Draft Genome Sequences of
            <i>Sphingobium</i>
            sp. Strain TCM1 and
            <i>Sphingomonas</i>
            sp. Strain TDK1, Haloalkyl Phosphate Flame Retardant- and Plasticizer-Degrading Bacteria

Kera, Yoshio; Abe, Katsumasa; Kasai, Daisuke; Fukuda, Masao; Takahashi, Shouji

doi:10.1128/genomea.00668-16

Cited by 9 publications

(9 citation statements)

References 8 publications

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“…Among these CDSs, 2388 (63.87%) genes were classified into clusters of orthologous group (COG) families comprised of 23 categories (Table S2). The genome size of LK11 falls within the expected range (based on other genomic studies) and a varying number of plasmid has been observed in other strains (Gai et al 2011a ; Kera et al 2016 ; Li et al 2016 ; Miller et al 2010 ; Pan et al 2016a ).…”

Section: Resultssupporting

confidence: 65%

“…Recent studies have also demonstrated the role of Sphingomonas spp. in the degradation of organic chemical compounds, such as bisphenol (Fujiwara et al 2016 ), phenol (Gong et al 2016 ), triclocarban (Mulla et al 2016 ), phenanthrene (Liu et al 2016 ), chlorogenic acid (Ma et al 2016 ), nonylphenol polyethoxylates (Bai et al 2016 ), astaxanthin (Ma et al 2016 ), dioxin (Miller et al 2010 ), γ-hexachlorocyclohexane (Tabata et al 2013 ), nicotine (Zhu et al 2016 ), plasticizers (Kera et al 2016 ), and hexachlorocyclohexane isomers (Kumari et al 2002 ) among others. In addition to these degradation abilities, the Sphingomonas genus can also produce bioactive metabolites, such as indole acetic acid, gibberellins, sphingan (Li et al 2016 ), and gellan gum (Gai et al 2011b ).…”

Section: Introductionmentioning

confidence: 99%

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Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth

Asaf

Khan

et al. 2018

3 Biotech

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Our study aimed to elucidate the plant growth-promoting characteristics and the structure and composition of Sphingomonas sp. LK11 genome using the single molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that LK11 produces different types of gibberellins (GAs) in pure culture and significantly improves soybean plant growth by influencing endogenous GAs compared with non-inoculated control plants. Detailed genomic analyses revealed that the Sphingomonas sp. LK11 genome consists of a circular chromosome (3.78 Mbp; 66.2% G+C content) and two circular plasmids (122,975 bps and 34,160 bps; 63 and 65% G+C content, respectively). Annotation showed that the LK11 genome consists of 3656 protein-coding genes, 59 tRNAs, and 4 complete rRNA operons. Functional analyses predicted that LK11 encodes genes for phosphate solubilization and nitrate/nitrite ammonification, which are beneficial for promoting plant growth. Genes for production of catalases, superoxide dismutase, and peroxidases that confer resistance to oxidative stress in plants were also identified in LK11. Moreover, genes for trehalose and glycine betaine biosynthesis were also found in LK11 genome. Similarly, Sphingomonas spp. analysis revealed an open pan-genome and a total of 8507 genes were identified in the Sphingomonas spp. pan-genome and about 1356 orthologous genes were found to comprise the core genome. However, the number of genomes analyzed was not enough to describe complete gene sets. Our findings indicated that the genetic makeup of Sphingomonas sp. LK11 can be utilized as an eco-friendly bioresource for cleaning contaminated sites and promoting growth of plants confronted with environmental perturbations.Electronic supplementary materialThe online version of this article (10.1007/s13205-018-1403-z) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 65%

Section: Introductionmentioning

confidence: 99%

Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth

Asaf

Khan

et al. 2018

3 Biotech

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“…strain TCM1 were determined to be EFVTQSDQRPP. We performed a Blast search against the draft genome of strain TCM1 20 using this N-terminal sequence as the query sequence and the putative gene (locus_tag A7Q26_24300) was found. However, no Shine-Dalgarno (SD) sequence was found around the putative translation initiation codon.…”

Section: Resultsmentioning

confidence: 99%

An atypical phosphodiesterase capable of degrading haloalkyl phosphate diesters from Sphingobium sp. strain TCM1

Abe

Mukai

Morooka

et al. 2017

Sci Rep

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Sphingobium sp. strain TCM1 can degrade tris(2-chloroethyl) phosphate (TCEP) to inorganic phosphate and 2-chloroethanol. A phosphotriesterase (PTE), phosphodiesterase (PDE) and phosphomonoesterase (PME) are believed to be involved in the degradation of TCEP. The PTE and PME that respectively catalyze the first and third steps of TCEP degradation in TCM1 have been identified. However, no information has been reported on a PDE catalyzing the second step. In this study, we identified, purified, and characterized a PDE capable of hydrolyzing haloalkyl phosphate diesters. The final preparation of the enzyme had a specific activity of 29 µmol min−1 mg−1 with bis(p-nitrophenyl) phosphate (BpNPP) as the substrate. It also possessed low PME activity with p-nitrophenyl phosphate (pNPP) as substrate. The catalytic efficiency (k cat/K m) with BpNPP was significantly higher than that with pNPP, indicating that the enzyme prefers the organophosphorus diester to the monoester. The enzyme degraded bis(2,3-dibromopropyl) phosphate, bis(1,3-dichloro-2-propyl) phosphate and bis(2-chloroethyl) phosphate, suggesting that it is involved in the metabolism of haloalkyl organophosphorus triesters. The primary structure of the PDE from TCM1 is distinct from those of typical PDE family members and the enzyme belongs to the polymerase and histidinol phosphatase superfamily.

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“…The OPs used in our MIX treatment are proven to be degradable and hence can be used as a resource for bacteria (Leahy and Colwell, ; Takahashi et al ., , , , ; Seo et al ., ; Abe et al ., , ; Joye et al ., ; Kera et al ., ; Vila‐Costa et al ., )). Yet, our study showed notably negative effects on bacterial growth of hydrocarbons and OPEs supplied at environmentally relevant concentrations.…”

Section: Discussionmentioning

confidence: 99%

Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacteriumRheinheimerasp.BAL341

Karlsson

Cerro‐Gálvez

Lundin

et al. 2019

Microbial Biotechnology

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Summary Organic pollutants (OPs) are critically toxic, bioaccumulative and globally widespread. Moreover, several OPs negatively influence aquatic wildlife. Although bacteria are major drivers of the ocean carbon cycle and the turnover of vital elements, there is limited knowledge of OP effects on heterotrophic bacterioplankton. We therefore investigated growth and gene expression responses of the Baltic Sea model bacterium Rheinheimera sp. BAL341 to environmentally relevant concentrations of distinct classes of OPs in 2‐h incubation experiments. During exponential growth, exposure to a mix of polycyclic aromatic hydrocarbons, alkanes and organophosphate esters (denoted MIX) resulted in a significant decrease (between 9% and 18%) in bacterial abundance and production compared with controls. In contrast, combined exposure to perfluorooctanesulfonic acids and perfluorooctanoic acids (denoted PFAS) had no significant effect on growth. Nevertheless, MIX and PFAS exposures both induced significant shifts in gene expression profiles compared with controls in exponential growth. This involved several functional metabolism categories (e.g. stress response and fatty acids metabolism), some of which were pollutant‐specific (e.g. phosphate acquisition and alkane‐1 monooxygenase genes). In stationary phase, only two genes in the MIX treatment were significantly differentially expressed. The substantial direct influence of OPs on metabolism during bacterial growth suggests that widespread OPs could severely alter biogeochemical processes governed by bacterioplankton.

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Draft Genome Sequences of Sphingobium sp. Strain TCM1 and Sphingomonas sp. Strain TDK1, Haloalkyl Phosphate Flame Retardant- and Plasticizer-Degrading Bacteria

Abstract: Sphingobium sp. strain TCM1 and Sphingomonas sp. strain TDK1 are haloalkyl phosphate flame retardant- and plasticizer-degrading bacteria. We report here the draft genome sequences of these strains to provide insights into the molecular mechanism underlying their degradation ability.

Cited by 9 publications

References 8 publications

Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth

Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth

An atypical phosphodiesterase capable of degrading haloalkyl phosphate diesters from Sphingobium sp. strain TCM1

Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacteriumRheinheimerasp.BAL341

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