interspersed repetitive sequences

Summary

Summary: Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.

Top Publications

  1. Queck S, Khan B, Wang R, Bach T, Kretschmer D, Chen L, et al. Mobile genetic element-encoded cytolysin connects virulence to methicillin resistance in MRSA. PLoS Pathog. 2009;5:e1000533 pubmed publisher
    ..Thus, our study reveals a previously unknown role of methicillin resistance clusters in staphylococcal pathogenesis and shows that important virulence and antibiotic resistance determinants may be combined in staphylococcal MGEs. ..
  2. Keane T, Wong K, Adams D. RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics. 2013;29:389-90 pubmed publisher
    ..We evaluate RetroSeq on a human trio from the 1000 Genomes Project, showing that it produces highly accurate TE calls. RetroSeq is open-source and available from https://github.com/tk2/RetroSeq. ..
  3. Affolabi D, Anyo G, Faïhun F, Sanoussi N, Shamputa I, Rigouts L, et al. First molecular epidemiological study of tuberculosis in Benin. Int J Tuberc Lung Dis. 2009;13:317-22 pubmed
    ..Spoligotype 61 and Beijing genotype are the most prevalent genotypes of M. tuberculosis in Cotonou. ..
  4. Mavrodi D, Loper J, Paulsen I, Thomashow L. Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5. BMC Microbiol. 2009;9:8 pubmed publisher
    ..In this study, we analyzed mobile genetic elements of the Pf-5 genome in an effort to identify determinants that might contribute to Pf-5's ability to adapt to changing environmental conditions and/or colonize new ecological niches...
  5. Romine M, Carlson T, Norbeck A, McCue L, Lipton M. Identification of mobile elements and pseudogenes in the Shewanella oneidensis MR-1 genome. Appl Environ Microbiol. 2008;74:3257-65 pubmed publisher
  6. Alonso Rodriguez N, Martínez Lirola M, Herranz M, Sanchez Benitez M, Barroso P, Bouza E, et al. Evaluation of the new advanced 15-loci MIRU-VNTR genotyping tool in Mycobacterium tuberculosis molecular epidemiology studies. BMC Microbiol. 2008;8:34 pubmed publisher
    ..If we add this to the speed with which it provides results, MIRU-15 could be considered a suitable tool for real-time genotyping. ..
  7. Bi D, Xu Z, Harrison E, Tai C, Wei Y, He X, et al. ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Res. 2012;40:D621-6 pubmed publisher
    ..The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community. ..
  8. Stokes H, Gillings M. Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. FEMS Microbiol Rev. 2011;35:790-819 pubmed publisher
    ..We also argue that human activities are exacerbating the problem by increasing the tempo of LGT and bacterial evolution for many traits that are important to humans. ..
  9. Monecke S, Coombs G, Shore A, Coleman D, Akpaka P, Borg M, et al. A field guide to pandemic, epidemic and sporadic clones of methicillin-resistant Staphylococcus aureus. PLoS ONE. 2011;6:e17936 pubmed publisher
    ..The data also indicate a high rate of genetic recombination in MRSA involving SCC elements, bacteriophages or other mobile genetic elements and large-scale chromosomal replacements. ..

Scientific Experts

More Information

Publications62

  1. Sitkiewicz I, Green N, Guo N, Mereghetti L, Musser J. Lateral gene transfer of streptococcal ICE element RD2 (region of difference 2) encoding secreted proteins. BMC Microbiol. 2011;11:65 pubmed publisher
    ..Ten RD2-encoded proteins have significant similarity to proteins involved in conjugative transfer of Streptococcus thermophilus integrative chromosomal elements (ICEs)...
  2. Smits W, Grossman A. The transcriptional regulator Rok binds A+T-rich DNA and is involved in repression of a mobile genetic element in Bacillus subtilis. PLoS Genet. 2010;6:e1001207 pubmed publisher
    ..In these ways, Rok appears to be functionally analogous to H-NS, a nucleoid associated protein found in Gram negative bacteria and Lsr2 of high G+C Mycobacteria...
  3. Garneau J, Dupuis M, Villion M, Romero D, Barrangou R, Boyaval P, et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature. 2010;468:67-71 pubmed publisher
    ..Our data show that the CRISPR/Cas immune system is remarkably adapted to cleave invading DNA rapidly and has the potential for exploitation to generate safer microbial strains. ..
  4. Haenni M, Saras E, Bertin S, Leblond P, Madec J, Payot S. Diversity and mobility of integrative and conjugative elements in bovine isolates of Streptococcus agalactiae, S. dysgalactiae subsp. dysgalactiae, and S. uberis. Appl Environ Microbiol. 2010;76:7957-65 pubmed publisher
    ..These ICEs could thus also be a vehicle for horizontal gene transfer between streptococci of animal and/or human origin. ..
  5. Wozniak R, Fouts D, Spagnoletti M, Colombo M, Ceccarelli D, Garriss G, et al. Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs. PLoS Genet. 2009;5:e1000786 pubmed publisher
    ..Furthermore, our analyses suggest that there may be a network of phylogenetic relationships among sequences found in all types of mobile genetic elements. ..
  6. Lowder B, Guinane C, Ben Zakour N, Weinert L, Conway Morris A, Cartwright R, et al. Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus. Proc Natl Acad Sci U S A. 2009;106:19545-50 pubmed publisher
    ..These data provide a new paradigm for the impact of human activities on the emergence of animal pathogens. ..
  7. Jeong H, Barbe V, Lee C, Vallenet D, Yu D, Choi S, et al. Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J Mol Biol. 2009;394:644-52 pubmed publisher
    ..coli and Shigella genomes, both commensals and pathogenic strains, identifies a minimal set of genes in common plus many strain-specific genes that constitute a large E. coli pan-genome. ..
  8. Makarova K, Wolf Y, van der Oost J, Koonin E. Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct. 2009;4:29 pubmed publisher
    ..Many prokaryotes also encode homologs of Argonaute-PIWI proteins but their functions remain unknown...
  9. Sorek R, Kunin V, Hugenholtz P. CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol. 2008;6:181-6 pubmed
    ..CRISPR arrays, together with a group of associated proteins, confer resistance to phages, possibly by an RNA-interference-like mechanism. This Progress discusses the structure and function of this newly recognized antiviral mechanism. ..
  10. Pi B, Yu M, Chen Y, Yu Y, Li L. Distribution of the ACME-arcA gene among meticillin-resistant Staphylococcus haemolyticus and identification of a novel ccr allotype in ACME-arcA-positive isolates. J Med Microbiol. 2009;58:731-6 pubmed publisher
    ..The results from this study revealed that MRSH is likely to be one of the potential reservoirs of ACME for Staphylococcus aureus...
  11. Möbius P, Luyven G, Hotzel H, Köhler H. High genetic diversity among Mycobacterium avium subsp. paratuberculosis strains from German cattle herds shown by combination of IS900 restriction fragment length polymorphism analysis and mycobacterial interspersed repetitive unit-variable-number t. J Clin Microbiol. 2008;46:972-81 pubmed publisher
    ..997. By using only BstEII and PstI digestion together with typing by MIRU-VNTR analysis, a discriminatory index of 0.993 was achieved. This is high enough to support epidemiological studies on a national as well as a global scale. ..
  12. Davies M, Shera J, Van Domselaar G, Sriprakash K, McMillan D. A novel integrative conjugative element mediates genetic transfer from group G Streptococcus to other {beta}-hemolytic Streptococci. J Bacteriol. 2009;191:2257-65 pubmed publisher
    ..We propose that ICESde3396 is a mobile genetic element that is capable of acquiring DNA from multiple bacterial sources and is a vehicle for dissemination of this DNA through the wider beta-hemolytic streptococcal population. ..
  13. Allix Béguec C, Fauville Dufaux M, Supply P. Three-year population-based evaluation of standardized mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing of Mycobacterium tuberculosis. J Clin Microbiol. 2008;46:1398-406 pubmed publisher
    ..g., large sequence polymorphisms. Our results reinforce the proposal of standardized MIRU-VNTR typing as a new reference genotyping method for the epidemiological and phylogenetic screening of M. tuberculosis strains. ..
  14. Bose B, Auchtung J, Lee C, Grossman A. A conserved anti-repressor controls horizontal gene transfer by proteolysis. Mol Microbiol. 2008;70:570-82 pubmed publisher
    ..subtilis phage phi105 is required for inactivation of the phi105 repressor (an ImmR homologue). ImmA-dependent proteolysis of ImmR repressors may be a conserved mechanism for regulating horizontal gene transfer...
  15. Osorio C, Marrero J, Wozniak R, Lemos M, Burrus V, Waldor M. Genomic and functional analysis of ICEPdaSpa1, a fish-pathogen-derived SXT-related integrating conjugative element that can mobilize a virulence plasmid. J Bacteriol. 2008;190:3353-61 pubmed publisher
    ..Our findings reveal the plasticity of ICE genomes and demonstrate that ICEs can enable virulence gene transfer...
  16. Ceccarelli D, Daccord A, René M, Burrus V. Identification of the origin of transfer (oriT) and a new gene required for mobilization of the SXT/R391 family of integrating conjugative elements. J Bacteriol. 2008;190:5328-38 pubmed publisher
    ..Instead, mobI appears to be involved in the recognition of oriT(SXT). ..
  17. Churchward G. Back to the future: the new ICE age. Mol Microbiol. 2008;70:554-6 pubmed publisher
    ..In the current issue, Bose et al. dissect the mechanism of induction of transfer of this element, and reveal a new, apparently widespread repressor anti-repressor system and a new mechanism of repressor destruction by proteolysis. ..
  18. Kawaguchiya M, Urushibara N, Kuwahara O, Ito M, Mise K, Kobayashi N. Molecular characteristics of community-acquired methicillin-resistant Staphylococcus aureus in Hokkaido, northern main island of Japan: identification of sequence types 6 and 59 Panton-Valentine leucocidin-positive community-acquired methicillin-resi. Microb Drug Resist. 2011;17:241-50 pubmed publisher
    ..These findings suggest a potential spread of these emerging CA-MRSA clones in Japan. ..
  19. Guinane C, Ben Zakour N, Tormo Mas M, Weinert L, Lowder B, Cartwright R, et al. Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation. Genome Biol Evol. 2010;2:454-66 pubmed publisher
    ..aureus biotyping scheme. Taken together, these data provide broad new insights into the origin and molecular basis of S. aureus ruminant host specificity. ..
  20. Brochet M, Couve E, Glaser P, Guédon G, Payot S. Integrative conjugative elements and related elements are major contributors to the genome diversity of Streptococcus agalactiae. J Bacteriol. 2008;190:6913-7 pubmed publisher
    ..Twelve are composite, likely resulting from site-specific accretions. Circular forms were detected for five elements. Macroarray analysis confirmed their high plasticity and wide distribution in S. agalactiae. ..
  21. Barbier F, Lebeaux D, Hernandez D, Delannoy A, Caro V, Francois P, et al. High prevalence of the arginine catabolic mobile element in carriage isolates of methicillin-resistant Staphylococcus epidermidis. J Antimicrob Chemother. 2011;66:29-36 pubmed publisher
    ..ACME is widely disseminated in MRSE strains colonizing outpatients and may contribute to their spread in a community environment with low antibiotic exposure, as suggested for USA300. ..
  22. Cui Y, Li Y, Gorgé O, Platonov M, Yan Y, Guo Z, et al. Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats. PLoS ONE. 2008;3:e2652 pubmed publisher
    ..The resulting data will make possible the development of very low cost and high-resolution assays for the systematic typing of any new isolate. ..
  23. Lintner N, Frankel K, Tsutakawa S, Alsbury D, Copi V, Young M, et al. The structure of the CRISPR-associated protein Csa3 provides insight into the regulation of the CRISPR/Cas system. J Mol Biol. 2011;405:939-55 pubmed publisher
    ..A similar N-terminal domain is also identified in Csx1, a second CRISPR-associated protein family of unknown function...
  24. Ceccarelli D, Spagnoletti M, Bacciu D, Danin Poleg Y, Mendiratta D, Kashi Y, et al. ICEVchInd5 is prevalent in epidemic Vibrio cholerae O1 El Tor strains isolated in India. Int J Med Microbiol. 2011;301:318-24 pubmed publisher
    ..In silico analysis showed the existence of at least 3 sibling ICEs of ICEVchInd5 in V. cholerae O1 El Tor reference strains, isolated in the Indian subcontinent after 1992. ..
  25. Aminian M, Shabbeer A, Bennett K. A conformal Bayesian network for classification of Mycobacterium tuberculosis complex lineages. BMC Bioinformatics. 2010;11 Suppl 3:S4 pubmed publisher
    ..The method can be readily extended as new biomarkers are introduced for TB tracking and control. An online tool (http://www.cs.rpi.edu/~bennek/tbinsight/tblineage) makes the CBN model available for TB control and research efforts. ..
  26. Allix Béguec C, Harmsen D, Weniger T, Supply P, Niemann S. Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates. J Clin Microbiol. 2008;46:2692-9 pubmed publisher
    ..The MIRU-VNTRplus database is a powerful tool for high-resolution clonal identification and has little equivalent in terms of functionalities among the bacterial genotyping databases available so far. ..
  27. Partridge S. Analysis of antibiotic resistance regions in Gram-negative bacteria. FEMS Microbiol Rev. 2011;35:820-55 pubmed publisher
  28. Chatterjee S, Chen L, Joo H, Cheung G, Kreiswirth B, Otto M. Distribution and regulation of the mobile genetic element-encoded phenol-soluble modulin PSM-mec in methicillin-resistant Staphylococcus aureus. PLoS ONE. 2011;6:e28781 pubmed publisher
    ..Our study gives new insight in the distribution, regulation, and role in virulence of the PSM-mec peptide and the psm-mec gene locus. ..
  29. Seth Smith H, Fookes M, Okoro C, Baker S, Harris S, Scott P, et al. Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae. J Bacteriol. 2012;194:1494-504 pubmed publisher
    ..We present a growing family of SPI-7-related ICEs whose mobility, abundance, and cargo variability indicate that these elements may have had a large impact on the evolution of the Enterobacteriaceae. ..
  30. Zaneveld J, Nemergut D, Knight R. Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns. Microbiology. 2008;154:1-15 pubmed publisher
    ..Finally, we describe software, databases and algorithms for identifying particular classes of mobile elements, and outline prospects for better detection of HGT based on specific mechanisms of transfer. ..
  31. Siefert J. Defining the mobilome. Methods Mol Biol. 2009;532:13-27 pubmed publisher
    ..This chapter provides a framework to describe our current understanding of the mobilome and a foundation on which appreciation of its impact on genome evolution can be understood. ..
  32. Ishmael N, Dunning Hotopp J, Ioannidis P, Biber S, Sakamoto J, Siozios S, et al. Extensive genomic diversity of closely related Wolbachia strains. Microbiology. 2009;155:2211-22 pubmed publisher
    ..Overall, these insect-associated Wolbachia have highly mosaic genomes, with lateral gene transfer playing an important role in their diversity and evolution. ..
  33. Leplae R, Lima Mendez G, Toussaint A. ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res. 2010;38:D57-61 pubmed publisher
    ..ulb.ac.be). The BLAST interface for querying the database has been extended and numerous tools for in-depth analysis of the results have been added. ..
  34. Lindsay J. Genomic variation and evolution of Staphylococcus aureus. Int J Med Microbiol. 2010;300:98-103 pubmed publisher
    ..Because of the mobility of MGE, there are prospects for increasingly virulent and resistant strains to emerge that could severely affect healthcare and agriculture more effectively than the current pathogens. ..
  35. Stegger M, Lindsay J, Sørum M, Gould K, Skov R. Genetic diversity in CC398 methicillin-resistant Staphylococcus aureus isolates of different geographical origin. Clin Microbiol Infect. 2010;16:1017-9 pubmed publisher
    ..However, the four isolates cluster into two distinct groups corresponding to differences in epidemiology based on mobile genetic elements and resistance patterns, suggesting that the two groups are epidemiologically distinct. ..
  36. Jensen S, Lyon B. Genetics of antimicrobial resistance in Staphylococcus aureus. Future Microbiol. 2009;4:565-82 pubmed publisher
    ..Nonetheless, chromosomal mutation is the catalyst of novel resistance determinants and is likely to have an enhanced influence with the ongoing introduction of synthetic antibiotics. ..
  37. Khan F, Furuta Y, Kawai M, Kaminska K, Ishikawa K, Bujnicki J, et al. A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI). Nucleic Acids Res. 2010;38:3019-30 pubmed publisher
    ..These results suggested that they constitute a restriction-modification system, present on the putative mobile element. Our approach thus allowed detection of a previously uncharacterized family of DNA-interacting proteins. ..
  38. Mao C, Bhardwaj K, Sharkady S, Fish R, Driscoll T, Wower J, et al. Variations on the tmRNA gene. RNA Biol. 2009;6:355-61 pubmed
  39. Makarova K, Wolf Y, Koonin E. Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct. 2009;4:19 pubmed publisher
  40. Otto M. Staphylococcus aureus toxin gene hitchhikes on a transferable antibiotic resistance element. Virulence. 2010;1:49-51 pubmed publisher
    ..aureus and other staphylococcal pathogens. ..
  41. Bonocora R, Shub D. A likely pathway for formation of mobile group I introns. Curr Biol. 2009;19:223-8 pubmed publisher
    ..Based on this evidence, we propose that introns and their homing endonucleases evolve separately to target the same highly conserved sequences, uniting afterwards to create a composite mobile element. ..
  42. Montgomery C, Boyle Vavra S, Daum R. The arginine catabolic mobile element is not associated with enhanced virulence in experimental invasive disease caused by the community-associated methicillin-resistant Staphylococcus aureus USA300 genetic background. Infect Immun. 2009;77:2650-6 pubmed publisher
    ..Nor was the presence of ACME associated with increased dermonecrosis in a model of skin infection. We conclude that ACME is not necessary for virulence in rodent models of CA-MRSA USA300 pneumonia or skin infection. ..
  43. Rosenstein R, Nerz C, Biswas L, Resch A, Raddatz G, Schuster S, et al. Genome analysis of the meat starter culture bacterium Staphylococcus carnosus TM300. Appl Environ Microbiol. 2009;75:811-22 pubmed publisher
    ..The genome lacks most of the toxins typical of S. aureus as well as genes involved in biofilm formation, underscoring the nonpathogenic status. ..
  44. Fuxelius H, Darby A, Cho N, Andersson S. Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction. Genome Biol. 2008;9:R42 pubmed publisher
    ..Thus, most of the variably present genes and pseudogenes in Rickettsia have arisen from recent acquisitions. ..
  45. Norman A, Hansen L, Sørensen S. Conjugative plasmids: vessels of the communal gene pool. Philos Trans R Soc Lond B Biol Sci. 2009;364:2275-89 pubmed publisher
    ..This communal pool provides the prokaryotes with an important mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized 'private genes'. ..
  46. Kaito C, Saito Y, Nagano G, Ikuo M, Omae Y, Hanada Y, et al. Transcription and translation products of the cytolysin gene psm-mec on the mobile genetic element SCCmec regulate Staphylococcus aureus virulence. PLoS Pathog. 2011;7:e1001267 pubmed publisher
    ..These findings suggest that both the psm-mec transcript, acting as a regulatory RNA, and the PSM-mec protein encoded by the gene on the mobile genetic element SCCmec regulate the virulence of Staphylococcus aureus. ..
  47. Fukuda E, Kaminska K, Bujnicki J, Kobayashi I. Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases. Genome Biol. 2008;9:R163 pubmed publisher
    ..To our knowledge, this represents the first report of a defense system against epigenetic systems through cell death. ..
  48. Gross R, Guzman C, Sebaihia M, dos Santos V, Pieper D, Koebnik R, et al. The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. BMC Genomics. 2008;9:449 pubmed publisher
    ..Recently, clinical isolates associated with bone degenerative disease or cystic fibrosis have also been described...
  49. Diep B, Stone G, Basuino L, Graber C, MILLER A, des Etages S, et al. The arginine catabolic mobile element and staphylococcal chromosomal cassette mec linkage: convergence of virulence and resistance in the USA300 clone of methicillin-resistant Staphylococcus aureus. J Infect Dis. 2008;197:1523-30 pubmed publisher
    ..These data are consistent with a model in which ACME enhances growth and survival of USA300, allowing for genetic "hitchhiking" of SCCmec. SCCmec in turn protects against exposure to beta-lactams. ..
  50. Wozniak R, Waldor M. Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol. 2010;8:552-63 pubmed publisher
    ..This Review compares and contrasts the core functions for some of the well-studied ICEs and discusses them in the broader context of mobile-element and genome evolution. ..
  51. Hegstad K, Mikalsen T, Coque T, Werner G, Sundsfjord A. Mobile genetic elements and their contribution to the emergence of antimicrobial resistant Enterococcus faecalis and Enterococcus faecium. Clin Microbiol Infect. 2010;16:541-54 pubmed publisher
    ..This review focuses on recent developments in the detection of MGEs and their contribution to the spread of antimicrobial resistance in clinically relevant enterococci. ..
  52. Hanekom M, van der Spuy G, Gey Van Pittius N, McEvoy C, Hoek K, Ndabambi S, et al. Discordance between mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing and IS6110 restriction fragment length polymorphism genotyping for analysis of Mycobacterium tuberculosis Beijing strains in a setting of high inciden. J Clin Microbiol. 2008;46:3338-45 pubmed publisher
  53. Jintaridth P, Mutirangura A. Distinctive patterns of age-dependent hypomethylation in interspersed repetitive sequences. Physiol Genomics. 2010;41:194-200 pubmed publisher
    b>Interspersed repetitive sequences (IRSs) are a major contributor to genome size and may contribute to cellular functions...