Insights and inferences about integron evolution from genomic data

<p>Abstract</p> <p>Background</p> <p>Integrons are mechanisms that facilitate horizontal gene transfer, allowing bacteria to integrate and express foreign DNA. These are important in the exchange of antibiotic resistance determinants, but can also transfer a diverse sui...

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Main Authors: Martin Andrew P, Kysela Robert F, Robeson Michael S, Nemergut Diana R, Schmidt Steven K, Knight Rob
Format: Article
Language:English
Published: BMC 2008-05-01
Series:BMC Genomics
Online Access:http://www.biomedcentral.com/1471-2164/9/261
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spelling doaj-146942d6e51d4b7c968460915127a79b2020-11-24T20:51:10ZengBMCBMC Genomics1471-21642008-05-019126110.1186/1471-2164-9-261Insights and inferences about integron evolution from genomic dataMartin Andrew PKysela Robert FRobeson Michael SNemergut Diana RSchmidt Steven KKnight Rob<p>Abstract</p> <p>Background</p> <p>Integrons are mechanisms that facilitate horizontal gene transfer, allowing bacteria to integrate and express foreign DNA. These are important in the exchange of antibiotic resistance determinants, but can also transfer a diverse suite of genes unrelated to pathogenicity. Here, we provide a systematic analysis of the distribution and diversity of integron <it>intI </it>genes and integron-containing bacteria.</p> <p>Results</p> <p>We found integrons in 103 different pathogenic and non-pathogenic bacteria, in six major phyla. Integrons were widely scattered, and their presence was not confined to specific clades within bacterial orders. Nearly 1/3 of the <it>intI </it>genes that we identified were pseudogenes, containing either an internal stop codon or a frameshift mutation that would render the protein product non-functional. Additionally, 20% of bacteria contained more than one integrase gene. dN/dS ratios revealed mutational hotspots in clades of <it>Vibrio </it>and <it>Shewanella intI </it>genes. Finally, we characterized the gene cassettes associated with integrons in <it>Methylobacillus flagellatus </it>KT and <it>Dechloromonas aromatica </it>RCB, and found a heavy metal efflux gene as well as genes involved in protein folding and stability.</p> <p>Conclusion</p> <p>Our analysis suggests that the present distribution of integrons is due to multiple losses and gene transfer events. While, in some cases, the ability to integrate and excise foreign DNA may be selectively advantageous, the gain, loss, or rearrangment of gene cassettes could also be deleterious, selecting against functional integrases. Thus, such a high fraction of pseudogenes may suggest that the selective impact of integrons on genomes is variable, oscillating between beneficial and deleterious, possibly depending on environmental conditions.</p> http://www.biomedcentral.com/1471-2164/9/261
collection DOAJ
language English
format Article
sources DOAJ
author Martin Andrew P
Kysela Robert F
Robeson Michael S
Nemergut Diana R
Schmidt Steven K
Knight Rob
spellingShingle Martin Andrew P
Kysela Robert F
Robeson Michael S
Nemergut Diana R
Schmidt Steven K
Knight Rob
Insights and inferences about integron evolution from genomic data
BMC Genomics
author_facet Martin Andrew P
Kysela Robert F
Robeson Michael S
Nemergut Diana R
Schmidt Steven K
Knight Rob
author_sort Martin Andrew P
title Insights and inferences about integron evolution from genomic data
title_short Insights and inferences about integron evolution from genomic data
title_full Insights and inferences about integron evolution from genomic data
title_fullStr Insights and inferences about integron evolution from genomic data
title_full_unstemmed Insights and inferences about integron evolution from genomic data
title_sort insights and inferences about integron evolution from genomic data
publisher BMC
series BMC Genomics
issn 1471-2164
publishDate 2008-05-01
description <p>Abstract</p> <p>Background</p> <p>Integrons are mechanisms that facilitate horizontal gene transfer, allowing bacteria to integrate and express foreign DNA. These are important in the exchange of antibiotic resistance determinants, but can also transfer a diverse suite of genes unrelated to pathogenicity. Here, we provide a systematic analysis of the distribution and diversity of integron <it>intI </it>genes and integron-containing bacteria.</p> <p>Results</p> <p>We found integrons in 103 different pathogenic and non-pathogenic bacteria, in six major phyla. Integrons were widely scattered, and their presence was not confined to specific clades within bacterial orders. Nearly 1/3 of the <it>intI </it>genes that we identified were pseudogenes, containing either an internal stop codon or a frameshift mutation that would render the protein product non-functional. Additionally, 20% of bacteria contained more than one integrase gene. dN/dS ratios revealed mutational hotspots in clades of <it>Vibrio </it>and <it>Shewanella intI </it>genes. Finally, we characterized the gene cassettes associated with integrons in <it>Methylobacillus flagellatus </it>KT and <it>Dechloromonas aromatica </it>RCB, and found a heavy metal efflux gene as well as genes involved in protein folding and stability.</p> <p>Conclusion</p> <p>Our analysis suggests that the present distribution of integrons is due to multiple losses and gene transfer events. While, in some cases, the ability to integrate and excise foreign DNA may be selectively advantageous, the gain, loss, or rearrangment of gene cassettes could also be deleterious, selecting against functional integrases. Thus, such a high fraction of pseudogenes may suggest that the selective impact of integrons on genomes is variable, oscillating between beneficial and deleterious, possibly depending on environmental conditions.</p>
url http://www.biomedcentral.com/1471-2164/9/261
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