Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression

نویسندگان

  • Lauren McDaniel
  • Mya Breitbart
  • Jennifer Mobberley
  • Amy Long
  • Matthew Haynes
  • Forest Rohwer
  • John H. Paul
چکیده

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 < or =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 x 10(7), 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 through their expression, as demonstrated by integrases in lysogeny.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Seasonal variation in lysogeny as depicted by prophage induction in Tampa Bay, Florida.

A seasonal study of the distribution of lysogenic bacteria in Tampa Bay, Florida, was conducted over a 13-month period. Biweekly water samples were collected and either were left unaltered or had the viral population reduced by filtration (pore size, 0.2 micro m) and resuspension in filtered (pore size, 0.2 micro m) water. Virus-reduced and unaltered samples were then treated by adding mitomyci...

متن کامل

Transcription termination controls prophage maintenance in Escherichia coli genomes.

Prophages represent a large fraction of prokaryotic genomes and often provide new functions to their hosts, in particular virulence and fitness. How prokaryotic cells maintain such gene providers is central for understanding bacterial genome evolution by horizontal transfer. Prophage excision occurs through site-specific recombination mediated by a prophage-encoded integrase. In addition, a rec...

متن کامل

Bacteria-Phage Models with a Focus on Prophage as a Genetic Reservoir

Temperate bacteriophages have the ability to incorporate their genetic material in the host’s DNA, which may be utilized by later generations of phage to overcome the host’s receptorbased defences. This effect of temperance can have major implications for the long-term survival of the phages as well as on bacteria-phage community evolution. To study the impact of prophage on microbial communiti...

متن کامل

Seasonal and Diel Abundance of Viruses and Occurrence of Lysogeny/Bacteriocinogeny in the Marine Environment

To understand the role of viruses in the marine environment, it is important to know the factors affecting their temporal distribution and the abundance of lysogens. We therefore performed a seasonal and a diel study on viral distribution in Tampa Bay, Florida, USA, and detected the abundance of lysogens and bacteriocinogens amongst marine bacterial isolates from diverse marine environments. We...

متن کامل

Escherichia coli nfuA is essential for maintenance of Shiga toxin phage Min27 lysogeny under iron-depleted condition.

It has been earlier hypothesized that lysogenic infection with Stx-encoding phages influences protein expression in the bacterial host, and therefore, some differentially expressed proteins could affect survival characteristics and pathogenicity. We compared the protein expression profiles of the host MG1655 and lysogens by 2D electrophoresis. Four different genes identified were all related to...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:
  • PLoS ONE

دوره 3  شماره 

صفحات  -

تاریخ انتشار 2008