scholarly journals Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24

PLoS ONE ◽  
2016 ◽  
Vol 11 (4) ◽  
pp. e0154233 ◽  
Author(s):  
Sang-Yeop Lee ◽  
Gun-Hwa Kim ◽  
Sung Ho Yun ◽  
Chi-Won Choi ◽  
Yoon-Sun Yi ◽  
...  
Keyword(s):  
Aromatic Hydrocarbon ◽  
Hydrocarbon Degradation ◽  
Degradation Pathways ◽  
Degrading Bacterium

scholarly journals Correction: Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-degrading Bacterium Burkholderia sp. K24

PLoS ONE ◽  
2016 ◽  
Vol 11 (6) ◽  
pp. e0157201
Author(s):  
Sang-Yeop Lee ◽  
Gun-Hwa Kim ◽  
Sung Ho Yun ◽  
Chi-Won Choi ◽  
Yoon-Sun Yi ◽  
...  
Keyword(s):  
Aromatic Hydrocarbon ◽  
Hydrocarbon Degradation ◽  
Degradation Pathways ◽  
Degrading Bacterium

scholarly journals Cloning, Expression, and Characterization of the katGGene, Encoding Catalase-Peroxidase, from the Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Mycobacterium sp. Strain PYR-1

2000 ◽  
Vol 66 (10) ◽  
pp. 4300-4304 ◽  
Author(s):  
Rong-Fu Wang ◽  
David Wennerstrom ◽  
Wei-Wen Cao ◽  
Ashraf A. Khan ◽  
Carl E. Cerniglia
Keyword(s):  
Polycyclic Aromatic Hydrocarbon ◽  
Aromatic Hydrocarbon ◽  
Genomic Library ◽  
Mycobacterium Fortuitum ◽  
Gene Encoding ◽  
Two Dimensional Gel Electrophoresis ◽  
Degrading Bacterium ◽  
Polycyclic Aromatic ◽  
Catalase Peroxidase

ABSTRACT A 81-kDa protein from Mycobacterium sp. strain PYR-1 was expressed in response to exposure of the strain to the polycyclic aromatic hydrocarbon pyrene and recovered by two-dimensional gel electrophoresis. The N-terminal sequence of the protein indicated that it was similar to catalase-peroxidase. An oligonucleotide probe designed from this sequence was used to screen a genomic library ofMycobacterium sp. strain PYR-1, and a positive clone, containing a part of the gene encoding the 81-kDa protein, was isolated. A gene-walking technique was used to sequence the entire gene, which was identified as katG for catalase-peroxidase. The deduced KatG protein sequence showed significant homology to KatGII of Mycobacterium fortuitum and clustered with catalase-peroxidase proteins from other Mycobacteriumspecies in a phylogenetic tree. The katG gene was expressed in Escherichia coli to produce a protein with catalase-peroxidase activity. Since the induction of this catalase-peroxidase occurred in pyrene-induced cultures and the exposure of these cultures to hydrogen peroxide reduced pyrene metabolism, our data suggest that this enzyme plays a role in polycyclic aromatic hydrocarbon metabolism by strain PYR-1.

scholarly journals CANT-HYD: A curated database of phylogeny-derived Hidden Markov Models for annotation of marker genes involved in hydrocarbon degradation

2021 ◽  
Author(s):  
Varada Khot ◽  
Jackie Zorz ◽  
Daniel A Gittins ◽  
Anirban Chakraborty ◽  
Emma Bell ◽  
...  
Keyword(s):  
Markov Models ◽  
Hydrocarbon Degradation ◽  
Marker Genes ◽  
Degradation Pathways ◽  
Metabolic Potential ◽  
Accurate Identification ◽  
Isolation And Characterization ◽  
Anaerobic Hydrocarbon Degradation ◽  
Aliphatic And Aromatic Hydrocarbons

Discovery of microbial hydrocarbon degradation pathways has traditionally relied on laboratory isolation and characterization of microorganisms. Although many metabolic pathways for hydrocarbon degradation have been discovered, the absence of tools dedicated to their annotation makes it difficult to identify the relevant genes and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Furthermore, sequence homology between hydrocarbon degradation genes and genes with other functions often results in misannotation. A tool that systematically identifies hydrocarbon metabolic potential is therefore needed. We present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database containing HMMs of 37 marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we show that hydrocarbon metabolic potential is widespread in the tree of life and identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate scalability by analyzing large metagenomic datasets for the prediction of hydrocarbon utilization in diverse environments. To the best of our knowledge, CANT-HYD is the first comprehensive tool for robust and accurate identification of marker genes associated with aerobic and anaerobic hydrocarbon degradation.

scholarly journals An Uncultivated Nitrate-Reducing Member of the Genus Herminiimonas Degrades Toluene

2014 ◽  
Vol 80 (10) ◽  
pp. 3233-3243 ◽  
Author(s):  
So-Jeong Kim ◽  
Soo-Je Park ◽  
Man-Young Jung ◽  
Jong-Geol Kim ◽  
Eugene L. Madsen ◽  
...  
Keyword(s):  
Aromatic Hydrocarbon ◽  
Sequence Similarity ◽  
Draft Genome ◽  
Stable Isotope Probing ◽  
Hydrocarbon Degradation ◽  
Metabolic Reconstruction ◽  
Content Type ◽  
Degrading Bacterium ◽  
Gene Acquisition ◽  
Catabolic Genes

ABSTRACTStable isotope probing (SIP) is a cultivation-free methodology that provides information about the identity of microorganisms participating in assimilatory processes in complex communities. In this study, aHerminiimonas-related bacterium was identified as the dominant member of a denitrifying microcosm fed [13C]toluene. The genome of the uncultivated toluene-degrading bacterium was obtained by applying pyrosequencing to the heavy DNA fraction. The draft genome comprised ∼3.8 Mb, in 131 assembled contigs. Metabolic reconstruction of aromatic hydrocarbon (toluene, benzoate,p-cresol, 4-hydroxybenzoate, phenylacetate, and cyclohexane carboxylate) degradation indicated that the bacterium might specialize in anaerobic hydrocarbon degradation. This characteristic is novel for the orderBurkholderialeswithin the classBetaproteobacteria. Under aerobic conditions, the benzoate oxidation gene cluster (BOX) system is likely involved in the degradation of benzoate via benzoyl coenzyme A. Many putative genes for aromatic hydrocarbon degradation were closely related to those in theRhodocyclaceae(particularlyAromatoleum aromaticumEbN1) with respect to organization and sequence similarity. Putative mobile genetic elements associated with these catabolic genes were highly abundant, suggesting gene acquisition byHerminiimonasvia horizontal gene transfer.

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