Biochemical and Genetic Characterization of a Gentisate 1,2-Dioxygenase from
            <i>Sphingomonas</i>
            sp. Strain RW5

Werwath, Jörn; Arfmann, Hans‐Adolf; Pieper, Dietmar H.; Timmis, Kenneth N.; Wittich, Rolf-Michael

doi:10.1128/jb.180.16.4171-4176.1998

Cited by 70 publications

(47 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Proteins for the modification and degradation of monoaryl and biaryl compounds were predicted, including a diversity of aromatic ring-cleaving dioxygenases 25–27 . A total of 42 ring-cleaving dioxygenases targeting compounds related to catechol, protocatechuate and gentisate were present in the six MAGs, with 25 dioxygenases predicted in SAR202-VII-2 alone (Fig.…”

Section: Resultsmentioning

confidence: 99%

Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria

Colatriano¹,

Tran²,

Guéguen

et al. 2018

Preprint

View full text Add to dashboard Cite

24The Arctic Ocean currently receives a large supply of global river discharge and terrestrial 25 dissolved organic matter. Moreover, an increase in freshwater runoff and riverine transport of 26 organic matter to the Arctic Ocean is a predicted consequence of thawing permafrost and 27 increased precipitation. The fate of the terrestrial humic-rich organic material and its impact on 28 the marine carbon cycle are largely unknown. Here, the first metagenomic survey of the Canada 29Basin in the Western Arctic Ocean showed that pelagic Chloroflexi from the Arctic Ocean are 30 replete with aromatic compound degradation genes, acquired in part by lateral transfer from 31 terrestrial bacteria. Our results imply marine Chloroflexi have the capacity to use terrestrial 32 organic matter and that their role in the carbon cycle may increase with the changing 33 hydrological cycle. 34 35 released to the Atlantic, at least in part by microbial processes 10 . As input of tDOM increases, 49 knowledge on its microbial transformation will be critical for understanding changes in Arctic 50 carbon cycling. 51The marine SAR202 is a diverse and uncultivated clade of Chloroflexi bacteria that 52 comprise roughly 10% of planktonic cells in the dark ocean [11][12][13][14][15] . SAR202 is also common in 53 marine sediments and deep lakes [16][17][18] . It has long been speculated that SAR202 may play a 54 role in the degradation of recalcitrant organic matter 12,15 , and the recent analysis of SAR202 55 single-cell amplified genomes (SAGs) lends support to this notion 19 . More generally, 56Chloroflexi, including those in the SAR202 clade, are also present in the upper layers of the 57 Arctic Ocean 20 , leading to the hypothesis that recalcitrant organic compounds present in high 58Arctic tDOM could be utilized by this group. 5960 Results 61In this study, we analyzed Chloroflexi metagenome assembled genomes (MAGs) 62 generated from samples collected from the vertically stratified waters of the Canada Basin in the 63 Western Arctic Ocean (Fig. 1a). A metagenomic co-assembly was generated from samples 64 originating from the surface layer (5 m to 7 m), the subsurface chlorophyll maximum (25 m to 79 65 m) and a layer corresponding to the terrestrially-derived DOM fluorescence (FDOM) maximum 66 previously described within the cold CB halocline comprised of Pacific-origin waters (177 m to 67 213 m) 21 . The Pacific-origin FDOM maximum is due to sea ice formation and interactions with 68 bottom sediments on the Beaufort and Chukchi shelves, which themselves are influenced by 69 coastal erosion and river runoff 21 . Binning based on tetranucleotide frequency and coverage 70 resulted in 360 MAGs from a diversity of marine microbes (Fig. 1b). Six near complete 71Chloroflexi MAGs were identified. Based on 16S rRNA gene phylogeny, these MAGs 72 represented 3 distinct SAR202 subclades (SAR202-II, -VI, -VII), the AncK29 clade and the TK10 73 Chloroflexi bacterium 5419 | Bioreactor (A0A1Q3SS95) Pseudomonas alcaligenes | Experimnetally validated (Q9S3...

show abstract

Section: Resultsmentioning

confidence: 99%

Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria

Colatriano¹,

Tran²,

Guéguen

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

“…[2] Gentisic acid (2,5-dihydroxybenzoic acid) is ak ey intermediate in the biodegradation of mono-and poly-cyclic aromatic,a nd hetero-aromatic compounds by microorganisms. [3,4] Gentisate-1,2-dioxygenase (GDO), [5][6][7][8][9][10] the nonheme iron enzyme isolated from avariety of sources,c atalyzes the aromatic C À Cb ond cleavage of gentisate to form maleyl pyruvate using dioxygen as the oxidant (Scheme 1). Ther ing cleavage product maleyl pyruvate is further degraded by direct hydrolysis to maleate and pyruvate or undergoes isomerization to form fumaryl pyruvate which hydrolyzes to form fumarate and pyruvate, the central metabolites of the Krebs cycle.…”

mentioning

confidence: 99%

“…In the next step of the reaction, the CT bands at 720 nm and 920 nm decay slowly over 8h (Figure 2b). The (7), N3-Fe1-O2 133.63 (7), N5-Fe1-O2 113.46(8), N1-Fe1-O1 98.95 (7), N3-Fe1-O1 92.63 (7), N5-Fe1-O1 166.61 (7), N1-Fe1-N3 90.59(8), N3-Fe1-N5 85.95- (7), O1-Fe1-O2 58.80 (7). decay of the CT bands suggests the oxidation of metal-bound naphthoate.S imilar spectral change is observed upon exposure of ab enzene solution of 1 Ox ,p repared in situ by mixing 1 and 1equivalent of 2,4,6-tri-tert-butylphenoxyl radical, to dioxygen.…”

mentioning

confidence: 99%

Mimicking the Aromatic‐Ring‐Cleavage Activity of Gentisate‐1,2‐Dioxygenase by a Nonheme Iron Complex

2016

View full text Add to dashboard Cite

Gentisate-1,2-dioxygenase (GDO), a nonheme iron enzyme in the cupin superfamily, catalyzes the cleavage of the aromatic-ring of 2,5-dihydroxybenzoic acid (gentisic acid) to form maleylpyruvic acid in the microbial aerobic degradation of aromatic compounds. To develop a functional model of GDO, we have isolated a nonheme iron(II) complex, [(Tp )Fe (DHN-H)] (Tp =hydrotris(3,5-diphenylpyrazole-1-yl)borate, DHN-H=1,4-dihydroxy-2-naphthoate). In the reaction with O , the biomimetic complex oxidatively cleaves the aromatic ring of the coordinated substrate with the incorporation of both the oxygen atoms from molecular oxygen into the cleavage product. The presence of para-hydroxy group on the substrate plays a crucial role in directing the aromatic-ring cleaving reaction.

show abstract

“…: WP_014075111.1), an enzyme that participates in the degradation of lignin‐derived biphenyl compounds through the nonoxidative decarboxylation of 5‐carboxyvanillate (Peng et al, ). gdo (model 2) is in the KEGG orthology group K00450, contains a conserved cupin‐fold (PF07883.10) and is related to bacterial gdo s that participate in gentisate degradation by catalysing the ring cleavage of gentisate to 3‐maleylpyruvate (Werwath, Arfmann, Pieper, Timmis, & Wittich, ). vao (model 3) contains FAD‐binding (PF01565.22) and FAD‐linked oxidase (PF02913.18) domains, and includes the only functionally characterized fungal vao from Penicillium simlissisum , vaoX (Accession no.…”

Section: Resultsmentioning

confidence: 99%

Fungal adaptation to plant defences through convergent assembly of metabolic modules

2018

View full text Add to dashboard Cite

The ongoing diversification of plant defence compounds exerts dynamic selection pressures on the microorganisms that colonize plant tissues. Evolutionary processes that generate resistance towards these compounds increase microbial fitness by giving access to plant resources and increasing pathogen virulence. These processes entail sequence‐based mechanisms that result in adaptive gene functions, and combinatorial mechanisms that result in novel syntheses of existing gene functions. However, the priority and interactions among these processes in adaptive resistance remain poorly understood. Using a combination of molecular genetic and computational approaches, we investigated the contributions of sequence‐based and combinatorial processes to the evolution of fungal metabolic gene clusters encoding stilbene cleavage oxygenases (SCOs), which catalyse the degradation of biphenolic plant defence compounds known as stilbenes into monophenolic molecules. We present phylogenetic evidence of convergent assembly among three distinct types of SCO gene clusters containing alternate combinations of phenolic catabolism. Multiple evolutionary transitions between different cluster types suggest recurrent selection for distinct gene assemblages. By comparison, we found that the substrate specificities of heterologously expressed SCO enzymes encoded in different clusters types were all limited to stilbenes and related molecules with a 4′‐OH group, and differed modestly in substrate range and activity under the experimental conditions. Together, this work suggests a primary role for genome structural rearrangement, and the importance of enzyme modularity, in promoting fungal metabolic adaptation to plant defence chemistry.

show abstract

Biochemical and Genetic Characterization of a Gentisate 1,2-Dioxygenase from Sphingomonas sp. Strain RW5

Cited by 70 publications

References 56 publications

Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria

Genomic evidence for the degradation of terrestrial organic matter by pelagic Arctic Ocean Chloroflexi bacteria

Mimicking the Aromatic‐Ring‐Cleavage Activity of Gentisate‐1,2‐Dioxygenase by a Nonheme Iron Complex

Fungal adaptation to plant defences through convergent assembly of metabolic modules

Contact Info

Product

Resources

About