Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-78c5997874-v9fdk Total loading time: 0 Render date: 2024-11-09T09:00:34.962Z Has data issue: false hasContentIssue false

5 - Genomic Islands in the Bacterial Chromosome – Paradigms of Evolution in Quantum Leaps

from PART II - Mobile Genetic Elements in Bacterial Evolution

Published online by Cambridge University Press:  16 September 2009

By
Tobias Ölschläger  and
Jörg Hacker
Edited by
Michael Hensel  and
Herbert Schmidt
Michael Hensel
Affiliation:
Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
Herbert Schmidt
Affiliation:
Universität Hohenheim, Stuttgart
Get access

Summary

INTRODUCTION

The bacterial genome, that is, the entirety of all genes of a bacterium, was once viewed as a rather stable entity. However, the observation of spreading resistance to antibiotics led to the discovery of extra-chromosomal elements encoding this property. Obviously, plasmids are able to transfer genes from one bacterium to another not only among one species but also from one species to another. Such transfer of genes is not restricted to antibiotic resistance genes. Examples of further traits often encoded by plasmids include resistance to heavy metals and production of toxins.

Another example of mobile genetic elements is phages, the viruses of bacteria. Phages are not just able to infect and finally lyse the bacterial host cell. Certain phages infect and then integrate their whole genome into the bacterial chromosome and thereby become a prophage. This may add another important factor to the property of the infected bacteria. In the case of pathogenic bacteria the production of toxins is frequently encoded by a prophage. A few medically important examples are bacteriophage β of Corynebacterium diphtheriae encoding diphtheria toxin, phage C1 of Clostridium botulinum coding for the C1 neurotoxin, and phage H-19B of Escherichia coli, which harbors the gene for Shiga toxin Stx1 (for a recent review, see Brüssow et al., 2004).

Smaller but still important mobile genetic units are insertion sequence (IS) elements. IS elements mediate DNA rearrangements by transposition, resulting in off/on switching of gene expression by insertion into, and excision from, open reading frames (ORFs), respectively.

Type
Chapter
Information
Horizontal Gene Transfer in the Evolution of Pathogenesis , pp. 113 - 134
Publisher: Cambridge University Press
Print publication year: 2008

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

,Anonymous (2000). Preventing pneumococcal disease among infants and young children. Recommendations of the Advisory Committee on Immunization Practices (ACIP). Morb Mortal Wkly Rep Recomm Rep, 49, 1–35.Google Scholar
Bach, S., Buchrieser, C., Prentice, M., et al. (1999). The high-pathogenicity island of Yersinia enterocolitica Ye8081 undergoes low-frequency deletion but not precise excision, suggesting recent stabilization in the genome. Infect Immun, 67, 5091–9.Google Scholar
Barocchi, M. A., Ries, J., Zogaj, X., et al. (2006). A pneumococcal pilus influences virulence and host inflammatory responses. Proc Natl Acad Sci USA, 103, 2857–62.CrossRefGoogle ScholarPubMed
Bennett, P. M. (2004). Genome plasticity: insertion sequence elements, transposons and integrons, and DNA rearrangement. Methods Mol Biol, 266, 71–113.Google ScholarPubMed
Bensing, B. A., Lopez, J. A., and Sullam, P. M. (2004). The Streptococcus gordonii surface proteins GspB and Hsa mediate binding to sialylated carbohydrate epitopes on the platelet membrane glycoprotein Ibα. Infect Immun, 72, 6528–37.CrossRefGoogle ScholarPubMed
Bessen, D. E., and Kalia, A. (2002). Genomic localization of a T serotype locus to a recombinatorial zone encoding extracellular matrix-binding proteins in Streptococcus pyogenes. Infect Immun, 70, 1159–67.CrossRefGoogle Scholar
Brown, J. S., Gilliland, S. M., and Holden, D. W. (2001). A Streptococcus pneumoniae pathogenicity island encoding an ABC transporter involved in iron uptake and virulence. Mol Microbiol, 40, 572–85.CrossRefGoogle ScholarPubMed
Brüssow, H., Canchaya, C., and Hardt, W. D. (2004). Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev, 68, 560–602.CrossRefGoogle ScholarPubMed
Brzuszkiewicz, E., Brüggemann, H., Liesegang, H., et al. (2006). How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc Natl Acad Sci USA, 103, 12879–84.CrossRefGoogle ScholarPubMed
Buchrieser, C., Brosch, R., Bach, S., Guiyoule, A., and Carniel, E. (1998). The high-pathogenicity island of Yersinia pseudotuberculosis can be inserted into any of the three chromosomal asn tRNA genes. Mol Microbiol, 30, 965–78.CrossRefGoogle ScholarPubMed
Cazalet, C., Rusniok, C., Brüggemann, H., et al. (2004). Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity. Nat Genet, 36, 1165–73.CrossRefGoogle ScholarPubMed
Censini, S., Lange, C., Xiang, Z., et al. (1996). cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors. Proc Natl Acad Sci USA, 93, 14648–53.CrossRefGoogle ScholarPubMed
Collyn, F., Billault, A., Mullet, C., Simonet, M., and Marceau, M. (2004). YAPI, a new Yersinia pseudotuberculosis pathogenicity island. Infect Immun, 72, 4784–90.CrossRefGoogle ScholarPubMed
Deng, W., Burland, V., Plunkett, G., et al. (2002). Genome sequence of Yersinia pestis KIM. J Bacteriol, 184, 4601–11.CrossRefGoogle ScholarPubMed
Deng, W., Puente, J. L., Gruenheid, S., et al. (2004). Dissecting virulence: systematic and functional analyses of a pathogenicity island. Proc Natl Acad Sci USA, 101, 3597–602.CrossRefGoogle ScholarPubMed
Dobrindt, U. (2005). (Patho-)Genomics of Escherichia coli. Int J Med Microbiol, 295, 357–71.CrossRefGoogle ScholarPubMed
Dobrindt, U., Hentschel, U., Kaper, J. B., and Hacker, J. (2002). Genome plasticity in pathogenic and nonpathogenic enterobacteria. Curr Top Microbiol Immunol, 264, 157–75.Google ScholarPubMed
Dobrindt, U., Hochhut, B., Hentschel, U., and Hacker, J. (2004). Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol, 2, 414–24.CrossRefGoogle ScholarPubMed
Doran, K. S., and Nizet, V. (2004). Molecular pathogenesis of neonatal group B streptococcal infection: no longer in its infancy. Mol Microbiol, 54, 23–31.CrossRefGoogle ScholarPubMed
Franco, A. A., Cheng, R. K., Chung, G. T., et al. (1999). Molecular evolution of the pathogenicity island of enterotoxigenic Bacteroides fragilis strains. J Bacteriol, 181, 6623–33.Google ScholarPubMed
Garmendia, J., Frankel, G., and Crepin, V. F. (2005). Enteropathogenic and enterohemorrhagic Escherichia coli infections: translocation, translocation, translocation. Infect Immun, 73, 2573–85.CrossRefGoogle ScholarPubMed
Germon, P., Roche, D., Melo, S., et al. (2007). tDNA locus polymorphism and ecto-chromosomal DNA insertion hot-spots are related to the phylogenetic group of Escherichia coli strains. Microbiology, 153, 826–37.CrossRefGoogle ScholarPubMed
Gill, S. R., Fouts, D. E., Archer, G. L., et al. (2005). Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J Bacteriol, 187, 2426–38.CrossRefGoogle Scholar
Groisman, E. A., and Ochman, H. (1996). Pathogenicity islands: bacterial evolution in quantum leaps. Cell, 87, 791–4.CrossRefGoogle ScholarPubMed
Hacker, J., and Carniel, E. (2001). Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep, 2, 376–81.CrossRefGoogle ScholarPubMed
Hacker, J., and Kaper, J. B. (1999). The concept of pathogenicity islands. In Hacker, J., and Kaper, J. B. (Eds.). Pathogenicity islands and other mobile virulence elements. Washington, DC: American Society for Microbiology.CrossRefGoogle Scholar
Hacker, J., and Kaper, J. B. (2000). Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol, 54, 641–79.CrossRefGoogle ScholarPubMed
Hacker, J., Bender, L., Ott, M., et al. (1990). Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia coli isolates. Microb Pathog, 8, 213–25.CrossRefGoogle ScholarPubMed
Hall, R. M., and Collis, C. M. (1995). Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination. Mol Microbiol, 15, 593–600.CrossRefGoogle ScholarPubMed
Hanssen, A. M., and Ericson Sollid, J. U. (2006). SCCmec in staphylococci: genes on the move. FEMS Immunol Med Microbiol, 46, 8–20.CrossRefGoogle ScholarPubMed
Hare, J. M., and McDonough, K. A. (1999). High-frequency RecA-dependent and -independent mechanisms of Congo red binding mutations in Yersinia pestis. J Bacteriol, 181, 4896–904.Google ScholarPubMed
Hava, D. L., and Camilli, A. (2002). Large-scale identification of serotype 4 Streptococcus pneumoniae virulence factors. Mol Microbiol, 45, 1389–406.Google ScholarPubMed
Herbert, M. A., Beveridge, C. J., McCormick, D., et al. (2005). Genetic islands of Streptococcus agalactiae strains NEM316 and 2603VR and their presence in other Group B streptococcal strains. BMC Microbiol, 5, 31.CrossRefGoogle ScholarPubMed
Hiramatsu, K., Cui, L., Kuroda, M., and Ito, T. (2001). The emergence and evolution of methicillin-resistant Staphylococcus aureus. Trends Microbiol, 9, 486–93.CrossRefGoogle ScholarPubMed
Hochhut, B., Dobrindt, U., and Hacker, J. (2006a). The contribution of pathogenicity islands to the evolution of bacterial pathogens. In Seifert, H. S., and Dirita, V. J. (Eds.). Evolution of microbial pathogens. Washington, DC: American Society for Microbiology.Google Scholar
Hochhut, B., Wilde, C., Balling, G., et al. (2006b). Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536. Mol Microbiol, 61, 584–95.CrossRefGoogle ScholarPubMed
Ito, T., Katayama, Y., Asada, K., et al. (2001). Structural comparison of three types of staphylococcal cassette chromosome mec integrated in the chromosome in methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother, 45, 1323–36.CrossRefGoogle ScholarPubMed
Jakubovics, N. S., Stromberg, N., Dolleweerd, C. J., Kelly, C. G., and Jenkinson, H. F. (2005). Differential binding specificities of oral streptococcal antigen I/II family adhesins for human or bacterial ligands. Mol Microbiol, 55, 1591–605.CrossRefGoogle ScholarPubMed
Janda, J. M., and Abbott, S. L. (2006). The genus Hafnia: from soup to nuts. Clin Microbiol Rev, 19, 12–8.CrossRefGoogle ScholarPubMed
Jores, J., Rumer, L., and Wieler, L. H. (2004). Impact of the locus of enterocyte effacement pathogenicity island on the evolution of pathogenic Escherichia coli. Int J Med Microbiol, 294, 103–13.CrossRefGoogle ScholarPubMed
Kelly, M., Hart, E., Mundy, R., et al. (2006). Essential role of the type III secretion system effector NleB in colonization of mice by Citrobacter rodentium. Infect Immun, 74, 2328–37.CrossRefGoogle ScholarPubMed
Lewis, D. A., Jones, A., Parkhill, J., et al. (2005). Identification of DNA markers for a transmissible Pseudomonas aeruginosa cystic fibrosis strain. Am J Respir Cell Mol Biol, 33, 56–64.CrossRefGoogle ScholarPubMed
Liang, X., Pham, X. Q., Olson, M. V., and Lory, S. (2001). Identification of a genomic island present in the majority of pathogenic isolates of Pseudomonas aeruginosa. J Bacteriol, 183, 843–53.CrossRefGoogle ScholarPubMed
Luong, T. T., Ouyang, S., Bush, K., and Lee, C. Y. (2002). Type 1 capsule genes of Staphylococcus aureus are carried in a staphylococcal cassette chromosome genetic element. J Bacteriol, 184, 3623–9.CrossRefGoogle Scholar
Maurelli, A. T., Fernandez, R. E., Bloch, C. A., Rode, C. K., and Fasano, A. (1998). “Black holes” and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc Natl Acad Sci USA, 95, 3943–8.CrossRefGoogle ScholarPubMed
Mazel, D. (2006). Integrons: agents of bacterial evolution. Nat Rev Microbiol, 4, 608–20.CrossRefGoogle ScholarPubMed
McDaniel, T. K., and Kaper, J. B. (1997). A cloned pathogenicity island from enteropathogenic Escherichia coli confers the attaching and effacing phenotype on E. coli K-12. Mol Microbiol, 23, 399–407.CrossRefGoogle ScholarPubMed
Middendorf, B., Hochhut, B., Leipold, K., et al. (2004). Instability of pathogenicity islands in uropathogenic Escherichia coli 536. J Bacteriol, 186, 3086–96.CrossRefGoogle ScholarPubMed
Mirold, S., Rabsch, W., Rohde, M., et al. (1999). Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain. Proc Natl Acad Sci USA, 96, 9845–50.CrossRefGoogle ScholarPubMed
Mongkolrattanothai, K., Boyle, S., Murphy, T. V., and Daum, R. S. (2004). Novel non-mecA-containing staphylococcal chromosomal cassette composite island containing pbp4 and tagF genes in a commensal staphylococcal species: a possible reservoir for antibiotic resistance islands in Staphylococcus aureus. Antimicrob Agents Chemother, 48, 1823–36.CrossRefGoogle Scholar
Mora, M., Bensi, G., Capo, S., et al. (2005). Group A Streptococcus produce pilus-like structures containing protective antigens and Lancefield T antigens. Proc Natl Acad Sci USA, 102, 15641–6.CrossRefGoogle ScholarPubMed
Nandi, S., Maurer, J. J., Hofacre, C., and Summers, A. O. (2004). Gram-positive bacteria are a major reservoir of Class 1 antibiotic resistance integrons in poultry litter. Proc Natl Acad Sci USA, 101, 7118–22.CrossRefGoogle ScholarPubMed
Navarre, W. W., Halsey, T. A., Walthers, D., et al. (2005). Co-regulation of Salmonella enterica genes required for virulence and resistance to antimicrobial peptides by SlyA and PhoP/PhoQ. Mol Microbiol, 56, 492–508.CrossRefGoogle ScholarPubMed
Nougayrede, J. P., Homburg, S., Taieb, F., et al. (2006). Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science, 313, 848–51.CrossRefGoogle ScholarPubMed
Obert, C., Sublett, J., Kaushal, D., et al. (2006). Identification of a candidate Streptococcus pneumoniae core genome and regions of diversity correlated with invasive pneumococcal disease. Infect Immun, 74, 4766–77.CrossRefGoogle ScholarPubMed
Oelschlaeger, T. A., Zhang, D., Schubert, S., et al. (2003). The high-pathogenicity island is absent in human pathogens of Salmonella enterica subspecies I but present in isolates of subspecies III and VI. J Bacteriol, 185, 1107–11.CrossRefGoogle ScholarPubMed
Okinaka, R. T., Cloud, K., Hampton, O., et al. (1999). Sequence and organization of pXO1, the large Bacillus anthracis plasmid harboring the anthrax toxin genes. J Bacteriol, 181, 6509–15.Google ScholarPubMed
Parkhill, J., Dougan, G., James, K. D., et al. (2001). Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature, 413, 848–52.CrossRefGoogle ScholarPubMed
Parks, A. R., and Peters, J. E. (2007). Transposon Tn7 is widespread in diverse bacteria and forms genomic islands. J Bacteriol, 189, 2170–3.CrossRefGoogle ScholarPubMed
Perna, N. T., Plunkett, G. 3rd, Burland, V., et al. (2001). Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature, 409, 529–33.CrossRefGoogle ScholarPubMed
Ruzin, A., Lindsay, J., and Novick, R. P. (2001). Molecular genetics of SaPI1 – a mobile pathogenicity island in Staphylococcus aureus. Mol Microbiol, 41, 365–77.CrossRefGoogle ScholarPubMed
Schubert, S., Rakin, A., and Heesemann, J. (2004). The Yersinia high-pathogenicity island (HPI): evolutionary and functional aspects. Int J Med Microbiol, 294, 83–94.CrossRefGoogle ScholarPubMed
Shankar, N., Coburn, P., Pillar, C., Haas, W., and Gilmore, M. (2004). Enterococcal cytolysin: activities and association with other virulence traits in a pathogenicity island. Int J Med Microbiol, 293, 609–18.CrossRefGoogle Scholar
Stabler, R. A., Gerding, D. N., Songer, J. G., et al. (2006). Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains. J Bacteriol, 188, 7297–305.CrossRefGoogle ScholarPubMed
Tettelin, H., Masignani, V., Cieslewicz, M. J., et al. (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome.”Proc Natl Acad Sci USA, 102, 13950–5.CrossRefGoogle ScholarPubMed
Thorne, C. (1993). Bacillus anthracis. In Soneshein, A. L. (Ed.). Bacillus subtilis and other gram-positive bacteria. Washington, DC: American Society for Microbiology.Google Scholar
Tong, H. H., James, M., Grants, I., et al. (2001). Comparison of structural changes of cell surface carbohydrates in the eustachian tube epithelium of chinchillas infected with a Streptococcus pneumoniae neuraminidase-deficient mutant or its isogenic parent strain. Microb Pathog, 31, 309–17.CrossRefGoogle ScholarPubMed
Auwera, G. A., Andrup, L., and Mahillon, J. (2005). Conjugative plasmid pAW63 brings new insights into the genesis of the Bacillus anthracis virulence plasmid pXO2 and of the Bacillus thuringiensis plasmid pBT9727. BMC Genomics 6, 103–110.CrossRefGoogle ScholarPubMed
Auwera, G.A., and Mahillon, J. (2005). TnXO1, a germination-associated class II transposon from Bacillus anthracis. Plasmid, 53, 251–7.CrossRefGoogle ScholarPubMed
Waterhouse, J. C., Swan, D. C., and Russell, R. R. (2007). Comparative genome hybridization of Streptococcus mutans strains. Oral Microbiol Immunol, 22, 103–10.CrossRefGoogle ScholarPubMed
Wolfgang, M. C., Kulasekara, B. R., Liang, X., et al. (2003). Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa. Proc Natl Acad Sci USA, 100, 8484–9.CrossRefGoogle ScholarPubMed
Zhang, S., Green, N. M., Sitkiewicz, I., Lefebvre, R. B., and Musser, J. M. (2006). Identification and characterization of an antigen I/II family protein produced by group A Streptococcus. Infect Immun, 74, 4200–13.CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×