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Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
Published on: June 11, 2015
Searching for a "hidden" prophage in a marine bacterium
Yanlin Zhao1, Kui Wang, Hans-Wolfgang Ackermann
1State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China.
Applied and Environmental Microbiology
|December 2, 2009
Summary
Hidden prophages, like ISM-pro1 in Roseovarius nubinhibens, can be missed by standard genomic analysis. Experimental induction and detailed genomic study are crucial for identifying inducible prophages in bacteria.
Area of Science:
- Microbiology
- Genomics
- Virology
Background:
- Prophages are integrated viral DNA within bacterial genomes, often challenging to identify.
- Standard bioinformatic analysis may miss cryptic or remnant prophages.
- The marine bacterium Roseovarius nubinhibens ISM was previously reported to lack intact prophages.
Purpose of the Study:
- To investigate the presence of inducible prophages in Roseovarius nubinhibens ISM.
- To characterize a newly identified prophage within the ISM genome.
- To explore the implications of this prophage for bacterial evolution and gene transfer.
Main Methods:
- Prophage induction using mitomycin C.
- Genomic sequencing and detailed bioinformatic analysis of the ISM genome.
- Comparative genomic analysis with other Rhodobacterales genomes.
- Reannotation of open reading frames (ORFs) within the putative prophage.
Main Results:
- Prophage induction experiments revealed a significant increase in virus-like particles.
- A cryptic prophage, ISM-pro1, was identified in the ISM genome.
- ISM-pro1 contains minimal phage-like genes, with most ORFs showing similarity to Rhodobacterales genes.
- ISM-pro1-like prophages are present in other Rhodobacterales genomes.
- Prophage-mediated lysis of ISM increased gene transfer agent (GTA) production.
Conclusions:
- A combination of in silico genomic analysis and experimental induction is essential for detecting cryptic prophages.
- The identified prophage (ISM-pro1) is inducible and represents a previously unrecognized lysogenic feature of Roseovarius nubinhibens.
- The presence of such prophages may influence bacterial evolution and the dissemination of genetic material.
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