Molecular mechanisms of bacteriocin evolution

Annual Review of Genetics

Volumn 32, Issue , 1998, Pages 255-278

  Riley, Margaret A ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Colicin; Diversifying selection; Pyocin; Recombination; Resistance

Indexed keywords

BACTERIOCIN;

ANTIMICROBIAL ACTIVITY; DNA SEQUENCE; GENE CLUSTER; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; REVIEW;

BACTERIOCINS; COLICINS; DRUG RESISTANCE, MICROBIAL; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; HALOBACTERIACEAE; HUMANS; MODELS, BIOLOGICAL; PYOCINS; SELECTION (GENETICS); VARIATION (GENETICS);

PROKARYOTA;

EID: 0032425481     PISSN: 00664197     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genet.32.1.255     Document Type: Review

References (116)

1. Achtman MA, Mercer B, Kusecek B, Pohl M, Heuzenroeder W, et al. 1983. Six widespread clones among Escherichia coli isolates. Infect. Immun. 39:315-35
2. Akutsu A, Masaki H, Ohta T. 1989. Molecular structure and immunity specificity of colicin E6, an evolutionary intermediate between E-group colicins and cloacin DF13. J. Bacteriol. 171:6430-36
3. Baty D, Knibiehler M, Verheij H, Pattus F, Shire D. 1987. Site-directed mutagenesis of the COOH-terminal region of colicin A: effect on secretion and voltage-dependent channel activity. Proc. Natl. Acad. Sci. USA 84:1152-56
4. Braude AI, Siemienski JS. 1968. The influence of bacteriocins on resistance to infection by gram-negative bacteria. J. Clin. Invest. 47:1763-73
5. Braun V, Pilsl H, Gross P. 1994. Colicins: structures, modes of actions, transfer through membranes, and evolution. Arch. Microbiol. 161:199-206
6. Cavard D, Batty D, Howard S, Verheij H, Lazdunski C. 1987. Lipoprotein nature of the colicin A lysis protein: effect of amino acid substitutions at the site of modification and processing. J. Bacteriol. 169:2187-94
7. Chak K-F, James R. 1986. Characterization of the ColE9-J plasmid and analysis of its genetic organization. J. Gen. Microbiol. 132:61-71
8. Chak K-F, Kuo W-S, Lu F-M, James R. 1991. Cloning and characterization of the ColEV plasmid. J. Gen. Microbiol. 137:91-100
9. Chak K-F, Safo M, Ku W, Hseih S, Yuan H. 1996. The crystal structure of the immunity protein of colicin E7 suggests a possible colicin-interacting surface. Proc. Natl. Acad. Sci. USA 93:6437-42
10. Chan PT, Ohmori H, Tomizawa J, Lebowitz J. 1985. Nucleotide sequence and gene organization of colE1 DNA. J. Biol. Chem. 260:8925-35
11. Chao L, Levin BR. 1977. A complex community in a simple habitat: an experimental study with bacteria and phage. Ecology 58:369-78
12. Chao L, Levin BR. 1981. Structured habitats and the evolution of anticompetitors in bacteria. Proc. Natl. Acad. Sci. USA 78:6324-28
13. Cheung J, Danna K, O'Connor E, Price L, Shand R. 1997. Isolation, sequence, and expression of the gene encoding halocin H4, a hacteriocin from the halophilic archaeon Huloferax mediterranei R4. J. Bactriol. 179:548-51
14. Chung K, Dickson J, Crouse J. 1989. Effects of Nisin on growth of bacteria attached to meat. Appl. Environ. Microbiol. 55:1329-33
15. Cohan R, King E, Zawadski P. 1994. Amelioration of the deleterious pleiotropic effects of an adaptive mutation in Bacillus subtilis. Evolution 48: 81-95
16. Curtis M, James R. 1991. Investigation of the specificity of the interaction between colicin E9 and its immunity protein by site-directed mutagenesis. Mol. Microbiol 5:2727-34
17. Curtis MD, James R, Coddington A. 1989. An evolutionary relationship between the colE5-099 and the colE9-J plasmids revealed by nucleotide sequencing. J. Gen. Microbiol 135:2783-88
18. Davies JK, Reeves P. 1975. Genetics of resistance to colicins in Escherichia coli K-12: cross-resistance among colicins of group B. J. Bacteriol. 123:96-101
19. Delves-Broughton J. 1990. Nisin and its use as a food preservative. Food Technol. 44:100, 102, 104, 106, 108, 111, 112, 117
20. de Vicente A, Codina J, Martinez-Mananares E, Aviles M, Borrego J. Romero P. 1990. Serotypes and pyocin types of Pseudomonas aeruginosa isolated from natural waters. Lett. Appl. Microbiol. 10:77-80
21. Dreher R, Braun V, Wittmann-Liebold B. 1985. Functional domains of colicin M. Arch. Microbiol. 140:343-46
22. Duché D, Letellier L, Géli V, Bénédetti H, Baty D. 1995. Quantification of group A colicin import sites. J. Bacteriol. 177: 4935-39
23. Duport C, Baysse C, Michel-Briand Y. 1995. Molecular characterization of pyocin S3, a novel S-type pyocin from Pseudomonas aeruginosa. J. Biol. Chem. 270:8920-27
24. Durrett R, Levin S. 1997. Allelopathy in spatially distributed populations. J. Theor. Biol. 185:165-71
25. Dykes GA, Hastings JW. 1997. Selection and fitness in bacteriocin-producing bacteria. Proc. R. Soc. London Ser. B 264:683-87
26. Dykhuizen DE, Hartl DL. 1983. Selection in chemostats. Microbiol. Rev. 47:150-68
27. Eaton T, James R. 1989. Complete nucleotide sequence of the colicin E9 (cei) gene. Nucleic Acids Res. 17:1761
28. Deleted in proof
29. Elkins P, Bunker A, Cramer W, Stauffacher C. 1995. The crystal structure of the channel-forming domain of colicin E1. Biophys. J. 68:369
30. Escuyer V, Mock M. 1987. DNA sequence analysis of three misense mutations affecting colicin E3 bacteriocidal activity. Mol. Microbiol. 1:82-85
31. Espesset D, Piet P, Lazdunski C, Geil V. 1994. Immunity proteins to pore-forming colicins: structure-function relationships. Mol. Microbiol. 13:1111-20
32. Feldgarden M, Golden S, Wilson H, Riley MA. 1995. Can phage defense maintain colicin plasmids in Escherichia coli? J. Microbiol. 141:2977-84
33. Feldgarden M, Riley MA. 1998. High levels of colicin resistance in Escherichia coli may be due to pleiotropy. Evolution. In press
34. Frank S. 1994. Spatial polymorphism of bacteriocins and other allelopathic traits. Evol. Ecol. 8:369-86
35. Fredericq P. 1957. Gene tics of two different mechanisms of resistance to colicins: resistance by loss of specific receptors and immunity by transfer of colicinogenic factors. Presented at Ciba Symp. Drug Resist. Microorg., Churchill, London
36. Fyfe J, Harris G, Govan J. 1984. Revised pyocin typing methods for Pseudomonas aeruginosa. J. Clin. Microbiol. 20:47-50
37. Gordon DM. 1992. The rate of plasmid transfer among Escherichia coli strains isolated from natural populations. J. Gen. Microbiol. 138:17-21
38. Gordon DM, Riley MA, Pinou T. 1998. Temporal changes in the frequency of colicinogeny in Escherichia coli from house mice. Microbiology. In press
39. Govan JRW. 1974. Studies on the pyocins of Pseudomonas aeruginosa: morphology and mode of action of contractile pyocins. J. Gen. Microbiol. 80:1-15
40. Govan JRW. 1978. Pyocin typing of Pseudomonas aeruginosa In Methods in Microbiology, ed. T Bergan, JR Morris, pp. 61-91. London: Academic
41. Hillman J, Dzuback A, Andrews S. 1987. Colonization of the human oral cavity by a Streptococcus mutans mutant producing increased bacteriocin. J. Dent. Res. 66:1092-1094
42. Howell T, Fiorellini J, Blackburn P, Projan S, Harpe JD, Williams R. 1993. The effect of a mouthrinse based on nisin, a bacteriocin, on developing plaque and gingivitis in beagle dogs. J. Clinic. Period. 20:335-39
43. Hoyt PR, Sizemore RK. 1982. Competitive dominance by a bacteriocin-producing Vibrio harveyi strain. Appl. Environ. Microbiol. 44:653-58
44. Hsieh S, Ko T, Tseng M, Ku W, Chak K, Yuan H. 1997. A novel role of ImmE7 in the autoregulatory expression of the ColE7 operon and identification of possible RNase active sites in the crystal structure of dimeric ImmE7. EMBO 16:1444-54
45. Hudson R, Kreitman M, Agaude M. 1987. A test of neutral molecular evolution based upon nucleotide data. Genetics 116:153-59
46. Jack RW, Tagg JR, Ray B. 1995. Bacteriocins of gram-positive bacteria. Microbiol. Rev. 59:171-200
47. James R. 1988. Molecular cloning and purification of Klebicin B. J. Gen. Microbiol. 134:2525-33
48. James R, Jarvis M, Barker DF. 1987. Nucleotide sequence of the immunity and lysis region of the ColE9-J plasmid. J. Gen. Microbiol. 133:1553-62
49. James R, Kleanthous C, Moore GR. 1996. The biology of E colicins: paradigms and paradoxes. Microbiology 142:1569-80
50. James R, Lazdunski C, Pattus F, eds. 1991. Bacteriocins, Microcins and Lantibiotics, p. 519. New York: Springer-Verlag
51. Jeanteur D, Schirmer T, Fourel D, Simonet V, Rummel G, et al. 1994. Structural and functional alterations of a colicin-resistant mutant of OmpF porin from Escherichia coli. Proc. Natl. Acad. Sci. USA 91:10675-79
52. Johnson I, Hayday H, Colman G. 1978. The effects of nisin on the microbial flora of the dental plaques of monkeys (Macaca fascicularis). J. Appl. Bacteriol. 45:99-109
53. Kageyama M. 1975. Bacteriocins and Bacteriophages in Pseudomonas deruginosa, pp. 291-305. Tokyo: Univ. Tokyo Press
54. Killiman H, Videnov G, Jung G, Schwarz H, Braun V. 1995. Identification of receptor binding sites by competitive peptide mapping: phages T1, T5, and φ80 and colicin M bind to the gating loop of FhuA. J. Bacteriol. 177:694-98
55. Kimura M. 1983. The Neutral Theory of Molecular Evolution. Cambridge: Cambridge Univ. Press
56. Kreitman M. 1983. Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304:412-17
57. Kuroda K, Kageyama M. 1981. Comparative study of F-type pyocins of Pseudomonas aeruginosa. J. Biochem. 89:1721-36
58. Lenski RE. 1988. Dynamics of interactions between bacteria and virulent phage. Adv. Microb. Ecol. 10:1-44
59. Lipuma J, Richman H, Stull T. 1990. Haemocin, the bacteriocin produced by Haemophilus influenzae species distribution and role in colonization. Infect. Immun. 58:1600-5
60. Lloubes RP, Chartier MJ, Journet AM, Varenne SG, Lazdunski CJ. 1984. Nucleotide sequence of the gene for the immunity protein to colicin A; analysis of codon usage of immunity proteins as compared to colicins. Eur. J. Biochem. 144:73-78
61. Maher DJ, Whelan K, Nuttall D, Colleran E. 1989. The extent of colicin B resistance among IncH plasmids. Microbios Lett. 41:143-49
62. Mankovich JA, Hsu C, Konisky J. 1986. DNA and amino acid sequence analysis of structural and immunity genes of colicins Ia and Ib. J. Bacteriol. 168:228-36
63. Masaki H. 1991. Identification of a unique specificity determinant of the colicin E3 immunity protein. Gene 107:133-38
64. McDonald J, Kreitman M. 1991. Adaptive protein evolution at the adh locus in Drosophila. Nature 351:652-54
65. Oren A. 1993. Ecology of extremely halophilic microorganisms. In The Bioogy of Halophilic Bacteria, ed. R Vreeland, L Hochstein, p. 26. Boca Raton, FL: CRC Press
66. Osborne M, Lian L, Wallis R, Reilly A, James R, et al. 1994. Sequential assignments and identification of secondary structure elements of the colicin E9 immunity protein in solution by homonuclear and heteronuclear NMR. Biochemistry 33:12347-55
67. Oschlager T, Schramm E, Braun V. 1984. Cloning and expression of the activity and immunity genes of colicins B and M on ColBM plasmids. Mol. Gen. Genet. 196:482-87
68. Padilla C, Salazar M, Faundez O. 1992. Range of action and genetic bacteriocin codification of Pseudomonas aeruginosa isolated from three different ecological niches. J. Appl. Bacteriol. 73:497-500
69. Pilsl H, Braun V. 1995. Novel colicin 10: assignment of four domains to TonB- and TolC-dependent uptake via the Tsx receptor and to pore formation. Mol. Microbiol. 16:57-67
70. Pilsl H, Braun V. 1995. Strong function-related homology between pore-forming colicins K and 5. J. Bacteriol. 177:6973-77
71. Pugsley A. 1984. The ins and outs of colicins. Microbiol. Sci. 1:168-75, 203-5
72. Pugsley A. 1985. Escherichia coli K12 strains for use in the identification and characterization of colicins. J. Gen. Microbiol. 131:369-76
73. Pugsley AP. 1988. The immunity and lysis genes of colN plasmid pCHAP4. Mol. Gen. Genet. 211:335-41
74. Pugsley AP, Oudega B. 1987. Methods for studying colicins and their plasmids. In Plasmids, ed. KG Hardy, pp. 105-61. Oxford: IRL Press
75. Rakin A, Boolgokowa E, Heesemann J. 1996. Structural and functional organisation of the Yersinia pestis bacteriocin pesticin gene cluster. Microbiology 142: 3415-24
76. Riley MA. 1993. Molecular mechanisms of colicin evolution. Mol. Biol. Evol. 10: 1380-95
77. Riley MA. 1993. Positive selection for colicin diversity in bacteria. Mol. Biol. Evol. 10:1048-59
78. Riley MA, Gordon DM. 1992. A survey of col plasmids in natural isolates of Escherichia coli and an investigation into the stability of col-plasmid lineages. J. Gen. Microbiol 138:1345-52
79. Riley MA, Gordon DM. 1995. Ecology and evolution of bacteriocins. J. Ind. Microbiol. 17:155-58
80. Riley MA, Tan Y, Wang J. 1994. Nucleotide polymorphism in colicin E1 and Ia plasmids from natural isolates of Escherichia coli. Proc. Natl. Acad. Sci. USA 91:11276-80
81. Rodriguez-Valera F, Juez G, Kushner DJ. 1982. Halocins: salt dependent bacteriocins produced by extremely halophilic rods. Can. J. Microbiol. 28:151-54
82. Roos U, Harkness RE, Braun V. 1989. Assembly of colicin genes from a few DNA fragments. Nucleotide sequence of colicin D. Mol. Microbiol. 3:891-902
83. Sano Y, Kagemaya M. 1993. A novel transposon-like structure carries the genes for pyocin AP41; a Pseudomonas aeruginosa bacteriocin with a DNAse homology to E2 group colicins. Mol. Gen. Genet. 237:161-70
84. Sano Y, Kobayashi M, Kagemaya M. 1993. Molecular structures and functions of pyocins S1 and S2 in Pseudomonas aeruginosa. J. Bacteriol. 175:2907-16
85. Sano Y, Matsui H, Kobayashi M, Kageyama M. 1990. Pyocins S1 and S2, bacteriocins of Pseudomonas aeruginosa. In Pseudomonas: Biotransformations, Pathogenesis, and Evolving Biotechnology, ed. S Silver, pp. 352-58. Washington. DC: Am. Soc. Microbiol.
86. Schramm E, Mende J, Braun V, Kamp R. 1987. Nucleotide sequence of the colicin B activity gene cba: consensus pentapeptide among TonB-dependent colicins and receptors. J. Bacteriol. 169:3350-57
87. Schramm E, Olschlager T, Troger W, Braun V. 1988. Sequence, expression and localization of the immunity protein for colicin B. Mol. Gen. Genet. 211:176-82
88. Shand R, Price L, O'Connor. 1998. Halocins: protein antibiotics from hypersaline environments. In Microbiology and Biogeochemistry of Hypersaline Environments, ed. A Oren. Boca Raton, FL: CRC Press
89. Smajs D, Pilsl H, Braun V. 1997. Colicin U, a novel colicin produced by Shigella baydii. J. Bacteriol. 179:4919-28
90. Smarda J. 1992. Resistance and tolerance of bacteria to E colicins. In Bacteriocins, Microcins, and Lantibiotics, ed. R James, C Lazdunski, F Pattus, pp. 493-502. Berlin: Springer-Verlag
91. Smith D, Dworkin M. 1994. Territorial interactions between two myxococcus species. J. Bacteriol. 176:1201-5
92. Stevens K, Klapes N, Sheldon B, Klaenhammer T. 1992. Antimicrobial action of nisin against Salmonella typhimurium lipopolysaccharide mutants. Appl. Environ. Microbiol. 58:1786-88
93. Stevens K, Sheldon B, Klapes N, Klaenhammer T. 1991. Nisin treatment for inactivation of Salmonells species and other gram-negative bacteria. Appl. Environ. Microbiol. 57:3613-15
94. Stevens K, Sheldon B, Klapes N, Klaenhammer T. 1992. Effect of treatment conditions on nisin inactivation of gram negative bacteria. J. Food Prot. 55:763-66
95. Stoltzfus A, Leslie JF, Milkman R. 1988. Molecular evolution of the Escherichia coli chromosome. 1. Analysis of structure and natural variation in a previously uncharacterized region between trp and tonB. Genetics 120:345-58
96. Streelman A, Snyder I, Six E. 1970. Modifying effect of colicin on experimental Shigella keratoconjunctivitis. Infect. Immun. 2:15-23
97. Tan Y, Riley MA. 1995. Rapid invasion of colicinogenic bacteria with novel immunity functions. Microbiology 142:2175-80
98. Tan Y, Riley MA. 1997. Nucleotide polymorphism in colicin E2 gene clusters: evidence for nonneutral evolution. Mol. Biol. Evol. 14:666-73
99. Tan Y, Riley MA. 1997. Positive selection and recombination: major molecular mechanisms in colicin diversification. TREE 12:348-51
100. Torreblanca M, Meseguer I, Rodriguez-Valera F. 1989. Halocin H6, a bacteriocin from Haloferax gibbonsii. J. Gen. Microbiol. 135:2655-61
101. Torreblanca M, Meseguer I, Ventosa A. 1994. Production of halocin is a practically universal feature of archael halophilic rods. Lett. Appl. Microbiol. 19: 201-5
102. Vaughan E, Caplice E, Looney R, O'Rourke N, Coveney H, et al. 1994. Isolation from food sources, of lactic acid bacteria that produced antimicrobials. J. Appl. Microbiol. 76:118-23
103. Viejo M, Gargallo D, Ferrer S, Enfedaque J, Regue M. 1992. Cloning and DNA sequence analysis of a bacteriocin gene of Serratia marcescens. J. Gen. Microbiol. 138:1737-43
104. Vuyst LD, Vandamme E, eds. 1994. Bacteriocins of Lactic Acid Bacteria, p. 539. London: Blackie
105. Wallis R, Leung K, Pommer A, Videler H, Moore G, et al. 1995. Protein-protein interactions in colicin E9 DNase-immunity protein complexes. 2. Cognate and noncognate interactions that span the millimolar to femtomolar range. Biochemistry 34:13751-59
106. Wallis R, Moore G, James R, Kleanthous C. 1995. Protein-protein interactions in colicin E9 DNase-immunity protein complexes. 1. Diffusion-controlled association and femtomolar binding for the cognate complex. Biochemistry 34: 13743-50
107. Wallis R, Moore G, Kleanthous C, James R. 1992. Molecular analysis of the protein-protein interaction between the E9 immunity protein and colicin E9. Eur. J. Biochem. 210:923-30
108. Wallis R, Reilly A, Barnes K, Abell C, Campbell D, et al. 1994. Tandem overproduction and characterisation of the nuclease domain of colicin E9 and its cognate inhibitor protein Im9. Eur J. Biochem. 220:447-54
109. Wallis R, Reilly A, Rowe A, Moore G, James R, Kleanthous C. 1992. In-vivo and in-vitro characterisation of overproduced colicin E9 immunity protein. Eur. J. Biochem. 207:687-95
110. Webster R. 1991. The toi gene products and the import of macromolecules into Escherichia coli. Mol. Microbiol. 5:1005-11
111. Weiner M, Freyman D, Ghosh P, Stroud R. 1997. Crystal structure of colicin Ia. Nature 385:461-64
112. Whelan KF, Colleran E, Taylor DE. 1995. Phage inhibition, colicin resistance, and tellurite resistance are encoded by a single cluster of genes on the IncHI2 plasmid R478. J. Bacteriol. 177:5016-27
113. Zhao D, Zappala A, Djebli A, Shoham M. 1997. Crystal structure of colicin E-3 immunity protein. Biophys. J 72:229
114. Zinder ND. 1973. Resistance of colicins E3 and K induced by infection with bacteriophage fl. Proc. Natl. Acad. Sci. USA 70:3160-64
115. Ziv G. 1971. Pyocin Typing as an epidemiological marker in Pseudomonas aeruginosa mastitis in cattle. J. Hyg. 69: 171-77
116. Zund P, Lebek G. 1980. Generation time-prolonging R plasmids: correlation between increase in the generation time of Escherichia coli caused by R plasmids and their molecular size. Plasmid 3:65-69