Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression
Phage integrase genes often play a role in the establishment of lysogeny in temperate phage by catalyzing the integration of the phage into one of the host's replicons. To investigate temperate phage gene expression, an induced viral metagenome from Tampa Bay was sequenced by 454/Pyrosequencing...
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ftpubmed:oai:pubmedcentral.nih.gov:2533394 2023-05-15T15:16:41+02:00 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression McDaniel, Lauren Breitbart, Mya Mobberley, Jennifer Long, Amy Haynes, Matthew Rohwer, Forest Paul, John H. 2008-09-23 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533394 http://www.ncbi.nlm.nih.gov/pubmed/18810270 https://doi.org/10.1371/journal.pone.0003263 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533394 http://www.ncbi.nlm.nih.gov/pubmed/18810270 http://dx.doi.org/10.1371/journal.pone.0003263 McDaniel et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Research Article Text 2008 ftpubmed https://doi.org/10.1371/journal.pone.0003263 2013-09-02T05:12:44Z Phage integrase genes often play a role in the establishment of lysogeny in temperate phage by catalyzing the integration of the phage into one of the host's replicons. To investigate temperate phage gene expression, an induced viral metagenome from Tampa Bay was sequenced by 454/Pyrosequencing. The sequencing yielded 294,068 reads with 6.6% identifiable. One hundred-three sequences had significant similarity to integrases by BLASTX analysis (e≤0.001). Four sequences with strongest amino-acid level similarity to integrases were selected and real-time PCR primers and probes were designed. Initial testing with microbial fraction DNA from Tampa Bay revealed 1.9×107, and 1300 gene copies of Vibrio-like integrase and Oceanicola-like integrase L−1 respectively. The other two integrases were not detected. The integrase assay was then tested on microbial fraction RNA extracted from 200 ml of Tampa Bay water sampled biweekly over a 12 month time series. Vibrio-like integrase gene expression was detected in three samples, with estimated copy numbers of 2.4-1280 L−1. Clostridium-like integrase gene expression was detected in 6 samples, with estimated copy numbers of 37 to 265 L−1. In all cases, detection of integrase gene expression corresponded to the occurrence of lysogeny as detected by prophage induction. Investigation of the environmental distribution of the two expressed integrases in the Global Ocean Survey Database found the Vibrio-like integrase was present in genome equivalents of 3.14% of microbial libraries and all four viral metagenomes. There were two similar genes in the library from British Columbia and one similar gene was detected in both the Gulf of Mexico and Sargasso Sea libraries. In contrast, in the Arctic library eleven similar genes were observed. The Clostridium-like integrase was less prevalent, being found in 0.58% of the microbial and none of the viral libraries. These results underscore the value of metagenomic data in discovering signature genes that play important roles in the environment ... Text Arctic PubMed Central (PMC) Arctic PLoS ONE 3 9 e3263 |
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Research Article McDaniel, Lauren Breitbart, Mya Mobberley, Jennifer Long, Amy Haynes, Matthew Rohwer, Forest Paul, John H. Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression |
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Research Article |
description |
Phage integrase genes often play a role in the establishment of lysogeny in temperate phage by catalyzing the integration of the phage into one of the host's replicons. To investigate temperate phage gene expression, an induced viral metagenome from Tampa Bay was sequenced by 454/Pyrosequencing. The sequencing yielded 294,068 reads with 6.6% identifiable. One hundred-three sequences had significant similarity to integrases by BLASTX analysis (e≤0.001). Four sequences with strongest amino-acid level similarity to integrases were selected and real-time PCR primers and probes were designed. Initial testing with microbial fraction DNA from Tampa Bay revealed 1.9×107, and 1300 gene copies of Vibrio-like integrase and Oceanicola-like integrase L−1 respectively. The other two integrases were not detected. The integrase assay was then tested on microbial fraction RNA extracted from 200 ml of Tampa Bay water sampled biweekly over a 12 month time series. Vibrio-like integrase gene expression was detected in three samples, with estimated copy numbers of 2.4-1280 L−1. Clostridium-like integrase gene expression was detected in 6 samples, with estimated copy numbers of 37 to 265 L−1. In all cases, detection of integrase gene expression corresponded to the occurrence of lysogeny as detected by prophage induction. Investigation of the environmental distribution of the two expressed integrases in the Global Ocean Survey Database found the Vibrio-like integrase was present in genome equivalents of 3.14% of microbial libraries and all four viral metagenomes. There were two similar genes in the library from British Columbia and one similar gene was detected in both the Gulf of Mexico and Sargasso Sea libraries. In contrast, in the Arctic library eleven similar genes were observed. The Clostridium-like integrase was less prevalent, being found in 0.58% of the microbial and none of the viral libraries. These results underscore the value of metagenomic data in discovering signature genes that play important roles in the environment ... |
format |
Text |
author |
McDaniel, Lauren Breitbart, Mya Mobberley, Jennifer Long, Amy Haynes, Matthew Rohwer, Forest Paul, John H. |
author_facet |
McDaniel, Lauren Breitbart, Mya Mobberley, Jennifer Long, Amy Haynes, Matthew Rohwer, Forest Paul, John H. |
author_sort |
McDaniel, Lauren |
title |
Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression |
title_short |
Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression |
title_full |
Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression |
title_fullStr |
Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression |
title_full_unstemmed |
Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression |
title_sort |
metagenomic analysis of lysogeny in tampa bay: implications for prophage gene expression |
publisher |
Public Library of Science |
publishDate |
2008 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533394 http://www.ncbi.nlm.nih.gov/pubmed/18810270 https://doi.org/10.1371/journal.pone.0003263 |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533394 http://www.ncbi.nlm.nih.gov/pubmed/18810270 http://dx.doi.org/10.1371/journal.pone.0003263 |
op_rights |
McDaniel et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0003263 |
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PLoS ONE |
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3 |
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9 |
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