'Big things in small packages: The genetics of filamentous phage and effects on fitness of their host'

FEMS Microbiology Reviews

Volumn 39, Issue 4, 2015, Pages 465-487

  Mai Prochnow, Anne ^a,d   Hui, Janice Gee Kay ^a   Kjelleberg, Staffan ^a,b   Rakonjac, Jasna ^c   McDougald, Diane ^a,b   Rice, Scott A ^a,b  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^c MASSEY UNIVERSITY   (New Zealand)

^d CSIRO   (Australia)

Author keywords

Bacteriophage; Biotechnology; CTX phage; Escherichia coli; Ff; Filamentous phage; Inoviridae; Inovirus; M13; Pseudomonas; Vibrio cholerae

Indexed keywords

CHOLERA TOXIN; INTEGRASE;

BACTERIOPHAGE; BIOFILM; BIOTECHNOLOGY; DEEP SEA SPECIES; ENTEROBACTERIACEAE; ESCHERICHIA COLI; GENE FUNCTION; GENOME ANALYSIS; GRAM NEGATIVE BACTERIUM; HORIZONTAL GENE TRANSFER; HOST; NEISSERIA; NONHUMAN; PHENOTYPE; PHYLOGENY; PROPHAGE; PROPIONIBACTERIUM; PSEUDOMONAS AERUGINOSA; RALSTONIA; RALSTONIA SOLANACEARUM; REVIEW; SHEWANELLA; STENOTROPHOMONAS; STRESS; THERMUS; VIBRIO CHOLERAE; VIRAL GENETICS; VIRION; VIRUS GENE; VIRUS INFECTION; VIRUS REPLICATION; VIRUS STRAIN; XANTHOMONAS; XANTHOMONAS CAMPESTRIS; XYLELLA; BACTERIUM; GENETICS; HOST PATHOGEN INTERACTION; HUMAN; INOVIRUS; MICROBIAL VIABILITY; PATHOGENICITY; VIROLOGY;

BACTERIA; BIOFILMS; GENES, VIRAL; HOST-PATHOGEN INTERACTIONS; HUMANS; INOVIRUS; MICROBIAL VIABILITY; PHENOTYPE;

EID: 84942577529     PISSN: 01686445     EISSN: 15746976     Source Type: Journal    
DOI: 10.1093/femsre/fuu007     Document Type: Review

References (209)

1. Addy HS, Askora A, Kawasaki T, et al. Loss of virulence of the phytopathogen Ralstonia solanacearum through infection by phiRSM filamentous phages. Phytopathology 2012a;102: 469-77.
2. Addy HS, Askora A, Kawasaki T, et al. The filamentous phage varphiRSS1 enhances virulence of phytopathogenic Ralstonia solanacearum on tomato. Phytopathology 2012b;102:244-51.
3. Antonara S, Chafel RM, LaFrance M, et al. Borrelia burgdorferi adhesins identified using in vivo phage display. Mol Microbiol 2007;66:262-76.
4. Askora A, Abdel-Haliem ME, Yamada T. Site-specific recombination systems in filamentous phages. Mol Genet Genomics 2012;287:525-30.
5. Askora A, Kawasaki T, Fujie M, et al. Resolvase-like serine recombinase mediates integration/excision in the bacteriophage [phi]RSM. J Biosci Bioeng 2011;111:109-16.
6. Askora A, Kawasaki T, Fujie M, et al. Insights into the diversity of φRSM phages infecting strains of the phytopathogen Ralstonia solanacearum complex: regulation and evolution. Mol Gen Genomics 2014;289:589-98.
7. Askora A, Kawasaki T, Usami S, et al. Host recognition and integration of filamentous phage φRSM in the phytopathogen, Ralstonia solanacearum. Virology 2009;384:69-76.
8. Ausmees N, Jacobsson K, Lindberg M. A unipolarly located, cell-surface-associated agglutinin, RapA, belongs to a family of Rhizobium-adhering proteins (Rap) in Rhizobium leguminosarum bv. trifolii. Microbiology 2001;147:549-59.
9. Bakhshi B, Pourshafie MR, Navabakbar F, et al. Genomic organisation of the CTX element among toxigenic Vibrio cholerae isolates. Clin Microbiol Infec 2008;14:562-8.
10. Baudry B, Fasano A, Ketley J, et al. Cloning of a gene (zot) encoding a new toxin produced by Vibrio cholerae. Infect Immun 1992;60:428-34.
11. Bayer ME, Bayer MH. Effects of bacteriophage fd infection on Escherichia coli HB11 envelope: a morphological and biochemical study. J Virol 1986;57:258-66.
12. Bentancor LV, Mejias MP, Pinto A, et al. Promoter sequence of shiga toxin 2 (Stx2) is recognized in vivo, leading to production of biologically active Stx2. Mbio 2013;4:501-13.
13. Bille E, Zahar JR, Perrin A, et al. A chromosomally integrated bacteriophage in invasive meningococci. J Exp Med 2005;201:1905-13.
14. Boeke J, Model P, Zinder N. Effects of bacteriophage f1 gene III protein on the host cell membrane. Mol Gen Genet 1982;186:185-92.
15. Bradbury ARM, Marks JD. Antibodies from phage antibody libraries. J Immunol Methods 2004;290:29-49.
16. Bradley DE. Length of filamentous Pseudomonas aeruginosa bacteriophage Pf. J Gen Virol 1973;20:249-51.
17. Brissette JL, Russel M, Weiner L, et al. Phage shock protein, a stress protein of Escherichia coli. P Natl Acad Sci USA 1990;87:862-6.
18. Campos J, Martinez E, Izquierdo Y, et al. VEJ{phi}, a novel filamentous phage of Vibrio cholerae able to transduce the cholera toxin genes. Microbiology 2010;156:108-15.
19. Campos J, Martinez E, Suzarte E, et al. VGJ phi, a novel filamentous phage of Vibrio cholerae, integrates into the same chromosomal site as CTX phi. J Bacteriol 2003;185: 5685-96.
20. Castang S, Dove SL. Basis for the essentiality of H-NS family members in Pseudomonas aeruginosa. J Bacteriol 2012;194:5101-9.
21. Chen J, Civerolo EL. Morphological evidence for phages in Xylella fastidiosa. Virol J 2008;5:75.
22. Chen J, Xie G, Han S, et al. Whole genome sequences of two Xylella fastidiosa strains (M12 and M23) causing almond leaf scorch disease in California. J Bacteriol 2010;192:4534.
23. Chen Y-Y, Wu C-C, Hsu J-L, et al. Surface rigidity change of Escherichia coli after filamentous bacteriophage infection. Langmuir 2009;25:4607-14.
24. Cheng CM, Wang HJ, Bau HJ, et al. The primary immunity determinant in modulating the lysogenic immunity of the filamentous bacteriophage cf. J Mol Biol 1999;287:867-76.
25. Cheng JL, Zhou X, Chou TF, et al. Identification of the amino acid-AZT-phosphoramidase by affinity T7 phage display selection. Bioorg Med Chem Lett 2009;19:6379-81.
26. Choi S, Dunams D, Jiang SC. Transfer of cholera toxin genes from O1 to non-O1/O139 strains by vibriophages from California coastal waters. J Appl Microbiol 2010;108:1015-22.
27. Chopin MC, Rouault A, Ehrlich SD, et al. Filamentous phage active on the gram-positive bacterium Propionibacterium freudenreichii. J Bacteriol 2002;184:2030-3.
28. Chouikha I, Charrier L, Filali S, et al. Insights into the infective properties of YpfPhi, the Yersinia pestis filamentous phage. Virology 2010;407:43-52.
29. Chung WJ, Oh JW, Kwak K, et al. Biomimetic self-templating supramolecular structures. Nature 2011;478:364-8.
30. Ciric M, Moon CD, Leahy SC, et al. Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. BMC Genomics 2014, 15:356.
31. Clackson T, Hoogenboom HR, Griffiths AD, et al. Making antibody fragments using phage display libraries. Nature 1991;352:624-8.
32. Crowther RA. Structure of bacteriophage Pf1. Nature 1980;286:440-1.
33. Dang X, Qi J, Klug MT, et al. Tunable localized surface plasmonenabled broadband light-harvesting enhancement for highefficiency panchromatic dye-sensitized solar cells. Nano Lett 2013;13:637-42.
34. Das B, Bischerour J, Barre FX. VGJφ integration and excision mechanisms contribute to the genetic diversity of Vibrio cholerae epidemic strains. P Natl Acad Sci USA 2011;108: 2516-21.
35. Davis BM, Lawson EH, Sandkvist M, et al. Convergence of the secretory pathways for cholera toxin and the filamentous phage, CTXφ. Science 2000;288:333-5.
36. Davis BM, Moyer KE, Boyd EF, et al. CTX prophages in classical biotype Vibrio cholerae: Functional phage genes but dysfunctional phage genomes. J Bacteriol 2000;182:6992-8.
37. Davis BM, Waldor MK. Filamentous phages linked to virulence of Vibrio cholerae. Curr Opin Microbiol 2003;6:35-42.
38. Day LA. Family Inoviridae. San Diego: Elsevier Academic Press, 2011.
39. Delbrock M. Bacterial viruses or bacteriophages. Biol Rev 1946;21:30-40.
40. Derbise A, Chenal-Francisque V, Pouillot F, et al. A horizontally acquired filamentous phage contributes to the pathogenicity of the plague bacillus. Mol Microbiol 2007;63:1145-57.
41. Dereeper A, Guignon V, Blanc G, et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 2008;36:W465-9.
42. Devlin JJ, Panganiban LC, Devlin PE. Random peptide libraries: a source of specific protein binding molecules. Science 1990;249:404-6.
43. Di Niro R, Sulic AM, Mignone F, et al. Rapid interactome profiling by massive sequencing. Nucleic Acids Res 2010;38:e110.
44. Di Pierro M, Lu R, Uzzau S, et al. Zonula occludens toxin structure-function analysis: identification of the fragment biologically active on the tight junctions and of the zonulin receptor binding domain. J Biol Chem 2001;276: 19160-5.
45. Dias-Neto E, Nunes DN, Giordano RJ, et al. Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis. Plos One 2009;4:e8338.
46. Endemann H, Model P. Location of filamentous phage minor coat proteins in phage and in infected cells. J Mol Biol 1995;250:496-506.
47. Faruque SM, Mekalanos JJ. Pathogenicity islands and phages in Vibrio cholerae evolution. Trends Microbiol 2003;11:505-10.
48. Faruque SM, Mekalonos JJ. Phage-bacterial interactions in the evolution of toxigenic Vibrio cholerae. Virulence 2014;3:556-65.
49. Fasano A, Baudry B, Pumplin DW, et al. Vibrio cholerae produces a second enterotoxin, which affects intestinal tight junctions. P Natl Acad Sci USA 1991;88:5242-6.
50. Feng JN, Model P, Russel M. A trans-envelope protein complex needed for filamentous phage assembly and export. Mol Microbiol 1999;34:745-55.
51. Feng JN, Russel M, Model P. A permeabilized cell system that assembles filamentous bacteriophage. P Natl Acad Sci USA 1997;94:4068-73.
52. Fozo EM, Hemm MR, Storz G. Small toxic proteins and the antisense RNAs that repress them. Microbiol Mol Biol Rev 2008;72:579-89.
53. Frost LS. Bacterial conjugation. In: Clewell DB (ed). Conjugative Pili and Pilus-Specific Phages. New York: Plenum Press, 1993, 189-221.
54. Fullner KJ, Boucher JC, Hanes MA, et al. The contribution of accessory toxins of Vibrio cholerae O1 El Tor to the proinflammatory response in a murine pulmonary cholera model. J Exp Med 2002;195:1455-62.
55. Gailus V, Rasched I. The adsorption protein of bacteriophage fd and its neighbour minor coat protein build a structural entity. Eur J Biochem 1994;222:927-31.
56. Gerdes K. Toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress. J Bacteriol 2000;182:561-72.
57. Gerdes K, Christensen SK, Lobner-Olesen A. Prokaryotic toxinantitoxin stress response loci. Nat Rev Microbiol 2005;3: 371-82.
58. Goeders N, Van Melderen L. Toxin-antitoxin systems as multilevel interaction systems. Toxins 2014;6:304-24.
59. Goff SP. Retroviral reverse transcriptase: synthesis, structure and function. J Acq Imm Def 1990;3:817-31.
60. Grant RA, Lin TC, Koningsberg V, et al. Structure of the filamentous bacteriophage f1. J Biol Chem 1981;256:539-46.
61. Gueguen E, Savitzky DC, Darwin AJ. Analysis of the Yersinia enterocolitica PspBC proteins defines functional domains, essential amino acids and new roles within the phage-shockprotein response. Mol Microbiol 2009;74:619-33.
62. Hagemann M, Hasse D, Berg G. Detection of a phage genome carrying a zonula occludens like toxin gene (zot) in clinical isolates of Stenotrophomonas maltophilia. Arch Microbiol 2006;185:449-58.
63. Haigh NG, Webster RE. The pI and pXI assembly proteins serve separate and essential roles in filamentous phage assembly. J Mol Biol 1999;293:1017-27.
64. Hansen MR, Rance M, Pardi A. Observation of long-range 1H-1H distances in solution by dipolar coupling interactions. J Am Chem Soc 1989;120:11210-1.
65. Hassan F, Kamruzzaman M, Mekalanos JJ, et al. Satellite phage TLC[phgr] enables toxigenic conversion by CTX phage through dif site alteration. Nature 2010;467440: 982-5.
66. Heilpern AJ, Waldor MK. pIIICTX, a predicted CTXφ minor coat protein, can expand the host range of coliphage fd to include Vibrio cholerae. J Bacteriol 2003;185:1037-44.
67. Hess GT, Cragnolini JJ, Popp MW, et al. M13 bacteriophage display framework that allows sortase-mediated modification of surface-accessible phage proteins. Bioconjugate Chem 2012;23:1478-87.
68. Higashitani A, Higashitani N, Horiuchi K. Minus-strand origin of filamentous phage versus transcriptional promoters in recognition of RNA polymerase. P Natl Acad Sci USA 1997;94:2909-14.
69. Hill DF, Short NJ, Perham RN, et al. DNA sequence of the filamentous bacteriophage Pf1. J Mol Biol 1991;218:349-64.
70. Hoang TT, Kutchma AJ, Becher A, et al. Integration-proficient plasmids for Pseudomonas aeruginosa: site-specific integration and use for engineering of reporter and expression strains. Plasmid 2000;43:59-72.
71. Hobbs M, Mattick JS. Common components in the assembly of type-4 fimbriae, DNA transfer systems, filamentous phage and protein-secretion apparatus-a general system for the formation of surface-associated protein complexes. Mol Microbiol 1993;10:233-43.
72. Hofschneider PH. Untersuchungen uber kleine E. coli K 12 bakteriophagen 1 und 2 Mitteilung. Z Naturforsch Pt B 1963;B 18:203.
73. Hohn B, Schutz HV, Marvin DA. Filamentous bacterial viruses. II. Killing of bacteria by abortive infection with Fd. J Mol Biol 1971;56:155-65.
74. Horabin JI, Webster RE. Morphogenesis of F1 filamentous bacteriophage-increased expression of gene-I inhibits bacterial-growth. J Mol Biol 1986;188:403-13.
75. Horabin JI, Webster RE. An amino-acid sequence which directs membrane insertion causes loss of membrane-potential. J Biol Chem 1988;263:11575-83.
76. Huang Y, Chiang CY, Lee SK, et al. Programmable assembly of nanoarchitectures using genetically engineered viruses. Nano Lett 2005;5:1429-34.
77. Huber KE, Waldor MK. Filamentous phage integration requires the host recombinases XerC and XerD. Nature 2002;417: 656-9.
78. Hufton SE, Moerkerk PT, Meulemans EV, et al. Phage display of cDNA repertoires: the pVI display system and its applications for the selection of immunogenic ligands. J Immunol Methods 1999;231:39-51.
79. Hui JGK. The genes and factors that drive the conversion of the Pseudomonas aeruginosa Pf4 prophage into the superinfective form. Ph. D. Thesis. University of New South Wales Sydney, Australia 2014.
80. Ikema M, Honma Y. A novel filamentous phage, fs-2, of Vibrio cholerae O139. Microbiology 1998;144:1901-6.
81. Ishimoto KS, Lory S. Formation of pilin in Pseudomonas aeruginosa requires the alternative sigma-factor (Rpon) of RNApolymerase. P Natl Acad Sci USA 1989;86:1954-7.
82. Iyer R, Darby V, Holland IB. Changes in membrane proteins of Escherichia coli K12 mediated by bacteriophage IKe-specific plasmids. Biochim Biophys Acta 1976;453:311-8.
83. Jankovic D, Collett MA, Lubbers MW, et al. Direct selection and phage display of a Gram-positive secretome. Genome Biol 2007;8:R266.
84. Jian H, Xiao X,Wang F. Role of filamentous phage SW1in regulating the lateral flagella of Shewanella piezotolerans strain WP3 at low temperatures. Appl Environ Microb 2013;79:7101-9.
85. Jian H, Xu J, Xiao X, et al. Dynamicmodulation of DNA replication and gene transcription in deep-sea filamentous phage SW1 in response to changes of host growth and temperature. PLoS One 2012;7:e41578.
86. Johnson JA, Morris JGJ, Kaper JB. Gene encoding zonula occludens toxin (zot) does not occur independently from cholera entertoxin genes (ctx) in Vibrio cholerae. J Clin Microbiol 1993;31:732-3.
87. Joly N, Engl C, Jovanovic G, et al. Managing membrane stress: the phage shock protein (Psp) response, from molecular mechanisms to physiology. FEMS Microbiol Rev 2010;34: 797-827.
88. Kamruzzaman M, Robins WP, Bari SM, et al. RS1 satellite phage promotes diversity of toxigenic Vibrio cholerae by driving CTX prophage loss and elimination of lysogenic immunity. Infect Immun 2014;82:3636-43.
89. Kar S, Ghosh RK, Ghosh AN, et al. Integration of the DNA of a novel filamentous bacteriophage VSK from Vibrio cholerae 0139 into the host chromosomal DNA. FEMS Microbiol Lett 1996;145:17-22.
90. Karaolis DKR, Somara S, Maneval DR, et al. A bacteriophage encoding a pathogenicity island, a type-IV pilus and a phage receptor in cholera bacteria. Nature 1999;399:375-9.
91. Karlsson F, Malmborg-Hager AC, Albrekt AS, et al. Genome-wide comparison of phage M13-infected vs. uninfected Escherichia coli. Can J Microbiol 2005;51:29-35.
92. Kawai M, Uchiyama I, Kobayashi I. Genome comparison in silico in Neisseria suggests integration of filamentous bacteriophages by their own transposase. DNA Res 2005;12: 389-401.
93. Kawasaki T, Nagata S, Fujiwara A, et al. Genomic characterization of the filamentous integrative bacteriophages phi RSSI and phi RSMI, which infect Ralstonia solanacearum. J Bacteriol 2007;189:5792-802.
94. Khatoon H, Iyer RV, Iyer VN. A new filamentous bacteriophage with sex-factor specificity. Virology 1972;48:145-55.
95. Kim AY, Blaschek HP. Isolation and characterization of a filamentous viruslike particle from Clostridium acetobutylicum NCIB 6444. J Bacteriol 1991;173:530-5.
96. Kirov SM, Webb JS, O'May CY, et al. Biofilm differentiation and dispersal inmucoid Pseudomonas aeruginosa isolates frompatients with cystic fibrosis. Microbiology 2007;153:3264-74.
97. Klockgether J, Munder A, Neugebauer J, et al. Genome diversity of Pseudomonas aeruginosa PAO1 laboratory strains. J Bacteriol 2010;192:1113-21.
98. Koonin EV. The second cholera toxin, Zot, and its plasmidencoded and phage-encoded homologues constitute a group of putative ATPases with an altered purine NTP-binding motif. FEBS Lett 1992;312:3-6.
99. Krogh A, Larsson B, von Heijne G, et al. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001;305:567-80.
100. Kunkel TA, Bebenek K, Mcclary J. Efficient site-directed mutagenesis using uracil-containing DNA. Method Enzymol 1991;204:125-39.
101. Kuo MY, Yang MK, Chen WP, et al. High-frequency interconversion of turbid and clear plaque strains of bacteriophage f1 and associated host cell death. Can J Microbiol 2000;46:841-7.
102. Kuo TT, Chiang CC, Chen SY, et al. A long lytic cycle in filamentous phage Cf1tv infecting Xanthomonas campestris pv. citri. Arch Virol 1994;135:253-64.
103. Kuo T-T, Tan M-S, Su M-T, et al. Complete nucleotide sequence of filamentous phage Cf1c from Xanthomonas campestris pv. citri. Nucleic Acids Res 1991;19:2498.
104. Lee JW, Song J, HwangMP, et al. Nanoscale bacteriophage biosensors beyond phage display. Int J Nanomed 2013;8:3917-25.
105. Lee YJ, Yi H, Kim WJ, et al. Fabricating genetically engineered high-power lithium-ion batteries usingmultiple virus genes. Science 2009;324:1051-5.
106. Lengeling A, Mahajan A, Gally DL. Bacteriophages as pathogens and immune modulators? mBio 2013;4:e00868.
107. Li CR, Wally H, Miller SJ, et al. The multifaceted proteins MvaT and MvaU, members of the H-NS family, control arginine metabolism, pyocyanin synthesis, and prophage activation in Pseudomonas aeruginosa PAO1. J Bacteriol 2009;191: 6211-8.
108. Li M, Kotetishvili M, Chen Y, et al. Comparative genomic analyses of the vibrio pathogenicity island and cholera toxin prophage regions in nonepidemic serogroup strains of Vibrio cholerae. Appl Environ Microb 2003;69:1728-38.
109. Lin JY,Wu CC, Kue TT. Amino acid analysis of the coat protein of the filamentous bacterial virus xf from Xanthomonas oryzae. Virology 1971;45:38-41.
110. Liu SS, Han WY, Sun CJ, et al. Subtractive screening with the Mycobacterium tuberculosis surface protein phage display library. Tuberculosis 2011;91:579-86.
111. Loeb T. Isolation of a bacteriophage specific for the F+ and Hfr mating types of Escherichia coli K-12. Science 1960;131:932-3.
112. Lopez J, Webster RE. Morphogenesis of filamentous bacteriophage-F1-orientation of extrusion and production of polyphage. Virology 1983;127:177-93.
113. Lu TK, Collins JJ. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. P Natl Acad Sci USA 2009;106:4629-34.
114. Luiten RG, Putterman DG, Schoenmakers JG, et al. Nucleotide sequence of the genome of Pf3, an IncP-1 plasmid-specific filamentous bacteriophage of Pseudomonas aeruginosa. J Virol 1985;56:268-76.
115. Luiten RGM, Schoenmakers JGG, Konings RNH. The major coat protein gene of the filamentous Pseudomonas aeruginosa phage-pf3-absence of an n-terminal leader signal sequence. Nucleic Acids Res 1983;11:8073-85.
116. McElroy K, Hui J, Woo JKK, et al. Strain-specific, parallel evolution drives short-term diversification during Pseudomonas aeruginosa biofilm formation. P Natl Acad Sci USA 2014;111: E1419-27.
117. McLeod SM, Kimsey HH, Davis BM, et al. CTX and Vibrio cholerae: exploring a newly recognized type of phage-host cell relationship. Mol Microbiol 2005;57:347-56.
118. McLeod SM, Waldor MK. Characterization of XerC- and XerDdependent CTX phage integration in Vibrio cholerae. Mol Microbiol 2004;54:935-47.
119. Mao CB, Solis DJ, Reiss BD, et al. Virus-based toolkit for the directed synthesis of magnetic and semiconducting nanowires. Science 2004;303:213-7.
120. Marciano DK, Russel M, Simon SM. An aqueous channel for filamentous phage export. Science 1999;284:1516-9.
121. Marciano DK, Russel M, Simon SM. Assembling filamentous phage occlude pIV channels. P Natl Acad Sci USA 2001;98:9359-64.
122. Marvin DA. Filamentous phage structure, infection and assembly. Curr Opin Struc Biol 1998;8:150-8.
123. Marvin DA, Hoffmann-Berling H. Physical and chemical properties of two new small bacteriophages. Nature 1963;197:517-8.
124. Marvin DA, Hohn B. Filamentous bacterial viruses. Bacteriol Rev 1969;33:172-209.
125. Marvin DA, Pigram WJ,Wiseman RL, et al. Filamentous bacterial viruses. XIL. Molecular architecture of the class I (fd, If1, IKe) virion. J Mol Biol 1974;88:581-98.
126. Marvin DA, Symmons MF, Straus SK. Structure and assembly of filamentous bacteriophages. Prog Biophys Mol Biol 2014;114:80-122.
127. Maxson ME, Darwin AJ. PspB and PspC of Yersinia enterocolitica are dual function proteins: regulators and effectors of the phageshock-protein response. Mol Microbiol 2006;59:1610-23.
128. Merril CR, Geier MR, Petricci JC. Bacterial virus gene expression in human cells. Nature 1971;233:398-400.
129. Messing J. Cloning in M13-phage or howto use biology at its best. Gene 1991;100:3-12.
130. Meynell GG, Lawn AM. Filamentous phages specific for the I Sex Factor. Nature 1968;217:1184-6.
131. Minamishima Y, Takeya K, Ohnishi Y, et al. Physicochemical and biological properties of fibrous Pseudomonas bacteriophages. J Virol 1968;2:208-13.
132. Mooij MJ, Drenkard E, Llamas MA, et al. Characterization of the integrated filamentous phage Pf5 and its involvement in small-colony formation. Microbiology 2007;153:1790-8.
133. Moreira LM, DeSouza RF, Digiampietri LA, et al. Comparative analyses of Xanthomonas and Xylella complete genomes. OMICS 2005;9:43-76.
134. Mullen LM, Nair SP, Ward JM, et al. Phage display in the study of infectious diseases. Trends Microbiol 2006;14:141-7.
135. Murugaiyan S, Bae JY,Wu J, et al. Characterization of filamentous bacteriophage PE226 infecting Ralstonia solanacearum strains. J Appl Microbiol 2011;110:296-303.
136. Nakasone N, Honma Y, Toma C, et al. Filamentous phage fs1 of Vibrio cholerae O139. Microbiol Immunol 1998;42:237-9.
137. Nakasone N, Ikema M, Higa N, et al. A filamentous phage of Vibrio parahaemolyticus O3:K6 isolated in Laos. Microbiol Immunol 1999;43:385-8.
138. Nasu H, Iida T, Sugahara T, et al. A filamentous phage associated with recent pandemic Vibrio parahaemolyticus O3:K6 strains. J Clin Microbiol 2000;38:2156-61.
139. Nguyen DT, Nguyen BM, Tran HH, et al. Filamentous vibriophage fs2 encoding the rstC gene integrates into the same chromosomal region as the CTX phage. FEMS Microbiol Lett 2008;284:225-30.
140. Ogura T, Wilkinson AJ. AAA+superfamily ATPase: common structure-diverse function. Genes Cells 2001;6:575-97.
141. Oh J-W, Chung W-J, Heo K, et al. Biomimetic virus-based colourimetric sensors. Nat Commun 2014;5:3043.
142. Oppenheim AB, Kobiler O, Stavans J, et al. Switches in bacteriophage lambda development. Annu Rev Genet 2005;39:409-29.
143. Pederson DM, Welsh LC, Marvin DA, et al. The protein capsid of filamentous bacteriophage PH75 from Thermus thermophilus. J Mol Biol 2001;309:401-21.
144. Peeters BP, Peters RM, Schoenmakers JG, et al. Nucleotide sequence and genetic organization of the genome of the Nspecific filamentous bacteriophage IKe. Comparison with the genome of the F-specific filamentous phages M13, fd and f1. J Mol Biol 1985;181:27-39.
145. Peterson C, Winter WT, Dalack GW, et al. Structure of the filamentous bacteriophage, Pf3, by X-ray fiber diffraction. J Mol Biol 1982;162:877-81.
146. Petrova OE, Sauer K. SagS contributes to the motile-sessile switch and acts in concert with BfiSR to enable Pseudomonas aeruginosa biofilm formation. J Bacteriol 2011;193:6614-28.
147. Piekarowicz A, Kłyz A, Majchrzak M, et al. Neisseria gonorrhoeae filamentous phage NgoΦ6 is capable of infecting a variety of gram-negative bacteria. J Virol 2014;88:1002-10.
148. Piekarowicz A, Majchrzak M, Klyz A, et al. Analysis of the filamentous bacteriophage genomes integrated into Neisseria gonorrhoeae FA1090 chromosome. Pol J Microbiol 2006;55: 251-60.
149. Platt MD, Schurr MJ, Sauer K, et al. Proteomic, microarray, and signature-tagged mutagenesis analyses of anaerobic Pseudomonas aeruginosa at pH 6.5, likely representing chronic, late-stage cystic fibrosis airway conditions. J Bacteriol 2008;190:2739-58.
150. Pratt D, Tzagoloff H, Erdahl WS. Conditional lethal mutants of the small filamentous coliphage M13. I. Isolation, complementation, cell killing, time of cistron action. Virology 1966;30:397-410.
151. Quinones M, Kinsey HH, Waldor MK. LexA cleavage is required for CTX propahge induction. Mol Cell 2005;17:291-300.
152. Rakonjac J, Feng JN, Model P. Filamentous phage are released from the bacterial membrane by a two-step mechanism involving a short C-terminal fragment of pIII. J Mol Biol 1999;289:1253-65.
153. Rakonjac K, Bennett NJ, Spagnuolo J, et al. Filamentous bacteriophage: biology, phage display and nanotechnology applications. Curr Issues Mol Biol 2011;13:51-76.
154. Ray DS. Single-stranded DNA phages. In: Denhardt DT, Dressler D, Ray DS (eds). In Viva Replication of Filamentous Phage DNA. New York: Cold Spring Harbor Laboratory, 1978, 325-39.
155. Reichmann L, Holliger P. The C-terminal domain of TolA is the coreceptor for filamentous phage infection of E. coli. Cell 1997;90:351-60.
156. Rice SA, Lampson BC. Bacterial reverse transcriptase and ms-DNA. Virus Genes 1996;11:95-104.
157. Rice SA, Tan CH, Mikkelsen PJ, et al. The biofilm life cycle and virulence of Pseudomonas aeruginosa are dependent on a filamentous prophage. ISME J 2009;3:271-82.
158. Rodi DJ, Makowski L. Phage-display technology-finding a needle in a vast molecular haystack. Curr Opin Biotech 1999;10: 87-93.
159. Roy A, Mitra S. Increased fragility of Escherichia coli after infection with bacteriphage M13. J Virol 1970a;6:333-9.
160. Roy A, Mitra S. Susceptibility of E. coli K-12 to actinomycinD after infection with phage-M13. Nature 1970b;228:365-6.
161. Russel M. Filamentous phage assembly. Mol Microbiol 1991;5:1607-13.
162. Russel M. Moving through the membrane with filamentous phages. Trends Microbiol 1995;3:223-8.
163. Russel M, Kazmierczak B. Analysis of the structure and subcellular location of filamentous phage-Piv. J Bacteriol 1993;175:3998-4007.
164. Russel M, Kidd S, Kelley MR. An improved filamentous helper phage for generating single-stranded plasmid DNA. Gene 1986;45:333-8.
165. Russel M, Model P. The role of thioredoxin in filamentous phage assembly - construction, isolation, and characterization of mutant thioredoxins. J Biol Chem 1986;261:4997-5005.
166. Russel M, Model P. Genetic analysis of the filamentous bacteriophage packaging signal and of the proteins that interactwith it. Virology 1989;63:3284-95.
167. Russel M, Model P. Filamentous phage. In: Calendar RC (ed). The Bacteriophages. New York: Oxford University Press Inc., 2006, 146-60.
168. Salivar WO, Tzagoloff H, Pratt D. Some physical-chemical and biological properties of the rod-shaped coliphage M13. Virology 1964;24:359-71.
169. Sanchez T, Chen DTN, DeCamp SJ, et al. Spontaneous motion in hierarchically assembled active matter. Nature 2012;491: 431-4.
170. Sanger F, Coulson AR, Barrell BG, et al. Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing. J Mol Biol 1980;143:161-78.
171. Schwartz FM, Zinder ND. Morphological changes in Escherichia coli infected with the DNA bacteriophage fl. Virology 1968;34:352-5.
172. Seo J, Brencic A, Darwin AJ. Analysis of secretin-induced stress in Pseudomonas aeruginosa suggests prevention rather than response and identifies a novel protein involved in secretin function. J Bacteriol 2009;191:898-908.
173. Sha Y, Melcher U, Davis RE, et al. Common elements of spiroplasma plectroviruses revealed by nucleotide sequence of SVTS2. Virus Genes 2000;20:47-56.
174. Sharma P, Ward A, Gibaud T, et al. Hierarchical organization of chiral rafts in colloidal membranes. Nature 2014;513:77-80.
175. Shieh GJ, Charng YC, Yang BC, et al. Identification and nucleotide sequence analysis of an open reading frame involved in highfrequency conversion of turbid to clear plaque mutants of filamentous phage Cf1t. Virology 1991;185:316-22.
176. Smith GP. Filamentous fusion phage-novel expression vectors that display cloned antigens on the virion surface. Science 1985;228:1315-7.
177. Snell DT, Offord RE. The amino acid sequence of the B-protein of bacteriophage ZJ-2. Biochem J 1972;127:167-78.
178. Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005;21:951-60.
179. Spagnuolo J, Opalka N, Wen WX, et al. Identification of the gate regions in the primary structure of the secretin pIV. Mol Microbiol 2010;76:133-50.
180. Stassen AP, Schoenmakers EF, Yu M, et al. Nucleotide sequence of the genome of the filamentous bacteriophage I2-2: module evolution of the filamentous phage genome. J Mol Evol 1992;34:141-52.
181. Stover CK, Pham XQ, Erwin AL, et al. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 2000;406:959-64.
182. Takeya K, Amako K. A rod-shaped Pseudomonas phage. Virology 1966;28:163-5.
183. Tam R, Saier MHJ. Structural, functional and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol Rev 1993;57:320-46.
184. Tay M. Identification of the secondary phage in Pseudomonas aeruginosa and determination of its role in biofilm development. Ph.D. Thesis. University of New South Wales Sydney, Australia, 2008.
185. Trucksis M, Galen JE, Michalski J, et al. Accessory cholera enterotoxin (Ace), the 3rd toxin of a Vibrio Cholerae virulence cassette. P Natl Acad Sci USA 1993;90:5267-71.
186. Tseng YH, Lo MC, Lin KC, et al. Characterization of filamentous bacteriophage phi Lf from Xanthomonas campestris pv. campestris. J Gen Virol 1990;71(Pt 8):1881-4.
187. van Houten NE, Henry KA, Smith GP, et al. Engineering filamentous phage carriers to improve focusing of antibody responses against peptides. Vaccine 2010;28: 2174-85.
188. Varani AM, Monteiro-Vitorello CB, Nakaya HI, et al. The role of prophage in plant-pathogenic bacteria. Annu Rev Phytopathol 2013;51:429-51.
189. Vieira J, Messing J. Production of single-stranded plasmid DNA. Method Enzymol 1987;153:3-11.
190. Waites KB, Canupp KC, DeVivo MJ. Efficacy and tolerance of norfloxacinin treatment of complicated urinary tract infection in outpatients with neurogenic bladder secondary to spinal cord injury. Urology 1991;38:589-96.
191. Waldor MK, Mekalanos JJ. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 1996;272:1910-4.
192. Waldor MK, Rubin EJ, Pearson GD, et al. Regulation, replication, and integration functions of the Vibrio cholerae CTX are encoded by region RS2. Mol Microbiol 1997;24:917-26.
193. Wang F,Wang FP, Li Q, et al. A novel filamentous phage fromthe deep-sea bacterium Shewanella piezotolerans WP3 is induced at low temperature. J Bacteriol 2007;189:7151-3.
194. Wang X, Wood TK. Toxin-antitoxin systems influence biofilm and persister cell formation and the general stress response. Appl Environ Microb 2011;77:5577-83.
195. Webb JS, Lau M, Kjelleberg S. Bacteriophage and phenotypic variation in Pseudomonas aeruginosa biofilm development. J Bacteriol 2004;186:8066-73.
196. Webb JS, Thompson LS, James S, et al. Cell death in Pseudomonas aeruginosa biofilm development. J Bacteriol 2003;185: 4585-92.
197. Webster RE. Phage display of peptides and proteins. In: Kay BK, Winter J, McCafferty J (eds). Biology of the Filamentous Bacteriophage. New York: Academic Press, 1996, 1-20.
198. Wei Q, Phu NLM, Dotsch A, et al. Global regulation of gene expression by OxyR in an important human opportunistic pathogen. Nucleic Acids Res 2012;40:4320-33.
199. Whitchurch CB, Tolker-Nielsen T, Ragas PC, et al. Extracellular DNA required for bacterial biofilm formation. Science 2002;295:1487.
200. Whiteley M, Bangera MG, Bumgarner RE, et al. Gene expression in Pseudomonas aeruginosa biofilms. Nature 2001;413: 860-4.
201. Williams PG, Fenwick ML. Degradation of the filamentous phage ZJ/2 by sodium dodecylsulphate. Nature 1967;214: 712-3.
202. Woo JKK, Webb JS, Kirov SM, et al. Biofilm dispersal cells of a cystic fibrosis Pseudomonas aeruginosa isolate exhibit variability in functional traits likely to contribute to persistent infection. FEMS Immunol Med Mic 2012;66: 251-64.
203. Xavier JB, Kim W, Foster KR. A molecular mechanism that stabilizes cooperative secretions in Pseudomonas aeruginosa. Mol Microbiol 2011;79:166-79.
204. Xue H, Xu Y, Boucher Y, et al. High frequency of a novel filamentous phage, VCY phi, within an environmental Vibrio cholerae population. Appl Environ Microb 2012;78:28-33.
205. Yamada T. Filamentous phages of Ralstonia solanacearum: double-edged swords for pathogenic bacteria. Front Microbiol 2013;4:325.
206. Yamada T, Kawasaki T, Nagata S, et al. New bacteriophages that infect the phytopathogen Ralstonia solanacearum. Microbiology 2007;153:2630-9.
207. Yang F, Pecina DA, Kelly SD, et al. Biosequestration via cooperative binding of copper by Ralstonia pickettii. Environ Technol 2010;31:1045-60.
208. Zweckstetter M, Bax A. Characterization ofmolecular alignment in aqueous suspensions of Pf1 bacteriophage. J Biomol NMR 2001;20:365-77.
209. Zwick MB, Shen JQ, Scott J. Phage-displayed peptide libraries. Curr Opin Biotech 1998;9:427-36.