Draft Genome Sequence of the Carbofuran-Mineralizing
            <i>Novosphingobium</i>
            sp. Strain KN65.2

Nguyen, Thi Phi Oanh; Mot, René De; Springael, Dirk

doi:10.1128/genomea.00764-15

Cited by 12 publications

(12 citation statements)

References 14 publications

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“…strain PP1Y ( 6 ) and N. pentaromaticivorans US6-1 ( 10 ). This clustering is likely a result of shared metabolic tendency, as strain KN65.2 can degrade carbofuran ( 2 ) and strains PP1Y and US6-1 can degrade polyaromatic hydrocarbon (PAH) compounds ( 6 , 10 ). Further ambiguity in habitat specificity was observed from the clustering of strains of marine, contaminated soil, and freshwater habitats ( N. malaysiense Musc273 [marine], N. naphthalenivorans NBRC102051 [contaminated soil], N. fuchskuhlense FNE08-7 [freshwater], Novosphingobium sp.…”

Section: Resultsmentioning

confidence: 99%

“…The genus Novosphingobium represents metabolically versatile members that belong to the class Alphaproteobacteria and family Sphingomonadaceae ( 1 ). Novosphingobium species have been isolated from a wide range of ecological habitats such as agricultural soil ( 2 ), pesticide-contaminated soil ( 3 , 4 ), plant surfaces ( 5 ), and aquatic environments ( 6 ) (see Table 1 ). Previous studies have investigated Novosphingobium strains for their bioremediation capacity ( 7 – 10 ), nutrient cycling ( 11 , 12 ), taxonomic characterization ( 3 , 13 ), analysis of extracellular products ( 7 ), mutagenesis experiments on certain genes or gene clusters ( 14 ), disease conditions ( 15 , 16 ), and application in nanoparticle formation for antibacterial activity ( 17 ).…”

Section: Introductionmentioning

confidence: 99%

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Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium

et al. 2017

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This study highlights the significant role of the genetic repertoire of a microorganism in the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe’s respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits for Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium

et al. 2017

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“…The enzyme which converts carbofuran to carbofuran phenol, however, could not yet be identified. The KN65.2 genome lacks the mcd gene but carries the gene cfdJ , a close homologue of the carbaryl hydrolase gene cehA (Nguyen et al ., ) of Rhizobium sp. strain AC100 that converts the carbamate compound carbaryl (1‐naphthyl methylcarbamate) to 1‐naphthol and methylamine (Hashimoto et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Expanded insecticide catabolic activity gained by a single nucleotide substitution in a bacterial carbamate hydrolase gene

Öztürk

Ghequire

Nguyen

et al. 2016

Environmental Microbiology

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Carbofuran-mineralizing strain Novosphingobium sp. KN65.2 produces the CfdJ enzyme that converts the N-methylcarbamate insecticide to carbofuran phenol. Purified CfdJ shows a remarkably low K towards carbofuran. Together with the carbaryl hydrolase CehA of Rhizobium sp. strain AC100, CfdJ represents a new protein family with several uncharacterized bacterial members outside the proteobacteria. Although both enzymes differ by only four amino acids, CehA does not recognize carbofuran as a substrate whereas CfdJ also hydrolyzes carbaryl. None of the CfdJ amino acids that differ from CehA were shown to be silent regarding carbofuran hydrolytic activity but one particular amino acid substitution, i.e., L152 to F152, proved crucial. CfdJ is more efficient in degrading methylcarbamate pesticides with an aromatic side chain whereas CehA is more efficient in degrading the oxime carbamate nematicide oxamyl. The presence of common flanking sequences suggest that the cfdJ gene is located on a remnant of the mobile genetic element Tnceh carrying cehA. Our results suggest that these enzymes can be acquired through horizontal gene transfer and can evolve to degrade new carbamate substrates by limited amino acid substitutions. We demonstrate that a carbaryl hydrolase can gain the additional capacity to degrade carbofuran by a single nucleotide transversion.

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“…cfdJ was found in the genome of Novosphingobium sp. strain KN65.2 (19), which is a close homologue of the carbaryl hydrolase-encoding gene cehA cloned from the Rhizobium sp. strain AC100.…”

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confidence: 99%

“…Strain CDS-1 was isolated from activated sludge in the Jiangsu province of China, and strain KN65.2 was isolated from soil sampled from a vegetable field with a long history of carbofuran treatment in the Soc Trang province of Vietnam. The draft genome sequence of strain KN65.2 was released recently (19). In this work, the draft genome of strain CDS-1 was sequenced; the genes involved in the carbofuran catabolism were first predicted from the open reading frames (ORFs) that share Ն95% nucleic acid similarities between strains CDS-1 and KN65.2 and then were subjected to experimental validation.…”

mentioning

confidence: 99%

Hydrolase CehA and Monooxygenase CfdC Are Responsible for Carbofuran Degradation in Sphingomonas sp. Strain CDS-1

Yan

Wen

et al. 2018

Appl Environ Microbiol

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Carbofuran, a broad-spectrum systemic insecticide, has been extensively used for approximately 50 years. Diverse carbofuran-degrading bacteria have been described, among which sphingomonads have exhibited an extraordinary ability to catabolize carbofuran; other bacteria can only convert carbofuran to carbofuran phenol, while all carbofuran-degrading sphingomonads can degrade both carbofuran and carbofuran phenol. However, the genetic basis of carbofuran catabolism in sphingomonads has not been well elucidated. In this work, we sequenced the draft genome of sp. strain CDS-1 that can transform both carbofuran and carbofuran phenol but fails to grow on them. On the basis of the hypothesis that the genes involved in carbofuran catabolism are highly conserved among carbofuran-degrading sphingomonads, two such genes, and , were predicted from the 84 open reading frames (ORFs) that share ≥95% nucleic acid similarities between strain CDS-1 and another sphingomonad sp. strain KN65.2 that is able to mineralize the benzene ring of carbofuran. The results of the gene knockout, genetic complementation, heterologous expression, and enzymatic experiments reveal that and are responsible for the conversion of carbofuran and carbofuran phenol, respectively, in strain CDS-1. CehA hydrolyzes carbofuran to carbofuran phenol. CfdC, a reduced flavin mononucleotide (FMNH)- or reduced flavin adenine dinucleotide (FADH)-dependent monooxygenase, hydroxylates carbofuran phenol at the benzene ring in the presence of NADH, FMN/FAD, and the reductase CfdX. It is worth noting that we found that carbaryl hydrolase CehA, which was previously demonstrated to have no activity toward carbofuran, can actually convert carbofuran to carbofuran phenol, albeit with very low activity. Due to the extensive use of carbofuran over the past 50 years, bacteria have evolved catabolic pathways to mineralize this insecticide, which plays an important role in eliminating carbofuran residue in the environment. This study revealed the genetic determinants of carbofuran degradation in sp. strain CDS-1. We speculate that the close homologues and are highly conserved among other carbofuran-degrading sphingomonads and play the same roles as those described here. These findings deepen our understanding of the microbial degradation mechanism of carbofuran and lay a foundation for the better use of microbes to remediate carbofuran contamination.

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Draft Genome Sequence of the Carbofuran-Mineralizing Novosphingobium sp. Strain KN65.2

Cited by 12 publications

References 14 publications

Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium

Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium

Expanded insecticide catabolic activity gained by a single nucleotide substitution in a bacterial carbamate hydrolase gene

Hydrolase CehA and Monooxygenase CfdC Are Responsible for Carbofuran Degradation in Sphingomonas sp. Strain CDS-1

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