Complete Genome Sequence of Sphingobium sp. Strain SYK-6, a Degrader of Lignin-Derived Biaryls and Monoaryls

Masai, Eiji; Kamimura, Naofumi; Kasai, Daisuke; Oguchi, Akio; Ankai, Akiho; Fukui, Shigehiro; Takahashi, Mikio; Yashiro, Isao; Sasaki, Hiroki; Harada, Takeshi; Nakamura, Sanae; Katano, Yoko; Narita-Yamada, Sachiko; Nakazawa, Hiromi; Hara, Hirofumi; Katayama, Yoshihiro; Fukuda, Masao; Yamazaki, Shuji; Fujita, Nobuyuki

doi:10.1128/jb.06254-11

Cited by 57 publications

(32 citation statements)

References 13 publications

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“…TKSγ-HCH degradation1_1164387identical repABC Ti, FCP00508526 pSLGP148,801 Sphingobium sp. SYK-6lignin degradation1_1164387identical repABC TiAP01222381 pSPHCH01123,733 Sphingobium chlorophenolicum L-1PCP degradation47083_48171_c362 c identical repABC TiCP00280011 pISP0275,840 Sphingomonas sp. MM-1γ-HCH degradation4081_524438798 (381/387) repABC Ti linF, linGHIJ CP00403723 pUT1 31,776 S. japonicum UT26γ-HCH degradation1_1104367—iteronAP01080618 pMI2 b 287,488 Sphingobium sp.…”

Section: Resultsmentioning

confidence: 99%

Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide

Tabata

Ohhata

Nikawadori

et al. 2016

DNA Res

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γ-Hexachlorocyclohexane (γ-HCH) is a recalcitrant man-made chlorinated pesticide. Here, the complete genome sequences of four γ-HCH-degrading sphingomonad strains, which are most unlikely to have been derived from one ancestral γ-HCH degrader, were compared. Together with several experimental data, we showed that (i) all the four strains carry almost identical linA to linE genes for the conversion of γ-HCH to maleylacetate (designated “specific” lin genes), (ii) considerably different genes are used for the metabolism of maleylacetate in one of the four strains, and (iii) the linKLMN genes for the putative ABC transporter necessary for γ-HCH utilization exhibit structural divergence, which reflects the phylogenetic relationship of their hosts. Replicon organization and location of the lin genes in the four genomes are significantly different with one another, and that most of the specific lin genes are located on multiple sphingomonad-unique plasmids. Copies of IS6100, the most abundant insertion sequence in the four strains, are often located in close proximity to the specific lin genes. Analysis of the footprints of target duplication upon IS6100 transposition and the experimental detection of IS6100 transposition strongly suggested that the IS6100 transposition has caused dynamic genome rearrangements and the diversification of lin-flanking regions in the four strains.

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Section: Resultsmentioning

confidence: 99%

Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide

Tabata

Ohhata

Nikawadori

et al. 2016

DNA Res

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“…Sphingobium SYK-6, a soil bacterium discovered in the ponds of a kraft pulp mill, has been one of the most studied bacterial lignin degraders, and its genome was sequenced by Eiji Masai and others in 2011 (22). SYK-6 can grow on a wide variety of lignin-derived monoaryls and biaryls, and most of the research thus far has focused on understanding its lignin catabolic pathways (23,24).…”

Section: Significancementioning

confidence: 99%

Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization

Varman

Follenfant

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Sphingobium sp. SYK-6 is a soil bacterium boasting a well-studied ligninolytic pathway and the potential for development into a microbial chassis for lignin valorization. An improved understanding of its metabolism will help researchers in the engineering of SYK-6 for the production of value-added chemicals through lignin valorization. We used 13 C-fingerprinting, 13C metabolic flux analysis ( 13 C-MFA), and RNA-sequencing differential expression analysis to uncover the following metabolic traits: (i) SYK-6 prefers alkaline conditions, making it an efficient host for the consolidated bioprocessing of lignin, and it also lacks the ability to metabolize sugars or organic acids; (ii) the CO 2 release (i.e., carbon loss) from the ligninolysis-based metabolism of SYK-6 is significantly greater than the CO 2 release from the sugar-based metabolism of Escherichia coli; (iii) the vanillin catabolic pathway (which is the converging point of majority of the lignin catabolic pathways) is coupled with the tetrahydrofolate-dependent C1 pathway that is essential for the biosynthesis of serine, histidine, and methionine; (iv) catabolic end products of lignin (pyruvate and oxaloacetate) must enter the tricarboxylic acid (TCA) cycle first and then use phosphoenolpyruvate carboxykinase to initiate gluconeogenesis; and (v) 13 C-MFA together with RNA-sequencing differential expression analysis establishes the vanillin catabolic pathway as the major contributor of NAD(P)H synthesis. Therefore, the vanillin catabolic pathway is essential for SYK-6 to obtain sufficient reducing equivalents for its healthy growth; cosubstrate experiments support this finding. This unique energy feature of SYK-6 is particularly interesting because most heterotrophs rely on the transhydrogenase, the TCA cycle, and the oxidative pentose phosphate pathway to obtain NADPH.

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“…The ligXa gene is located approximately 3.3 kb downstream of ligZ-orf1-orf2-ligY and located approximately 6.6 kb downstream of ligW and 570 kb upstream of ligW2 (Fig. 1B) (29). However, genes encoding ETCs were not found in the vicinity of ligXa and other DDVA catabolism genes.…”

mentioning

confidence: 88%

“…In this study, in order to thoroughly characterize DDVA O-demethylase of SYK-6, we searched for possible genes encoding ETCs of DDVA O-demethylase in the SYK-6 genome (29). Based on the gene disruption analyses and in vitro reconstitution of the DDVA O-demethylase activity with the products of the candidate genes, the essential ETC genes responsible for the DDVA conversion were identified.…”

mentioning

confidence: 99%

Three-Component O -Demethylase System Essential for Catabolism of a Lignin-Derived Biphenyl Compound in Sphingobium sp. Strain SYK-6

Yoshikata

Suzuki

Kamimura

et al. 2014

Appl Environ Microbiol

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c Sphingobium sp. strain SYK-6 is able to assimilate lignin-derived biaryls, including a biphenyl compound, 5,5=-dehydrodivanillate (DDVA). Previously, ligXa (SLG_07770), which is similar to the gene encoding oxygenase components of Rieske-type nonheme iron aromatic-ring-hydroxylating oxygenases, was identified to be essential for the conversion of DDVA; however, the genes encoding electron transfer components remained unknown. Disruption of putative electron transfer component genes scattered through the SYK-6 genome indicated that SLG_08500 and SLG_21200, which showed approximately 60% amino acid sequence identities with ferredoxin and ferredoxin reductase of dicamba O-demethylase, were essential for the normal growth of SYK-6 on DDVA. LigXa and the gene products of SLG_08500 (LigXc) and SLG_21200 (LigXd) were purified and were estimated to be a trimer, a monomer, and a monomer, respectively. LigXd contains FAD as the prosthetic group and showed much higher reductase activity toward 2,6-dichlorophenolindophenol with NADH than with NADPH. A mixture of purified LigXa, LigXc, and LigXd converted DDVA into 2,2=,3-trihydroxy-3=-methoxy-5,5=-dicarboxybiphenyl in the presence of NADH, indicating that DDVA O-demethylase is a three-component monooxygenase. This enzyme requires Fe(II) for its activity and is highly specific for DDVA, with a K m value of 63.5 M and k cat of 6.1 s ؊1 . Genome searches in six other sphingomonads revealed genes similar to ligXc and ligXd (>58% amino acid sequence identities) with a limited number of electron transfer component genes, yet a number of diverse oxygenase component genes were found. This fact implies that these few electron transfer components are able to interact with numerous oxygenase components and the conserved LigXc and LigXd orthologs are important in sphingomonads.

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Complete Genome Sequence of Sphingobium sp. Strain SYK-6, a Degrader of Lignin-Derived Biaryls and Monoaryls

Cited by 57 publications

References 13 publications

Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide

Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide

Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization

Three-Component O -Demethylase System Essential for Catabolism of a Lignin-Derived Biphenyl Compound in Sphingobium sp. Strain SYK-6

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