Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes

Hudson, Corey M.; Lau, Britney Y.; Williams, Kelly P.

doi:10.1093/nar/gku1072

Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes

Journal Article · Tue Nov 04 23:00:00 EST 2014 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gku1072· OSTI ID:1213420

Hudson, Corey M. ^[1]; Lau, Britney Y. ^[1]; Williams, Kelly P. ^[1]

Sandia National Lab. (SNL-CA), Livermore, CA (United States)

Genomic islands are mobile DNAs that are major agents of bacterial and archaeal evolution. Integration into prokaryotic chromosomes usually occurs site-specifically at tRNA or tmRNA gene (together, tDNA) targets, catalyzed by tyrosine integrases. This splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm identifies tDNAs, finds fragments of those tDNAs in the same replicon and removes unlikely candidate islands through a series of filters. A search for islands in 2168 whole prokaryotic genomes produced 3919 candidates. The website Islander (recently moved to http://bioinformatics.sandia.gov/islander/) presents these precisely mapped candidate islands, the gene content and the island sequence. The algorithm further insists that each island encode an integrase, and attachment site sequence identity is carefully noted; therefore, the database also serves in the study of integrase site-specificity and its evolution.

View Accepted Manuscript (DOE)

Research Organization:: Sandia National Laboratories (SNL), Albuquerque, NM, and Livermore, CA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC04-94AL85000

OSTI ID:: 1213420

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 43; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

References (32)

Genomic islands are dynamic, ancient integrative elements in bacterial evolution Boyd, E. Fidelma; Almagro-Moreno, Salvador; Parent, Michelle A. Trends in Microbiology, Vol. 17, Issue 2 https://doi.org/10.1016/j.tim.2008.11.003	journal	February 2009
tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features Marck, Christian; Grosjean, Henri RNA, Vol. 8, Issue 10, p. 1189-1232 https://doi.org/10.1017/s1355838202022021	journal	October 2002
Filamentous phage integration requires the host recombinases XerC and XerD Huber, Kathryn E.; Waldor, Matthew K. Nature, Vol. 417, Issue 6889 https://doi.org/10.1038/nature00782	journal	June 2002
Genomic islands in pathogenic and environmental microorganisms Dobrindt, Ulrich; Hochhut, Bianca; Hentschel, Ute Nature Reviews Microbiology, Vol. 2, Issue 5 https://doi.org/10.1038/nrmicro884	journal	May 2004
Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene Sullivan, J. T.; Ronson, C. W. Proceedings of the National Academy of Sciences, Vol. 95, Issue 9 https://doi.org/10.1073/pnas.95.9.5145	journal	April 1998
Complete Genome Sequence of Enterohemorrhagic Eschelichia coli O157:H7 and Genomic Comparison with a Laboratory Strain K-12 Hayashi, T. DNA Research, Vol. 8, Issue 1 https://doi.org/10.1093/dnares/8.1.11	journal	January 2001
Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements Reiter, Wolf-Dieter; Palm, Peter; Yeats, Siobhan Nucleic Acids Research, Vol. 17, Issue 5 https://doi.org/10.1093/nar/17.5.1907	journal	January 1989
Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies Williams, K. P. Nucleic Acids Research, Vol. 30, Issue 4 https://doi.org/10.1093/nar/30.4.866	journal	February 2002
BRUCE: a program for the detection of transfer-messenger RNA genes in nucleotide sequences Laslett, D. Nucleic Acids Research, Vol. 30, Issue 15 https://doi.org/10.1093/nar/gkf459	journal	August 2002
Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities Mantri, Y. Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh059	journal	January 2004
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Laslett, Dean; Canback, Bjorn Nucleic Acids Research, Vol. 32, Issue 1, p. 11-16 https://doi.org/10.1093/nar/gkh152	journal	January 2004
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
PHAST: A Fast Phage Search Tool Zhou, Y.; Liang, Y.; Lynch, K. H. Nucleic Acids Research, Vol. 39, Issue suppl https://doi.org/10.1093/nar/gkr485	journal	June 2011
HAMAP in 2013, new developments in the protein family classification and annotation system Pedruzzi, I.; Rivoire, C.; Auchincloss, A. H. Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1157	journal	November 2012
Evidence for the horizontal transfer of an integrase gene from a fusellovirus to a pRN-like plasmid within a single strain of Sulfolobus and the implications for plasmid survival Peng, X. Microbiology, Vol. 154, Issue 2, p. 383-391 https://doi.org/10.1099/mic.0.2007/012963-0	journal	February 2008
Integration of bacteriophage Mx8 into the Myxococcus xanthus chromosome causes a structural alteration at the C-terminal region of the IntP protein. Tojo, N.; Sanmiya, K.; Sugawara, H. Journal of Bacteriology, Vol. 178, Issue 14 https://doi.org/10.1128/jb.178.14.4004-4011.1996	journal	July 1996
Traffic at the tmRNA Gene Williams, K. P. Journal of Bacteriology, Vol. 185, Issue 3 https://doi.org/10.1128/jb.185.3.1059-1070.2003	journal	February 2003
Interactive metagenomic visualization in a Web browser Ondov, Brian D.; Bergman, Nicholas H.; Phillippy, Adam M. BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-385	journal	September 2011
The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation Guglielmini, Julien; Quintais, Leonor; Garcillán-Barcia, Maria Pilar PLoS Genetics, Vol. 7, Issue 8 https://doi.org/10.1371/journal.pgen.1002222	journal	August 2011
Ends of the line for tmRNA-SmpB Hudson, Corey M.; Lau, Britney Y.; Williams, Kelly P. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00421	journal	August 2014
Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extra intestinal Escherichia coli isolates Hacker, Jörg; Bender, Larisa; Ott, Manfred Microbial Pathogenesis, Vol. 8, Issue 3 https://doi.org/10.1016/0882-4010(90)90048-U	journal	March 1990
tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features Marck, Christian; Grosjean, Henri RNA, Vol. 8, Issue 10, p. 1189-1232 https://doi.org/10.1017/S1355838202022021	journal	October 2002
A bacterial virulence determinant encoded by lysogenic coliphage λ Barondess, James J.; Beckwfth, Jon Nature, Vol. 346, Issue 6287 https://doi.org/10.1038/346871a0	journal	August 1990
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7 Perna, Nicole T.; Plunkett, Guy; Burland, Valerie Nature, Vol. 409, Issue 6819 https://doi.org/10.1038/35054089	journal	January 2001
DNA extraction approaches substantially influence the assessment of the human breast milk microbiome Douglas, Chloe A.; Ivey, Kerry L.; Papanicolas, Lito E. Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-019-55568-y	journal	January 2020
Conjugative transposons: the tip of the iceberg: Conjugative transposons Burrus, Vincent; Pavlovic, Guillaume; Decaris, Bernard Molecular Microbiology, Vol. 46, Issue 3 https://doi.org/10.1046/j.1365-2958.2002.03191.x	journal	October 2002
PROSITE: A documented database using patterns and profiles as motif descriptors Sigrist, C. J. A. Briefings in Bioinformatics, Vol. 3, Issue 3 https://doi.org/10.1093/bib/3.3.265	journal	January 2002
Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands Vernikos, Georgios S.; Parkhill, Julian Bioinformatics, Vol. 22, Issue 18 https://doi.org/10.1093/bioinformatics/btl369	journal	July 2006
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.0955	journal	March 1997
HMMER web server: interactive sequence similarity searching Finn, R. D.; Clements, J.; Eddy, S. R. Nucleic Acids Research, Vol. 39, Issue suppl https://doi.org/10.1093/nar/gkr367	journal	May 2011
Traffic at the tmRNA Gene Williams, K. P. Journal of Bacteriology, Vol. 185, Issue 3 https://doi.org/10.1128/JB.185.3.1059-1070.2003	journal	February 2003
Towards a more accurate annotation of tyrosine-based site-specific recombinases in bacterial genomes Van Houdt, Rob; Leplae, Raphael; Lima-Mendez, Gipsi Mobile DNA, Vol. 3, Issue 1 https://doi.org/10.1186/1759-8753-3-6	journal	January 2012

Cited By (26)

Computational methods for predicting genomic islands in microbial genomes Lu, Bingxin; Leong, Hon Wai Computational and Structural Biotechnology Journal, Vol. 14 https://doi.org/10.1016/j.csbj.2016.05.001	journal	January 2016
Comparative and phylogenetic analysis of a novel family of Enterobacteriaceae-associated genomic islands that share a conserved excision/integration module Piña-Iturbe, Alejandro; Ulloa-Allendes, Diego; Pardo-Roa, Catalina Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-28537-0	journal	July 2018
Cumulative acquisition of pathogenicity islands has shaped virulence potential and contributed to the emergence of LEE-negative Shiga toxin-producing Escherichia coli strains Montero, David Arturo; Canto, Felipe Del; Velasco, Juliana Emerging Microbes & Infections, Vol. 8, Issue 1 https://doi.org/10.1080/22221751.2019.1595985	journal	January 2019
panRGP: a pangenome-based method to predict genomic islands and explore their diversity Bazin, Adelme; Gautreau, Guillaume; Médigue, Claudine Bioinformatics, Vol. 36, Issue Supplement_2 https://doi.org/10.1093/bioinformatics/btaa792	journal	December 2020
Improved genomic island predictions with IslandPath-DIMOB Bertelli, Claire; Brinkman, Fiona S. L. Bioinformatics, Vol. 34, Issue 13 https://doi.org/10.1093/bioinformatics/bty095	journal	February 2018
PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning Fang, Zhencheng; Tan, Jie; Wu, Shufang GigaScience, Vol. 8, Issue 6 https://doi.org/10.1093/gigascience/giz066	journal	June 2019
The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection Galperin, Michael Y.; Rigden, Daniel J.; Fernández-Suárez, Xosé M. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1241	journal	January 2015
Experimental single-strain mobilomics reveals events that shape pathogen emergence Schoeniger, Joseph S.; Hudson, Corey M.; Bent, Zachary W. Nucleic Acids Research, Vol. 44, Issue 14 https://doi.org/10.1093/nar/gkw601	journal	July 2016
xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria Bush, Eliot C.; Clark, Anne E.; DeRanek, Carissa A. https://doi.org/10.1101/188599	posted_content	September 2017
Precise mapping of new group I introns in tRNA genes Williams, Kelly P. BioRxiv https://doi.org/10.1101/2020.01.27.920355	posted_content	January 2020
Draft Genome Sequence of Sinorhizobium meliloti Strain CXM1-105 Baturina, Olga A.; Muntyan, Victoria S.; Afonin, Alexey M. Microbiology Resource Announcements, Vol. 8, Issue 2 https://doi.org/10.1128/mra.01621-18	journal	January 2019
Identifying genomic islands with deep neural networks Assaf, Rida; Xia, Fangfang; Stevens, Rick BMC Genomics, Vol. 22, Issue S3 https://doi.org/10.1186/s12864-021-07575-5	journal	June 2021
A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands Uchiyama, Ikuo; Albritton, Jacob; Fukuyo, Masaki PLOS ONE, Vol. 11, Issue 8 https://doi.org/10.1371/journal.pone.0159419	journal	August 2016
Pan-genome analysis of Riemerella anatipestifer reveals its genomic diversity and acquired antibiotic resistance associated with genomic islands Zhu, Dekang; Yang, Zhishuang; Xu, Jinge Functional & Integrative Genomics, Vol. 20, Issue 3 https://doi.org/10.1007/s10142-019-00715-x	journal	October 2019
Impacts of horizontal gene transfer on the compact genome of the clavulanic acid-producing Streptomyces strain F613-1 Li, Jun; Zhao, Zhilong; Zhong, Weihong 3 Biotech, Vol. 8, Issue 11 https://doi.org/10.1007/s13205-018-1498-2	journal	November 2018
Microbial genomic island discovery, visualization and analysis Bertelli, Claire; Tilley, Keith E.; Brinkman, Fiona S. L. Briefings in Bioinformatics, Vol. 20, Issue 5 https://doi.org/10.1093/bib/bby042	journal	June 2018
New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements Mageeney, Catherine M.; Lau, Britney Y.; Wagner, Julian M. Nucleic Acids Research, Vol. 48, Issue 8 https://doi.org/10.1093/nar/gkaa156	journal	March 2020
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets Bertelli, Claire; Laird, Matthew R.; Williams, Kelly P. Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx343	journal	May 2017
Genome Sequences of Burkholderia thailandensis strains E421, E426, and DW503 Mageeney, Catherine M.; Sinha, Anupama; Williams, Kelly P. Microbiology Resource Announcements https://doi.org/10.1101/2020.01.24.915645	journal	January 2020
Systematic discovery of natural CRISPR-Cas12a inhibitors Watters, Kyle E.; Fellmann, Christof; Bai, Hua B. Science, Vol. 362, Issue 6411 https://doi.org/10.1126/science.aau5138	journal	September 2018
Genome Sequences of Burkholderia thailandensis Strains E421, E426, and DW503 Mageeney, Catherine M.; Sinha, Anupama; Williams, Kelly P. Microbiology Resource Announcements, Vol. 9, Issue 21 https://doi.org/10.1128/mra.00312-20	journal	May 2020
xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria Bush, Eliot C.; Clark, Anne E.; DeRanek, Carissa A. BMC Bioinformatics, Vol. 19, Issue 1 https://doi.org/10.1186/s12859-018-2038-0	journal	February 2018
Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2 Gonnella, Giorgio; Adam, Nicole; Perner, Mirjam BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-5710-5	journal	May 2019
Identification of virulence factors and antibiotic resistance markers using bacterial genomics Bakour, Sofiane; Sankar, Senthil Alias; Rathored, Jaishriram Future Microbiology, Vol. 11, Issue 3 https://doi.org/10.2217/fmb.15.149	journal	March 2016
Horizontally Acquired Homologs of Xenogeneic Silencers: Modulators of Gene Expression Encoded by Plasmids, Phages and Genomic Islands Piña-Iturbe, Alejandro; Suazo, Isidora D.; Hoppe-Elsholz, Guillermo Genes, Vol. 11, Issue 2 https://doi.org/10.3390/genes11020142	journal	January 2020
Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic Genus Pectobacterium Arizala, Dario; Arif, Mohammad Pathogens, Vol. 8, Issue 4 https://doi.org/10.3390/pathogens8040247	journal	November 2019

Similar Records

The tmRNA website

Journal Article · Tue Nov 04 23:00:00 EST 2014 · Nucleic Acids Research · OSTI ID:1183117

Ends of the line for tmRNA-SmpB

Journal Article · Wed Aug 13 00:00:00 EDT 2014 · Frontiers in Microbiology · OSTI ID:1137319

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
96 KNOWLEDGE MANAGEMENT AND PRESERVATION

Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes

Citation Formats

References (32)

Cited By (26)

Similar Records

Related Subjects