Draft Genome Sequence of Rhodococcus erythropolis DN1, a Crude Oil Biodegrader

Shevtsov, Alexandr; Tarlykov, Pavel; Zholdybayeva, Elena; Momynkulov, Dauren; Sarsenova, Ainur; Moldagulova, Nazira; Momynaliev, Kuvat

doi:10.1128/genomea.00846-13

Cited by 14 publications

(11 citation statements)

References 6 publications

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“…Most of the selected bacterial species in this study have been reported to catabolize aromatic compounds [71][72][73][74][75][76][77] , depolymerize lignin 78 , or both depolymerize and uptake aromatics from lignin. Most of the selected bacterial species in this study have been reported to catabolize aromatic compounds [71][72][73][74][75][76][77] , depolymerize lignin 78 , or both depolymerize and uptake aromatics from lignin.…”

Section: Discussionmentioning

confidence: 99%

Towards lignin consolidated bioprocessing: simultaneous lignin depolymerization and product generation by bacteria

et al. 2015

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Lignin represents an untapped resource in lignocellulosic biomass, primarily due to its recalcitrance to depolymerization and its intrinsic heterogeneity. In Nature, microorganisms have evolved mechanisms to both depolymerize lignin using extracellular oxidative enzymes and to uptake the aromatic species generated during depolymerization for carbon and energy sources. The ability of microbes to conduct both of these processes simultaneously could enable a Consolidated Bioprocessing concept to be applied to lignin, similar to what is done today with polysaccharide conversion to ethanol via ethanologenic, cellulolytic microbes. To that end, here we examine the ability of 14 bacteria to secrete ligninolytic enzymes, depolymerize lignin, uptake aromatic and other compounds present in a biomass-derived, lignin-enriched stream, and, under nitrogen-limiting conditions, accumulate intracellular carbon storage compounds that can be used as fuel, chemical, or material precursors. In shake flask conditions using a substrate produced during alkaline pretreatment, we demonstrate that up to nearly 30% of the initial lignin can be depolymerized and catabolized by a subset of bacteria. In particular, Amycolatopsis sp., two Pseudomonas putida strains, Acinetobacter ADP1, and Rhodococcus jostii are able to depolymerize high molecular weight lignin species and catabolize a significant portion of the low molecular weight aromatics, thus representing good starting hosts for metabolic engineering. This study also provides a comprehensive set of experimental tools to simultaneously study lignin depolymerization and aromatic catabolism in bacteria, and provides a foundation towards the concept of Lignin Consolidated Bioprocessing, which may eventually be an important route for biological lignin valorization. Electronic Supplementary Information (ESI) available: Additional resultsdescribing the HPAE-PAD findings, growth curves of the bacteria over the 7-day experiments, the full set of ligninolytic enzyme profiles, and genomic analyses for ligninolytic enzymes and aromatic catabolic enzymes. See

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Section: Discussionmentioning

confidence: 99%

Towards lignin consolidated bioprocessing: simultaneous lignin depolymerization and product generation by bacteria

et al. 2015

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“…A Kwasiborski et al soil, SK121 from human skin and CCM2595 from soil (Sekine et al, 2006;Vesely et al, 2007;Shevtsov et al, 2013). By contrast, number, size and functions of plasmids differed when the R. erythropolis strains were compared.…”

Section: Functional Genomics Of R Erythropolismentioning

confidence: 99%

Transcriptome of the quorum-sensing signal-degrading Rhodococcus erythropolis responds differentially to virulent and avirulent Pectobacterium atrosepticum

et al. 2015

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Social bacteria use chemical communication to coordinate and synchronize gene expression via the quorum-sensing (QS) regulatory pathway. In Pectobacterium, a causative agent of the blackleg and soft-rot diseases on potato plants and tubers, expression of the virulence factors is collectively controlled by the QS-signals N-acylhomoserine lactones (NAHLs). Several soil bacteria, such as the actinobacterium Rhodococcus erythropolis, are able to degrade NAHLs, hence quench the chemical communication and virulence of Pectobacterium. Here, next-generation sequencing was used to investigate structural and functional genomics of the NAHL-degrading R. erythropolis strain R138. The R. erythropolis R138 genome (6.7 Mbp) contained a single circular chromosome, one linear (250 kbp) and one circular (84 kbp) plasmid. Growth of R. erythropolis and P. atrosepticum was not altered in mixed-cultures as compared with monocultures on potato tuber slices. HiSeq-transcriptomics revealed that no R. erythropolis genes were differentially expressed when R. erythropolis was cultivated in the presence vs absence of the avirulent P. atrosepticum mutant expI, which is defective for QS-signal synthesis. By contrast 50 genes (o1% of the R. erythropolis genome) were differentially expressed when R. erythropolis was cultivated in the presence vs absence of the NAHL-producing virulent P. atrosepticum. Among them, quantitative real-time reverse-transcriptase-PCR confirmed that the expression of some alkyl-sulfatase genes decreased in the presence of a virulent P. atrosepticum, as well as deprivation of organic sulfur such as methionine, which is a key precursor in the synthesis of NAHL by P. atrosepticum.

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“…In the current era of genomics, rhodococci have generated some interest due to their wide biotechnological applications and 26 genome sequencing projects are currently ongoing, of which five are already completed and represent four species: R. erythropolis , R. equi , R. opacus , and R. jostii (National Center for Biotechnology Information, 2005 ). The analysis of these genomes revealed different structures, R. equi and R. erythropolis present smaller circular genomes (5 and 6.9 Mb) whereas R. opacus and R. jostii have larger linear chromosomes (8.8 and 9.7 Mb) (National Center for Biotechnology Information, 2005 ; McLeod et al, 2006 ; Letek et al, 2010 ; Pathak et al, 2013 ; Shevtsov et al, 2013 ). Another characteristic of rhodococcal genomes is the common presence of plasmids, one to five per strain, either circular or linear, that range in size from 3 kb to more than 1 Mb, accounting for up to 20% of the entire genome (e.g., R. jostii strain RHA1) (Letek et al, 2008 , 2010 ).…”

Section: Transport Systems Present In the Rhodococcus mentioning

confidence: 99%

Membrane transport systems and the biodegradation potential and pathogenicity of genus Rhodococcus

et al. 2014

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The Rhodococcus genus contains species with remarkable ability to tolerate toxic compounds and to degrade a myriad of substrates. These substrates have to cross a distinctive cell envelope dominated by mycolic acids anchored in a scaffold of arabinogalactan covalently attached to the cell wall peptidoglycan, and a cellular membrane with phospholipids, whose composition in fatty acids can be rapidly altered in response to environmental conditions. The hydrophobic nature of the cell envelope facilitates the entrance of hydrophobic molecules but some substrates require active transport systems. Additionally, toxic compounds may also be extruded by energy spending efflux systems. In this review, physiological evidences of the use of transport systems by Rhodococcus strains and genomic studies that corroborate their existence are presented and discussed. The recently released complete genomes of several Rhodococcus strains will be the basis for an in silico correlation analysis between the efflux pumps present in the genome and their role on active transport of substrates. These transport systems will be placed on an integrative perspective of the impact of this important genus on biotechnology and health, ranging from bioremediation to antibiotic and biocide resistance.

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Draft Genome Sequence of Rhodococcus erythropolis DN1, a Crude Oil Biodegrader

Abstract: We report the 6,548-Mb genome sequence of Rhodococcus erythropolis strain DN1, isolated from the oil-contaminated soil in the Karagandy region of Kazakhstan. The draft genome sequence of strain DN1 might provide new insights into the genetic mechanisms of crude oil biodegradation.

Cited by 14 publications

References 6 publications

Towards lignin consolidated bioprocessing: simultaneous lignin depolymerization and product generation by bacteria

Towards lignin consolidated bioprocessing: simultaneous lignin depolymerization and product generation by bacteria

Transcriptome of the quorum-sensing signal-degrading Rhodococcus erythropolis responds differentially to virulent and avirulent Pectobacterium atrosepticum

Membrane transport systems and the biodegradation potential and pathogenicity of genus Rhodococcus

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