl. 1 (1994)______________________________________ L. L. McKay, University of Minnesota; W. E. Sandine, Oregon State University; Lac, lactosefermenting ability; Ap.sup.4, ampicillin resistance; Cm.sup.r, chloramphenicol resistance; Em.sup.r, erythromycin resistance. TABLE 2______________________________________Plasmids used in this study.Plasmid Relevant characteristics Source______________________________________pSA3 Shuttle vector, Cm, Tc, Em, 10.2 kb. Dao, M. L., et al., Appl. Env. Microb. 49:115-119 (1985)pBS KS(+) Cloning vector for sequencing, Ap, 2.9 kb. StratagenepSRQ700 Resident plasmid of DCH-4, R.sup.+ /M.sup.+, 7.8 This studypSRQ701 7.0-kb EcoRI fragment from pSRQ700 This study cloned into pSA3, R.sup.+ /M.sup.+, Cm.sup.s, Tc.sup.r, Em.sup.r.pSRQ702 5.3-kb Ncol-EcoRI fragment from pSRQ700 This study cloned into pSA3, R.sup.- /M.sup.+, Cm.sup.s, Tc.sup.r, Em.sup.r.pSRQ703 6.6-kb Ncol fragment from pSRQ700 This study cloned into pSA3, R.sup.- /M.sup.+, Cm.sup.s, Tc.sup.r, Em.sup.r.pSRQ704 7.8-kb EcoRV fragment from pSRQ700 This study cloned into pSA3, R.sup.+ /M.sup.+, Cm.sup.r, Tc.sup.s, Em.sup.r.pSRQ706 3.0-kb Nrul-EcoRV fragment from pSRQ700 This study cloned into pSA3, R.sup.+ /M.sup.+, Cm.sup.r, Tc.sup.s, Em.sup.r.pSRQ708 3.0-kb Nrul-EcoRV fragment from pSRQ700 This study cloned into pBS, R.sup.+ /M.sup.+, Ap.sup.r.______________________________________ Ap.sup.r, ampicillin resistance; Cm.sup.r, chloramphenicol resistance; Cm.sup.s, sensitive to chloramphenicol; Em.sup.r, erythromycin resistance Tc.sup.r, tetracycline resistance; Tc.sup.s, tetracycline resistance; R.sup.+ /M.sup.+, active restriction/active modification enzymes; Escherichia coli was grown at 37.degree. C. in Luria-Bertani (Sambrooke, J., et al., Molecular cloning: a laboratory manual. 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989)). Lactococcus lactis strains were grown at 30.degree. C. in M17 (Terzaghi, B. E., et al., Appl. Microbiol. 29: 807-813 (1975)) supplemented with 0.5% glucose (GM17) or 0.5% lactose (LM17). When appropriate, antibiotics were added as follows: for E. coli, 50 .mu.g/ml of ampicillin (Ap), 10 .mu.g/ml of tetracycline (Tc), and 20 .mu.g/ml of chloramphenicol (Cm); for L. lactis, 5 .mu.g/ml of erythromycin (Em).

Bacteriophage Propagation and Assays

Bacteriophages used in this invention are listed in Table 1. Bacteriophages were propagated and titrated by the method of Jarvis (Jarvis, A. W., Appl. Environ. Microbiol. 36: 785-789 (1978)). Efficiency of plaguing (EOP) assays were performed as described by Sanders and Klaenhammer (Sanders, M. E., et al., Appl. Environ. Microbiol. 40: 500-506 (1980)). Bacteriophages c2, p2, sk1 and jj50 were supplied by T. R. Klaenhammer (North Carolina State University).

DNA Isolation and Manipulation

Plasmid DNA from E. coli was isolated as described previously (Moineau, S., et al., Appl. Environ. Microbiol. 60: 1832-1841 (1994)). Large quantities of E. coli plasmid DNA was isolated by using plasmid MIDI or MAXI kit (Qiagen Inc., Chatsworth, Calif.). Plasmid DNA from L. lactis was isolated as described by O'Sullivan and Klaenhammer (O'Sullivan, D. J., et al., Appl. Environ. Microbiol. 59: 2730-2733 (1993)). Large quantity of lactococcal plasmid DNA was obtained using the Leblanc and Lee procedure (Leblanc, D. J., et al., J. Bacteriol. 140: 1112-1115 (1979)) as modified by Gonzalez and Kunka (Gonzalez, C. F., et al., Appl. Environ. Microbiol. 46: 81-89 (1983)). Restriction endonucleases (Gibco/BRL, Grand Island, N.Y.) and T4 DNA ligase (Boehringer Manheim, Indianapolis, Ind.) were used according to manufacturer's instructions. When needed, DNA fragments were obtained from low-melting agarose using a QIAEX gel extraction kit (Qiagen, Inc., Chatsworth, Calif.).

Electroporation

E. coli was grown, electroporated, incubated, and plated as described previously (Moineau, S., et al., Appl. Environ. Microbiol. 60: 1832-1841 (1994)). L. lactis was grown in GM17 supplemented with 0.5 M sucrose (SGM17) and 1% glycine and electroporated as described by Holo and Nes (Holo, H., et al., Appl. Environ. Microbiol. 55: 3119-3123 (1989)). The Gene Pulser apparatus (Bio-Rad Laboratories, Richmond, Calif.) was set at 25 .mu.F and 2.45 kV, and the Pulse Controller was set at 200 .OMEGA.. Plasmid DNA was mixed with 40 .mu.l of cells in a chilled cuvette (0.2 cm). After electroporation, L. lactis cells were resuspended in SGM17, incubated for 2 h at 30.degree. C., plated on GM17 supplemented with erythromycin (5 .mu.g/ml) and incubated for 2 days at 30.degree. C.

Sequencing

The entire LlaII system (3 kb NruI-EcoRV fragment from pSRQ700) was cloned into E. coli pBluescript. The resulting clone was named pSRQ708. Nested deletions were made in both orientations from pSRQ708 using the ERASE-A-BASE kit (Promega, Madison, Wis.). For the first set of deletions, the endonucleases SstI was used for protection and XbaI to start the deletion. The restriction pairs KpnI-DraII were used to obtain the nested deletions in the other orientation. Plasmid DNA was extracted from the nested clones with QIAGEN and directly used for sequencing. The sequencing reactions were performed using the DYEDEOXY TERMINATOR TAQ sequencing kit for use on the 373A automated DNA sequencing system (Applied Biosystems, Foster City, Calif.). The T7 and T3 primers were used for annealing.

Restriction enzyme purification

L. lactis SMQ-17 was grown in 2L, concentrated by centrifugation (10,000 rpm, 15 min.) and washed twice in saline. The cells were then resuspended in 30 ml of PME buffer (10 mM NaH.sub.2 PO.sub.4 pH 7.4, 0.1 mM EDTA and 10 mM .beta.-mercaptoethanol). Cells were lysed by 15 bursts (30 seconds each followed by one minute rest) with glass beads and a bead beater (BIOSPEC, Bartlesville, Okla.). After centrifugation to remove cell debris and glass beads, the supernatant was used for ion exchange chromatography. Successive chromatographies were performed on phosphocellulose (Whatman P11, Maidstone, England) and dimethylaminoethyl cellulose (Whatman DE5, Maidstone, England) using a salt gradient in PME buffer. Restriction endonuclease activity was found in the fractions around 0.5 M NaCl. Lactococcal phage ul36 DNA was used as substrate and the digestions were performed at 37.degree. C. for 2-4 h using the buffer system #2 from GIBCO/BRL (50 mM Tris-HCl pH 8.0, 10 mM MgCl.sub.2, 50 mM NaCl). DNA samples were analyzed as described by Sambrooke et al in Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989) in 0.7% agarose gels in TAE.

DNA and Protein Analysis

The DNA sequence was analyzed with DNA strider 1.2. The SwissProt database (release 29, Jun. 1994) was searched for homology to all three LlaII amino acid sequences of SEQ ID NO: 1.

Isolation of pSRQ700

For many years, Lactococcus lactis subsp. cremoris DCH-4 has performed very well during the industrial buttermilk and sour cream production. One reason for continued good performance is the natural resistance of DCH-4 to lactococcal bacteriophages. One objective of this invention was to identify and transfer the DNA responsible for the phage resistance of DCH-4. The total plasmid DNA of DCH-4 was isolated and co-electroporated with the vector pSA3 into the phage sensitive-plasmid free L. lactis LM0230. The latter strain was selected because it can propagate phages from two species, 936 and c2. The DNA ratio of DCH-4:pSA3 used for electroporation was about 10:1. Em-resistant colonies were tested for phage resistance by spot assay (10.sup.3 -10.sup.4 pfu of .O slashed.p2/spot). A few phage resistant colonies were obtained, analyzed, and found to contain pSA3 and a 7.8 kb low copy plasmid which was named pSRQ700 (FIG. 1). The transformant containing pSRQ700 was named L. lactis SMQ-17 (NRRL-B-21337). Plasmid pSRQ700 was also electroporated into L. lactis UL8 which can propagate phages from the P335 species. The transformant was named L. lactis SMQ-87.

Effectiveness of pSRQ700 on lactococcal Phage Species

L. lactis SMQ-17 and SMQ-87 were tested for phage resistance against a total of 9 phages belonging to 3 species (3 phages/species). Phages p2, sk1 and jj50 were selected as representatives of the 936 species (Table 1). The lactococcal phage species c2 was represented by the phages c2, ml3 and eb1. These six phages were individually tested on SMQ-17 and their EOPs are presented in Table 3.

TABLE 3______________________________________Comparison between the efficiency of plaquingof lactococcal phages on L. lactis SMQ-17 andthe number of Mbol sites in the phage genome. EOP on Number of SMQ-17 Mbol sites*______________________________________936 species.o slashed.p2 1.7 .times. 10.sup.-6 11.o slashed.sk1 2.5 .times. 10.sup.-6 9.o slashed.jj50 2.0 .times. 10.sup.-6 10c2 species.o slashed.c2* 1.0 .times. 10.sup.-4 3.o slashed.ml3 6.1 .times. 10.sup.-3 2.o slashed.eb1 5.5 .times. 10.sup.-3 2P335 species.o slashed.ul36 2.7 .times. 10.sup.-7 13.o slashed.Q30 5.2 .times. 10.sup.-6 12.o slashed.Q33 1.3 .times. 10.sup.-7 15______________________________________ *Only number of fragments > 0.5 kb were determined. The new emerging P335 species was represented by the phages ul36, Q30 and Q33. They were tested separately on SMQ-87 and their EOPs are also presented in Table 3. All three 936 phages had similar EOPs in the range of 10.sup.-6. More variability was observed with the c2 species where EOPs ranged from 10.sup.-3 to 10.sup.-4. The P335 phages were the most affected by pSRQ700 since EOPs of 10.sup.-7 were observed (Table 3). Identical results were obtained when phage resistance was tested at 21.degree., 30.degree.and 38.degree. C. (data not shown). These results indicated that the phage resistance mechanism encoded on pSRQ700 is temperature insensitive.

Identification of the Phage Resistance Mechanism on pSRQ700

Phages capable of overcoming the defense mechanism encoded on pSRQ700 were isolated. These phages had EOPs of 1.0 on L. lactis SMQ-17. When these resistant (modified) phages were propagated back on their original host, they became sensitive (restricted) to pSRQ700 at the same previous level (data not shown). This temporary host specific immunity, demonstrates the presence of a classical R/M system encoded on pSRQ700. The R/M system was named LlaII.

Isolation of the Restriction Endonuclease

The non-specific nucleases were removed after ion exchange chromatographies performed on phosphocellulose (Whatman P11) and dimethylaminoethyl cellulose (Whatman DE5) using a salt gradient in PME (10 mM NaH.sub.2 PO.sub.4 pH 7.4, 0.1 mM EDTA and 10 mM .beta.-mercaptoethanol) buffer. DNAs from the well-characterized lactococcal phage ul36 (Moineau, S., et al., Can. J. Microbiol. 38: 875-882 (1992: Moineau, S., et al., Appl. Environ. Microbiol. 59: 197-202 (1993); and Moineau, S., et al., Appl. Environ. Microbiol. 60: ;1832-1841 (1994)) was digested with LlaII. The digestions were conducted overnight at 37.degree. C. since the R/M encoded on pSRQ700 is temperature-insensitive (up to 38.degree. C.). Defined DNA fragments were identified on agarose gels (data not shown). No attempts were made to determine the number of activity units in the collected fractions nor the percentage of recovery from the crude supernatant. Unexpectedly, the restriction patterns obtained corresponded to MboI restriction patterns. Attempts to cut pSRQ700 with MboI were unsuccessful. It was concluded that the R/M system present on pSRQ700 was similar to the MboI system which recognized the sequence 5'-GATC-3' and cleaved it before the guanine.

Mapping of pSRQ700

Single, double and triple digestions were performed with endonucleases to obtain a map of pSRQ700. The results are presented in FIG. 2. The following endonucleases did not cut pSRQ700: ApaI, AvaI, AvaII, BalI, BamHI, HpaI, MboI, PstI, PvuII, SalI, SmaI, SphI, XbaI, XhoI.

Localization of the LlaII System on pSRQ700

The LlaII R/M system was entirely cloned into E. coli using the E. coli-L. lactis shuttle vector pSA3 (FIG. 3). Since appropriate unique restriction sites were present on PSA3 and PSRQ700, total plasmid DNA from L. lactis SMQ-17 was directly used for cloning. Plasmid DNA from SMQ-17 was digested with selected endonucleases, phenol extracted, ethanol precipitated, ligated and the ligation mixture electroporated in E. coli DH5.alpha.. This strategy was very effective because expected clones were rapidly obtained. The clones were electroporated into L. lactis LM0230 and phage resistance was determined. The relevant clones are presented in FIG. 3. The entire R/M system of PSRQ700 was localized on a 3-kb NruI-EcoRV fragment. The PSA3 clone containing this 3 kb fragment was named pSRQ706. Similar EOPs were obtained with PSRQ700 and PSRQ706 (FIG. 3). This is due to the similar low copy number of PSA3 and PSRQ700 (FIG. 1).

DNA Sequence Analysis of the LlaII

The 3-kb NruI-EcoRV fragment containing the LlaII genes was sequenced in both directions and found to contain 2,987 bp (FIGS. 4A to 4C; SEQ ID NO: 1). This fragment was 65.7% A+T rich, typical of lactococcal genes (Van de Guchte, M., et al., FEMS Microbiol. Rev. 88: 73-92 (1992)). Three overlapping open reading frames (orfs) were found and the genes were named LlaIIA, LlaIIB and LlaIIC. In reference to FIGS. 4A to 4C and SEQ ID NO: 1, the gene LlaIIA was localized from position 97 to position 948 and coded for a protein of 284 amino acids with an estimated weight of 33,031 Da. The gene LlaIIB was localized from position 941 to position 1747 and coded for a protein of 269 amino acids with an estimated weight of 30,904 Da. The gene LlaIIC was localized from position 1740 to position 2651 and coded for a protein of 304 amino acids with an estimated weight of 34,720 Da. Phage p2 EOP of 1.0 on L. lactis harboring pSRQ702 or pSRQ703 suggested that LlaIIC coded for the endonuclease (FIG. 3). No putative ribosome binding site (RBS) was found for LlaIIA and LlaIIB. A putative RBS (GGAG) was found preceding LlaIIC. Atypical RBS have been identified for the DpnII methylases which are similar to LlaII (FIGS. 5A to 5C). They were not found in the LlaII system. Atypical RBS may be related to translational control of the methylase gene expression (Lacks, S. A., et al., In: Genetics and Molecular Biology of Streptococci, Lactococci and Enterococci, Dunny, G. M., P. P. Cleary and L. L. McKay. (eds) ASM, Washington , D.C. p.71-76 (1991)). All three genes appear to be under the control of the same promoter. However, no definite consensus E. coli-10 and -35 promoter sequences could be identified. Because EOPs were the same in PSRQ700, pSRQ701 and PSRQ703 (FIG. 3), it is believed that the promoter was present in the 3.0-kb fragment. The putative promoter sequences upstream of LlaIIA is of interest. A putative -35 region was localized at position 27, followed by a 18 bp spacer, and a putative -10 region at position 51 (FIGS. 4A to 4C). A search for palindromic sequences identified two perfect inverted repeats of 19 bp, typical of a strong rho-independent terminator, at the very end of LlaIIC (FIGS. 4A to 4C). Interestingly, the stop codon of LlaIIC was within the beginning of the stemloop structure.

Protein Analysis

Homology searches showed that the deduced protein coded by LlaIIA was 75.4% identical to DpnII methylase (Mannarelli, B. M., et al., Proc. Natl. Acad. Sci. 82: 4468-4472 (1985)), 41.5% identical MboI methylase (Ueno, T., et al., Nucleic Acids Res. 10: 2309-2313 (1993)) and 30.1% to the Dam methylase of E. coli (Brooks, J. E., et al., Nucleic Acids Res. 11: 837-851 (1983)). It was concluded that LlaIIA codes for a methylase and was named M.LlaIIA. All three methylases (M.DpnII, M.MboA and Dam) homologous to LlaIIA are N-6 adenine methyltransferase (m.sup.6 A-MTases). The most conserved amino acid sequence motifs among the m.sup.6 A-Mtases are F-G-G (motif I) and DPPY (motif II). Their organization in the protein allowed the division of the m.sup.6 A-Mtases in three subclasses (.alpha., .beta. and .gamma.). In the m.sup.6 A-Mtase subclass .alpha., the motif I is found close to the N-terminal followed by a variable region of 100-200 aa and the motif II close to the C-terminal. The reverse situation is found in the subclass .beta., where the motif II appears before the motif I. M.LlaIIA has all the characteristics of a m.sup.6 A-Mtase subclass a: F-G-G motif, a 146 aa variable region and a DPPY motif (FIG. 5). The F-G-G motif probably contained the S-adenosylmethionine binding site and DPPY might be involved in the methylation of exocyclic amino acids (Klimasauskas, S., et al., Nucleic Acids Res. 17: 9823-9832 (1989)).

The deduced protein coded by LlaIIB was found to be 88.9% identical to the second methylase of DpnII (Cerritelli, S., et al., Proc. Natl. Acad. Sci. USA, 86: 9223-9227 (1989)), 50.2% identical to the second methylase of MboI (Ueno, T., et al., Nucleic Acids Res. 10: 2309-2313 (1993)) and 43.6% identical to the HinfI methylase (Chandrasegaran, S., et al., Gene 70: 387-392 (1988)). It was concluded that LlaIIB also codes for a methylase and was named M.LlaIIB. All three methylases (M.DpnA, M.MboC and HinfI) homologous to LlaIIB are m.sup.6 A-Mtases but subclass .beta.. M.LlaIIB has all the subclass .beta. characteristics: a DPPY motif, a 175 aa variable region and a F-G-G motif. Interestingly, FIGS. 5A to 5C also show the amino acid comparison between two sets of four m.sup.6 A-Mtases isolated from two Gram-positive and two Gram-negative bacteria. This enzyme methylates the same 5'-GATC-3' sequence. Despite the various origins, about 20% and 28% of the amino acids are respectively conserved in the four .alpha. and .beta. methylases studied. Interestingly, almost all tryptophan residues are conserved in the methylases studied (FIGS. 5A to 5C).

The deduced protein coded by LlaIIC was 34% and 31% identical to MboI (Ueno, T., et al., Nucleic Acids Res. 10: 2309-2313 (1993)) and DpnII (de la Campa, A. G., et al., J. Biol. chem. 263: 14696-14702 (1987)) endonucleases, respectively. These results confirmed that LlaIIC coded for an endonuclease and was named R.LlaII. Conserved aa motifs were observed among the three isoschizomers but their functionality is unknown.

It was thus found that Lactococcus lactis subsp cremoris DCH-4 harbors a 7.8-kb low copy plasmid (PSRQ700) coding for a temperature-insensitive R/M system similar to DpnII (Lacks, S. A., et al., In: Genetics and Molecular biology of Streptococci, Lactococci and Enterococci. Dunny, G. M., P. P. Cleary and L. L. McKay. (eds) ASM, Washington , D.C. p-71-76 (1991)) and MboI (Ueno, T., et al., Nucleic Acids Res. 10: 2309-2313 (1993)). These systems recognize the non-methylated DNA sequence 5'-GATC-3' where the endonuclease cleaved before the guanine (Lacks, S. A., et al., In: Genetics and Molecular biology of Streptococci, Lactococci and Enterococci. Dunny, G. M., P. P. Cleary and L. L. McKay. (eds) ASM, Washington , D.C. p-71-76 (1991); and (Ueno, T., et al., Nucleic Acids Res. 10: 2309-2313 (1993)). The plasmid PSRQ700 is probably one reason for the strong phage resistance shown by DCH-4 over the years. Any phage containing the non-methylated GATC sequence in its genome will be restricted when infecting a L. lactis strain containing PSRQ700.

Members of the three most common lactococcal phage species were strongly restricted by PSRQ700 as shown by their reduced EOPs (Table 3). The small isometric-headed phages of the P335 and 936 species were particularly affected by PSRQ700. This is due in part to their larger genomes. The average genome size for the P335, 936 and c2 phages used in this study was 31.8, 29.7 and 20.2-kb, respectively. However, the most important factor was the number of LlaII sites in the phage genome. Three LlaII sites in the prolate .O slashed.c2 genome were enough to restrict its EOP by 4 logs on L. lactis SMQ-17 (Table 3). Two LlaII sites in the .O slashed.ml3 and .O slashed.eb1 genomes were still enough to reduce the EOP by 3 logs. These data are in agreement with the single hit kinetic of R/M system and shows that restriction at one site is enough to prevent phage proliferation (Wilson, G. G., et al., Annu. Rev. Genet. 25: 585-627 (1991)). For the small isometric phages which had more LlaII sites in their genome, the presence of 9 to 12 sites gave a 6 log reduction in EOP, whereas 13 to 15 sites were needed for a 7 log reduction. As reported previously, the EOP decreases logarithmically as the number of sites in the phage genome increases (Wilson, G. G., et al., Annu. Rev. Genet. 25: 585-627 (1991)).

Thus, phage resistance conferred by PSRQ700 was substantial against members of the 3-lactococcal phage species tested.

Close gene linkage is a feature of all R/M system and accordingly LlaII genes are adjacent (Wilson, G. G., Nucleic Acids Res. 19: 2539-2566 (1991); and Wilson, G. G., et al. Annu. Rev. Genet. 25: 585-627 (1991)). The LlaII system is highly related to DpnII (Lacks, S. A., et al., In: Genetics and Molecular Biology of Streptococci, Lactococci and Enterococci. Dunny, G. M., P. P. Cleary and L. L. McKay. (eds) ASM, Washington, D.C. p. 71-76 (1991)). They share the same genetic structure: two methylases followed by an endonuclease (de la Campa, A. G., et al., J. Mol. Biol. 196: 457-469 (1987)). There is also gene overlapping in both systems. The most striking similarity is their methylases (Cerritelli, S., et al., Proc. Natl. Acad. Sci. USA. 86: 9223-9227); and Mannarelli, B. M., et al., Proc. Natl. Acad. Sci. 82: 4468-4472 (1985)). Amino acids comparison showed 75% identity between M.LlaIIA and M.DpnII and 88% between M.LlaIIB and M.DpnA (FIG. 5).

Despite the strong homology between LlaII and DpnII methylases, the endonucleases are still divergent. Only 31% of the amino acids are identical. In fact, the endonuclease of LlaII is more homologous to MboI than to DpnII. One might suggest that the methylase had a common ancestor whereas endonucleases evolved independently (Bickle, T. A., et al., Microbiol. Rev. 57: 434-450 (1993); (Wilson, G. G., Nucleic Acids Res. 19: 2539-2566 (1991); and Wilson, G. G., et al. Annu. Rev. Genet. 25: 585-627 (1991)). Many type II R/M system appear to have formed partnerships with miscellaneous genes that were initially separated. They became linked due to a persistent selective advantage (Bickle, T. A., et al., Microbiol. Rev. 57: 434-450 (1993); (Wilson, G. G., Nucleic Acids Res. 19: 2539-2566 (1991); and Wilson, G. G., et al. Annu. Rev. Genet. 25: 585-627 (1991)).

Finally, from a culture manufacturer standpoint, the introduction of the natural low copy number PSRQ700 into industrial Lactococcus lactis strains can confer strong phage resistance against phages of the 936 species and the newly emerging P335 species. Its effectiveness against c2 species will be variable. The temperature insensitivity nature of LlaII (up to 38.degree. C.) makes this phage resistance mechanism amenable to various types of high-temperature dairy fermentations, especially cheese. The use of PSRQ700 as part of a starter rotation scheme (to avoid the build up of modified phages) can improve the overall phage resistance of starter cultures.

EXAMPLE 2

The native LlaII R/M system from Lactococcus lactis was expressed by and conferred strong phage resistance to various industrial S. thermophilus strains. Resistance was observed against phages isolated from yogurt and Mozzarella wheys.

Bacteria, Bacteriophages, and Media

The strains used in this study are listed in Table 4. S. thermophilus strains were confirmed by Rapid ID 32 Strep (BioMerieux Vitek, Inc., Hazelwood, Mo.). Streptococcus thermophilus strains were grown at 42.degree. C. in GM17. When needed, antibiotics were added at 5 .mu.g of chloramphenicol per ml. Bacteriophages used in this study are listed in Table 4.

TABLE 4______________________________________Bacteria and bacteriophages used in this study.Bacteriaor phage Relevant characteristics.sup.a Source______________________________________E. coliDH5.alpha. Transformation host. Gibco/BRLL. lactisLM0230 Plasmid-free, Lac-, host for .o slashed.p2. 38SMQ-17 LM0230 (pSRQ700). This InventionSMQ-151 LM0230 (pSRQ707), Cm.sup.r. This InventionS. thermophilusSMQ-119 Industrial strain used in yogurt, host This Invention for .o slashed.Q1 and .o slashed.Q3.SMQ-146 SMQ-119 (pNZ123), Cm.sup.r. This InventionSMQ-154 SMQ-119 (pSRQ707), Cm.sup.r. This InventionSMQ-173 Industrial strain used for Mozzarella, This Invention host for .o slashed.Q5.SMQ-174 Industrial strain used for Mozzarella, This Invention host for .o slashed.Q6.SMQ-211 SMQ-173 (pSRQ707), Cm.sup.r. This InventionSMQ-212 SMQ-174 (pSRQ707), Cm.sup.r. This InventionPhages.o slashed.p2 L. lactis phage, small isometric-head, L. L. McKay 936 species..o slashed.Q1 S. thermophilus phage isolated from This Invention yogurt..o slashed.Q3 S. thermophilus phage isolated from This Invention yogurt..o slashed.Q5 S. thermophilus phage isolated from This Invention Mozzarella whey..o slashed.Q6 S. thermophilus phage isolated from This Invention Mozzarella whey.______________________________________ L. L. McKay, University of Minnesota; Cm.sup.r, chloramphenicol resistance; Lac.sup.-, deficient in lactose fermenting ability. Streptococcal phages were propagated by the method of Jarvis et al (Jarvis, A. W., et al., Intervirology 32: 2-9 (1991)). EOP assays on S. thermophilus hosts were performed as follows: strains were grown in GM17 overnight at 37 C., 500 .mu.l of cells and 100 .mu.l of diluted phages were mixed with 2.5 ml of soft agar (GM17 supplemented with 10 mM CaCl.sub.2) and layered onto bottom agar (GM17+CaCl.sub.2) Plates were incubated overnight 42.degree. C. in an anaerobic jar (BBL GasPaK Plus, Beckton Dickinson, Cockeysville, Md.).

DNA Isolation and Manipulation

Plasmid DNA from S. thermophilus was isolated by using the method of O'Sullivan and Klaenhammer (O'Sullivan, D. J., et al., Appl. Environ. Microbiol. 59: 2730-2733 (1993)). Phage DNA was isolated as described previously (Moineau, S., et al., Appl. Environ. Microbiol. 60: 1832-1841 (1994)).

Electroporation

S. thermophilus cells were electroporated as follows: cells were grown in GM17 until mid-exponential phase, centrifuged, washed twice with SG buffer (0.5 M sucrose and 10% glycerol) and put on ice until use. Plasmid DNA (1 .mu.g) was mixed with 40 .mu.l of cells in a chilled Gene Pulser cuvette (0.2 cm). The Gene Pulser apparatus (Bio-Rad Laboratories, Richmond, Calif.) was set at 25 .mu.F and 2.45 kV, and the Pulse Controller at 200 .OMEGA.. After electroporation, the S. thermophilus cells were immediately resuspended in the rescue broth used for L. lactis cells (Hill, C., FEMS Microbiol. Rev. 12: 87-108 (1993)) and incubated for 2 hours at 42.degree. C. before they were plated on GM17 supplemented with the appropriate antibiotic.

Phage isolation

Phages .O slashed.Q1 and .O slashed.Q3 were recently isolated from yogurt samples whereas .O slashed.Q5 and .O slashed.Q6 were isolated also in our laboratory but from Mozzarella whey samples. Phages .O slashed.Q1 and .O slashed.Q3 were then propagated on S. thermophilus SMQ-119, .O slashed.Q5 on SMQ-173 and .O slashed.Q6 on SMQ-174. The genomic DNAs of these streptococcal phages were compared after digestion with EcoRV and MboI (FIG. 6). All four S. thermophilus phages had different restriction patterns (FIG. 6) and consequently they were different.

Expression of LlaII in Streptococcus thermophilus

To verify if LlaII system could be functional in S. thermophilus, the LlaII genes were cloned into a vector with an origin of replication functional in L. lactis and S. thermophilus. The lactic acid bacteria shuttle vector pNZ123 (2.5 kb) (DeVos, W. M., FEMS Microbiol. Rev. 46: 281-295 (1987)) was selected. A 7.0-kb EcoRI fragment from pSRQ700 was cloned into the unique EcoRI site of pNZ123 (FIG. 7). The ligation mixture was electroporated directly into the phage sensitive strain L. lactis LM0230. Cm-resistant transformants were obtained and tested for resistance to .O slashed.p2. A phage-resistant transformant thus obtained was named SMQ-151. The resulting pNZ123 clone containing the 7.0 kb fragment from pSRQ700 was named pSRQ707. This plasmid was electroporated into S. thermophilus SMQ-119 and a Cmr-transformant was named SMQ-154. This clone was tested for resistance against two S. thermophilus phages (.O slashed.Q1 and .O slashed.Q3). Both phages were severely restricted on SMQ-154 since they had EOPs of 10.sup.-8 (Table 5).

TABLE 5______________________________________Efficiency of Plaquing of S. thermophilusphages on various hosts.Phage/Host EOP______________________________________.O slashed.Q1/SMQ-119 1.0.O slashed.Q1/SMQ-146 1.0.O slashed.Q1/SMQ-151 2.4 .times. 10.sup.-8.O slashed.Q3/SMQ-119 1.0.O slashed.Q3/SMQ-151 6.1 .times. 10.sup.-8.O slashed.Q5/SMQ-173 1.0.O slashed.Q5/SMQ-211 3.9 .times. 10.sup.-6.O slashed.Q6/SMQ-174 1.0.O slashed.Q6/SMQ-212 1.2 .times. 10.sup.-5______________________________________

Plasmid pSRQ707 was also electroporated into S. thermophilus SMQ-173 and SMQ-174 which are commercially used for Mozzarella cheese production. Transformants were obtained for both strains, and named SMQ-211 and SMQ-212, respectively. Both transformants were tested for phage resistance. Phage Q5 had an EOP of 10.sup.-6 on SMQ-211 whereas .O slashed.Q6 and an EOP of 10.sup.-5 on SMQ-212 (Table 5). The phage resistance observed against Mozzarella phages was slightly weaker than with the yogurt phages, but still significant. These results show that the LlaII R/M system is functional in various S. thermophilus strains and can confer strong phage resistance in this lactic acid bacteria. This is the first report of increased phage resistance in S. thermophilus.

Thus, in general the present invention relates to an isolated and purified Streptococcus thermophilus naturally lacking in at least one phage resistance and containing recombinant DNA encoding an endonuclease from a Lactococcus lactis to impart the phage resistance.

Further, it relates to a method for fermenting a dairy product, the improvement which comprises using a dairy culture of Streptococcus thermophilus lacking in at least one phage resistance for the fermentation incorporating recombinant DNA encoding an endonuclease of Lactococcus lactis to impart the phage resistance.

Still further, it relates to a method of imparting phage resistance to a Streptococcus thermophilus which is lacking in at least one phage resistance which comprises incorporating recombinant DNA encoding an endonuclease of Lactococcus lactis into the Streptococcus thermophilus to impart the phage resistance.

The foregoing description is only illustrative of the present invention and the present invention is limited only by the hereinafter appended claims.

__________________________________________________________________________SEQUENCE LISTING(1) GENERAL INFORMATION:(iii) NUMBER OF SEQUENCES: 12(2) INFORMATION FOR SEQ ID NO:1:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 2987 base pairs(B) TYPE: Nucleic Acid(C) STRANDEDNESS: Double(D) TOPOLOGY: Linear(ii) MOLECULE TYPE: Peptide(xi) SEQUENCE DESCRIPTION: SEQ ID NO:1:TCGCGAGCTTTCTAATGCTTAGTGCTTTAAGATTAGGATAGCACGACTTA50TTTATTTTCCAATGAAATTAACTAGCAATTCGGGTATAATATATTTATGA100ATTTATTACAAAAAAACAAGATCAACTTACGTCCGTTTACTAAATGGACA150GGTGGGAAAAGGCAACTACTGCCACACATTCAATACCTAATGCCAGAAAA200ATACAATCATTTTTTCGAACCTTTTATTGGTGGTGGCGCTTTGTTTTTTG250AACCCGCTCCTCAAAAAGCAGTTATTAACGACTTCAATTCTGAGCTTATA300AACTGTTACCGGCAGATGAAAGATAATCCTGAGCAATTGATAGAATTGTT350GACTAATCATCAGCGGGAAAATTCTAAAGAATATTATTTAGACTTACGTT400CTTCTGATAGAGATGGAAGAATTGATAAGATGAGCGAAGTTGAACGTGCT450GCTAGAATTATGTATATGCTACGTGTTGATTTTAATGGTTTATATCGTGT500TAATTCGAAAAACCAGTTTAATGTGCCTTATGGAAGATATAAAAATCCTA550AGATAGTTGATAAAGAATTGATTGAAAGTATTTCCGAGTACTTGAATAAC600AATTCTATTAAGATCATGAGTGGAGATTTTGAAAAAGCCGTTAAAGAAGC650ACAGGATGGAGATTTTGTTTATTTCGACCCTCCATACATTCCACTTTCTG700AAACTAGCGCCTTTACTTCTTATACACACGAAGGCTTTAGCTACGAAGAT750CAAGTTAGGCTAAGAGATTGTTTCAAACAGTTAGATTCAAAAGGGGTATT800CGTCATGCTTTCAAATTCTTCAAGCCCTTTAGCGGAGGAATTATATAAAG850ATTTTAACATCCATAAAATTGAAGCTACTCGAACAAATGGGGCTAAATCA900TCTAGTCGTGGAAAAATCACTGAAATCATCGTAACCAATTATGGCAATTA950ACGAATATAAGTATGGAGGTGTTTTAATGACAAAACCATACTATGAAAAA1000GAAAACGCAATTCTCGTTCACGCAGATTCATTTAAATTATTAGAAAAAAT1050TAAACCTGAAAGCATGGACATGATATTTGCTGACCCTCCTTACTTTTTAA1100GTAATGGAGGAATGTCAAATTCAGGTGGTCAAATTGTTTCTGTTGATAAA1150GGGGATTGGGATAAAATTTCTTCATTTGAAGAAAAACATGACTTTAATAG1200ACGTTGGATTAGGTTAGCAAGATTGGTTTTAAAACCCAACGGAACTATTT1250GGGTTTCCGGAAGCCTTCATAACATATATTCTGTCGGGATGGCGCTGGAA1300CAGGAAGGTTTCAAAATCTTAAATAATATAACTTGGCAAAAGACAAATCC1350TGCACCTAATCTATCATGTCGGTACTTCACCCACTCTACAGAGACAATTT1400TATGGGCAAGAAAGAACGATAAAAAATCTCGCCATTATTATAACTATGAA1450TTGATGAAAGAGTTTAATGACGGGAAACAAATGAAAGATGTTTGGACAGG1500TAGTCTGACAAAAAAATCAGAAAAATGGGCTGGGAAACATCCAACTCAGA1550AGCCAGAGTATATTTTAGAACGGATAATCTTAGCTAGTACAAAGGAAAAT1600GATTATATTTTAGACCCTTTCGTCGGAAGTGGAACTACTGGTGTAGTAGC1650CAAGAGATTGGGGCGTAAATTTATTGGGATTGATTCTGAGAAAGAATATC1700TTAAAATTGCTAAAAAAAGGCTAAATAAAGGAGCAACATATGGACTTTAA1750TAATTACATCGGTTTAGAATCTGACGATAGATTAAATGCTTTTATGGCAA1800CACTTTCCGTAACTAATAGAACTCCCGAATACTACGTGAACTGGGAAAAA1850GTTGAACGTGAAACACGAAAATTTGAATTAGAACTAAATACTTTAAACTA1900TCTCATTGGGAAAGAAGATATTTATAGTGAAGCACTTGAACTATTTACCA1950ATCAACCTGAATTGCTTAAAGCTATTCCTAGTTTGATTGCTAGTAGAGAT2000ACATCTTTAGATATACTAAACATTGACGAAAATGATGATATGAGTTTTGA2050ACAACTTAACTTTCTTGTTATCGACGAAAATTGTATCGCTGATTATGTAG2100ACTTTATTAACCAGGCAGGTTTACTAGATTTTCTACAGAATAAAGCAAAA2150CGTTCTCTGGTAGACTATGTGTATGGTGTTGAAGCAGGGCTTGATAGCAA2200TGCTCGAAAAAACCGAAGCGGTACAACCATGGAGGGGATTTTAGAACGTA2250CTGTTTCAAAAATAGCTCAAGAGAAAGGGCTTGAATGGAAGCCACAGGCA2300ACCGCTTCTTTTATCAAGTCTCAATGGGACATAGAAGTCCCTGTAGATAA2350ATCAAAAAGACGCTTTGATGCAGCAGTTTACTCTCGTGCGCTCAATAAGG2400TTTGGCTCATAGAAACAAATTACTACGGCGGTGGAGGAAGTAAACTCAAA2450GCAGTTGCTGGAGAATTTACAGAATTGAGTCAGTTTGTAAAAACATCAAA2500AGATAATGTTGAATTTGTATGGGTAACAGACGGCCAAGGGTGGAAATTTT2550CCCGCTTACCACTTGCAGAAGCTTTCGGACACATCGATAACGTTTTCAAT2600CTAACCATGTTGAAAGAAGGTTTCTTATCTGATTTATTCGAAAAAGAAAT2650TTAAAAAGACAGAGAATCTCTGTCTTTTTAAATTTCAATTCCTTCCTTCT2700GCTAGCTATAACTTTCCAAAAAACCTGAAAAACGGTTCTGTTGCAATTGT2750ATGTGGGGTCGGAACTTACTACTATATCATGAGAAATGAAGATTAAAGTT2800GAAACAAAAAAACAGATTATTTTAAAATGTAAATCTGTTTTTGTTTGGGC2850TGATTTTATCACACCAATTCTATGTTCAGAAAATGGTCATTTTCTGGACA2900CTCTTCTTTTGTTATTAAAACTCTCAAAATCATTTACATTTATTGTTCAT2950TAACCCGTAATTTATTCTATGTTCATTTATAGATATC2987(2) INFORMATION FOR SEQ ID NO:2:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 284 Amino Acids(B) TYPE: Amino Acid(C) STRANDEDNESS: Single(D) TOPOLOGY: Linear(ii) MOLECULE TYPE: Peptide(xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:MetAsnLeuLeuGlnLysAsnLysIleAsnLeuArgProPheThr51015LysTrpThrGlyGlyLysArgGlnLeuLeuProHisIleGlnTyr202530LeuMetProGluLysTyrAsnHisPhePheGluProPheIleGly354045GlyGlyAlaLeuPhePheGluProAlaProGlnLysAlaValIle505560AsnAspPheAsnSerGluLeuIleAsnCysTyrArgGlnMetLys657075AspAsnProGluGlnLeuIleGluLeuLeuThrAsnHisGlnArg808590GluAsnSerLysGluTyrTyrLeuAspLeuArgSerSerAspArg95100105AspGlyArgIleAspLysMetSerGluValGluArgAlaAlaArg110115120IleMetTyrMetLeuArgValAspPheAsnGlyLeuTyrArgVal125130135AsnSerLysAsnGlnPheAsnValProTyrGlyArgTyrLysAsn140145150ProLysIleValAspLysGluLeuIleGluSerIleSerGluTyr155160165LeuAsnAsnAsnSerIleLysIleMetSerGlyAspPheGluLys170175180AlaValLysGluAlaGlnAspGlyAspPheValTyrPheAspPro185190195ProTyrIleProLeuSerGluThrSerAlaPheThrSerTyrThr200205210HisGluGlyPheSerTyrGluAspGlnValArgLeuArgAspCys215220225PheLysGlnLeuAspSerLysGlyValPheValMetLeuSerAsn230235240SerSerSerProLeuAlaGluGluLeuTyrLysAspPheAsnIle245250255HisLysIleGluAlaThrArgThrAsnGlyAlaLysSerSerSer260265270ArgGlyLysIleThrGluIleIleValThrAsnTyrGlyAsn275280(2) INFORMATION FOR SEQ ID NO:3:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 269 Amino Acids(B) TYPE: Amino Acid(C) STRANDEDNESS: Single(D) TOPOLOGY: Linear(ii) MOLECULE TYPE: Peptide(xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:MetAlaIleAsnGluTyrLysTyrGlyGlyValLeuMetThrLys51015ProTyrTyrGluLysGluAsnAlaIleLeuValHisAlaAspSer202530PheLysLeuLeuGluLysIleLysProGluSerMetAspMetIle354045PheAlaAspProProTyrPheLeuSerAsnGlyGlyMetSerAsn505560SerGlyGlyGlnIleValSerValAspLysGlyAspTrpAspLys657075IleSerSerPheGluGluLysHisAspPheAsnArgArgTrpIle808590ArgLeuAlaArgLeuValLeuLysProAsnGlyThrIleTrpVal95100105SerGlySerLeuHisAsnIleTyrSerValGlyMetAlaLeuGlu110115120GlnGluGlyPheLysIleLeuAsnAsnIleThrTrpGlnLysThr125130135AsnProAlaProAsnLeuSerCysArgTyrPheThrHisSerThr140145150GluThrIleLeuTrpAlaArgLysAsnAspLysLysSerArgHis155160165TyrTyrAsnTyrGluLeuMetLysGluPheAsnAspGlyLysGln170175180MetLysAspValTrpThrGlySerLeuThrLysLysSerGluLys185190195TrpAlaGlyLysHisProThrGlnLysProGluTyrIleLeuGlu200205210ArgIleIleLeuAlaSerThrLysGluAsnAspTyrIleLeuAsp215220225ProPheValGlySerGlyThrThrGlyValValAlaLysArgLeu230235240GlyArgLysPheIleGlyIleAspSerGluLysGluTyrLeuLys245250255IleAlaLysLysArgLeuAsnLysGlyAlaThrTyrGlyLeu260265(2) INFORMATION FOR SEQ ID NO:4:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 304 Amino Acids(B) TYPE: Amino Acid(C) STRANDEDNESS: Single(D) TOPOLOGY: Linear(ii) MOLECULE TYPE: Peptide(xi) SEQUENCE DESCRIPTION: SEQ ID NO:4:MetAspPheAsnAsnTyrIleGlyLeuGluSerAspAspArgLeu51015AsnAlaPheMetAlaThrLeuSerValThrAsnArgThrProGlu202530TyrTyrValAsnTrpGluLysValGluArgGluThrArgLysPhe354045GluLeuGluLeuAsnThrLeuAsnTyrLeuIleGlyLysGluAsp505560IleTyrSerGluAlaLeuGluLeuPheThrAsnGlnProGluLeu657075LeuLysAlaIleProSerLeuIleAlaSerArgAspThrSerLeu808590AspIleLeuAsnIleAspGluAsnAspAspMetSerPheGluGln95100105LeuAsnPheLeuValIleAspGluAsnCysIleAlaAspTyrVal110115120AspPheIleAsnGlnAlaGlyLeuLeuAspPheLeuGlnAsnLys125130135AlaLysArgSerLeuValAspTyrValTyrGlyValGluAlaGly140145150LeuAspSerAsnAlaArgLysAsnArgSerGlyThrThrMetGlu155160165GlyIleLeuGluArgThrValSerLysIleAlaGlnGluLysGly170175180LeuGluTrpLysProGlnAlaThrAlaSerPheIleLysSerGln185190195TrpAspIleGluValProValAspLysSerLysArgArgPheAsp200205210AlaAlaValTyrSerArgAlaLeuAsnLysValTrpLeuIleGlu215220225ThrAsnTyrTyrGlyGlyGlyGlySerLysLeuLysAlaValAla230235240GlyGluPheThrGluLeuSerGlnPheValLysThrSerLysAsp245250255AsnValGluPheValTrpValThrAspGlyGlnGlyTrpLysPhe260265270SerArgLeuProLeuAlaGluAlaPheGlyHisIleAspAsnVal275280285PheAsnLeuThrMetLeuLysGluGlyPheLeuSerAspLeuPhe290295300GluLysGluIle(2) INFORMATION FOR SEQ ID NO:5:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 284 Amino Acids(B) TYPE: Amino Acid(C) STRANDEDNESS: Single(D) TOPOLOGY: Linear(ii) MOLECULE TYPE: Peptide(xi) SEQUENCE DESCRIPTION: SEQ ID NO:5:MetLysIleLysGluIleLysLysValThrLeuGlnProPheThr51015LysTrpThrGlyGlyLysArgGlnLeuLeuProValIleArgGlu202530LeuIleProLysThrTyrAsnArgTyrPheGluProPheValGly354045GlyGlyAlaLeuPhePheAspLeuAlaProLysAspAlaValIle505560AsnAspPheAsnAlaGluLeuIleAsnCysTyrGlnGlnIleLys657075AspAsnProGlnGluLeuIleGluIleLeuLysValHisGlnGlu808590TyrAsnSerLysGluTyrTyrLeuAspLeuArgSerAlaAspArg95100105AspGluArgIleAspMetMetSerGluValGlnArgAlaAlaArg110115120IleLeuTyrMetLeuArgValAsnPheAsnGlyLeuTyrArgVal125130135AsnSerLysAsnGlnPheAsnValProTyrGlyArgTyrLysAsn140145150ProLysIleValAspGluGluLeuIleSerAlaIleSerValTyr155160165IleAsnAsnAsnGlnLeuGluIleLysValGlyAspPheGluLys170175180AlaIleValAspValArgThrGlyAspPheValTyrPheAspPro185190195ProTyrIleProLeuSerGluThrSerAlaPheThrSerTyrThr200205210HisGluGlyPheSerPheAlaAspGlnValArgLeuArgAspAla215220225PheLysArgLeuSerAspThrGlyAlaTyrValMetLeuSerAsn230235240SerSerSerAlaLeuValGluGluLeuTyrLysAspPheAsnIle245250255HisTyrValGluAlaThrArgThrAsnGlyAlaLysSerSerSer260265270ArgGlyLysIleSerGluIleIleValThrAsnTyrGluLys275280(2) INFORMATION FOR SEQ ID NO:6:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 294 Amino Acids(B) TYPE: Amino Acid(C) STRANDEDNESS: Single(D) TOPOLOGY: Linear(ii) MOLECULE TYPE: Peptide(xi) SEQUENCE DESCRIPTION: SEQ ID NO:6:MetLysProPheIleLysTrpAlaGlyGlyLysAsnSerLeuLeu51015AspGluIleGlnLysArgLeuProAspPheValHisSerGlnAsp202530PheCysLeuValGluProPheValGlyGlyGlyAlaValSerLeu354045TrpAlaLeuSerAspLeuProHisLeuLysGlnLeuValIleAsn505560AspCysAsnAlaAspLeuIleAsnValTyrGlnValIleLysAsn657075AsnProAspAspLeuIleGlyTyrIleGluAsnLeuGlnSerHis808590TyrAspLysLeuThrAspLeuGluSerLysLysProTyrPheTyr95100105HisLysArgAspValPheAsnGlnArgThrSerAsnAspIleGlu110115120GlnAlaGlyLeuPheIlePheLeuAsnLysSerAlaPheAsnGly125130135LeuTyrArgValAsnLysAsnAsnGlnPheAsnValProIleGly140145150AsnTyrLysLysProThrPheValAspLysGluAsnIleLeuAsn155160165IleSerLysLysLeuGlnAsnThrLysIleLeuSerGlyAspPhe170175180GluLeuValLeuAlaHisLeuProAsnAsnPheProCysLeuPhe185190195TyrLeuAspProProTyrArgProIleSerAspThrAlaSerPhe200205210ThrSerTyrSerAspAsnGlyPheAspAspAsnGluGlnLysArg215220225LeuAlaAsnPheCysLysLysIleAspLysLeuGlyHisTyrPhe230235240LeuLeuSerAsnSerAspProLysAsnThrAsnSerSerAspGlu245250255PhePheAspGluLeuTyrGlnAspPheLysIleGluArgIleGln260265270AlaAsnArgThrIleSerAlaAsnSerAsnGlyArgLysLysVal275280285AsnGluIleIleValSerAsnGlyVal290(2) INFORMATION FOR SEQ ID NO:7:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 278 Amino Acids(B) TYPE: Amino Acid(C) STRANDEDNESS: Single(D) TOPOLOGY: Linear(ii) MOLECULE TYPE: Peptide(xi) SEQUENCE DESCRIPTION: SEQ ID NO:7:MetLysLysAsnArgAlaPheLeuLysTrpAlaGlyGlyLysTyr51015ProLeuLeuAspAspIleLysArgHisLeuProLysGlyGluCys202530LeuValGluProPheValGlyAlaGlySerValPheLeuAsnThr354045AspPheSerArgTyrIleLeuAlaAspIleAsnSerAspLeuIle505560SerLeuTyrAsnIleValLysMetArgThrAspGluTyrValGln657075AlaAlaArgGluLeuPheValProGluThrAsnCysAlaGluVal808590TyrTyrGlnPheArgGluGluPheAsnLysSerGlnAspProPhe95100105ArgArgAlaValLeuPheLeuTyrLeuAsnArgTyrGlyTyrAsn110115120GlyLeuCysArgTyrAsnLeuArgGlyGluPheAsnValProPhe125130135GlyArgTyrLysLysProTyrPheProGluAlaGluLeuTyrHis140145150PheAlaGluLysAlaGlnAsnAlaPhePheTyrCysGluSerTyr155160165AlaAspSerMetAlaArgAlaAspAspAlaSerValValTyrCys170175180AspProProTyrAlaProLeuSerAlaThrAlaAsnPheThrAla185190195TyrHisThrAsnSerPheThrLeuGluGlnGlnAlaHisLeuAla200205210GluIleAlaGluGlyLeuValGluArgHisIleProValLeuIle215220225SerAsnHisAspThrMetLeuThrArgGluTrpTyrGlnArgAla230235240LysLeuHisValValLysValArgArgSerIleSerSerAsnGly245250255GlyThrArgLysLysValAspGluLeuLeuAlaLeuTyrLysPro260265270GlyValValSerProAlaLysLys275(2) INFORMATION FOR SEQ ID NO:8:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 268 Amino Acids(B) TYPE: Amino Acid(C) STRANDEDNESS: Single(D) TOPOLOGY: Linear(ii) MOLECULE TYPE: Peptide(xi) SEQUENCE DESCRIPTION: SEQ ID NO:8:MetLysAsnAsnGluTyrLysTyrGlyGlyValLeuMetThrLys51015ProTyrTyrAsnLysAsnLysMetIleLeuValHisSerAspThr202530PheLysPheLeuSerLysMetLysProGluSerMetAspMetIle354045PheAlaAspProProTyrPheLeuSerAsnGlyGlyIleSerAsn505560SerGlyGlyGlnValValSerValAspLysGlyAspTrpAspLys657075IleSerSerPheGluGluLysHisGluPheAsnArgLysTrpIle808590ArgLeuAlaLysGluValLeuLysProAsnGlyThrValTrpIle95100105SerGlySerLeuHisAsnIleTyrSerValGlyMetAlaLeuGlu110115120GlnGluGlyPheLysIleLeuAsnAsnIleThrTrpGlnLysThr125130135AsnProAlaProAsnLeuSerCysArgTyrPheThrHisSerThr140145150GluThrIleLeuTrpAlaArgLysAsnAspLysLysAlaArgHis155160165TyrTyrAsnTyrAspLeuMetLysGluLeuAsnAspGlyLysGln170175180MetLysAspValTrpThrGlySerLeuThrLysLysValGluLys185190195TrpAlaGlyLysHisProThrGlnLysProGluTyrLeuLeuGlu200205210ArgIleIleLeuAlaSerThrLysGluGlyAspTyrIleLeuAsp215220225ProPheValGlySerGlyThrThrGlyValValAlaLysArgLeu230235240GlyArgArgPheIleGlyIleAspAlaGluLysGluTyrLeuLys245250255IleAlaArgLysArgLeuGluAlaGluAsnGluThrAsn260265(2) INFORMATION FOR SEQ ID NO:9:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 273 Amino Acids(B) TYPE: Amino Acid(C) STRANDEDNESS: Single(D) TOPOLOGY: Linear(ii) MOLECULE TYPE: Peptide(xi) SEQUENCE DESCRIPTION: SEQ ID NO:9:MetArgIleLysProTyrPheGluSerAspAspLysAsnPheAsn51015IleTyrGlnGlyAsnCysIleAspPheMetSerHisPheGlnAsp202530AsnSerIleAspMetIlePheAlaAspProProTyrPheLeuSer354045AsnAspGlyLeuThrPheLysAsnSerIleIleGlnSerValAsn505560LysGlyGluTrpAspLysAsnAspAsnGluAlaSerIleTyrAsn657075PheAsnHisGluTrpIleAlaGlnAlaArgGlnLeuLeuLysAsp808590AsnGlyThrIleTrpIleSerGlyThrHisHisAsnIlePheThr95100105ValGlyGlnValLeuLysGluAsnAsnPheLysIleLeuAsnIle110115120IleThrTrpGluLysProAsnProProProAsnPheSerCysArg125130135TyrPheThrTyrSerSerGluTrpIleIleTrpAlaArgLysHis140145150SerLysIleProHisTyrPheAsnTyrAspLeuMetLysLysLeu155160165AsnGlyAspLysGlnGlnLysAspIleTrpArgLeuProAlaVal170175180GlySerTrpGluLysThrGlnGlyLysHisProThrGlnLysPro185190195LeuGlyLeuLeuSerArgIleIleLeuSerSerThrGlnLysAsp200205210AspLeuIleLeuAspProPheSerGlySerGlyThrThrGlyIle215220225AlaGlyValLeuLeuAspArgAsnTyrIleGlyIleGluGlnGlu230235240LeuGluPheLeuGluLeuSerLysArgArgTyrHisGluIleThr245250255ProValLeuLysAsnGluPheLysGlnLysIleArgLysGlnIle260265270SerAlaIle(2) INFORMATION FOR SEQ ID NO:10:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 287 Amino Acids(B) TYPE: Amino Acid(C) STRANDEDNESS: Single(D) TOPOLOGY: Linear(ii) MOLECULE TYPE: Peptide(xi) SEQUENCE DESCRIPTION: SEQ ID NO:10:MetMetLysGluAsnIleAsnAspPheLeuAsnThrIleLeuLys51015GlyAspCysIleGluLysLeuLysThrIleProAsnGluSerIle202530AspLeuIlePheAlaAspProProTyrPheMetGlnThrGluGly354045LysLeuLeuArgThrAsnGlyAspGluPheSerGlyValAspAsp505560GluTrpAspLysPheAsnAspPheValGluTyrAspSerPheCys657075GluLeuTrpLeuLysGluCysLysArgIleLeuLysSerThrGly808590SerIleTrpValIleGlySerPheGlnAsnIleTyrArgIleGly95100105TyrIleMetGlnAsnLeuAspPheTrpIleLeuAsnAspValIle110115120TrpAsnLysThrAsnProValProAsnPheGlyGlyThrArgPhe125130135CysAsnAlaHisGluThrMetLeuTrpCysSerLysCysLysLys140145150AsnLysPheThrPheAsnTyrLysThrMetLysHisLeuAsnGln155160165GluLysGlnGluArgSerValTrpSerLeuSerLeuCysThrGly170175180LysGluArgIleLysAspGluGluGlyLysLysAlaHisSerThr185190195GlnLysProGluSerLeuLeuTyrLysValIleLeuSerSerSer200205210LysProAsnAspValValLeuAspProPhePheGlyThrGlyThr215220225ThrGlyAlaValAlaLysAlaLeuGlyArgAsnTyrIleGlyIle230235240GluArgGluGlnLysTyrIleAspValAlaGluLysArgLeuArg245250255GluIleLysProAsnProAsnAspIleGluLeuLeuSerLeuGlu260265270IleLysProProLysValProMetLysThrLeuIleGluAlaAsp275280285PheLeu(2) INFORMATION FOR SEQ ID NO:11:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 288 Amino Acids(B) TYPE: Amino Acid(C) STRANDEDNESS: Single(D) TOPOLOGY: Linear(ii) MOLECULE TYPE: Peptide(xi) SEQUENCE DESCRIPTION: SEQ ID NO:11:MetLysGlnThrArgAsnPheAspGluTrpLeuSerThrMetThr51015AspThrValAlaAspTrpThrTyrTyrThrAspPheProLysVal202530TyrLysAsnValSerSerIleLysValAlaLeuAsnIleMetAsn354045SerLeuIleGlySerLysAsnIleGlnGluAspPheLeuAspLeu505560TyrGlnAsnTyrProGluIleLeuLysValValProLeuLeuIle657075AlaLysArgLeuArgAspThrIleIleValLysAspProIleLys808590AspPheTyrPheAspPheSerLysArgAsnTyrSerIleGluGlu95100105TyrThrMetPheLeuGluLysSerGlyIlePheAspLeuLeuGln110115120AsnHisLeuValSerAsnLeuValAspTyrValThrGlyValGlu125130135ValGlyMetAspThrAsnGlyArgLysAsnArgThrGlyAspAla140145150MetGluAsnIleValGlnSerTyrLeuGluAlaGluGlyTyrIle155160165LeuGlyGluAsnLeuPheLysGluIleGluGlnAsnGluIleGlu170175180GluIlePheSerValAspLeuSerAlaIleThrAsnAspGlyAsn185190195ThrValLysArgPheAspPheValIleLysAsnGluGlnValLeu200205210TyrLeuIleGluValAsnPheTyrSerGlySerGlySerLysLeu215220225AsnGluThrAlaArgSerTyrLysMetIleAlaGluGluThrLys230235240AlaIleProAsnValGluPheMetTrpIleThrAspGlyGlnGly245250255TrpTyrLysAlaLysAsnAsnLeuArgGluThrPheAspIleLeu260265270ProPheLeuTyrAsnIleAsnAspLeuGluHisAsnIleLeuLys275280285AsnLeuLys(2) INFORMATION FOR SEQ ID NO:12:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 280 Amino Acids(B) TYPE: Amino Acid(C) STRANDEDNESS: Single(D) TOPOLOGY: Linear(ii) MOLECULE TYPE: Peptide(xi) SEQUENCE DESCRIPTION: SEQ ID NO:12:MetLysLeuAlaPheAspAspPheLeuAsnSerMetSerGluThr51015AsnThrThrLeuAspTyrPheThrAspPheAspLysValLysLys202530AsnValAlaGlnIleGluIleHisLeuAsnGlnLeuAsnTyrLeu354045LeuGlyLysAspAspLeuLysGlnAlaValTyrAspLeuTyrAla505560GluCysProAsnAlaPheSerIleLeuGluIleLeuIleAlaVal657075ArgLysLysGluGlnLysLysSerLeuAspGluLysGlyGlnVal808590ValThrLeuAsnSerTyrPheGlnSerAlaAspLysIleIleAsp95100105PheLeuAsnAsnThrGlyLeuAlaAspValPheArgAspLysAsn110115120IleLysAsnLeuValAspTyrValPheGlyIleGluValGlyLeu125130135AspThrAsnAlaArgLysAsnArgGlyGlyAspAsnMetSerLys140145150AlaValGlnLeuLeuPheAspAsnAlaAspIleTyrTyrLysLys155160165GluValArgAsnThrIlePheThrAspIleGluSerLeuGlyAla170175180AspValLysGlnPheAspPheValIleLysThrLysArgLysThr185190195TyrValIleGluThrAsnTyrTyrAsnSerGlyGlySerLysLeu200205210AsnGluValAlaArgAlaTyrThrAspValAlaProLysIleAsn215220225GlnTyrSerGlnTyrGluPheValTrpIleThrAspGlyGlnGly230235240TrpLysThrAlaLysAsnLysLeuGlnGluAlaTyrThrHisIle245250255ProSerValTyrAsnLeuTyrThrLeuHisGlyPheIleGluGln260265270LeuAsnSerGluGlyValIleLysAspTrp275280__________________________________________________________________________

Claims

1. An isolated DNA encoding only an enzyme which is selected from the group consisting of LlaIIA, LlaIIB and LlaIIC wherein the DNA is in a sequence which encodes one or more of the enzymes and wherein the enzymes restrict or modify a phage DNA.

2. An isolated DNA having a nucleotide sequence as set forth in SEQ ID NO. 1 and selected from the group consisting of ORF1 (positions 97 to 948), ORF2 (positions 941 to 1747) and ORF3 (positions 1740 to 2651) and combinations thereof.

3. An isolated DNA encoding an enzyme LlaIIA and having a nucleotide sequence as set forth in SEQ ID NO. 1.

4. An isolated DNA encoding an enzyme LlaIIB and having a nucleotide sequence as set forth in SEQ ID NO.1.

5. An isolated DNA sequence encoding an enzyme LlaIIC and having a nucleotide as set forth in SEQ ID NO.1.

6. A recombinant plasmid containing DNA encoding an enzyme which is selected from the group consisting of LlaIIA, LlaIIB and LlaIIC wherein the DNA is in a sequence which encodes one or more of the enzymes and wherein the enzymes restrict or modify a phage DNA.

7. The plasmid of claim 6 which is a shuttle vector PSA3 containing the DNA.

8. A bacterium harboring a recombinant plasmid containing DNA encoding for an enzyme which is selected from the group consisting of LlaIIA, LlaIIB and LlaIIC wherein the DNA is in a sequence which encodes one or more of the enzymes and wherein the enzymes restrict or modify a phage DNA.

9. The bacterium of claim 8 which is Escherichia coli.

10. The bacterium of claim 8 which is selected from the group consisting of a Lactococcus lactis and Streptococcus thermophilus.

11. A method of imparting phage resistance to a bacterium which is sensitive to the phage which comprises incorporating recombinant DNA into the bacterium encoding an enzyme selected from the group consisting of LlaIIA, LlaIIB and LlaIIC wherein the DNA is in a sequence which encodes one or more of the enzymes and wherein the enzymes impart the phage resistance, wherein the DNA is contained in strain Lactococcus lactis SMQ-17 deposited as NRRL-B-21337.

12. The method of claim 11 wherein the DNA is in a plasmid.

13. The method of claim 11 wherein the DNA is in a vector for transforming the bacterium.

14. The method of claim 11 wherein the bacterium is selected from the group consisting of a Lactococcus lactis and a Streptococcus salivarius subsp. thermophilus.

15. A bacterium selected from the group consisting of Streptococcus salivarius subsp. thermophilus and Lactococcus lactis which group naturally lacks phage resistance which bacterium contains recombinant DNA encoding an enzyme selected from the group consisting of LlaIIA, LlaIIB and LlaIIC wherein the DNA is in a sequence which encodes one or more of the enzymes and has a sequence as set forth in SEQ ID NO: 1 and wherein the enzyme imparts phage resistance.

16. The Lactococcus lactis of claim 15 wherein the DNA is contained in Lactococcus lactis SMQ-17 deposited as NRRL-B-21337.

17. The Lactococcus lactis of claim 15 wherein the DNA is in a plasmid.

18. The Lactococcus lactis of claim 15 wherein the DNA is in a vector for transformation.

19. A Streptococcus thermophilus naturally lacking in a phage resistance mechanism and containing recombinant DNA encoding at least one endonuclease from Lactococcus lactis SMO-17 deposited as NRRL-B-21337 to impart the phage resistance.

20. The Streptococcus thermophilus of claim 19 wherein the DNA is in a plasmid.

21. The Streptococcus thermophilus of claim 19 wherein the DNA is in a vector for transformation.

22. A method of imparting phage resistance to a Streptococcus thermophilus which lacks phage resistance which comprises incorporating recombinant DNA encoding at least one endonuclease of Lactococcus lactis SMO-17 deposited as NRRL-B-21337 into the Streptococcus thermophilus to impart the phage resistance.

23. The method of claim 22 wherein the DNA is in a plasmid.

24. The method of claim 22 wherein the DNA is in a vector for transforming the bacterium.