Genome of a Novel Isolate of Paracoccus denitrificans Capable of Degrading
            <i>N</i>
            ,
            <i>N</i>
            -Dimethylformamide

Siddavattam, Dayananda; Karegoudar, T. B.; Mudde, Santosh Kumar; Kumar, Narender; Baddam, Ramani; Tiruvayipati, Suma; Ahmed, Niyaz

doi:10.1128/jb.05667-11

Cited by 45 publications

(25 citation statements)

References 16 publications

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“…For example, the Paracoccus denitrificans SD1 genome (Siddavattam et al 2011) at IMG (id: 2511231195) was estimated to be only 59% complete by CheckM (Supplemental Table S19). Comparing this genome to Paracoccus denitrificans PD1222 suggests that this species has two chromosomes and a plasmid, and that the SD1 genome is currently missing both a chromosome and its plasmid.…”

Section: Assessment Of Isolate Genomesmentioning

confidence: 99%

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

et al. 2015

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Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of "marker" genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene-and genome-centric analyses of microbial communities.

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Section: Assessment Of Isolate Genomesmentioning

confidence: 99%

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

et al. 2015

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“…The announcement of genomic sequences for P. denitrificans such as strain PD1222 (http://genome.jgi-psf.org/parde/parde.home.html) (Siddavattam et al. ) greatly facilitated the development of being a model organism for extensive investigations of molecular mechanism (endosymbiotic theory) implicated into denitrifications and possible ancestors for the eukaryotic mitochondrion (http://en.wikipedia.org/wiki/Paracoccus_denitrificans) (John and Whatley ). In views of genomic contents, we noted that P. denitrificans is unusual in that the gene duplication and/or redundancy (especially two BioR orthologs) is prevalent in the context of biotin metabolism, unlike the scenarios observed with its close relatives A. tumefaciens and B. melitensis (Fig.…”

Section: Introductionmentioning

confidence: 99%

Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism

et al. 2015

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Recently, we determined that BioR, the GntR family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain species of α-proteobacteria, including the zoonotic agent Brucella melitensis and the plant pathogen Agrobacterium tumefaciens. However, the scenario is unusual in Paracoccus denitrificans, another closely related member of the same phylum α-proteobacteria featuring with denitrification. Not only does it encode two BioR homologs Pden_1431 and Pden_2922 (designated as BioR1 and BioR2, respectively), but also has six predictive BioR-recognizable sites (the two bioR homolog each has one site, whereas the two bio operons (bioBFDAGC and bioYB) each contains two tandem BioR boxes). It raised the possibility that unexpected complexity is present in BioR-mediated biotin regulation. Here we report that this is the case. The identity of the purified BioR proteins (BioR1 and BioR2) was confirmed with LC-QToF-MS. Phylogenetic analyses combined with GC percentage raised a possibility that the bioR2 gene might be acquired by horizontal gene transfer. Gel shift assays revealed that the predicted BioR-binding sites are functional for the two BioR homologs, in much similarity to the scenario seen with the BioR site of A. tumefaciens bioBFDAZ. Using the A. tumefaciens reporter system carrying a plasmid-borne LacZ fusion, we revealed that the two homologs of P. denitrificans BioR are functional repressors for biotin metabolism. As anticipated, not only does the addition of exogenous biotin stimulate efficiently the expression of bioYB operon encoding biotin transport/uptake system BioY, but also inhibits the transcription of the bioBFDAGC operon resembling the de novo biotin synthetic pathway. EMSA-based screening failed to demonstrate that the biotin-related metabolite is involved in BioR-DNA interplay, which is consistent with our former observation with Brucella BioR. Our finding defined a complex regulatory network for biotin metabolism in P. denitrificans by two BioR proteins.

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“…About 95ϫ and 105ϫ coverage was achieved for strains UJ308A and UJ816A, respectively, comprising 1.9 and 2.0 Gb of data, respectively. De novo assembly was done as described previously (1,2,4,8,19); initial assembly generated 416 and 335 contigs for UJ308A and UJ816A, respectively, using Velvet (23) with a hash length of 39. The scaffolds were generated from contigs by using SSPACE (5) and further assembled and curated to give a consensus draft.…”

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confidence: 99%

Whole-Genome Sequences and Comparative Genomics of Salmonella enterica Serovar Typhi Isolates from Patients with Fatal and Nonfatal Typhoid Fever in Papua New Guinea

et al. 2012

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Many of the developing countries of the Southeast Asian region are significantly affected by endemic typhoid fever, possibly as a result of marginal living standards. It is an important public health problem in countries such as Papua New Guinea, which is geographically close to some of the foci of endemicity in Asia. The severity of the disease varies in different regions, and this may be attributable to genetic diversity among the native strains. Genome sequence data on strains from different countries are needed to clearly understand their genetic makeup and virulence potential. We describe the genomes of two Salmonella Typhi isolates from patients with fatal and nonfatal cases of typhoid fever in Papua New Guinea. We discuss in brief the underlying sequencing methodology, assembly, genome statistics, and important features of the two draft genomes, which form an essential step in our functional molecular infection epidemiology program centering on typhoid fever. The comparative genomics of these and other isolates would enable us to identify genetic rearrangements and mechanisms responsible for endemicity and the differential severity of pathogenic salmonellae in Papua New Guinea and elsewhere.

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Genome of a Novel Isolate of Paracoccus denitrificans Capable of Degrading N , N -Dimethylformamide

Cited by 45 publications

References 16 publications

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism

Whole-Genome Sequences and Comparative Genomics of Salmonella enterica Serovar Typhi Isolates from Patients with Fatal and Nonfatal Typhoid Fever in Papua New Guinea

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