<i>De Novo</i>
            Genome Project of Cupriavidus basilensis OR16

Cserháti, Mátyás; Kriszt, Balázs; Szoboszlay, Sándor; Tóth, Ákos; Szabó, István; Táncsics, Andräs; Nagy, István; Horváth, Balázs; Kukolya, József

doi:10.1128/jb.06752-11

Cited by 19 publications

(13 citation statements)

References 14 publications

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“…The cat and pca gene products of C. basilensis B-8 were significantly similar to proteins of known function from other bacteria, mainly Cupriavidus basilensis OR16 (Table 2), which has been reported earlier [32]. However, unlike many other bacteria whose cat and ben genes are usually organized in a single cluster, these genes in C. basilensis B-8 were organized in three clusters at different positions (see alignment result in supplementary files).…”

Section: Resultssupporting

confidence: 76%

Characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium Cupriavidus basilensis B-8

Shi

Chai

Tang

et al. 2013

Biotechnol Biofuels

466

328

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BackgroundLignin materials are abundant and among the most important potential sources for biofuel production. Development of an efficient lignin degradation process has considerable potential for the production of a variety of chemicals, including bioethanol. However, lignin degradation using current methods is inefficient. Given their immense environmental adaptability and biochemical versatility, bacterial could be used as a valuable tool for the rapid degradation of lignin. Kraft lignin (KL) is a polymer by-product of the pulp and paper industry resulting from alkaline sulfide treatment of lignocellulose, and it has been widely used for lignin-related studies.ResultsBeta-proteobacterium Cupriavidus basilensis B-8 isolated from erosive bamboo slips displayed substantial KL degradation capability. With initial concentrations of 0.5–6 g L-1, at least 31.3% KL could be degraded in 7 days. The maximum degradation rate was 44.4% at the initial concentration of 2 g L-1. The optimum pH and temperature for KL degradation were 7.0 and 30°C, respectively. Manganese peroxidase (MnP) and laccase (Lac) demonstrated their greatest level of activity, 1685.3 U L-1 and 815.6 U L-1, at the third and fourth days, respectively. Many small molecule intermediates were formed during the process of KL degradation, as determined using GC-MS analysis. In order to perform metabolic reconstruction of lignin degradation in this bacterium, a draft genome sequence for C. basilensis B-8 was generated. Genomic analysis focused on the catabolic potential of this bacterium against several lignin-derived compounds. These analyses together with sequence comparisons predicted the existence of three major metabolic pathways: β-ketoadipate, phenol degradation, and gentisate pathways.ConclusionThese results confirmed the capability of C. basilensis B-8 to promote KL degradation. Whole genomic sequencing and systematic analysis of the C. basilensis B-8 genome identified degradation steps and intermediates from this bacterial-mediated KL degradation method. Our findings provide a theoretical basis for research into the mechanisms of lignin degradation as well as a practical basis for biofuel production using lignin materials.

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Section: Resultssupporting

confidence: 76%

Characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium Cupriavidus basilensis B-8

Shi

Chai

Tang

et al. 2013

Biotechnol Biofuels

466

328

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“…The relationship between the CR3 and HPC (L) strains was also shown in their genome composition analysis. As shown in Table 2 , other Cupriavidus genome sizes [ 4 – 7 , 11 , 17 ] range from 5.49 Mb to 8.55 Mb, and the smallest genome is HPC (L); CR3 comes second. Whereas, GC content of all these other members of Cupriavidus varies from 63.53% to 67.54%, and the highest GC content genome is HPC (L).…”

Section: Resultsmentioning

confidence: 99%

“…eutropha HPC(L) and C . basilensis OR16 [ 11 ]. We also gathered other public and completed 16S rRNA genes from NCBI to present a full taxonomic analysis.…”

Section: Methodsmentioning

confidence: 99%

Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3

et al. 2015

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Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3 encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other non-coding genes. Many genes were associated with xenobiotic biodegradation and metal resistance functions. Pathway prediction for degradation of cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that naphthenic acid undergoes initial ring-cleavage, after which the ring fission products can be degraded via several plausible degradation pathways including a mechanism similar to that used for fatty acid oxidation. The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals, which was mainly achieved by self-detoxification through ion efflux, metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism. Our genomic analysis suggests that CR3 is well adapted to survive the harsh environment in natural asphalts containing naphthenic acids and high concentrations of heavy metals.

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“…To develop a bacterial strain to efficient biodegradation of OTA, selection of the most active and environmentally safe microbes is required. The aim of the present work was to evaluate the OTA-degrading and detoxifying potential of a Cupriavidus basilensis strain, which mycotoxin- degrading ability was presumable based on its genome project [22] .…”

Section: Introductionmentioning

confidence: 99%

A New Ochratoxin A Biodegradation Strategy Using Cupriavidus basilensis Őr16 Strain

et al. 2014

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Ochratoxin-A (OTA) is a mycotoxin with possibly carcinogenic and nephrotoxic effects in humans and animals. OTA is often found as a contaminant in agricultural commodities. The aim of the present work was to evaluate OTA-degrading and detoxifying potential of Cupriavidus basilensis ŐR16 strain. In vivo administration of OTA in CD1 male mice (1 or 10 mg/kg body weight for 72 hours or 0.5 mg/kg body weight for 21 days) resulted in significant elevation of OTA levels in the blood, histopathological alterations- and transcriptional changes in OTA-dependent genes (annexinA2, clusterin, sulphotransferase and gadd45 and gadd153) in the renal cortex. These OTA-induced changes were not seen in animals that have been treated with culture supernatants in which OTA was incubated with Cupriavidus basilensis ŐR16 strain for 5 days. HPLC and ELISA methods identified ochratoxin α as the major metabolite of OTA in Cupriavidus basilensis ŐR16 cultures, which is not toxic in vivo. This study has demonstrated that Cupriavidus basilensis ŐR16 efficiently degrade OTA without producing toxic adventitious metabolites.

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De Novo Genome Project of Cupriavidus basilensis OR16

Cited by 19 publications

References 14 publications

Characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium Cupriavidus basilensis B-8

Characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium Cupriavidus basilensis B-8

Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3

A New Ochratoxin A Biodegradation Strategy Using Cupriavidus basilensis Őr16 Strain

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