TY - JOUR
T1 - Searching for a "Hidden" Prophase in a marine bacterium
AU - Zhao, Yanlin
AU - Wang, Kui
AU - Ackermann, Hans Wolfgang
AU - Halden, Rolf
AU - Jiao, Nianzhi
AU - Chen, Feng
PY - 2010/1
Y1 - 2010/1
N2 - Prophages are common in many bacterial genomes. Distinguishing putatively viable prophages from nonviable sequences can be a challenge, since some prophages are remnants of once-functional prophages that have been rendered inactive by mutational changes. In some cases, a putative prophage may be missed due to the lack of recognizable prophage loci. The genome of a marine roseobacter, Roseovarius nubinhibens ISM (hereinafter referred to as ISM), was recently sequenced and was reported to contain no intact prophage based on customary bioinformatic analysis. However, prophage induction experiments performed with this organism led to a different conclusion. In the laboratory, virus-like particles in the ISM culture increased more than 3 orders of magnitude following induction with mitomycin C. After careful examination of the ISM genome sequence, a putative prophage (ISM-prol) was identified. Although this prophage contains only minimal phage-like genes, we demonstrated that this "hidden" prophage is inducible. Genomic analysis and reannotation showed that most of the ISM-prol open reading frames (ORFs) display the highest sequence similarity with Rhodobacterales bacterial genes and some ORFs are only distantly related to genes of other known phages or prophages. Comparative genomic analyses indicated that ISM-prol-like prophages or prophage remnants are also present in other Rhodobacterales genomes. In addition, the lysis of ISM by this previously unrecognized prophage appeared to increase the production of gene transfer agents (GTAs). Our study suggests that a combination of in silico genomic analyses and experimental laboratory work is needed to fully understand the lysogenic features of a given bacterium
AB - Prophages are common in many bacterial genomes. Distinguishing putatively viable prophages from nonviable sequences can be a challenge, since some prophages are remnants of once-functional prophages that have been rendered inactive by mutational changes. In some cases, a putative prophage may be missed due to the lack of recognizable prophage loci. The genome of a marine roseobacter, Roseovarius nubinhibens ISM (hereinafter referred to as ISM), was recently sequenced and was reported to contain no intact prophage based on customary bioinformatic analysis. However, prophage induction experiments performed with this organism led to a different conclusion. In the laboratory, virus-like particles in the ISM culture increased more than 3 orders of magnitude following induction with mitomycin C. After careful examination of the ISM genome sequence, a putative prophage (ISM-prol) was identified. Although this prophage contains only minimal phage-like genes, we demonstrated that this "hidden" prophage is inducible. Genomic analysis and reannotation showed that most of the ISM-prol open reading frames (ORFs) display the highest sequence similarity with Rhodobacterales bacterial genes and some ORFs are only distantly related to genes of other known phages or prophages. Comparative genomic analyses indicated that ISM-prol-like prophages or prophage remnants are also present in other Rhodobacterales genomes. In addition, the lysis of ISM by this previously unrecognized prophage appeared to increase the production of gene transfer agents (GTAs). Our study suggests that a combination of in silico genomic analyses and experimental laboratory work is needed to fully understand the lysogenic features of a given bacterium
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U2 - 10.1128/AEM.01450-09
DO - 10.1128/AEM.01450-09
M3 - Article
C2 - 19948862
AN - SCOPUS:75249087084
SN - 0099-2240
VL - 76
SP - 589
EP - 595
JO - Applied and environmental microbiology
JF - Applied and environmental microbiology
IS - 2
ER -