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Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin.

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Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman C, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN
OpenAccess logo J Biol Chem 291 5234-46 (2016)
Related entries: 4xt0, 4yan

Cited: 20 times
EuropePMC logo PMID: 26637355

Abstract

Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50-70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.

Articles - 4yam mentioned but not cited (1)

  1. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin. Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman C, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN. J Biol Chem 291 5234-5246 (2016)


Reviews citing this publication (6)

  1. Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism. Kamimura N, Takahashi K, Mori K, Araki T, Fujita M, Higuchi Y, Masai E. Environ Microbiol Rep 9 679-705 (2017)
  2. Biochemical transformation of lignin for deriving valued commodities from lignocellulose. Gall DL, Ralph J, Donohue TJ, Noguera DR. Curr. Opin. Biotechnol. 45 120-126 (2017)
  3. Profiling microbial lignocellulose degradation and utilization by emergent omics technologies. Rosnow JJ, Anderson LN, Nair RN, Baker ES, Wright AT. Crit. Rev. Biotechnol. 37 626-640 (2017)
  4. Microbial β-etherases and glutathione lyases for lignin valorisation in biorefineries: current state and future perspectives. Husarcíková J, Voß H, Domínguez de María P, Schallmey A. Appl. Microbiol. Biotechnol. 102 5391-5401 (2018)
  5. Efficient, environmentally-friendly and specific valorization of lignin: promising role of non-radical lignolytic enzymes. Wang W, Zhang C, Sun X, Su S, Li Q, Linhardt RJ. World J. Microbiol. Biotechnol. 33 125 (2017)
  6. The chemical logic of enzymatic lignin degradation. Bugg TDH. Chem Commun (Camb) 60 804-814 (2024)

Articles citing this publication (13)

  1. Structural and functional divergence of GDAP1 from the glutathione S-transferase superfamily. Googins MR, Woghiren-Afegbua AO, Calderon M, St Croix CM, Kiselyov KI, VanDemark AP. FASEB J 34 7192-7207 (2020)
  2. Effect of sulfonated lignin on enzymatic activity of the ligninolytic enzymes Cα-dehydrogenase LigD and β-etherase LigF. Wang C, Ouyang X, Su S, Liang X, Zhang C, Wang W, Yuan Q, Li Q. Enzyme Microb. Technol. 93-94 59-69 (2016)
  3. In Vitro Enzymatic Depolymerization of Lignin with Release of Syringyl, Guaiacyl, and Tricin Units. Gall DL, Kontur WS, Lan W, Kim H, Li Y, Ralph J, Donohue TJ, Noguera DR. Appl. Environ. Microbiol. 84 (2018)
  4. Lignin Degradation and Its Use in Signaling Development by the Coprophilous Ascomycete Podospora anserina. Dicko M, Ferrari R, Tangthirasunun N, Gautier V, Lalanne C, Lamari F, Silar P. J Fungi (Basel) 6 E278 (2020)
  5. Roles of two glutathione S-transferases in the final step of the β-aryl ether cleavage pathway in Sphingobium sp. strain SYK-6. Higuchi Y, Sato D, Kamimura N, Masai E. Sci Rep 10 20614 (2020)
  6. A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases. Kontur WS, Olmsted CN, Yusko LM, Niles AV, Walters KA, Beebe ET, Vander Meulen KA, Karlen SD, Gall DL, Noguera DR, Donohue TJ. J. Biol. Chem. 294 1877-1890 (2019)
  7. Acidic Versus Alkaline Bacterial Degradation of Lignin Through Engineered Strain E. coli BL21(Lacc): Exploring the Differences in Chemical Structure, Morphology, and Degradation Products. Morales GM, Ali SS, Si H, Zhang W, Zhang R, Hosseini K, Sun J, Zhu D. Front Bioeng Biotechnol 8 671 (2020)
  8. Bacterial Catabolism of β-Hydroxypropiovanillone and β-Hydroxypropiosyringone Produced in the Reductive Cleavage of Arylglycerol-β-Aryl Ether in Lignin. Higuchi Y, Aoki S, Takenami H, Kamimura N, Takahashi K, Hishiyama S, Lancefield CS, Ojo OS, Katayama Y, Westwood NJ, Masai E. Appl. Environ. Microbiol. 84 (2018)
  9. Cloning, expression, and biochemical characterization of β-etherase LigF from Altererythrobacter sp. B11. Robles-Machuca M, Aviles-Mejía L, Romero-Soto IC, Rodríguez JA, Armenta-Pérez VP, Camacho-Ruiz MA. Heliyon 9 e21006 (2023)
  10. Database Mining for Novel Bacterial β-Etherases, Glutathione-Dependent Lignin-Degrading Enzymes. Voß H, Heck CA, Schallmey M, Schallmey A. Appl Environ Microbiol 86 (2020)
  11. Mitochondrial sorting and assembly machinery operates by β-barrel switching. Takeda H, Tsutsumi A, Nishizawa T, Lindau C, Busto JV, Wenz LS, Ellenrieder L, Imai K, Straub SP, Mossmann W, Qiu J, Yamamori Y, Tomii K, Suzuki J, Murata T, Ogasawara S, Nureki O, Becker T, Pfanner N, Wiedemann N, Kikkawa M, Endo T. Nature 590 163-169 (2021)
  12. Nucleophilic Thiols Reductively Cleave Ether Linkages in Lignin Model Polymers and Lignin. Klinger GE, Zhou Y, Foote JA, Wester AM, Cui Y, Alherech M, Stahl SS, Jackson JE, Hegg EL. ChemSusChem 13 4394-4399 (2020)
  13. Rapid characterization of the activities of lignin-modifying enzymes based on nanostructure-initiator mass spectrometry (NIMS). Deng K, Zeng J, Cheng G, Gao J, Sale KL, Simmons BA, Singh AK, Adams PD, Northen TR. Biotechnol Biofuels 11 266 (2018)


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