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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ftusouthflorida:oai:digitalcommons.usf.edu:msc_facpub-1775 |
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Open Polar |
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University of South Florida St. Petersburg: Digital USFSP |
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ftusouthflorida |
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Life Sciences |
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Life Sciences McDaniel, Lauren D. Breitbart, Mya Mobberley, Jennifer M Long, Amy Haynes, Matthew Rohwer, Forest Paul, John Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression |
topic_facet |
Life Sciences |
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 |
Article in Journal/Newspaper |
author |
McDaniel, Lauren D. Breitbart, Mya Mobberley, Jennifer M Long, Amy Haynes, Matthew Rohwer, Forest Paul, John |
author_facet |
McDaniel, Lauren D. Breitbart, Mya Mobberley, Jennifer M Long, Amy Haynes, Matthew Rohwer, Forest Paul, John |
author_sort |
McDaniel, Lauren D. |
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 |
Digital Commons @ University of South Florida |
publishDate |
2008 |
url |
https://digitalcommons.usf.edu/msc_facpub/769 https://doi.org/10.1371/journal.pone.0003263 https://digitalcommons.usf.edu/context/msc_facpub/article/1775/viewcontent/Breitbart__Metagenomic_Analysis_of_Lysogeny_in_Tampa_Bay__Implications_for_Prophage_Gene_Expression.pdf https://digitalcommons.usf.edu/context/msc_facpub/article/1775/filename/0/type/additional/viewcontent/Breitbart__Metagenomic_Analysis__Supplementary__Table_1.DOC https://digitalcommons.usf.edu/context/msc_facpub/article/1775/filename/1/type/additional/viewcontent/Breitbart__Metagenomic_Analysis__Supplementary__Figure_1.TIF https://digitalcommons.usf.edu/context/msc_facpub/article/1775/filename/2/type/additional/viewcontent/Breitbart__Metagenomic_Analysis__Supplementary__Figure_2.TIF |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Marine Science Faculty Publications |
op_relation |
https://digitalcommons.usf.edu/msc_facpub/769 doi:10.1371/journal.pone.0003263 https://digitalcommons.usf.edu/context/msc_facpub/article/1775/viewcontent/Breitbart__Metagenomic_Analysis_of_Lysogeny_in_Tampa_Bay__Implications_for_Prophage_Gene_Expression.pdf https://digitalcommons.usf.edu/context/msc_facpub/article/1775/filename/0/type/additional/viewcontent/Breitbart__Metagenomic_Analysis__Supplementary__Table_1.DOC https://digitalcommons.usf.edu/context/msc_facpub/article/1775/filename/1/type/additional/viewcontent/Breitbart__Metagenomic_Analysis__Supplementary__Figure_1.TIF https://digitalcommons.usf.edu/context/msc_facpub/article/1775/filename/2/type/additional/viewcontent/Breitbart__Metagenomic_Analysis__Supplementary__Figure_2.TIF |
op_doi |
https://doi.org/10.1371/journal.pone.0003263 |
container_title |
PLoS ONE |
container_volume |
3 |
container_issue |
9 |
container_start_page |
e3263 |
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1772812849710628864 |
spelling |
ftusouthflorida:oai:digitalcommons.usf.edu:msc_facpub-1775 2023-07-30T04:02:08+02:00 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression McDaniel, Lauren D. Breitbart, Mya Mobberley, Jennifer M Long, Amy Haynes, Matthew Rohwer, Forest Paul, John 2008-01-01T08:00:00Z application/pdf https://digitalcommons.usf.edu/msc_facpub/769 https://doi.org/10.1371/journal.pone.0003263 https://digitalcommons.usf.edu/context/msc_facpub/article/1775/viewcontent/Breitbart__Metagenomic_Analysis_of_Lysogeny_in_Tampa_Bay__Implications_for_Prophage_Gene_Expression.pdf https://digitalcommons.usf.edu/context/msc_facpub/article/1775/filename/0/type/additional/viewcontent/Breitbart__Metagenomic_Analysis__Supplementary__Table_1.DOC https://digitalcommons.usf.edu/context/msc_facpub/article/1775/filename/1/type/additional/viewcontent/Breitbart__Metagenomic_Analysis__Supplementary__Figure_1.TIF https://digitalcommons.usf.edu/context/msc_facpub/article/1775/filename/2/type/additional/viewcontent/Breitbart__Metagenomic_Analysis__Supplementary__Figure_2.TIF unknown Digital Commons @ University of South Florida https://digitalcommons.usf.edu/msc_facpub/769 doi:10.1371/journal.pone.0003263 https://digitalcommons.usf.edu/context/msc_facpub/article/1775/viewcontent/Breitbart__Metagenomic_Analysis_of_Lysogeny_in_Tampa_Bay__Implications_for_Prophage_Gene_Expression.pdf https://digitalcommons.usf.edu/context/msc_facpub/article/1775/filename/0/type/additional/viewcontent/Breitbart__Metagenomic_Analysis__Supplementary__Table_1.DOC https://digitalcommons.usf.edu/context/msc_facpub/article/1775/filename/1/type/additional/viewcontent/Breitbart__Metagenomic_Analysis__Supplementary__Figure_1.TIF https://digitalcommons.usf.edu/context/msc_facpub/article/1775/filename/2/type/additional/viewcontent/Breitbart__Metagenomic_Analysis__Supplementary__Figure_2.TIF Marine Science Faculty Publications Life Sciences article 2008 ftusouthflorida https://doi.org/10.1371/journal.pone.0003263 2023-07-13T20:45:39Z 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 ... Article in Journal/Newspaper Arctic University of South Florida St. Petersburg: Digital USFSP Arctic PLoS ONE 3 9 e3263 |