Abstract
Bacteriophages are probably the oldest viruses, having appeared early during bacterial evolution. Therefore, bacteria and bacteriophages have a long history of co-evolution in which bacteria have developed multiple resistance mechanisms against bacteriophages. These mechanisms, that are very diverse and are in constant evolution, allow the survival of the bacteria. Bacteriophages have adapted to bacterial defense systems, devised strategies to evade these anti-phage mechanisms and restored their infective capacity. In this chapter, we review the bacterial strategies that hinder the phage infection as well as the counter-defense mechanisms developed
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Hoskisson PA, Smith MCM. Hypervariation and phase variation in the bacteriophage ‘resistome’. Curr Opin Microbiol 2007; 10:396–400.
Labrie SJ, Samson JE, Moineau S. Bacteriophage resistance mechanism. Nat Rev Microbiol 2010; 5:317–327.
McAuliffe O, Ross RP, Fitzgerald GF. The new phage biology: from genomics to applications. In: McGrath S and van Sinderen D, eds. Bacteriophage Genetics and Molecular Biology. Norfolk: Caister Academic Press 2007: 1–42.
Ackermann H-W. Bacteriophage obserations and evolution. Res Microbiol 2003; 154:245–251.
Cuttman B, Raya R, Kutter E. Basic phage biology. In: Kutter E and Sulakvelidze A, eds. Bacteriophages. Biology and Applications. Boca Raton: CRC Press 2005: 29–66.
Casjens S. Prophages and bacterial genomics: what have we learned so far? Mol Microbiol 2003; 49:277–300.
Liu M, Deora R, Doulatov SR et al. Reverse transcriptase-meditated tropism switching in Bordetella bacteriophage. Science 2002; 295:2091–2094.
Doulatov S, Hodes A, Dai L et al. Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements. Nature 2004; 431:473–481.
Destoumieux-Garzond, Duquesne S, Peduzzi J et al. The iron-siderophore transporter FhuA is the receptor for the antimicrobial peptide microcin J25: role of the microcin Val11-Pro16 β-hairpin region in the recognition mechanism. Biochem J 2005; 389:869–876.
Vicent PA, Morero RD. The structure and biological aspects of peptide antibiotic microcin J25. Curr Med Chem 2009; 16:538–549.
Riede I, Eschbach M-L. Evidence that TraT interacts with OmpA of Escherichia coli. FEBS Lett 1986; 205:241–245.
Bruttin A, Desiere F, Lucchini S et al. Characterization of the lysogeny DNA module from teteperate Streptococcus thermophilus bacteriophage φSfi21. Virology 1997; 233:136–148.
McGrath S, Fitzgerald GF, van Sinderen D. Identification and characterization of phage-resistance genes in temperate lactococcal bacteriophages. Mol Microbiol 2002; 43:509–520.
Lopez D, Vlamakis H, Kolter R. Biofilms. Cold Spring Harb Perspect Biol 2010; 2:a000398.
Sutherland IW, Hughes KA, Skillman LC et al. The interaction of phage and biofilms. FEMS Microbiol Lett 2004; 232:1–6.
Tait K, Sutherland IW. The efficacy of bacteriophages as a method of biofilm eradication. Biofouling 2002; 18:305–310.
Richard AH, Gilbert P, High NJ et al. Bacterial coaggregation: an integral process in the development of multi-species biofilms. Trends microbial 2003; 11:94–100.
Ghosh D, Roy K, Williamson KE et al. Acyl-homoserine lactones can induce virus production in lysogenic bacteria: an alternative paradigm for prophage induction. Appl Environ Microbiol 2009; 75:7142–7152.
Wilson GG. Restriction and modification systems. Annu Rev Genet 1991; 25:585–627.
Price C, Bickle TA. A possible role for DNA restriction in bacterial evolution. Microbiol Sci 1986; 3:296–299.
Tock MR, Dryden DTF. The biology of restriction and anti-restriction. Curr Opin Microbiol 2005; 8:466–472.
Roberts RJ et al. A nomenclature for restriction enzymes, DNA methytransferases, homing endonucelases and their genes. Nucleic Acids Res 2003; 31:1805–1812.
Kruger DH, Barcak GJ, Smith HO. Abolition of DNA recognition site resistance to the restriction endonuclease EcoRII. Biomed Biochim Acta 1988; 47:K1–K5.
Blair CL, Black LW. A type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs. J Mol Biol 2007; 366:768–778.
Blair CL, Rifat D, Black LW. Exclusion of glucosyl-hydroxymethylcytosine DNA containing bacteriophages is overcome by the injected protein inhibitor IPI*. J Mol Biol 2007; 366:779–789.
Bedford D, Laity C, Buttner MJ. Two genes involved in the phase-variable phi C31 resistance mechanism of Streptomyces coelicolor A3(2). J Bacteriol 1995; 177:4681–4689.
Sumby P, Smit MCM. Phase variation in the phage growth limitation system of Streptomices coelicor A3(2). J Bacteriol 2003; 4558–4563.
Studier FW, Novva NR. SAMase gene of bacteriophage T3 is responsible for overcoming host restriction. J Virol 1976; 19:136–145.
Walkinshaw MD, Taylor P, Sturrock SS et al. Structure of OCR from bacteriophage T7, a protein that mimics B-form DNA. Mol Cell 2002; 9:18–94.
Barrangou R, Fremaux C, Deveau H et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007; 315:1709–1712.
Andersson AF, Banfield JF. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 2008; 320:1047–1050.
Ishino Y, Shinagawa H, Makino K et al. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli and identification of the gene product. J Bacteriol 1987; 169:5429–5433.
Jansen R, Embden JD, Gaastra W et al. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 2002; 43:1565–1575.
Marraffini LA, Sontheimer EJ. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 2010; 11:181–190.
Bult CJ, White O, Olsen GJ et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 1996; 273:1058–1073.
Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 2007; 8:172.
Kunin V, Sorek R, Hugenholtz P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol 2007; 8:R61.
Mojica FJ, Díez-Villaseñor C, García-Martínez J et al. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 2005; 60:174–182.
Lillestøl RK, Shah SA, Brügger K et al. CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties. Mol Microbiol 2009; 72:259–272.
Hale C, Kleppe K, Terns RM et al. Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus. RNA 2008; 14:2572–2579.
Haft DH, Selengut J, Mongodin EF et al. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol 2005; 1:e60.
Wiedenheft B, Zhou K, Jinek M et al. Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure 2009; 17:904–912.
Beloglazova N, Brown G, Zimmerman MD et al. A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J Biol Chem 2008; 283:20361–20371.
Brouns SJ, Jore MM, Lundgren M et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 2008; 321:960–964.
Carte J, Wang R, Li H et al. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev 2008; 22:3489–3496.
Makarova KS, Grishin NV, Shabalina SA et al. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi and hypothetical mechanisms of action. Biol Direct 2006; 1:7.
Marraffini LA, Sontheimer EJ. Self versus nonself discrimination during CRISPR RNA-directed immunity. Nature 2010; 463:568–571.
Snyder L. Phage-exclusion enzymes: a bonanza of biochemical and cell biology reagent? Mol Microbiol 1995; 15:415–420.
Slavcev RA, Hayes S. Over-expression of rexA nullifies T4rII exclusion in Escherichia coli K(γ) lysogens. Can J Microbiol 2004; 50:133–136.
Amitsur M, Levitz R, Kaufmann G. Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. EMBO J 1987; 6:2499–2503.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Landes Bioscience and Springer Science+Business Media
About this chapter
Cite this chapter
Martínez-Borra, J., González, S., López-Larrea, C. (2012). The Origin of the Bacterial Immune Response. In: López-Larrea, C. (eds) Self and Nonself. Advances in Experimental Medicine and Biology, vol 738. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-1680-7_1
Download citation
DOI: https://doi.org/10.1007/978-1-4614-1680-7_1
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4614-1679-1
Online ISBN: 978-1-4614-1680-7
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)