Genetic and Biochemical Investigations on Bacterial Catabolic Pathways for Lignin-Derived Aromatic Compounds

Masai, Eiji; Katayama, Yoshihiro; Fukuda, Masao

doi:10.1271/bbb.60437

Cited by 447 publications

(435 citation statements)

References 68 publications

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“…As an example, the lignin model biphenyl compound 5,5 ′ -dehydrodivanillate (∼332 Da) can be transformed by bacterial degradation via an O-demethylation followed by a subsequent ring cleavage (Masai et al, 2007). If the resulting product is further hydrolyzed, decarboxylated, and then demethylated, protocatechuic acid is generated.…”

Section: Discussion Temporal Changes In Dom Transformationmentioning

confidence: 99%

Microbially-Mediated Transformations of Estuarine Dissolved Organic Matter

et al. 2017

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Microbially-mediated transformations of dissolved organic matter (DOM) in a marsh-dominated estuarine system were investigated at the molecular level using ultrahigh resolution mass spectrometry. In addition to observing spatial and temporal variability in DOM sources in the estuary, multiple incubations with endogenous microorganisms identified the influence of DOM composition on biodegradation. A clear microbial preference for degradation of compounds associated with marine DOM relative to those of terrestrial origin was observed, resulting in an overall shift of the remaining DOM toward a stronger terrigenous signature. During short, 1-day long incubations of samples rich in marine DOM, the molecular formulae that were enriched had slightly smaller mass (20-30 Da) and number of carbon atoms compared to the molecular formulae that were depleted. Over longer time scales (70 days), the mean differences in molecular mass between formulae that were depleted and enriched were substantially larger (∼270 Da). The differences in elemental composition over daily time scales were consistent with transformations in functional groups; over longer time scales, the differences in elemental composition may be related to progressive transformations of functional groups of intermediate products and/or other reactions. Our results infused new data toward the understanding of DOM processing by bacterioplankton in estuarine systems.

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Section: Discussion Temporal Changes In Dom Transformationmentioning

confidence: 99%

Microbially-Mediated Transformations of Estuarine Dissolved Organic Matter

et al. 2017

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“…In contrast, galD homologs are frequently found in lig operons and is found in the same gene cluster as the canonical protocatechuate 4,5-cleavage pathway of Sphingo- bium sp. SYK-6 (9,47). The presence of a GalD homolog in the Lig pathways suggests that the product of 2-pyrone-4,6-dicarboxylate (PDC) lactonase, LigI, is OMA rather than (2Z,4E)-CHM, which is subsequently tautomerized to (2E,4E)-CHM by the GalD homolog to be used by either GalB or LigJ (Fig.…”

Section: Enzymementioning

confidence: 99%

Structural and Kinetic Characterization of the 4-Carboxy-2-hydroxymuconate Hydratase from the Gallate and Protocatechuate 4,5-Cleavage Pathways of Pseudomonas putida KT2440

Mazurkewich

Brott

Kimber

et al. 2016

Journal of Biological Chemistry

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The bacterial catabolism of lignin and its breakdown products is of interest for applications in industrial processing of lignobiomass. The gallate degradation pathway of Pseudomonas putida KT2440 requires a 4-carboxy-2-hydroxymuconate (CHM) hydratase (GalB), which has a 12% sequence identity to a previously identified CHM hydratase (LigJ) from Sphingomonas sp. SYK-6. The structure of GalB was determined and found to be a member of the PIG-L N-acetylglucosamine deacetylase family; GalB is structurally distinct from the amidohydrolase fold of LigJ. LigJ has the same stereospecificity as GalB, providing an example of convergent evolution for catalytic conversion of a common metabolite in bacterial aromatic degradation pathways. Purified GalB contains a bound Zn 2؉ cofactor; however the enzyme is capable of using Fe 2؉ and Co 2؉ with similar efficiency. The general base aspartate in the PIG-L deacetylases is an alanine in GalB; replacement of the alanine with aspartate decreased the GalB catalytic efficiency for CHM by 9.5 ؋ 10 4 -fold, and the variant enzyme did not have any detectable hydrolase activity. Kinetic analyses and pH dependence studies of the wild type and variant enzymes suggested roles for Glu-48 and His-164 in the catalytic mechanism. A comparison with the PIG-L deacetylases led to a proposed mechanism for GalB wherein Glu-48 positions and activates the metal-ligated water for the hydration reaction and His-164 acts as a catalytic acid.

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“…The catabolic lignin degradation pathway and the corresponding gene clusters were well studied in Sphingomonas paucimobilis SYK-6 using various lignin derived biaryls and monoaryls (Masai et al 2007). It was clear that bacteria mineralized lignin via protocatechuic acid 4, 5-cleavage pathway and the multiple 3MGA catabolic pathways which may be more significant on lignin degradation than previous thought (Bugg et al 2011).…”

Section: Introductionmentioning

confidence: 99%