Zhao Y.,Xiamen University |
Zhao Y.,University of Maryland, Baltimore |
Wang K.,University of Maryland, Baltimore |
Ackermann H.-W.,Laval University |
And 4 more authors.
Applied and Environmental Microbiology | Year: 2010
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 Copyright © 2010, American Society for Microbiology. All Rights Reserved.
Identification of putative biomarkers for toluene-degrading burkholderia and pseudomonads by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and peptide mass fingerprinting
Hartmann E.M.,Arizona State University |
Hartmann E.M.,Center for Water and Health |
Colquhoun D.R.,Center for Water and Health |
Halden R.U.,Arizona State University |
Halden R.U.,Center for Water and Health
Bioscience, Biotechnology and Biochemistry | Year: 2010
The use of peptide mass fingerprinting with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was demonstrated to identify and phenotypically characterize toluene-degrading bacteria via biomarkers of degradation and taxonomical classification. Pseudomonas putida F1, P. mendocina KR1, and Burkholderia sp. JS150 were grown on toluene, extracted, electrophoretically separated, and analyzed by MALDI-TOF MS. Catabolic enzymes were identified and results substantiated using tandem MS.