Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis

Xu, Zhangyang; Peng, Bo; Kitata, Reta Birhanu; Nicora, Carrie D.; Weitz, Karl K.; Pu, Yunqiao; Shi, Tujin; Cort, John R.; Ragauskas, Arthur J.; Yang, Bin

doi:10.1186/s13068-022-02214-x

Title: Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis

Journal Article · Mon Oct 31 00:00:00 EDT 2022 · Biotechnology for Biofuels and Bioproducts

DOI:https://doi.org/10.1186/s13068-022-02214-x· OSTI ID:1895510

Xu, Zhangyang; Peng, Bo; Kitata, Reta Birhanu; Nicora, Carrie D.; Weitz, Karl K.; Pu, Yunqiao; Shi, Tujin; Cort, John R.; Ragauskas, Arthur J.; Yang, Bin

Abstract Background Bacterial lignin degradation is believed to be primarily achieved by a secreted enzyme system. Effects of such extracellular enzyme systems on lignin structural changes and degradation pathways are still not clearly understood, which remains as a bottleneck in the bacterial lignin bioconversion process. Results This study investigated lignin degradation using an isolated secretome secreted by Pseudomonas putida KT2440 that grew on glucose as the only carbon source. Enzyme assays revealed that the secretome harbored oxidase and peroxidase/Mn ²⁺ -peroxidase capacity and reached the highest activity at 120 h of the fermentation time. The degradation rate of alkali lignin was found to be only 8.1% by oxidases, but increased to 14.5% with the activation of peroxidase/Mn ²⁺ -peroxidase. Gas chromatography–mass spectrometry (GC–MS) and two-dimensional ¹ H– ¹³ C heteronuclear single-quantum coherence (HSQC) NMR analysis revealed that the oxidases exhibited strong C–C bond ( β-β , β -5, and β -1) cleavage. The activation of peroxidases enhanced lignin degradation by stimulating C–O bond ( β -O-4) cleavage, resulting in increased yields of aromatic monomers and dimers. Further mass spectrometry-based quantitative proteomics measurements comprehensively identified different groups of enzymes particularly oxidoreductases in P. putida secretome, including reductases, peroxidases, monooxygenases, dioxygenases, oxidases, and dehydrogenases, potentially contributed to the lignin degradation process. Conclusions Overall, we discovered that bacterial extracellular degradation of alkali lignin to vanillin, vanillic acid, and other lignin-derived aromatics involved a series of oxidative cleavage, catalyzed by active DyP-type peroxidase, multicopper oxidase, and other accessory enzymes. These results will guide further metabolic engineering design to improve the efficiency of lignin bioconversion. Graphical Abstract

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Center for Bioenergy Innovation (CBI)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Energy Efficiency and Renewable Energy (EERE)

Grant/Contract Number:: EE0007104; AC05-76RL01830; AC05-00OR22725; EE0006112; EE0008250

OSTI ID:: 1895510

Alternate ID(s):: OSTI ID: 1909377

Report Number(s):: PNNL-SA-172168; 117; PII: 2214

Journal Information:: Biotechnology for Biofuels and Bioproducts, Journal Name: Biotechnology for Biofuels and Bioproducts Vol. 15 Journal Issue: 1; ISSN 2731-3654

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (65)

Biological valorization strategies for converting lignin into fuels and chemicals Chen, Zhu; Wan, Caixia Renewable and Sustainable Energy Reviews, Vol. 73 https://doi.org/10.1016/j.rser.2017.01.166	journal	June 2017
Advances in microbial lignin degradation and its applications Kamimura, Naofumi; Sakamoto, Shingo; Mitsuda, Nobutaka Current Opinion in Biotechnology, Vol. 56 https://doi.org/10.1016/j.copbio.2018.11.011	journal	April 2019
Oxidative Mechanisms Involved in Lignin Degradation by White-Rot Fungi ten Have, Rimko; Teunissen, Pauline J. M. Chemical Reviews, Vol. 101, Issue 11 https://doi.org/10.1021/cr000115l	journal	November 2001
Pathways for biomass-derived lignin to hydrocarbon fuels Laskar, Dhrubojyoti D.; Yang, Bin; Wang, Huamin Biofuels, Bioproducts and Biorefining, Vol. 7, Issue 5 https://doi.org/10.1002/bbb.1422	journal	July 2013
Decoding lignin valorization pathways in the extremophilic Bacillus ligniniphilus L1 for vanillin biosynthesis Zhu, Daochen; Xu, Lingxia; Sethupathy, Sivasamy Green Chemistry, Vol. 23, Issue 23 https://doi.org/10.1039/D1GC02692E	journal	January 2021
From lignin to valuable products–strategies, challenges, and prospects Wang, Hongliang; Pu, Yunqiao; Ragauskas, Arthur Bioresource Technology, Vol. 271 https://doi.org/10.1016/j.biortech.2018.09.072	journal	January 2019
New dye-decolorizing peroxidases from Bacillus subtilis and Pseudomonas putida MET94: towards biotechnological applications Santos, Ana; Mendes, Sónia; Brissos, Vânia Applied Microbiology and Biotechnology, Vol. 98, Issue 5 https://doi.org/10.1007/s00253-013-5041-4	journal	July 2013
Strengths, challenges, and opportunities for hydrothermal pretreatment in lignocellulosic biorefineries Yang, Bin; Tao, Ling; Wyman, Charles E. Biofuels, Bioproducts and Biorefining, Vol. 12, Issue 1 https://doi.org/10.1002/bbb.1825	journal	October 2017
Towards lignin consolidated bioprocessing: simultaneous lignin depolymerization and product generation by bacteria Salvachúa, Davinia; Karp, Eric M.; Nimlos, Claire T. Green Chemistry, Vol. 17, Issue 11 https://doi.org/10.1039/C5GC01165E	journal	January 2015
Energy savings combined with lignin extraction for production increase: case study at a eucalyptus mill in Portugal Laaksometsä, Catherine; Axelsson, Erik; Berntsson, Thore Clean Technologies and Environmental Policy, Vol. 11, Issue 1 https://doi.org/10.1007/s10098-008-0169-0	journal	October 2008
Transforming biorefinery designs with ‘Plug-In Processes of Lignin’ to enable economic waste valorization Liu, Zhi-Hua; Hao, Naijia; Wang, Yun-Yan Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-23920-4	journal	June 2021
Extremophiles and extremozymes in lignin bioprocessing Zhu, Daochen; Qaria, Majjid A.; Zhu, Bin Renewable and Sustainable Energy Reviews, Vol. 157 https://doi.org/10.1016/j.rser.2021.112069	journal	April 2022
Identification of DypB from Rhodococcus jostii RHA1 as a Lignin Peroxidase Ahmad, Mark; Roberts, Joseph N.; Hardiman, Elizabeth M. Biochemistry, Vol. 50, Issue 23 https://doi.org/10.1021/bi101892z	journal	June 2011
Characterization and use of a bacterial lignin peroxidase with an improved manganese-oxidative activity Vignali, Elisa; Tonin, Fabio; Pollegioni, Loredano Applied Microbiology and Biotechnology, Vol. 102, Issue 24 https://doi.org/10.1007/s00253-018-9409-3	journal	October 2018
Biomass-derived lignin to jet fuel range hydrocarbons via aqueous phase hydrodeoxygenation Wang, Hongliang; Ruan, Hao; Pei, Haisheng Green Chemistry, Vol. 17, Issue 12 https://doi.org/10.1039/C5GC01534K	journal	January 2015
Critical enzyme reactions in aromatic catabolism for microbial lignin conversion Erickson, Erika; Bleem, Alissa; Kuatsjah, Eugene Nature Catalysis, Vol. 5, Issue 2 https://doi.org/10.1038/s41929-022-00747-w	journal	February 2022
Bacterial enzymes involved in lignin degradation de Gonzalo, Gonzalo; Colpa, Dana I.; Habib, Mohamed H. M. Journal of Biotechnology, Vol. 236 https://doi.org/10.1016/j.jbiotec.2016.08.011	journal	October 2016
One-Pot Process for Hydrodeoxygenation of Lignin to Alkanes Using Ru-Based Bimetallic and Bifunctional Catalysts Supported on Zeolite Y Wang, Hongliang; Ruan, Hao; Feng, Maoqi ChemSusChem, Vol. 10, Issue 8 https://doi.org/10.1002/cssc.201700160	journal	March 2017
Defining lignin nanoparticle properties through tailored lignin reactivity by sequential organosolv fragmentation approach (SOFA) Liu, Zhi-Hua; Hao, Naijia; Shinde, Somnath Green Chemistry, Vol. 21, Issue 2 https://doi.org/10.1039/C8GC03290D	journal	January 2019
Ligninolytic enzymes and its mechanisms for degradation of lignocellulosic waste in environment Kumar, Adarsh; Chandra, Ram Heliyon, Vol. 6, Issue 2 https://doi.org/10.1016/j.heliyon.2020.e03170	journal	February 2020
Enhancement of polyhydroxyalkanoate production by co-feeding lignin derivatives with glycerol in Pseudomonas putida KT2440 Xu, Zhangyang; Pan, Chunmei; Li, Xiaolu Biotechnology for Biofuels, Vol. 14, Issue 1 https://doi.org/10.1186/s13068-020-01861-2	journal	January 2021
Identifying and creating pathways to improve biological lignin valorization Liu, Zhi-Hua; Le, Rosemary K.; Kosa, Matyas Renewable and Sustainable Energy Reviews, Vol. 105 https://doi.org/10.1016/j.rser.2019.02.009	journal	May 2019
Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440 Salvachúa, Davinia; Werner, Allison Z.; Pardo, Isabel Proceedings of the National Academy of Sciences, Vol. 117, Issue 17 https://doi.org/10.1073/pnas.1921073117	journal	April 2020
Enzymatic "Combustion": The Microbial Degradation of Lignin Kirk, T. K.; Farrell, R. L. Annual Review of Microbiology, Vol. 41, Issue 1, p. 465-501 https://doi.org/10.1146/annurev.mi.41.100187.002341	journal	October 1987
Enhanced biocatalytic degradation of lignin using combinations of lignin-degrading enzymes and accessory enzymes Rashid, Goran M. M.; Bugg, Timothy D. H. Catalysis Science & Technology, Vol. 11, Issue 10 https://doi.org/10.1039/D1CY00431J	journal	January 2021
Oxidative Catabolism of (+)-Pinoresinol Is Initiated by an Unusual Flavocytochrome Encoded by Translationally Coupled Genes within a Cluster of (+)-Pinoresinol-Coinduced Genes in Pseudomonas sp. Strain SG-MS2 Shettigar, Madhura; Balotra, Sahil; Kasprzak, Annette Applied and Environmental Microbiology, Vol. 86, Issue 10 https://doi.org/10.1128/AEM.00375-20	journal	May 2020
Characterization of multicopper oxidase CopA from Pseudomonas putida KT2440 and Pseudomonas fluorescens Pf-5: Involvement in bacterial lignin oxidation Granja-Travez, Rommel Santiago; Bugg, Timothy D. H. Archives of Biochemistry and Biophysics, Vol. 660 https://doi.org/10.1016/j.abb.2018.10.012	journal	December 2018
Elucidating the mechanisms of enhanced lignin bioconversion by an alkali sterilization strategy Zhao, Zhi-Min; Zhang, Shuyang; Meng, Xianzhi Green Chemistry, Vol. 23, Issue 13 https://doi.org/10.1039/D1GC00911G	journal	January 2021
Bacterial laccases Sharma, P.; Goel, R.; Capalash, N. World Journal of Microbiology and Biotechnology, Vol. 23, Issue 6 https://doi.org/10.1007/s11274-006-9305-3	journal	November 2006
Lignin valorization through integrated biological funneling and chemical catalysis Linger, J. G.; Vardon, D. R.; Guarnieri, M. T. Proceedings of the National Academy of Sciences, Vol. 111, Issue 33, p. 12013-12018 https://doi.org/10.1073/pnas.1410657111	journal	August 2014
Improved Manganese-Oxidizing Activity of DypB, a Peroxidase from a Lignolytic Bacterium Singh, Rahul; Grigg, Jason C.; Qin, Wei ACS Chemical Biology, Vol. 8, Issue 4 https://doi.org/10.1021/cb300608x	journal	January 2013
Kinetic understanding of nitrogen supply condition on biosynthesis of polyhydroxyalkanoate from benzoate by Pseudomonas putida KT2440 Xu, Zhangyang; Li, Xiaolu; Hao, Naijia Bioresource Technology, Vol. 273 https://doi.org/10.1016/j.biortech.2018.11.046	journal	February 2019
Lignin depolymerization by fungal secretomes and a microbial sink Salvachúa, Davinia; Katahira, Rui; Cleveland, Nicholas S. Green Chemistry, Vol. 18, Issue 22 https://doi.org/10.1039/C6GC01531J	journal	January 2016
Systems biology-guided biodesign of consolidated lignin conversion Lin, Lu; Cheng, Yanbing; Pu, Yunqiao Green Chemistry, Vol. 18, Issue 20 https://doi.org/10.1039/C6GC01131D	journal	January 2016
Lignin-modifying enzymes from selected white-rot fungi: production and role from in lignin degradation Hatakka, Annele FEMS Microbiology Reviews, Vol. 13, Issue 2-3 https://doi.org/10.1111/j.1574-6976.1994.tb00039.x	journal	March 1994
Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants Aylward, Frank O.; Khadempour, Lily; Tremmel, Daniel M. PLOS ONE, Vol. 10, Issue 8 https://doi.org/10.1371/journal.pone.0134752	journal	August 2015
Characterisation and optimisation of three potential aerobic bacterial strains for kraft lignin degradation from pulp paper waste Chandra, R.; Raj, A.; Purohit, H. J. Chemosphere, Vol. 67, Issue 4 https://doi.org/10.1016/j.chemosphere.2006.10.011	journal	March 2007
Revealing the Molecular Structural Transformation of Hardwood and Softwood in Dilute Acid Flowthrough Pretreatment Zhang, Libing; Pu, Yunqiao; Cort, John R. ACS Sustainable Chemistry & Engineering, Vol. 4, Issue 12 https://doi.org/10.1021/acssuschemeng.6b01491	journal	October 2016
LsdD has a critical role in the dehydrodiconiferyl alcohol catabolism among eight lignostilbene α,β-dioxygenase isozymes in Sphingobium sp. strain SYK-6 Kamimura, Naofumi; Hirose, Yusaku; Masuba, Ryuto International Biodeterioration & Biodegradation, Vol. 159 https://doi.org/10.1016/j.ibiod.2021.105208	journal	April 2021
A bionic system with Fenton reaction and bacteria as a model for bioprocessing lignocellulosic biomass Zhang, Kejing; Si, Mengying; Liu, Dan Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1035-x	journal	February 2018
Lignin Valorization: Improving Lignin Processing in the Biorefinery Ragauskas, A. J.; Beckham, G. T.; Biddy, M. J. Science, Vol. 344, Issue 6185, p. 1246843-1246843 https://doi.org/10.1126/science.1246843	journal	May 2014
Exploring bacterial lignin degradation Brown, Margaret E.; Chang, Michelle CY Current Opinion in Chemical Biology, Vol. 19 https://doi.org/10.1016/j.cbpa.2013.11.015	journal	April 2014
Lignin valorization: Status, challenges and opportunities Sethupathy, Sivasamy; Murillo Morales, Gabriel; Gao, Lu Bioresource Technology, Vol. 347 https://doi.org/10.1016/j.biortech.2022.126696	journal	March 2022
Structural and functional analysis of lignostilbene dioxygenases from Sphingobium sp. SYK-6 Kuatsjah, Eugene; Chan, Anson C. K.; Katahira, Rui Journal of Biological Chemistry, Vol. 296 https://doi.org/10.1016/j.jbc.2021.100758	journal	January 2021
Proteogenomic and metabolomic characterization of human glioblastoma Wang, Liang-Bo; Karpova, Alla; Gritsenko, Marina A. Cancer Cell, Vol. 39, Issue 4 https://doi.org/10.1016/j.ccell.2021.01.006	journal	April 2021
Pathways for degradation of lignin in bacteria and fungi Bugg, Timothy D. H.; Ahmad, Mark; Hardiman, Elizabeth M. Natural Product Reports, Vol. 28, Issue 12, p. 1883-1896 https://doi.org/10.1039/c1np00042j	journal	January 2011
Lipid Production from Dilute Alkali Corn Stover Lignin by Rhodococcus Strains He, Yucai; Li, Xiaolu; Ben, Haoxi ACS Sustainable Chemistry & Engineering, Vol. 5, Issue 3 https://doi.org/10.1021/acssuschemeng.6b02627	journal	January 2017
Isolation of the (+)-Pinoresinol-Mineralizing Pseudomonas sp. Strain SG-MS2 and Elucidation of Its Catabolic Pathway Shettigar, Madhura; Balotra, Sahil; Cahill, David Applied and Environmental Microbiology, Vol. 84, Issue 4 https://doi.org/10.1128/AEM.02531-17	journal	February 2018
Flowthrough Pretreatment of Softwood under Water-Only and Alkali Conditions Zhang, Libing; Xu, Zhangyang; Cort, John R. Energy & Fuels, Vol. 34, Issue 12 https://doi.org/10.1021/acs.energyfuels.0c03374	journal	November 2020
Discovery of potential pathways for biological conversion of poplar wood into lipids by co-fermentation of Rhodococci strains Li, Xiaolu; He, Yucai; Zhang, Libing Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1395-x	journal	March 2019
The production of scientific knowledge on renewable energies: Worldwide trends, dynamics and challenges and implications for management Rizzi, Francesco; van Eck, Nees Jan; Frey, Marco Renewable Energy, Vol. 62 https://doi.org/10.1016/j.renene.2013.08.030	journal	February 2014
Cooperative valorization of lignin and residual sugar to polyhydroxyalkanoate (PHA) for enhanced yield and carbon utilization in biorefineries Liu, Zhi-Hua; Shinde, Somnath; Xie, Shangxian Sustainable Energy & Fuels, Vol. 3, Issue 8 https://doi.org/10.1039/C9SE00021F	journal	January 2019
Lignin catabolic pathways reveal unique characteristics of dye‐decolorizing peroxidases in Pseudomonas putida Lin, Lu; Wang, Xiaopeng; Cao, Lanfang Environmental Microbiology, Vol. 21, Issue 5 https://doi.org/10.1111/1462-2920.14593	journal	March 2019
Opportunities and challenges in biological lignin valorization Beckham, Gregg T.; Johnson, Christopher W.; Karp, Eric M. Current Opinion in Biotechnology, Vol. 42 https://doi.org/10.1016/j.copbio.2016.02.030	journal	December 2016
Breaking Down Lignin to High-Value Chemicals: The Conversion of Lignocellulose to Vanillin in a Gene Deletion Mutant of Rhodococcus jostii RHA1 Sainsbury, Paul D.; Hardiman, Elizabeth M.; Ahmad, Mark ACS Chemical Biology, Vol. 8, Issue 10 https://doi.org/10.1021/cb400505a	journal	August 2013
Recent developments in chemical degradation of lignin: catalytic oxidation and ionic liquids Dai, Jinhuo; Patti, Antonio F.; Saito, Kei Tetrahedron Letters, Vol. 57, Issue 45 https://doi.org/10.1016/j.tetlet.2016.09.084	journal	November 2016
Improvement of biomass through lignin modification Li, Xu; Weng, Jing-Ke; Chapple, Clint The Plant Journal, Vol. 54, Issue 4 https://doi.org/10.1111/j.1365-313X.2008.03457.x	journal	May 2008
Techno‐economic analysis of jet‐fuel production from biorefinery waste lignin Shen, Rongchun; Tao, Ling; Yang, Bin Biofuels, Bioproducts and Biorefining, Vol. 13, Issue 3 https://doi.org/10.1002/bbb.1952	journal	December 2018
Catalytic routes for the conversion of lignocellulosic biomass to aviation fuel range hydrocarbons Wang, Hongliang; Yang, Bin; Zhang, Qian Renewable and Sustainable Energy Reviews, Vol. 120 https://doi.org/10.1016/j.rser.2019.109612	journal	March 2020
Intracellular pathways for lignin catabolism in white-rot fungi del Cerro, Carlos; Erickson, Erika; Dong, Tao Proceedings of the National Academy of Sciences, Vol. 118, Issue 9 https://doi.org/10.1073/pnas.2017381118	journal	February 2021
Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism: Bacterial catabolism of lignin-derived aromatics Kamimura, Naofumi; Takahashi, Kenji; Mori, Kosuke Environmental Microbiology Reports, Vol. 9, Issue 6 https://doi.org/10.1111/1758-2229.12597	journal	November 2017
Microbial degradation of lignin: Role of lignin peroxidase, manganese peroxidase, and laccase Higuchi, Takayoshi Proceedings of the Japan Academy, Series B, Vol. 80, Issue 5 https://doi.org/10.2183/pjab.80.204	journal	January 2004
Pathway discovery and engineering for cleavage of a β-1 lignin-derived biaryl compound Presley, Gerald N.; Werner, Allison Z.; Katahira, Rui Metabolic Engineering, Vol. 65 https://doi.org/10.1016/j.ymben.2021.02.003	journal	May 2021
Lignocellulose degradation mechanisms across the Tree of Life Cragg, Simon M.; Beckham, Gregg T.; Bruce, Neil C. Current Opinion in Chemical Biology, Vol. 29 https://doi.org/10.1016/j.cbpa.2015.10.018	journal	December 2015
Catalytic Mechanism of Aryl-Ether Bond Cleavage in Lignin by LigF and LigG Prates, Erica Teixeira; Crowley, Michael F.; Skaf, Munir S. The Journal of Physical Chemistry B, Vol. 123, Issue 48 https://doi.org/10.1021/acs.jpcb.9b06243	journal	November 2019

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Title: Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis

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