Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria.

A variety of bacteria in the environment can utilize xenobiotic compounds as a source of carbon and energy. The bacterial strains degrading xenobiotics are suitable models to investigate the adaptation and evolutionary processes of bacteria because they appear to have emerged relatively soon after the release of these compounds into the natural environment. Analyses of bacterial genome sequences indicate that horizontal gene transfer (HGT) is the most important contributor to the bacterial evolution of genetic architecture.

A New ICE Subfamily Integrative and Conjugative Element Responsible for Horizontal Transfer of Biphenyl and Salicylic Acid Catabolic Pathway in the PCB-Degrading Strain KF716.

Integrative and conjugative elements (ICEs) are chromosomally integrated self-transmissible mobile genetic elements. Although some ICEs are known to carry genes for the degradation of aromatic compounds, information on their genetic features is limited. We identified a new member of the ICE family carrying biphenyl catabolic genes and salicylic acid catabolic genes from the PCB-degrading strain KF716.

Biphenyl/PCB Degrading Genes of Ten Bacterial Strains Isolated from Biphenyl-Contaminated Soil in Kitakyushu, Japan: Comparative and Dynamic Features as Integrative Conjugative Elements (ICEs).

We sequenced the entire genomes of ten biphenyl/PCB degrading bacterial strains (KF strains) isolated from biphenyl-contaminated soil in Kitakyushu, Japan. All the strains were Gram-negative bacteria belonging to β- and γ-proteobacteria. Out of the ten strains, nine strains carried a biphenyl catabolic gene cluster as integrative conjugative elements (ICEs), and they were classified into four groups based on the structural features of the genes.

Pseudomonas furukawaii sp. nov., a polychlorinated biphenyl-degrading bacterium isolated from biphenyl-contaminated soil in Japan.

Strain KF707 was isolated from a biphenyl-contaminated site in Kitakyushu, Japan. Analysis of 16S rRNA gene sequences, retrieved from the whole-genome sequence, revealed that the isolate was closely related to members of the genus Pseudomonas, sharing the highest sequence similarities with Pseudomonas balearica strain SP1402 (DSM 6083) (97.8 %).

Insights into the genomic plasticity of Pseudomonas putida KF715, a strain with unique biphenyl-utilizing activity and genome instability properties.

Pseudomonas putida KF715 exhibits unique properties in both catabolic activity and genome plasticity. Our previous studies revealed that the DNA region containing biphenyl and salycilate metabolism gene clusters (termed the bph-sal element) was frequently deleted and transferred by conjugation to closely related P. putida strains.

Complete Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium KF715 (NBRC 110667) Isolated from Biphenyl-Contaminated Soil.

KF715 (NBRC 110667) utilizes biphenyl as a sole source of carbon and degrades polychlorinated biphenyls (PCBs). Here, we report a complete genome sequence of the KF715 strain, which comprises a circular chromosome and four plasmids. Biphenyl catabolic genes were located on the largest plasmid, pKF715A.

Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas stutzeri KF716 (NBRC 110668).

Pseudomonas stutzeri KF716 (NBRC 110668) utilizes biphenyl as a sole source of carbon and energy and degrades polychlorinated biphenyls. Here, we report the first draft genome sequence of a biphenyl-degrading strain of the species P. stutzeri.

Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Comamonas testosteroni KF712 (NBRC 110673).

We present a 5.89-Mb draft genome sequence of Comamonas testosteroni KF712 (NBRC 110673), a polychlorinated biphenyl degrader. The genome sequence clarified that KF712 harbors the gene clusters coding for the catabolism of biphenyl and at least seven other aromatic compounds.

Draft Genome Sequence of Pseudomonas aeruginosa KF702 (NBRC 110665), a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated Soil.

Pseudomonas aeruginosa KF702 (NBRC 110665) utilizes biphenyl as a sole source of carbon and degrades polychlorinated biphenyls (PCBs). Here, we report the 7,167,540-bp draft genome sequence of KF702, which contains 6,714 coding sequences and a 65.8 mol% G+C content.

Draft Genome Sequence of Pseudomonas abietaniphila KF701 (NBRC110664), a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated Soil.

Pseudomonas abietaniphila KF701 utilizes biphenyl as a sole source of carbon and degrades polychlorinated biphenyls (PCBs). Here, we report the 6,886,250-bp draft genome sequence of KF701, which contains 6,315 coding sequences and 59.4 mol% G+C content.

Draft Genome Sequence of Pseudomonas toyotomiensis KF710, a Polychlorinated Biphenyl-Degrading Bacterium Isolated from Biphenyl-Contaminated Soil.

Pseudomonas toyotomiensis KF710 utilizes biphenyl and degrades polychlorinated biphenyls (PCBs). Here, we report the genome sequence of the KF710 strain, consisting of 5,596,721 bp with 5,155 coding sequences. The biphenyl catabolic genes were almost identical to those of Pseudomonas pseudoalcaligenes KF707, one of the most well-characterized biphenyl-utilizing strains.

Draft Genome Sequence of Cupriavidus pauculus Strain KF709, a Biphenyl-Utilizing Bacterium Isolated from Biphenyl-Contaminated Soil.

We report the draft genome sequence of Cupriavidus pauculus strain KF709, which comprises 6,826,799 bp with 6,272 coding sequences. The strain KF709 utilizes biphenyl and degrades low-chlorinated biphenyls; however, it possesses fewer coding sequences involved in the degradation of aromatic compounds than other strains belonging to the Betaproteobacteria.

Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Cupriavidus basilensis KF708 (NBRC 110671) Isolated from Biphenyl-Contaminated Soil.

We report the draft genome sequence of Cupriavidus basilensis KF708 (NBRC 110671), which utilizes biphenyl as a sole carbon source and degrades polychlorinated biphenyls (PCBs). The KF708 strain possesses genes for biphenyl catabolism and other genes involved in various aromatic compounds.

Draft Genome Sequence of the Polychlorinated Biphenyl-Degrading Bacterium Pseudomonas putida KF703 (NBRC 110666) Isolated from Biphenyl-Contaminated Soil.

Pseudomonas putida KF703 (NBRC 110666) utilizes biphenyl as a sole source of carbon and degrades polychlorinated biphenyls (PCBs). Here, we report the draft genome sequence of the KF703 strain, which provides insight into the molecular mechanisms of adaptation to an environment polluted by aromatic compounds.

Draft Genome Sequence of Pseudomonas abietaniphila KF717 (NBRC 110669), Isolated from Biphenyl-Contaminated Soil in Japan.

Pseudomonas abietaniphila KF717 utilizes biphenyl as a sole source of carbon and energy and degrades polychlorinated biphenyls (PCBs). We report here the 6,930,016-bp genome sequence of this strain, which contains 6,323 predicted coding sequences (CDSs), including the biphenyl-utilizing bph gene cluster.

Efficient screening of environmental isolates for Saccharomyces cerevisiae strains that are suitable for brewing.

We developed an efficient screening method for Saccharomyces cerevisiae strains from environmental isolates. MultiPlex PCR was performed targeting four brewing S. cerevisiae genes (SSU1, AWA1, BIO6, and FLO1).

Evaluation of the inhibitory effects of chloroform on ortho-chlorophenol- and chloroethene-dechlorinating Desulfitobacterium strains.

Organohalide-respiring Desulfitobacterium strains are believed to play an important role in the bioremediation and natural attenuation of chlorinated aliphatic and aromatic hydrocarbons. However, several studies have reported that chloroform significantly inhibits microbial reductive dechlorination of chloroethene. In this study, we examined the effect of chloroform on several Desulfitobacterium strains, including ortho-chlorophenol-dechlorinating Desulfitobacterium dehalogenans JW/IU-1 and Desulfitobacterium hafniense DCB-2, and also the chloroethene-dechlorinating strain D.

Hybrid pseudomonads engineered by two-step homologous recombination acquire novel degradation abilities toward aromatics and polychlorinated biphenyls.

Pseudomonas pseudoalcaligenes KF707 possesses a chromosomally encoded bph gene cluster responsible for the catabolism of biphenyl and polychlorinated biphenyls. Previously, we constructed chimeric versions of the bphA1 gene, which encodes a large subunit of biphenyl dioxygenase, by using DNA shuffling between bphA1 genes from P. pseudoalcaligenes KF707 and Burkholderia xenovorans LB400.

Microbial degradation of polychlorinated biphenyls: biochemical and molecular features.

It is more than 40 years since the environmental contamination of polychlorinated biphenyls (PCBs) was first reported in wildlife samples. Since then, a huge number of papers on PCBs have been published, which include the biodegradation of PCBs and toxicology of PCBs. The studies on the microbial degradation of PCBs during the few decades provided significant insight into the areas of microbial ecology, biochemistry, and molecular genetics.

Cross-regulation of biphenyl- and salicylate-catabolic genes by two regulatory systems in Pseudomonas pseudoalcaligenes KF707.

Pseudomonas pseudoalcaligenes KF707 grows on biphenyl and salicylate as sole sources of carbon. The biphenyl-catabolic (bph) genes are organized as bphR1A1A2(orf3)A3A4BCX0X1X2X3D, encoding the enzymes for conversion of biphenyl to acetyl coenzyme A. In this study, the salicylate-catabolic (sal) gene cluster encoding the enzymes for conversion of salicylate to acetyl coenzyme A were identified 6.

Characterization of the second LysR-type regulator in the biphenyl-catabolic gene cluster of Pseudomonas pseudoalcaligenes KF707.

Pseudomonas pseudoalcaligenes KF707 possesses a biphenyl-catabolic (bph) gene cluster consisting of bphR1A1A2-(orf3)-bphA3A4BCX0X1X2X3D. The bphR1 (formerly orf0) gene product, which belongs to the GntR family, is a positive regulator for itself and bphX0X1X2X3D. Further analysis in this study revealed that a second regulator belonging to the LysR family (designated bphR2) is involved in the regulation of the bph genes in KF707.