title: Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization.
abstract: 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 used13C-fingerprinting,13C metabolic flux analysis (13C-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 CO2release (i.e., carbon loss) from the ligninolysis-based metabolism of SYK-6 is significantly greater than the CO2release 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)13C-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.
authors.affiliation: Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94550.
authors.forename: Arul M
authors.initials: AM
authors.lastname: Varman
authors.affiliation: Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130.
authors.forename: Lian
authors.initials: L
authors.lastname: He
authors.affiliation: Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94550.
authors.forename: Rhiannon
authors.initials: R
authors.lastname: Follenfant
authors.affiliation: Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94550.
authors.forename: Weihua
authors.initials: W
authors.lastname: Wu
authors.affiliation: Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94550.
authors.forename: Sarah
authors.initials: S
authors.lastname: Wemmer
authors.affiliation: Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94550.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Wrobel
authors.affiliation: Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130.
authors.forename: Yinjie J
authors.initials: YJ
authors.lastname: Tang
authors.affiliation: Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94550; Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN 55108 seesing@sandia.gov.
authors.forename: Seema
authors.initials: S
authors.lastname: Singh
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D001419:Bacteria / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D001547:Benzaldehydes / Q000737:chemistry / Q000378:metabolism; D002244:Carbon / Q000378:metabolism; D002247:Carbon Isotopes; D004734:Energy Metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D006863:Hydrogen-Ion Concentration; D008031:Lignin / Q000378:metabolism*; D064688:Metabolic Flux Analysis; D009249:NADP / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012987:Soil; D012988:Soil Microbiology; D014641:Vanillic Acid / Q000737:chemistry / Q000378:metabolism
chemical_list: D000596:Amino Acids; D001547:Benzaldehydes; D002247:Carbon Isotopes; D012987:Soil; D009249:NADP; D002244:Carbon; D008031:Lignin; C100058:vanillin; D014641:Vanillic Acid
keywords: 13C-MFA; NADPH; fingerprinting; gluconeogenesis; lignin