title: Comparative Genomics and Metabolic Analysis Reveals Peculiar Characteristics of Rhodococcus opacus Strain M213 Particularly for Naphthalene Degradation.
abstract: The genome of Rhodococcus opacus strain M213, isolated from a fuel-oil contaminated soil, was sequenced and annotated which revealed a genome size of 9,194,165 bp encoding 8680 putative genes and a G+C content of 66.72%. Among the protein coding genes, 71.77% were annotated as clusters of orthologous groups of proteins (COGs); 55% of the COGs were present as paralog clusters. Pulsed field gel electrophoresis (PFGE) analysis of M213 revealed the presence of three different sized replicons- a circular chromosome and two megaplasmids (pNUO1 and pNUO2) estimated to be of 750Kb 350Kb in size, respectively. Conversely, using an alternative approach of optical mapping, the plasmid replicons appeared as a circular ~1.2 Mb megaplasmid and a linear, ~0.7 Mb megaplasmid. Genome-wide comparative analysis of M213 with a cohort of sequenced Rhodococcus species revealed low syntenic affiliation with other R. opacus species including strains B4 and PD630. Conversely, a closer affiliation of M213, at the functional (COG) level, was observed with the catabolically versatile R. jostii strain RHA1 and other Rhodococcii such as R. wratislaviensis strain IFP 2016, R. imtechensis strain RKJ300, Rhodococcus sp. strain JVH1, and Rhodococcus sp. strain DK17, respectively. An in-depth, genome-wide comparison between these functional relatives revealed 971 unique genes in M213 representing 11% of its total genome; many associating with catabolic functions. Of major interest was the identification of as many as 154 genomic islands (GEIs), many with duplicated catabolic genes, in particular for PAHs; a trait that was confirmed by PCR-based identification of naphthalene dioxygenase (NDO) as a representative gene, across PFGE-resolved replicons of strain M213. Interestingly, several plasmid/GEI-encoded genes, that likely participate in degrading naphthalene (NAP) via a peculiar pathway, were also identified in strain M213 using a combination of bioinformatics, metabolic analysis and gene expression measurements of selected catabolic genes by RT-PCR. Taken together, this study provides a comprehensive understanding of the genome plasticity and ecological competitiveness of strain M213 likely facilitated by horizontal gene transfer (HGT), bacteriophage attacks and genomic reshuffling- aspects that continue to be understudied and thus poorly understood, in particular for the soil-borne Rhodococcii.
authors.affiliation: School of the Environment, Florida A&M University, Tallahassee, Florida, United States of America.
authors.forename: Ashish
authors.initials: A
authors.lastname: Pathak
authors.affiliation: School of the Environment, Florida A&M University, Tallahassee, Florida, United States of America.
authors.forename: Ashvini
authors.initials: A
authors.lastname: Chauhan
authors.affiliation: Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany.
authors.forename: Jochen
authors.initials: J
authors.lastname: Blom
authors.affiliation: Environmental Processes Branch, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America.
authors.forename: Karl J
authors.initials: KJ
authors.lastname: Indest
authors.affiliation: Environmental Processes Branch, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America.
authors.forename: Carina M
authors.initials: CM
authors.lastname: Jung
authors.affiliation: Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.
authors.forename: Paul
authors.initials: P
authors.lastname: Stothard
authors.affiliation: Geochemical and Environmental Research Group, Texas A&M University, College Station, Texas, United States of America.
authors.forename: Gopal
authors.initials: G
authors.lastname: Bera
authors.affiliation: DNA Services Facility, University of Illinois at Chicago, Chicago, Illinois, United States of America.
authors.forename: Stefan J
authors.initials: SJ
authors.lastname: Green
authors.affiliation: Soil and Water Science Department, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Andrew
authors.initials: A
authors.lastname: Ogram
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001673:Biodegradation, Environmental; D049308:Dioxygenases / Q000235:genetics; D004785:Environmental Pollutants / Q000378:metabolism; D015321:Gene Rearrangement; D016680:Genome, Bacterial; D044404:Genomic Islands; D053858:Metabolic Networks and Pathways / Q000235:genetics; D009097:Multienzyme Complexes / Q000235:genetics; D009281:Naphthalenes / Q000378:metabolism*; D010802:Phylogeny; D012093:Replicon; D012240:Rhodococcus / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism*; D012988:Soil Microbiology; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins; D004785:Environmental Pollutants; D009097:Multienzyme Complexes; D009281:Naphthalenes; C031721:naphthalene; D049308:Dioxygenases; C038703:naphthalene dioxygenase