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Cazier EA, Pham TN, Cossus L, Abla M, Ilc T, Lawrence P. Exploring industrial lignocellulosic waste: Sources, types, and potential as high-value molecules. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 188:11-38. [PMID: 39094219 DOI: 10.1016/j.wasman.2024.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Lignocellulosic biomass has a promising role in a circular bioeconomy and may be used to produce valuable molecules for green chemistry. Lignocellulosic biomass, such as food waste, agricultural waste, wood, paper or cardboard, corresponded to 15.7% of all waste produced in Europe in 2020, and has a high potential as a secondary raw material for industrial processes. This review first presents industrial lignocellulosic waste sources, in terms of their composition, quantities and types of lignocellulosic residues. Secondly, the possible high added-value chemicals obtained from transformation of lignocellulosic waste are detailed, as well as their potential for applications in the food industry, biomedical, energy or chemistry sectors, including as sources of polyphenols, enzymes, bioplastic precursors or biofuels. In a third part, various available transformation treatments, such as physical treatments with ultrasound or heat, chemical treatments with acids or bases, and biological treatments with enzymes or microorganisms, are presented. The last part discusses the perspectives of the use of lignocellulosic waste and the fact that decreasing the cost of transformation is one of the major issues for improving the use of lignocellulosic biomass in a circular economy and green chemistry approach, since it is currently often more expensive than petroleum-based counterparts.
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Affiliation(s)
- Elisabeth A Cazier
- UCLy (Lyon Catholic University), ESTBB, Lyon, France; UCLy (Lyon Catholic University), UR CONFLUENCE : Sciences et Humanités (EA 1598), Lyon, France; Nantes Université, Oniris, GEPEA, UMR 6144, F-44600 Saint-Nazaire, France(1).
| | - Thanh-Nhat Pham
- UCLy (Lyon Catholic University), ESTBB, Lyon, France; UCLy (Lyon Catholic University), UR CONFLUENCE : Sciences et Humanités (EA 1598), Lyon, France
| | - Louis Cossus
- UCLy (Lyon Catholic University), ESTBB, Lyon, France; UCLy (Lyon Catholic University), UR CONFLUENCE : Sciences et Humanités (EA 1598), Lyon, France
| | - Maher Abla
- UCLy (Lyon Catholic University), ESTBB, Lyon, France; UCLy (Lyon Catholic University), UR CONFLUENCE : Sciences et Humanités (EA 1598), Lyon, France.
| | - Tina Ilc
- UCLy (Lyon Catholic University), ESTBB, Lyon, France; UCLy (Lyon Catholic University), UR CONFLUENCE : Sciences et Humanités (EA 1598), Lyon, France.
| | - Philip Lawrence
- UCLy (Lyon Catholic University), ESTBB, Lyon, France; UCLy (Lyon Catholic University), UR CONFLUENCE : Sciences et Humanités (EA 1598), Lyon, France.
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2
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Gao J, Ali MY, Kamaraj Y, Zhang Z, Weike L, Sethupathy S, Zhu D. A comprehensive review on biological funnel mechanism in lignin valorization: Pathways and enzyme dynamics. Microbiol Res 2024; 287:127835. [PMID: 39032264 DOI: 10.1016/j.micres.2024.127835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/17/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
Lignin, a significant byproduct of the paper and pulp industry, is attracting interest due to its potential utilization in biomaterial-based sectors and biofuel production. Investigating biological methods for converting lignin into valuable products is crucial for effective utilization and has recently gained growing attention. Several microorganisms effectively decomposed low molecular weight lignins, transforming them into intermediate compounds via upper and lower metabolic pathways. This review focuses on assessing bacterial metabolic pathways involved in the breakdown of lignin into aromatic compounds and their subsequent utilization by different bacteria through various metabolic pathways. Understanding these pathways is essential for developing efficient synthetic metabolic systems to valorize lignin and obtain valuable industrial aromatic chemicals. The concept of "biological funneling," which involves examining key enzymes, their interactions, and the complex metabolic pathways associated with lignin conversion, is crucial in lignin valorization. By manipulating lignin metabolic pathways and utilizing biological routes, many aromatic compounds can be synthesized within cellular factories. Although there is insufficient evidence regarding the complete metabolism of polyaromatic hydrocarbons by particular microorganisms, understanding lignin-degrading enzymes, regulatory mechanisms, and interactions among various enzyme systems is essential for optimizing lignin valorization. This review highlights recent advancements in lignin valorization, bio-funneling, multi-omics, and analytical characterization approaches for aromatic utilization. It provides up-to-date information and insights into the latest research findings and technological innovations. The review offers valuable insights into the future potential of biological routes for lignin valorization.
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Affiliation(s)
- Jiayue Gao
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Mohamed Yassin Ali
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China; Department of Biochemistry, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt
| | - Yoganathan Kamaraj
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Zhenghao Zhang
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Li Weike
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Sivasamy Sethupathy
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Daochen Zhu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China.
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3
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Liu A, Ellis D, Mhatre A, Brahmankar S, Seto J, Nielsen DR, Varman AM. Biomanufacturing of value-added chemicals from lignin. Curr Opin Biotechnol 2024; 89:103178. [PMID: 39098292 DOI: 10.1016/j.copbio.2024.103178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 07/16/2024] [Accepted: 07/22/2024] [Indexed: 08/06/2024]
Abstract
Lignin valorization faces persistent biomanufacturing challenges due to the heterogeneous and toxic carbon substrates derived from lignin depolymerization. To address the heterogeneous nature of aromatic feedstocks, plant cell wall engineering and 'lignin first' pretreatment methods have recently emerged. Next, to convert the resulting aromatic substrates into value-added chemicals, diverse microbial host systems also continue to be developed. This includes microbes that (1) lack aromatic metabolism, (2) metabolize aromatics but not sugars, and (3) co-metabolize both aromatics and sugars, each system presenting unique pros and cons. Considering the intrinsic complexity of lignin-derived substrate mixtures, emerging and non-model microbes with native metabolism for aromatics appear poised to provide the greatest impacts on lignin valorization via biomanufacturing.
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Affiliation(s)
- Arren Liu
- Biological Design Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA
| | - Dylan Ellis
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA
| | - Apurv Mhatre
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA
| | - Sumant Brahmankar
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA
| | - Jong Seto
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA
| | - David R Nielsen
- Biological Design Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA; Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA
| | - Arul M Varman
- Biological Design Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA; Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA.
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4
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Silva JP, Frederico TD, Ticona ARP, Pinto OHB, Williams TCR, Krüger RH, Noronha EF. Insights on kraft lignin degradation in an anaerobic environment. Enzyme Microb Technol 2024; 179:110468. [PMID: 38850683 DOI: 10.1016/j.enzmictec.2024.110468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/14/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
Lignin is an aromatic macromolecule and one of the main constituents of lignocellulosic materials. Kraft lignin is generated as a residual by-product of the lignocellulosic biomass industrial process, and it might be used as a feedstock to generate low molecular weight aromatic compounds. In this study, we seek to understand and explore the potential of ruminal bacteria in the degradation of kraft lignin. We established two consortia, KLY and KL, which demonstrated significant lignin-degrading capabilities. Both consortia reached maximum growth after two days, with KLY showing a higher growth and decolorization rate. Additionally, SEM analysis revealed morphological changes in the residual lignin from both consortia, indicating significant degradation. This was further supported by FTIR spectra, which showed new bands corresponding to the C-H vibrations of guaiacyl and syringyl units, suggesting structural transformations of the lignin. Taxonomic analysis showed enrichment of the microbial community with members of the Dickeya genus. Seven metabolic pathways related to lignin metabolism were predicted for the established consortia. Both consortia were capable of consuming aromatic compounds such as 4-hydroxybenzoic acid, syringaldehyde, acetovanillone, and syringic acid, highlighting their capacity to convert aromatic compounds into commercially valuable molecules presenting antifungal activity and used as food preservatives as 4-hydroxyphenylacetic, 3-phenylacetic, and phenylacetic acids. Therefore, the microbial consortia shown in the present work are models for understanding the process of lignin degradation and consumption in bacterial anaerobic communities and developing biological processes to add value to industrial processes based on lignocellulosic biomass as feedstock.
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Affiliation(s)
- Jéssica P Silva
- Enzymology Laboratory, Cell Biology Department, Universidade de Brasília (UnB), Brasília 70910-900, Brazil
| | - Tayná D Frederico
- Enzymology Laboratory, Cell Biology Department, Universidade de Brasília (UnB), Brasília 70910-900, Brazil
| | - Alonso R P Ticona
- Enzyme Biotechnology Research Laboratory, Science Faculty, Universidad Nacional Jorge Basadre Grohmann, Tacna 23003, Peru
| | - Otávio H B Pinto
- Genomic for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil
| | - Thomas C R Williams
- Plant Biochemistry Laboratory, Department of Botany, University of Brasilia, Brasília 70910-900, Brazil
| | - Ricardo H Krüger
- Enzymology Laboratory, Cell Biology Department, Universidade de Brasília (UnB), Brasília 70910-900, Brazil
| | - Eliane F Noronha
- Enzymology Laboratory, Cell Biology Department, Universidade de Brasília (UnB), Brasília 70910-900, Brazil.
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5
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Ji T, Liaqat F, Khazi MI, Liaqat N, Nawaz MZ, Zhu D. Lignin biotransformation: Advances in enzymatic valorization and bioproduction strategies. INDUSTRIAL CROPS AND PRODUCTS 2024; 216:118759. [DOI: 10.1016/j.indcrop.2024.118759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
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6
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Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted CN, Majumder ELW, Kumar D, Awasthi D, Mukhopadhyay A, Singer SW, Gladden JM, Simmons BA, Choudhary H. Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries. CHEMSUSCHEM 2024; 17:e202301460. [PMID: 38669480 DOI: 10.1002/cssc.202301460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shubhasish Goswami
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Valentina Garcia
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Elizabeth Zhou
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
| | - Charles N Olmsted
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA 94550, United States
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7
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Metz F, Olsen AM, Lu F, Myers KS, Allemann MN, Michener JK, Noguera DR, Donohue TJ. Catabolism of β-5 linked aromatics by Novosphingobium aromaticivorans. mBio 2024; 15:e0171824. [PMID: 39012147 PMCID: PMC11323797 DOI: 10.1128/mbio.01718-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 07/17/2024] Open
Abstract
Aromatic compounds are an important source of commodity chemicals traditionally produced from fossil fuels. Aromatics derived from plant lignin can potentially be converted into commodity chemicals through depolymerization followed by microbial funneling of monomers and low molecular weight oligomers. This study investigates the catabolism of the β-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) by the bacterium Novosphingobium aromaticivorans. We used genome-wide screens to identify candidate genes involved in DC-A catabolism. Subsequent in vivo and in vitro analyses of these candidate genes elucidated a catabolic pathway composed of four required gene products and several partially redundant dehydrogenases that convert DC-A to aromatic monomers that can be funneled into the central aromatic metabolic pathway of N. aromaticivorans. Specifically, a newly identified γ-formaldehyde lyase, PcfL, opens the phenylcoumaran ring to form a stilbene and formaldehyde. A lignostilbene dioxygenase, LsdD, then cleaves the stilbene to generate the aromatic monomers vanillin and 5-formylferulate (5-FF). We also showed that the aldehyde dehydrogenase FerD oxidizes 5-FF before it is decarboxylated by LigW, yielding ferulic acid. We found that some enzymes involved in the β-5 catabolism pathway can act on multiple substrates and that some steps in the pathway can be mediated by multiple enzymes, providing new insights into the robust flexibility of aromatic catabolism in N. aromaticivorans. A comparative genomic analysis predicted that the newly discovered β-5 aromatic catabolic pathway is common within the order Sphingomonadales. IMPORTANCE In the transition to a circular bioeconomy, the plant polymer lignin holds promise as a renewable source of industrially important aromatic chemicals. However, since lignin contains aromatic subunits joined by various chemical linkages, producing single chemical products from this polymer can be challenging. One strategy to overcome this challenge is using microbes to funnel a mixture of lignin-derived aromatics into target chemical products. This approach requires strategies to cleave the major inter-unit linkages of lignin to release monomers for funneling into valuable products. In this study, we report newly discovered aspects of a pathway by which the Novosphingobium aromaticivorans DSM12444 catabolizes aromatics joined by the second most common inter-unit linkage in lignin, the β-5 linkage. This work advances our knowledge of aromatic catabolic pathways, laying the groundwork for future metabolic engineering of this and other microbes for optimized conversion of lignin into products.
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Affiliation(s)
- Fletcher Metz
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, USA
| | - Abigail M. Olsen
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Fachuang Lu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Kevin S. Myers
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Marco N. Allemann
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Joshua K. Michener
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Daniel R. Noguera
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
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8
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Kim M, Cha IT, Li M, Park SJ. Unraveling interspecies cross-feeding during anaerobic lignin degradation for bioenergy applications. CHEMOSPHERE 2024; 361:142588. [PMID: 38866340 DOI: 10.1016/j.chemosphere.2024.142588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/14/2024]
Abstract
Lignin, a major component of plant biomass, remains underutilized for renewable biofuels due to its complex and heterogeneous structure. Although investigations into depolymerizing lignin using fungi are well-established, studies of microbial pathways that enable anaerobic lignin breakdown linked with methanogenesis are limited. Through an enrichment cultivation approach with inoculation of freshwater sediment, we enriched a microbial community capable of producing methane during anaerobic lignin degradation. We reconstructed the near-complete population genomes of key lignin degraders and methanogens using metagenome-assembled genomes finally selected in this study (MAGs; 92 bacterial and 4 archaeal MAGs affiliated into 45 and 2 taxonomic groups, respectively). This study provides genetic evidence of microbial interdependence in conversion of lignin to methane in a syntrophic community. Metagenomic analysis revealed metabolic linkages, with lignin-hydrolyzing and/or fermentative bacteria such as the genera Alkalibaculum and Propionispora transforming lignin breakdown products into compounds such as acetate to feed methanogens (two archaeal MAGs classified into the genus Methanosarcina or UBA6 of the family Methanomassiliicoccaceae). Understanding the synergistic relationships between microbes that convert lignin could inform strategies for producing renewable bioenergy and treating aromatic-contaminated environments through anaerobic biodegradation processes. Overall, this study offers fundamental insights into complex community-level anaerobic lignin metabolism, highlighting hitherto unknown players, interactions, and pathways in this biotechnologically valuable process.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea
| | - In-Tae Cha
- Climate Change and Environmental Biology Research Division, National Institute of Biological Resources, Incheon, 22689, South Korea
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Soo-Je Park
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea.
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Bleem AC, Kuatsjah E, Johnsen J, Mohamed ET, Alexander WG, Kellermyer ZA, Carroll AL, Rossi R, Schlander IB, Peabody V GL, Guss AM, Feist AM, Beckham GT. Evolution and engineering of pathways for aromatic O-demethylation in Pseudomonas putida KT2440. Metab Eng 2024; 84:145-157. [PMID: 38936762 DOI: 10.1016/j.ymben.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
Biological conversion of lignin from biomass offers a promising strategy for sustainable production of fuels and chemicals. However, aromatic compounds derived from lignin commonly contain methoxy groups, and O-demethylation of these substrates is often a rate-limiting reaction that influences catabolic efficiency. Several enzyme families catalyze aromatic O-demethylation, but they are rarely compared in vivo to determine an optimal biocatalytic strategy. Here, two pathways for aromatic O-demethylation were compared in Pseudomonas putida KT2440. The native Rieske non-heme iron monooxygenase (VanAB) and, separately, a heterologous tetrahydrofolate-dependent demethylase (LigM) were constitutively expressed in P. putida, and the strains were optimized via adaptive laboratory evolution (ALE) with vanillate as a model substrate. All evolved strains displayed improved growth phenotypes, with the evolved strains harboring the native VanAB pathway exhibiting growth rates ∼1.8x faster than those harboring the heterologous LigM pathway. Enzyme kinetics and transcriptomics studies investigated the contribution of selected mutations toward enhanced utilization of vanillate. The VanAB-overexpressing strains contained the most impactful mutations, including those in VanB, the reductase for vanillate O-demethylase, PP_3494, a global regulator of vanillate catabolism, and fghA, involved in formaldehyde detoxification. These three mutations were combined into a single strain, which exhibited approximately 5x faster vanillate consumption than the wild-type strain in the first 8 h of cultivation. Overall, this study illuminates the details of vanillate catabolism in the context of two distinct enzymatic mechanisms, yielding a platform strain for efficient O-demethylation of lignin-related aromatic compounds to value-added products.
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Affiliation(s)
- Alissa C Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Eugene Kuatsjah
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Josefin Johnsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Elsayed T Mohamed
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - William G Alexander
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN, USA
| | - Zoe A Kellermyer
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Austin L Carroll
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN, USA
| | - Riccardo Rossi
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark; Department of Bioengineering, University of California, San Diego, CA, USA
| | - Ian B Schlander
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - George L Peabody V
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN, USA
| | - Adam M Guss
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN, USA
| | - Adam M Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark; Joint BioEnergy Institute, Emeryville, CA, USA; Department of Bioengineering, University of California, San Diego, CA, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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10
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Dixon RA, Puente-Urbina A, Beckham GT, Román-Leshkov Y. Enabling Lignin Valorization Through Integrated Advances in Plant Biology and Biorefining. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:239-263. [PMID: 39038247 DOI: 10.1146/annurev-arplant-062923-022602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Despite lignin having long been viewed as an impediment to the processing of biomass for the production of paper, biofuels, and high-value chemicals, the valorization of lignin to fuels, chemicals, and materials is now clearly recognized as a critical element for the lignocellulosic bioeconomy. However, the intended application for lignin will likely require a preferred lignin composition and form. To that end, effective lignin valorization will require the integration of plant biology, providing optimal feedstocks, with chemical process engineering, providing efficient lignin transformations. Recent advances in our understanding of lignin biosynthesis have shown that lignin structure is extremely diverse and potentially tunable, while simultaneous developments in lignin refining have resulted in the development of several processes that are more agnostic to lignin composition. Here, we review the interface between in planta lignin design and lignin processing and discuss the advances necessary for lignin valorization to become a feature of advanced biorefining.
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Affiliation(s)
- Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, Texas, USA;
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Allen Puente-Urbina
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Gregg T Beckham
- Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Yuriy Román-Leshkov
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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11
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Lequan Q, Yanan F, Xianda Z, Mengyuan B, Chenyu L, Shijin W. Mechanisms and high-value applications of phthalate isomers degradation pathways in bacteria. World J Microbiol Biotechnol 2024; 40:247. [PMID: 38904858 DOI: 10.1007/s11274-024-04060-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024]
Abstract
Phthalate isomers are key intermediates in the biodegradation of pollutants including waste polyethylene terephthalate (PET) plastics and plasticizers. So far, an increasing number of phthalate isomer-degrading strains have been isolated, and their degradation pathways show significant diversity. In this paper, we comprehensively review the current status of research on the degrading bacteria, degradation characteristics, aerobic and anaerobic degradation pathways, and degradation genes (clusters) of phthalate isomers, and discuss the current shortcomings and challenges. Moreover, the degradation process of phthalate isomers produces many important aromatic precursor molecules, which can be used to produce higher-value derivative chemicals, and the modification of their degradation pathways holds good prospects. Therefore, this review also highlights the current progress made in modifying the phthalate isomer degradation pathway and explores its potential for high-value applications.
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Affiliation(s)
- Qiu Lequan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.
| | - Fu Yanan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhou Xianda
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Bao Mengyuan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Li Chenyu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Wu Shijin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.
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12
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Riddell LA, de Peinder P, Polizzi V, Vanbroekhoven K, Meirer F, Bruijnincx PCA. Predicting Molecular Weight Characteristics of Reductively Depolymerized Lignins by ATR-FTIR and Chemometrics. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2024; 12:8968-8977. [PMID: 38872958 PMCID: PMC11167637 DOI: 10.1021/acssuschemeng.4c03100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024]
Abstract
Recent scientific advances in the valorization of lignin, through e.g., (partial-)catalytic depolymerization, require equally state-of-the-art approaches for the analysis of the obtained depolymerized lignins (DLs) or lignin bio-oils. The use of chemometrics in combination with infrared (IR) spectroscopy is one avenue to provide rapid access to pertinent lignin parameters, such as molecular weight (MW) characteristics, which typically require analysis via time-consuming size-exclusion methods, or diffusion-ordered NMR spectroscopy. Importantly, MW serves as a marker for the degree of depolymerization (or recondensation) that the lignin has undergone, and thus probing this parameter is essential for the optimization of depolymerization conditions to achieve DLs with desired properties. Here, we show that our ATR-IR-based chemometrics approach used previously for technical lignin analysis can be extended to analyze these more processed, lignin-derived samples as well. Remarkably, also at this lower end of the MW scale, the use of partial least-squares (PLS) regression models well-predicted the MW parameters for a sample set of 57 depolymerized lignins, with relative errors of 9.9-11.2%. Furthermore, principal component analysis (PCA) showed good correspondence with features in the regression vectors for each of the biomass classes (hardwood, herbaceous/grass, and softwood) obtained from PLS-discriminant analysis (PLS-DA). Overall, we show that the IR spectra of DLs are still amenable to chemometric analysis and specifically to rapid, predictive characterization of their MW, circumventing the time-consuming, tedious, and not generally accessible methods typically employed.
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Affiliation(s)
- Luke A. Riddell
- Faculty
of Science, Organic Chemistry & Catalysis, Institute for Sustainable
and Circular Chemistry, Utrecht University
institution, Utrecht 3584CG, The Netherlands
| | - Peter de Peinder
- Faculty
of Science, Inorganic Chemistry & Catalysis, Institute for Sustainable
and Circular Chemistry, Utrecht University, Utrecht 3584CG, The Netherlands
- VibSpec, Haaftenlaan 28, Tiel 4006
XL, The Netherlands
| | - Viviana Polizzi
- Sustainable
Polymer Technologies team, Materials & Chemistry unit, Flemish Institute for Technological Research (VITO), Mol 2400, Belgium
| | - Karolien Vanbroekhoven
- Sustainable
Polymer Technologies team, Materials & Chemistry unit, Flemish Institute for Technological Research (VITO), Mol 2400, Belgium
| | - Florian Meirer
- Faculty
of Science, Inorganic Chemistry & Catalysis, Institute for Sustainable
and Circular Chemistry, Utrecht University, Utrecht 3584CG, The Netherlands
| | - Pieter C. A. Bruijnincx
- Faculty
of Science, Organic Chemistry & Catalysis, Institute for Sustainable
and Circular Chemistry, Utrecht University
institution, Utrecht 3584CG, The Netherlands
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13
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Ali NS, Thakur S, Ye M, Monteil-Rivera F, Pan Y, Qin W, Yang TC. Uncovering the lignin-degrading potential of Serratia quinivorans AORB19: insights from genomic analyses and alkaline lignin degradation. BMC Microbiol 2024; 24:181. [PMID: 38789935 PMCID: PMC11127350 DOI: 10.1186/s12866-024-03331-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Lignin is an intricate phenolic polymer found in plant cell walls that has tremendous potential for being converted into value-added products with the possibility of significantly increasing the economics of bio-refineries. Although lignin in nature is bio-degradable, its biocatalytic conversion is challenging due to its stable complex structure and recalcitrance. In this context, an understanding of strain's genomics, enzymes, and degradation pathways can provide a solution for breaking down lignin to unlock the full potential of lignin as a dominant valuable bioresource. A gammaproteobacterial strain AORB19 has been isolated previously from decomposed wood based on its high laccase production. This work then focused on the detailed genomic and functional characterization of this strain based on whole genome sequencing, the identification of lignin degradation products, and the strain's laccase production capabilities on various agro-industrial residues. RESULTS Lignin degrading bacterial strain AORB19 was identified as Serratia quinivorans based on whole genome sequencing and core genome phylogeny. The strain comprised a total of 123 annotated CAZyme genes, including ten cellulases, four hemicellulases, five predicted carbohydrate esterase genes, and eight lignin-degrading enzyme genes. Strain AORB19 was also found to possess genes associated with metabolic pathways such as the β-ketoadipate, gentisate, anthranilate, homogentisic, and phenylacetate CoA pathways. LC-UV analysis demonstrated the presence of p-hydroxybenzaldehyde and vanillin in the culture media which constitutes potent biosignatures indicating the strain's capability to degrade lignin. Finally, the study evaluated the laccase production of Serratia AORB19 grown with various industrial raw materials, with the highest activity detected on flax seed meal (257.71 U/L), followed by pea hull (230.11 U/L), canola meal (209.56 U/L), okara (187.67 U/L), and barley malt sprouts (169.27 U/L). CONCLUSIONS The whole genome analysis of Serratia quinivorans AORB19, elucidated a repertoire of genes, pathways and enzymes vital for lignin degradation that widens the understanding of ligninolytic metabolism among bacterial lignin degraders. The LC-UV analysis of the lignin degradation products coupled with the ability of S. quinivorans AORB19 to produce laccase on diverse agro-industrial residues underscores its versatility and its potential to contribute to the economic viability of bio-refineries.
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Affiliation(s)
- Nadia Sufdar Ali
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Ottawa, ON, Canada
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
| | - Subarna Thakur
- Department of Bioinformatics, University of North Bengal, Siliguri, India
| | - Mengwei Ye
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Fanny Monteil-Rivera
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Youlian Pan
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada.
| | - Trent Chunzhong Yang
- Aquatic and Crop Resource Development Research Centre, National Research Council Canada, Ottawa, ON, Canada.
- BioWise Technologies Inc, Ottawa, Canada.
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14
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Manoli MT, Gargantilla-Becerra Á, Del Cerro Sánchez C, Rivero-Buceta V, Prieto MA, Nogales J. A model-driven approach to upcycling recalcitrant feedstocks in Pseudomonas putida by decoupling PHA production from nutrient limitation. Cell Rep 2024; 43:113979. [PMID: 38517887 DOI: 10.1016/j.celrep.2024.113979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 03/24/2024] Open
Abstract
Bacterial polyhydroxyalkanoates (PHAs) have emerged as promising eco-friendly alternatives to petroleum-based plastics since they are synthesized from renewable resources and offer exceptional properties. However, their production is limited to the stationary growth phase under nutrient-limited conditions, requiring customized strategies and costly two-phase bioprocesses. In this study, we tackle these challenges by employing a model-driven approach to reroute carbon flux and remove regulatory constraints using synthetic biology. We construct a collection of Pseudomonas putida-overproducing strains at the expense of plastics and lignin-related compounds using growth-coupling approaches. PHA production was successfully achieved during growth phase, resulting in the production of up to 46% PHA/cell dry weight while maintaining a balanced carbon-to-nitrogen ratio. Our strains are additionally validated under an upcycling scenario using enzymatically hydrolyzed polyethylene terephthalate as a feedstock. These findings have the potential to revolutionize PHA production and address the global plastic crisis by overcoming the complexities of traditional PHA production bioprocesses.
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Affiliation(s)
- Maria-Tsampika Manoli
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Álvaro Gargantilla-Becerra
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain; 3Systems Biotechnology Group, Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain
| | - Carlos Del Cerro Sánchez
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Virginia Rivero-Buceta
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), 28040 Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
| | - Juan Nogales
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain; 3Systems Biotechnology Group, Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid 28049, Spain; CNB DNA Biofoundry (CNBio), CSIC, Madrid, Spain.
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15
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Godoy P, Udaondo Z, Duque E, Ramos JL. Biosynthesis of fragrance 2-phenylethanol from sugars by Pseudomonas putida. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:51. [PMID: 38566218 PMCID: PMC10986128 DOI: 10.1186/s13068-024-02498-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Petrochemicals contribute to environmental issues, with concerns ranging from energy consumption and carbon emission to pollution. In contrast, microbial biorefineries offer eco-friendly alternatives. The solvent-tolerant Pseudomonas putida DOT-T1E serves as a suitable host for producing aromatic compounds, specifically L-phenylalanine and its derivative, 2-phenylethanol (2-PE), which find widespread applications in various industries. RESULTS This study focuses on enhancing 2-PE production in two L-phenylalanine overproducing strains of DOT-T1E, namely CM12-5 and CM12-5Δgcd (xylABE), which grow with glucose and glucose-xylose, respectively. To synthesize 2-PE from L-phenylalanine, these strains were transformed with plasmid pPE-1, bearing the Ehrlich pathway genes, and it was found higher 2-PE production with glucose (about 50-60 ppm) than with xylose (< 3 ppm). To understand the limiting factors, we tested the addition of phenylalanine and intermediates from the Ehrlich and shikimate pathways. The results identified intracellular L-phenylalanine as a key limiting factor for 2-PE production. To overcame this limitation, a chorismate mutase/prephenate dehydratase variant-insentive to feedback inhibition by aromatic amino acids-was introduced in the producing strains. This led to increased L-phenylalanine production and subsequently produced more 2-PE (100 ppm). Random mutagenesis of the strains also produced strains with higher L-phenylalanine titers and increased 2-PE production (up to 120 ppm). The improvements resulted from preventing dead-end product accumulation from shikimate and limiting the catabolism of potential pathway intermediates in the Ehrlich pathway. The study explored agricultural waste substrates, such as corn stover, sugarcane straw and corn-syrup as potential C sources. The best results were obtained using 2G substrates at 3% (between 82 and 100 ppm 2-PE), with glucose being the preferred sugar for 2-PE production among the monomeric sugars in these substrates. CONCLUSIONS The findings of this study offer strategies to enhance phenylalanine production, a key substrate for the synthesis of aromatic compounds. The ability of P. putida DOT-T1E to thrive with various C-sources and its tolerance to substrates, products, and potential toxicants in industrial wastes, are highlighted. The study identified and overcome possible bottlenecks for 2-PE production. Ultimately, the strains have potential to become efficient microbial platforms for synthesizing 2-PE from agro-industrial waste materials.
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Affiliation(s)
- Patricia Godoy
- Department of Environmental Protection, Estación Experimental del Zaidín, CSIC, c/ Profesor Albareda 1, 1808, Granada, Spain
| | - Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Science, Little Rock, AR, 72205, USA
| | - Estrella Duque
- Department of Environmental Protection, Estación Experimental del Zaidín, CSIC, c/ Profesor Albareda 1, 1808, Granada, Spain
| | - Juan L Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, CSIC, c/ Profesor Albareda 1, 1808, Granada, Spain.
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16
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Jin X, Li X, Zou L, Zheng Z, Ouyang J. Biological Valorization of Lignin-Derived Aromatics in Hydrolysate to Protocatechuic Acid by Engineered Pseudomonas putida KT2440. Molecules 2024; 29:1555. [PMID: 38611834 PMCID: PMC11013400 DOI: 10.3390/molecules29071555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Alongside fermentable sugars, weak acids, and furan derivatives, lignocellulosic hydrolysates contain non-negligible amounts of lignin-derived aromatic compounds. The biological funnel of lignin offers a new strategy for the "natural" production of protocatechuic acid (PCA). Herein, Pseudomonas putida KT2440 was engineered to produce PCA from lignin-derived monomers in hydrolysates by knocking out protocatechuate 3,4-dioxygenase and overexpressing vanillate-O-demethylase endogenously, while acetic acid was used for cell growth. The sugar catabolism was further blocked to prevent the loss of fermentable sugar. Using the engineered strain, a total of 253.88 mg/L of PCA was obtained with a yield of 70.85% from corncob hydrolysate 1. The highest titer of 433.72 mg/L of PCA was achieved using corncob hydrolysate 2 without any additional nutrients. This study highlights the potential ability of engineered strains to address the challenges of PCA production from lignocellulosic hydrolysate, providing novel insights into the utilization of hydrolysates.
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Affiliation(s)
| | | | | | | | - Jia Ouyang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; (X.J.); (X.L.); (L.Z.); (Z.Z.)
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17
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Borchert AJ, Bleem AC, Lim HG, Rychel K, Dooley KD, Kellermyer ZA, Hodges TL, Palsson BO, Beckham GT. Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440. mSystems 2024; 9:e0094223. [PMID: 38323821 PMCID: PMC10949508 DOI: 10.1128/msystems.00942-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/07/2024] [Indexed: 02/08/2024] Open
Abstract
There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules ("functional modules"), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida. Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.
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Affiliation(s)
- Andrew J. Borchert
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Alissa C. Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Agile BioFoundry, Emeryville, California, USA
| | - Hyun Gyu Lim
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Biological Engineering, Inha University, Incheon, Korea
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Keven D. Dooley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Agile BioFoundry, Emeryville, California, USA
| | - Zoe A. Kellermyer
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Tracy L. Hodges
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Agile BioFoundry, Emeryville, California, USA
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Joint BioEnergy Institute, Emeryville, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Department of Pediatrics, University of California, San Diego, California, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Agile BioFoundry, Emeryville, California, USA
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18
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Tavis S, Hettich RL. Multi-Omics integration can be used to rescue metabolic information for some of the dark region of the Pseudomonas putida proteome. BMC Genomics 2024; 25:267. [PMID: 38468234 PMCID: PMC10926591 DOI: 10.1186/s12864-024-10082-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/02/2024] [Indexed: 03/13/2024] Open
Abstract
In every omics experiment, genes or their products are identified for which even state of the art tools are unable to assign a function. In the biotechnology chassis organism Pseudomonas putida, these proteins of unknown function make up 14% of the proteome. This missing information can bias analyses since these proteins can carry out functions which impact the engineering of organisms. As a consequence of predicting protein function across all organisms, function prediction tools generally fail to use all of the types of data available for any specific organism, including protein and transcript expression information. Additionally, the release of Alphafold predictions for all Uniprot proteins provides a novel opportunity for leveraging structural information. We constructed a bespoke machine learning model to predict the function of recalcitrant proteins of unknown function in Pseudomonas putida based on these sources of data, which annotated 1079 terms to 213 proteins. Among the predicted functions supplied by the model, we found evidence for a significant overrepresentation of nitrogen metabolism and macromolecule processing proteins. These findings were corroborated by manual analyses of selected proteins which identified, among others, a functionally unannotated operon that likely encodes a branch of the shikimate pathway.
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Affiliation(s)
- Steven Tavis
- Genome Science and Technology Graduate Program, University of Tennessee Knoxville, Knoxville, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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19
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Rani S, Aslam S, Lal K, Noreen S, Alsader KAM, Hussain R, Shirinfar B, Ahmed N. Electrochemical C-H/C-C Bond Oxygenation: A Potential Technology for Plastic Depolymerization. CHEM REC 2024; 24:e202300331. [PMID: 38063812 DOI: 10.1002/tcr.202300331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/23/2023] [Indexed: 03/10/2024]
Abstract
Herein, we provide eco-friendly and safely operated electrocatalytic methods for the selective oxidation directly or with water, air, light, metal catalyst or other mediators serving as the only oxygen supply. Heavy metals, stoichiometric chemical oxidants, or harsh conditions were drawbacks of earlier oxidative cleavage techniques. It has recently come to light that a crucial stage in the deconstruction of plastic waste and the utilization of biomass is the selective activation of inert C(sp3 )-C/H(sp3 ) bonds, which continues to be a significant obstacle in the chemical upcycling of resistant polyolefin waste. An appealing alternative to chemical oxidations using oxygen and catalysts is direct or indirect electrochemical conversion. An essential transition in the chemical and pharmaceutical industries is the electrochemical oxidation of C-H/C-C bonds. In this review, we discuss cutting-edge approaches to chemically recycle commercial plastics and feasible C-C/C-H bonds oxygenation routes for industrial scale-up.
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Affiliation(s)
- Sadia Rani
- Department of Chemistry, The Women University Multan, Multan, 60000, Pakistan
| | - Samina Aslam
- Department of Chemistry, The Women University Multan, Multan, 60000, Pakistan
| | - Kiran Lal
- Department of Chemistry, The Women University Multan, Multan, 60000, Pakistan
| | - Sobia Noreen
- Institute of Chemistry, University of Sargodha, Sargodha, 40100, Pakistan
| | | | - Riaz Hussain
- Department of Chemistry, University of Education Lahore, D.G. Khan Campus, 32200, Pakistan
| | - Bahareh Shirinfar
- West Herts College - University of Hertfordshire, Watford, WD17 3EZ, London, United Kingdom
| | - Nisar Ahmed
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, United Kingdom
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20
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Banerjee D, Yunus IS, Wang X, Kim J, Srinivasan A, Menchavez R, Chen Y, Gin JW, Petzold CJ, Martin HG, Magnuson JK, Adams PD, Simmons BA, Mukhopadhyay A, Kim J, Lee TS. Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida. Metab Eng 2024; 82:157-170. [PMID: 38369052 DOI: 10.1016/j.ymben.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 01/10/2024] [Accepted: 02/10/2024] [Indexed: 02/20/2024]
Abstract
Sustainable aviation fuel (SAF) will significantly impact global warming in the aviation sector, and important SAF targets are emerging. Isoprenol is a precursor for a promising SAF compound DMCO (1,4-dimethylcyclooctane) and has been produced in several engineered microorganisms. Recently, Pseudomonas putida has gained interest as a future host for isoprenol bioproduction as it can utilize carbon sources from inexpensive plant biomass. Here, we engineer metabolically versatile host P. putida for isoprenol production. We employ two computational modeling approaches (Bilevel optimization and Constrained Minimal Cut Sets) to predict gene knockout targets and optimize the "IPP-bypass" pathway in P. putida to maximize isoprenol production. Altogether, the highest isoprenol production titer from P. putida was achieved at 3.5 g/L under fed-batch conditions. This combination of computational modeling and strain engineering on P. putida for an advanced biofuels production has vital significance in enabling a bioproduction process that can use renewable carbon streams.
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Affiliation(s)
- Deepanwita Banerjee
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ian S Yunus
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xi Wang
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jinho Kim
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Aparajitha Srinivasan
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Russel Menchavez
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer W Gin
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hector Garcia Martin
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jon K Magnuson
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Energy Processes & Materials Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Paul D Adams
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joonhoon Kim
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Energy Processes & Materials Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - Taek Soon Lee
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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21
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Fan Y, Ji H, Ji X, Tian Z, Chen J. Lignocellulosic biomass pretreatment with a lignin stabilization strategy and valorization toward multipurpose fractionation. Int J Biol Macromol 2024; 259:129186. [PMID: 38184047 DOI: 10.1016/j.ijbiomac.2023.129186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/20/2023] [Accepted: 12/30/2023] [Indexed: 01/08/2024]
Abstract
Lignocellulosic biomass has emerged as a promising alternative with sustainable advantages for the production of a wide range of renewable products and value-added chemicals. In this study, a pretreatment strategy that use a fully recyclable acid hydrotrope (p-TsOH aqueous solution) to extract lignin and employ glyoxylic acid (GA) to stabilize lignin was proposed for biomass valorization toward multipurpose fractionation. 83.0 % of lignin was dissolved out by p-TsOH hydrotrope (80 wt%) with GA addition to form GA-stabilized product at 80 o C for 15 min. The stabilized lignin was subsequently used as an additive in the preparation of lignin-based suncream. Notably, the incorporation of 4 wt% lignin nanospheres into an SPF15 sunscreen yielded a measured SPF of 59.94. Furthermore, the depolymerization of uncondensed lignin into aromatic monomers yielded a high lignin-oil yield of 84.2 %. Additionally, direct heating of the pretreatment liquor facilitated the conversion of monosaccharides into furfural, achieving a desired yield of 53.7 % without the addition of any acid catalyst. The pretreatment also enhanced the enzymatic hydrolysis of glucan, resulting in a saccharification yield of 98.4 %. Moreover, short-term ultrasonication of the pretreated substrate yielded pulp suitable for papermaking. Incorporating 15 wt% fibers into the produced paper sheets led to a 5.3 % increase in tear index and a 25.4 % increase in tensile index. This study presents a viable pretreatment strategy for the multipurpose fractionation of lignocellulosic biomass, offering potential avenues for biomass valorization.
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Affiliation(s)
- Yufei Fan
- Key Laboratory of Pulp and Paper Science & Technology of Ministry of Education, State Key Laboratory of Biobased Material and Green Papermaking, Faculty of Light Industry, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Hairui Ji
- Key Laboratory of Pulp and Paper Science & Technology of Ministry of Education, State Key Laboratory of Biobased Material and Green Papermaking, Faculty of Light Industry, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China.
| | - Xingxiang Ji
- Key Laboratory of Pulp and Paper Science & Technology of Ministry of Education, State Key Laboratory of Biobased Material and Green Papermaking, Faculty of Light Industry, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Zhongjian Tian
- Key Laboratory of Pulp and Paper Science & Technology of Ministry of Education, State Key Laboratory of Biobased Material and Green Papermaking, Faculty of Light Industry, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Jiachuan Chen
- Key Laboratory of Pulp and Paper Science & Technology of Ministry of Education, State Key Laboratory of Biobased Material and Green Papermaking, Faculty of Light Industry, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
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22
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Nain P, Dickey RM, Somasundaram V, Sulzbach M, Kunjapur AM. Reductive amination cascades in cell-free and resting whole cell formats for valorization of lignin deconstruction products. Biotechnol Bioeng 2024; 121:593-604. [PMID: 37986639 PMCID: PMC10872919 DOI: 10.1002/bit.28604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 10/22/2023] [Indexed: 11/22/2023]
Abstract
The selective introduction of amine groups within deconstruction products of lignin could provide an avenue for valorizing waste biomass while achieving a green synthesis of industrially relevant building blocks from sustainable sources. Here, we built and characterized enzyme cascades that create aldehydes and subsequently primary amines from diverse lignin-derived carboxylic acids using a carboxylic acid reductase (CAR) and an ω-transaminase (TA). Unlike previous studies that have paired CAR and TA enzymes, here we examine multiple homologs of each of these enzymes and a broader set of candidate substrates. In addition, we compare the performance of these systems in cell-free and resting whole-cell biocatalysis formats using the conversion of vanillate to vanillyl amine as model chemistry. We also demonstrate that resting whole cells can be recycled for multiple batch reactions. We used the knowledge gained from this study to produce several amines from carboxylic acid precursors using one-pot biocatalytic reactions, several of which we report for the first time. These results expand our knowledge of these industrially relevant enzyme families to new substrates and contexts for environmentally friendly and potentially low-cost synthesis of diverse aryl aldehydes and amines.
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Affiliation(s)
- Priyanka Nain
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716
| | - Roman M. Dickey
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716
| | - Vishal Somasundaram
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716
| | - Morgan Sulzbach
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716
| | - Aditya M. Kunjapur
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716
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23
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Palumbo CT, Gu NX, Bleem AC, Sullivan KP, Katahira R, Stanley LM, Kenny JK, Ingraham MA, Ramirez KJ, Haugen SJ, Amendola CR, Stahl SS, Beckham GT. Catalytic carbon-carbon bond cleavage in lignin via manganese-zirconium-mediated autoxidation. Nat Commun 2024; 15:862. [PMID: 38286984 PMCID: PMC10825196 DOI: 10.1038/s41467-024-45038-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024] Open
Abstract
Efforts to produce aromatic monomers through catalytic lignin depolymerization have historically focused on aryl-ether bond cleavage. A large fraction of aromatic monomers in lignin, however, are linked by various carbon-carbon (C-C) bonds that are more challenging to cleave and limit the yields of aromatic monomers from lignin depolymerization. Here, we report a catalytic autoxidation method to cleave C-C bonds in lignin-derived dimers and oligomers from pine and poplar. The method uses manganese and zirconium salts as catalysts in acetic acid and produces aromatic carboxylic acids as primary products. The mixtures of the oxygenated monomers are efficiently converted to cis,cis-muconic acid in an engineered strain of Pseudomonas putida KT2440 that conducts aromatic O-demethylation reactions at the 4-position. This work demonstrates that autoxidation of lignin with Mn and Zr offers a catalytic strategy to increase the yield of valuable aromatic monomers from lignin.
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Affiliation(s)
- Chad T Palumbo
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Nina X Gu
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Alissa C Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Kevin P Sullivan
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Rui Katahira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Lisa M Stanley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Jacob K Kenny
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, 80303, CO, USA
| | - Morgan A Ingraham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Kelsey J Ramirez
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Stefan J Haugen
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Caroline R Amendola
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Shannon S Stahl
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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24
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Li X, Li Z, Li M, Li J, Wang Q, Wang S, Li S, Li H. Transcriptomic and metabolomic analysis reveals the influence of carbohydrates on lignin degradation mediated by Bacillus amyloliquefaciens. Front Microbiol 2024; 15:1224855. [PMID: 38333584 PMCID: PMC10850570 DOI: 10.3389/fmicb.2024.1224855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/05/2024] [Indexed: 02/10/2024] Open
Abstract
Introduction Ligninolytic bacteria can secrete extracellular enzymes to depolymerize lignin into small-molecular aromatics that are subsequently metabolized and funneled into the TCA cycle. Carbohydrates, which are the preferred carbon sources of bacteria, influence the metabolism of lignin-derived aromatics through bacteria. Methods In this study, untargeted metabolomics and transcriptomics analyses were performed to investigate the effect of carbohydrates on lignin degradation mediated by Bacillus amyloliquefaciens MN-13, a strain with lignin-degrading activity that was isolated in our previous work. Results The results demonstrated that the cell growth of the MN-13 strain and lignin removal were promoted when carbohydrates such as glucose and sodium carboxymethyl cellulose were added to an alkaline lignin-minimal salt medium (AL-MSM) culture. Metabolomics analysis showed that lignin depolymerization took place outside the cells, and the addition of glucose regulated the uptake and metabolism of lignin-derived monomers and activated the downstream metabolism process in cells. In the transcriptomics analysis, 299 DEGs were screened after 24 h of inoculation in AL-MSM with free glucose and 2 g/L glucose, respectively, accounting for 8.3% of the total amount of annotated genes. These DEGs were primarily assigned to 30 subcategories, including flagellar assembly, the PTS system, RNA degradation, glycolysis/gluconeogenesis, the TCA cycle, pyruvate metabolism, and tryptophan metabolism. These subcategories were closely associated with the cell structure, generation of cellular energy, and precursors for biosynthetic pathways, based on a - log 10 (P adjust) value in the KEGG pathway analysis. Conclusion In summary, the addition of glucose increased lignin degradation mediated by the MN-13 strain through regulating glycolysis, TCA cycle, and central carbon metabolism.
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Affiliation(s)
- Xiaodan Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zhuofan Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Ming Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Jingwen Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Quan Wang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
| | - Shuxiang Wang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
| | - Shuna Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
| | - Hongya Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Forage Microbial Technology Innovation Center, Baoding, Hebei, China
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25
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Ma JX, Wang H, Jin C, Ye YF, Tang LX, Si J, Song J. Whole genome sequencing and annotation of Daedaleopsis sinensis, a wood-decaying fungus significantly degrading lignocellulose. Front Bioeng Biotechnol 2024; 11:1325088. [PMID: 38292304 PMCID: PMC10826855 DOI: 10.3389/fbioe.2023.1325088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/15/2023] [Indexed: 02/01/2024] Open
Abstract
Daedaleopsis sinensis is a fungus that grows on wood and secretes a series of enzymes to degrade cellulose, hemicellulose, and lignin and cause wood rot decay. Wood-decaying fungi have ecological, economic, edible, and medicinal functions. Furthermore, the use of microorganisms to biodegrade lignocellulose has high application value. Genome sequencing has allowed microorganisms to be analyzed from the aspects of genome characteristics, genome function annotation, metabolic pathways, and comparative genomics. Subsequently, the relevant information regarding lignocellulosic degradation has been mined by bioinformatics. Here, we sequenced and analyzed the genome of D. sinensis for the first time. A 51.67-Mb genome sequence was assembled to 24 contigs, which led to the prediction of 12,153 protein-coding genes. Kyoto Encyclopedia of Genes and Genomes database analysis of the D. sinensis data revealed that 3,831 genes are involved in almost 120 metabolic pathways. According to the Carbohydrate-Active Enzyme database, 481 enzymes are found in D. sinensis, of which glycoside hydrolases are the most abundant. The genome sequence of D. sinensis provides insights into its lignocellulosic degradation and subsequent applications.
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Affiliation(s)
- Jin-Xin Ma
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Hao Wang
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Can Jin
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yi-Fan Ye
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Lu-Xin Tang
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jing Si
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jie Song
- Department of Horticulture and Food, Guangdong Eco-Engineering Polytechnic, Guangzhou, China
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26
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Gu J, Qiu Q, Yu Y, Sun X, Tian K, Chang M, Wang Y, Zhang F, Huo H. Bacterial transformation of lignin: key enzymes and high-value products. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:2. [PMID: 38172947 PMCID: PMC10765951 DOI: 10.1186/s13068-023-02447-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024]
Abstract
Lignin, a natural organic polymer that is recyclable and inexpensive, serves as one of the most abundant green resources in nature. With the increasing consumption of fossil fuels and the deterioration of the environment, the development and utilization of renewable resources have attracted considerable attention. Therefore, the effective and comprehensive utilization of lignin has become an important global research topic, with the goal of environmental protection and economic development. This review focused on the bacteria and enzymes that can bio-transform lignin, focusing on the main ways that lignin can be utilized to produce high-value chemical products. Bacillus has demonstrated the most prominent effect on lignin degradation, with 89% lignin degradation by Bacillus cereus. Furthermore, several bacterial enzymes were discussed that can act on lignin, with the main enzymes consisting of dye-decolorizing peroxidases and laccase. Finally, low-molecular-weight lignin compounds were converted into value-added products through specific reaction pathways. These bacteria and enzymes may become potential candidates for efficient lignin degradation in the future, providing a method for lignin high-value conversion. In addition, the bacterial metabolic pathways convert lignin-derived aromatics into intermediates through the "biological funnel", achieving the biosynthesis of value-added products. The utilization of this "biological funnel" of aromatic compounds may address the heterogeneous issue of the aromatic products obtained via lignin depolymerization. This may also simplify the separation of downstream target products and provide avenues for the commercial application of lignin conversion into high-value products.
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Affiliation(s)
- Jinming Gu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Qing Qiu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Yue Yu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Xuejian Sun
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Kejian Tian
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Menghan Chang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Yibing Wang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Fenglin Zhang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China
| | - Hongliang Huo
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun, 130117, China.
- Engineering Lab for Water Pollution Control and Resources Recovery of Jilin Province, Changchun, 130117, China.
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Changchun, 130117, China.
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27
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Shen Z, Shi C, Liu F, Wang W, Ai M, Huang Z, Zhang X, Pan L, Zou J. Advances in Heterogeneous Catalysts for Lignin Hydrogenolysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306693. [PMID: 37964410 PMCID: PMC10767463 DOI: 10.1002/advs.202306693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/04/2023] [Indexed: 11/16/2023]
Abstract
Lignin is the main component of lignocellulose and the largest source of aromatic substances on the earth. Biofuel and bio-chemicals derived from lignin can reduce the use of petroleum products. Current advances in lignin catalysis conversion have facilitated many of progress, but understanding the principles of catalyst design is critical to moving the field forward. In this review, the factors affecting the catalysts (including the type of active metal, metal particle size, acidity, pore size, the nature of the oxide supports, and the synergistic effect of the metals) are systematically reviewed based on the three most commonly used supports (carbon, oxides, and zeolites) in lignin hydrogenolysis. The catalytic performance (selectivity and yield of products) is evaluated, and the emerging catalytic mechanisms are introduced to better understand the catalyst design guidelines. Finally, based on the progress of existing studies, future directions for catalyst design in the field of lignin depolymerization are proposed.
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Affiliation(s)
- Zhensheng Shen
- Key Laboratory for Green Chemical Technology of Ministry of EducationSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China
- Collaborative Innovative Center of Chemical Science and Engineering (Tianjin)Tianjin300072China
- Haihe Laboratory of Sustainable Chemical TransformationsTianjin300192China
| | - Chengxiang Shi
- Key Laboratory for Green Chemical Technology of Ministry of EducationSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China
- Collaborative Innovative Center of Chemical Science and Engineering (Tianjin)Tianjin300072China
- Haihe Laboratory of Sustainable Chemical TransformationsTianjin300192China
| | - Fan Liu
- Key Laboratory for Green Chemical Technology of Ministry of EducationSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China
- Collaborative Innovative Center of Chemical Science and Engineering (Tianjin)Tianjin300072China
- Haihe Laboratory of Sustainable Chemical TransformationsTianjin300192China
| | - Wei Wang
- Key Laboratory for Green Chemical Technology of Ministry of EducationSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China
- Collaborative Innovative Center of Chemical Science and Engineering (Tianjin)Tianjin300072China
- Haihe Laboratory of Sustainable Chemical TransformationsTianjin300192China
| | - Minhua Ai
- Key Laboratory for Green Chemical Technology of Ministry of EducationSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China
- Collaborative Innovative Center of Chemical Science and Engineering (Tianjin)Tianjin300072China
- Haihe Laboratory of Sustainable Chemical TransformationsTianjin300192China
| | - Zhenfeng Huang
- Key Laboratory for Green Chemical Technology of Ministry of EducationSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China
- Collaborative Innovative Center of Chemical Science and Engineering (Tianjin)Tianjin300072China
- Haihe Laboratory of Sustainable Chemical TransformationsTianjin300192China
| | - Xiangwen Zhang
- Key Laboratory for Green Chemical Technology of Ministry of EducationSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China
- Collaborative Innovative Center of Chemical Science and Engineering (Tianjin)Tianjin300072China
- Haihe Laboratory of Sustainable Chemical TransformationsTianjin300192China
| | - Lun Pan
- Key Laboratory for Green Chemical Technology of Ministry of EducationSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China
- Collaborative Innovative Center of Chemical Science and Engineering (Tianjin)Tianjin300072China
- Haihe Laboratory of Sustainable Chemical TransformationsTianjin300192China
| | - Ji‐Jun Zou
- Key Laboratory for Green Chemical Technology of Ministry of EducationSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China
- Collaborative Innovative Center of Chemical Science and Engineering (Tianjin)Tianjin300072China
- Haihe Laboratory of Sustainable Chemical TransformationsTianjin300192China
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28
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Chacόn M, Percival E, Bugg TDH, Dixon N. Engineered co-culture for consolidated production of phenylpropanoids directly from aromatic-rich biomass. BIORESOURCE TECHNOLOGY 2024; 391:129935. [PMID: 37923228 DOI: 10.1016/j.biortech.2023.129935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023]
Abstract
Consolidated bioprocesses for the in situ hydrolysis and conversion of biomass feedstocks into value-added products offers great potential for both process and cost reduction. However, to date few consolidated bioprocesses have been developed that target aromatic rich feedstock fractions. Reported here is the development of synthetic co-cultivation for the consolidated hydrolysis and valorisation of corncob hydroxycinnamic acids. Biomass hydrolysis was achieved via a secretion module developed in B. subtilis using a genetically encoded biosensor-actuator to secrete hydrolytic enzymes. Conversion was achieved via a biotransformation module developed in E. coli using a suite of plug-and-play encoded enzymes to convert the released hydroxycinnamic acids into high-value phenylpropanoid target compounds. Finally, employing cellulolytic pre-treatment, extractive fermentation and in situ product recovery multiple aromatic products, coniferol and chavicol, were isolated from the same process in high purity.
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Affiliation(s)
- Micaela Chacόn
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester M1 7DN, UK
| | - Ellen Percival
- Department of Chemistry, University of Warwick, Coventry CV4 7AK, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AK, UK
| | - Neil Dixon
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, University of Manchester, Manchester M1 7DN, UK.
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29
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Amendola CR, Cordell WT, Kneucker CM, Szostkiewicz CJ, Ingraham MA, Monninger M, Wilton R, Pfleger BF, Salvachúa D, Johnson CW, Beckham GT. Comparison of wild-type KT2440 and genome-reduced EM42 Pseudomonas putida strains for muconate production from aromatic compounds and glucose. Metab Eng 2024; 81:88-99. [PMID: 38000549 DOI: 10.1016/j.ymben.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/12/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023]
Abstract
Pseudomonas putida KT2440 is a robust, aromatic catabolic bacterium that has been widely engineered to convert bio-based and waste-based feedstocks to target products. Towards industrial domestication of P. putida KT2440, rational genome reduction has been previously conducted, resulting in P. putida strain EM42, which exhibited characteristics that could be advantageous for production strains. Here, we compared P. putida KT2440- and EM42-derived strains for cis,cis-muconic acid production from an aromatic compound, p-coumarate, and in separate strains, from glucose. To our surprise, the EM42-derived strains did not outperform the KT2440-derived strains in muconate production from either substrate. In bioreactor cultivations, KT2440- and EM42-derived strains produced muconate from p-coumarate at titers of 45 g/L and 37 g/L, respectively, and from glucose at 20 g/L and 13 g/L, respectively. To provide additional insights about the differences in the parent strains, we analyzed growth profiles of KT2440 and EM42 on aromatic compounds as the sole carbon and energy sources. In general, the EM42 strain exhibited reduced growth rates but shorter growth lags than KT2440. We also observed that EM42-derived strains resulted in higher growth rates on glucose compared to KT2440-derived strains, but only at the lowest glucose concentrations tested. Transcriptomics revealed that genome reduction in EM42 had global effects on transcript levels and showed that the EM42-derived strains that produce muconate from glucose exhibit reduced modulation of gene expression in response to changes in glucose concentrations. Overall, our results highlight that additional studies are warranted to understand the effects of genome reduction on microbial metabolism and physiology, especially when intended for use in production strains.
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Affiliation(s)
- Caroline R Amendola
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA
| | - William T Cordell
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Colin M Kneucker
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Caralyn J Szostkiewicz
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Morgan A Ingraham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Michela Monninger
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Rosemarie Wilton
- Agile BioFoundry, Emeryville, CA, 94608, USA; Biosciences Division Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Davinia Salvachúa
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA.
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30
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Gu NX, Palumbo CT, Bleem AC, Sullivan KP, Haugen SJ, Woodworth SP, Ramirez KJ, Kenny JK, Stanley LD, Katahira R, Stahl SS, Beckham GT. Autoxidation Catalysis for Carbon-Carbon Bond Cleavage in Lignin. ACS CENTRAL SCIENCE 2023; 9:2277-2285. [PMID: 38161372 PMCID: PMC10755848 DOI: 10.1021/acscentsci.3c00813] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 01/03/2024]
Abstract
Selective lignin depolymerization is a key step in lignin valorization to value-added products, and there are multiple catalytic methods to cleave labile aryl-ether bonds in lignin. However, the overall aromatic monomer yield is inherently limited by refractory carbon-carbon linkages, which are abundant in lignin and remain intact during most selective lignin deconstruction processes. In this work, we demonstrate that a Co/Mn/Br-based catalytic autoxidation method promotes carbon-carbon bond cleavage in acetylated lignin oligomers produced from reductive catalytic fractionation. The oxidation products include acetyl vanillic acid and acetyl vanillin, which are ideal substrates for bioconversion. Using an engineered strain of Pseudomonas putida, we demonstrate the conversion of these aromatic monomers to cis,cis-muconic acid. Overall, this study demonstrates that autoxidation enables higher yields of bioavailable aromatic monomers, exceeding the limits set by ether-bond cleavage alone.
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Affiliation(s)
- Nina X. Gu
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Chad T. Palumbo
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Alissa C. Bleem
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Kevin P. Sullivan
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Stefan J. Haugen
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Sean P. Woodworth
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Kelsey J. Ramirez
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Jacob K. Kenny
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Lisa D. Stanley
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Rui Katahira
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Shannon S. Stahl
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United
States
| | - Gregg T. Beckham
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
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31
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Radley E, Davidson J, Foster J, Obexer R, Bell EL, Green AP. Engineering Enzymes for Environmental Sustainability. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202309305. [PMID: 38516574 PMCID: PMC10952289 DOI: 10.1002/ange.202309305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 03/23/2024]
Abstract
The development and implementation of sustainable catalytic technologies is key to delivering our net-zero targets. Here we review how engineered enzymes, with a focus on those developed using directed evolution, can be deployed to improve the sustainability of numerous processes and help to conserve our environment. Efficient and robust biocatalysts have been engineered to capture carbon dioxide (CO2) and have been embedded into new efficient metabolic CO2 fixation pathways. Enzymes have been refined for bioremediation, enhancing their ability to degrade toxic and harmful pollutants. Biocatalytic recycling is gaining momentum, with engineered cutinases and PETases developed for the depolymerization of the abundant plastic, polyethylene terephthalate (PET). Finally, biocatalytic approaches for accessing petroleum-based feedstocks and chemicals are expanding, using optimized enzymes to convert plant biomass into biofuels or other high value products. Through these examples, we hope to illustrate how enzyme engineering and biocatalysis can contribute to the development of cleaner and more efficient chemical industry.
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Affiliation(s)
- Emily Radley
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - John Davidson
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Jake Foster
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Richard Obexer
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Elizabeth L Bell
- Renewable Resources and Enabling Sciences Center National Renewable Energy Laboratory Golden CO USA
- BOTTLE Consortium Golden CO USA
| | - Anthony P Green
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
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32
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Radley E, Davidson J, Foster J, Obexer R, Bell EL, Green AP. Engineering Enzymes for Environmental Sustainability. Angew Chem Int Ed Engl 2023; 62:e202309305. [PMID: 37651344 PMCID: PMC10952156 DOI: 10.1002/anie.202309305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/02/2023]
Abstract
The development and implementation of sustainable catalytic technologies is key to delivering our net-zero targets. Here we review how engineered enzymes, with a focus on those developed using directed evolution, can be deployed to improve the sustainability of numerous processes and help to conserve our environment. Efficient and robust biocatalysts have been engineered to capture carbon dioxide (CO2 ) and have been embedded into new efficient metabolic CO2 fixation pathways. Enzymes have been refined for bioremediation, enhancing their ability to degrade toxic and harmful pollutants. Biocatalytic recycling is gaining momentum, with engineered cutinases and PETases developed for the depolymerization of the abundant plastic, polyethylene terephthalate (PET). Finally, biocatalytic approaches for accessing petroleum-based feedstocks and chemicals are expanding, using optimized enzymes to convert plant biomass into biofuels or other high value products. Through these examples, we hope to illustrate how enzyme engineering and biocatalysis can contribute to the development of cleaner and more efficient chemical industry.
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Affiliation(s)
- Emily Radley
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - John Davidson
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Jake Foster
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Richard Obexer
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Elizabeth L. Bell
- Renewable Resources and Enabling Sciences CenterNational Renewable Energy LaboratoryGoldenCOUSA
- BOTTLE ConsortiumGoldenCOUSA
| | - Anthony P. Green
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
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33
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Hall BW, Kontur WS, Neri JC, Gille DM, Noguera DR, Donohue TJ. Production of carotenoids from aromatics and pretreated lignocellulosic biomass by Novosphingobium aromaticivorans. Appl Environ Microbiol 2023; 89:e0126823. [PMID: 38014958 PMCID: PMC10734531 DOI: 10.1128/aem.01268-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/04/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE There is economic and environmental interest in generating commodity chemicals from renewable resources, such as lignocellulosic biomass, that can substitute for chemicals derived from fossil fuels. The bacterium Novosphingobium aromaticivorans is a promising microbial platform for producing commodity chemicals from lignocellulosic biomass because it can produce these from compounds in pretreated lignocellulosic biomass, which many industrial microbial catalysts cannot metabolize. Here, we show that N. aromaticivorans can be engineered to produce several valuable carotenoids. We also show that engineered N. aromaticivorans strains can produce these lipophilic chemicals concurrently with the extracellular commodity chemical 2-pyrone-4,6-dicarboxylic acid when grown in a complex liquor obtained from alkaline pretreated lignocellulosic biomass. Concurrent microbial production of valuable intra- and extracellular products can increase the economic value generated from the conversion of lignocellulosic biomass-derived compounds into commodity chemicals and facilitate the separation of water- and membrane-soluble products.
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Affiliation(s)
- Benjamin W. Hall
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, USA
| | - Wayne S. Kontur
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Jeanette C. Neri
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Derek M. Gille
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
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34
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Chainani Y, Bonnanzio G, Tyo KE, Broadbelt LJ. Coupling chemistry and biology for the synthesis of advanced bioproducts. Curr Opin Biotechnol 2023; 84:102992. [PMID: 37688985 DOI: 10.1016/j.copbio.2023.102992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/30/2023] [Accepted: 08/05/2023] [Indexed: 09/11/2023]
Abstract
Chemical and biological syntheses can both lead to a myriad of compounds. Biology enables us to harness the metabolism of microbial cell factories to produce key target molecules from renewable biomass-derived substrates. Although bio-based feedstocks are sustainably sourced and more benign than the rapidly depleting fossil fuels that chemical processes have historically relied on, limiting pathways solely to biological reactions may not equate to a greener process overall. In fact, bioreactors rely on substantial quantities of water and can be inefficient since organisms typically operate around ambient conditions and are sensitive to perturbations in their environment. Hybridizing biosynthetic pathways with green chemistry can instead be a more potent strategy to reduce our net manufacturing footprint. Emerging chemistries have demonstrated considerable success in performing complex transformations on biological feedstocks without significant solvent use. Many of these transformations would be too slow to perform enzymatically or infeasible altogether. Here, we put forth the concept that by carefully considering the merits and drawbacks of synthetic biology and chemistry as well as one's own use case, there exist many opportunities for coupling the two. Merging these syntheses can unlock a wider suite of functional group transformations, thereby enabling future manufacturing processes to sustainably access a larger space of valuable, platform chemicals.
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Affiliation(s)
- Yash Chainani
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Geoffrey Bonnanzio
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Keith Ej Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
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35
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Silva D, Sousa AC, Robalo MP, Martins LO. A wide array of lignin-related phenolics are oxidized by an evolved bacterial dye-decolourising peroxidase. N Biotechnol 2023; 77:176-184. [PMID: 36563877 DOI: 10.1016/j.nbt.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Lignin is the second most abundant natural polymer next to cellulose and by far the largest renewable source of aromatic compounds on the planet. Dye-decolourising peroxidases (DyPs) are biocatalysts with immense potential in lignocellulose biorefineries to valorize emerging lignin building blocks for environmentally friendly chemicals and materials. This work investigates the catalytic potential of the engineered PpDyP variant 6E10 for the oxidation of 24 syringyl, guaiacyl and hydroxybenzene lignin-phenolic derivatives. Variant 6E10 exhibited up to 100-fold higher oxidation rates at pH 8 for all the tested phenolic substrates compared to the wild-type enzyme and other acidic DyPs described in the literature. The main products of reactions were dimeric isomers with molecular weights of (2 × MWsubstrate - 2 H). Their structure depends on the substitution pattern of the aromatic ring of substrates, i.e., of the coupling possibilities of the primarily formed radicals upon enzymatic oxidation. Among the dimers identified were syringaresinol, divanillin and diapocynin, important sources of structural scaffolds exploitable in medicinal chemistry, food additives and polymers.
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Affiliation(s)
- Diogo Silva
- Institute of Chemical and Biological Technology António Xavier, NOVA New University of Lisbon, Av da República, 2780-157 Oeiras, Portugal
| | - Ana Catarina Sousa
- Department of Chemical Engineering, Instituto Superior de Engenharia de Lisboa, Polytechnic Institute of Lisbon, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal; Centre for Structural Chemistry, Institute of Molecular Sciences, Complexo I; Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - M Paula Robalo
- Department of Chemical Engineering, Instituto Superior de Engenharia de Lisboa, Polytechnic Institute of Lisbon, R. Conselheiro Emídio Navarro, 1, 1959-007 Lisboa, Portugal; Centre for Structural Chemistry, Institute of Molecular Sciences, Complexo I; Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Lígia O Martins
- Institute of Chemical and Biological Technology António Xavier, NOVA New University of Lisbon, Av da República, 2780-157 Oeiras, Portugal.
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36
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Wang Y, Luo CB, Li YQ. Biofuneling lignin-derived compounds into lipids using a newly isolated Citricoccus sp. P2. BIORESOURCE TECHNOLOGY 2023; 387:129669. [PMID: 37573985 DOI: 10.1016/j.biortech.2023.129669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
Lignin-derived compounds (LDCs) bioconversion into lipids is a promising yet challenging task. This study focuses on the isolation of the ligninolytic bacterium Citricoccus sp. P2 and investigates its mechanism for producing lipids from LDCs. Although strain P2 exhibits a relatively low lignin degradation rate of 44.63%, it efficiently degrades various concentrations of LDCs. The highest degradation rate is observed when incubated with 0.6 g/L vanillic acid, 0.6 g/L syringic acid, 0.8 g/L p-coumaric acid, and 0.4 g/L phenol, resulting in respective lipid yields of 0.16 g/L, 0.13 g/L, 0.24 g/L, and 0.13 g/L. The genome of strain P2 provides insights into LDCs bioconversion into lipids and stress tolerance. Moreover, Citricoccus sp. P2 has been successfully developed a non-sterilized lipid production using its native alkali-halophilic characteristics, which significantly enhances the lipid yield. This study presents a promising platform for lipids production from LDCs and has potential to promote valorization of lignin.
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Affiliation(s)
- Yan Wang
- College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Chao-Bing Luo
- College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Yuan-Qiu Li
- College of Life Science, Leshan Normal University, Leshan 614000, China.
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37
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Lee S, Kang M, Jung CD, Bae JH, Lee JY, Park YK, Joo JC, Kim H, Sohn JH, Sung BH. Development of novel recombinant peroxidase secretion system from Pseudomonas putida for lignin valorisation. BIORESOURCE TECHNOLOGY 2023; 388:129779. [PMID: 37739186 DOI: 10.1016/j.biortech.2023.129779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023]
Abstract
Pseudomonas putida is a promising strain for lignin valorisation. However, there is a dearth of stable and efficient systems for secreting enzymes to enhance the process. Therefore, a novel secretion system for recombinant lignin-depolymerising peroxidase was developed. By adopting a flagellar type III secretion system, P. putida KT-M2, a secretory host strain, was constructed and an optimal secretion signal fusion partner was identified. Application of the dye-decolourising peroxidase of P. putida to this system resulted in efficient oxidation activity of the cell-free supernatant against various chemicals, including lignin model compounds. This peroxidase-secreting strain was examined to confirm its lignin utilisation capability, resulting in the efficient assimilation of various lignin substrates with 2.6-fold higher growth than that of the wild-type strain after 72 h of cultivation. Finally, this novel system will lead efficient bacterial lignin breakdown and utilization through enzyme secretion, paving the way for sustainable lignin-consolidated bioprocessing.
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Affiliation(s)
- Siseon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Minsik Kang
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Biosystems and Bioengineering Program, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Chan-Duck Jung
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Republic of Korea
| | - Jung-Hoon Bae
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Ju Young Lee
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Republic of Korea
| | - Young-Kwon Park
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea
| | - Hoyong Kim
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Republic of Korea
| | - Jung-Hoon Sohn
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Biosystems and Bioengineering Program, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Biosystems and Bioengineering Program, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
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38
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Manoli MT, Blanco FG, Rivero-Buceta V, Kniewel R, Alarcon SH, Salgado S, Prieto MA. Heterologous constitutive production of short-chain-length polyhydroxyalkanoates in Pseudomonas putida KT2440: the involvement of IbpA inclusion body protein. Front Bioeng Biotechnol 2023; 11:1275036. [PMID: 38026847 PMCID: PMC10646324 DOI: 10.3389/fbioe.2023.1275036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Designing cell factories for the production of novel polyhydroxyalkanoates (PHAs) via smart metabolic engineering is key to obtain à la carte materials with tailored physicochemical properties. To this end, we used the model medium-chain-length-PHA producing bacterium, P. putida KT2440 as a chassis, which is characterized by its metabolic versatility and stress tolerance. Different PHA biosynthetic modules were assembled in expression plasmids using the Golden gate/MoClo modular assembly technique to implement an orthogonal short-chain-lengh-PHA (scl-PHA) switch in a "deaf" PHA mutant. This was specifically constructed to override endogenous multilevel regulation of PHA synthesis in the native strain. We generated a panel of engineered approaches carrying the genes from Rhodospirillum rubrum, Cupriavidus necator and Pseudomonas pseudoalcaligenes, demonstrating that diverse scl-PHAs can be constitutively produced in the chassis strain to varying yields from 23% to 84% PHA/CDW. Co-feeding assays of the most promising engineered strain harboring the PHA machinery from C. necator resulted to a panel of PHBV from 0.6% to 19% C5 monomeric incorporation. Chromosomally integrated PHA machineries with high PhaCCn synthase dosage successfully resulted in 68% PHA/CDW production. Interestingly, an inverse relationship between PhaC synthase dosage and granule size distribution was demonstrated in the heterologous host. In this vein, it is proposed the key involvement of inclusion body protein IbpA to the heterologous production of tailored PHA in P. putida KT2440.
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Affiliation(s)
- Maria-Tsampika Manoli
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Francisco G. Blanco
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Virginia Rivero-Buceta
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Ryan Kniewel
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Sandra Herrera Alarcon
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Sergio Salgado
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - M. Auxiliadora Prieto
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Polymer Biotechnology Group, Department of Microbial and Plant Biotechnology, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
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39
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Shrestha S, Awasthi D, Chen Y, Gin J, Petzold CJ, Adams PD, Simmons BA, Singer SW. Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2. Appl Environ Microbiol 2023; 89:e0085223. [PMID: 37724856 PMCID: PMC10617552 DOI: 10.1128/aem.00852-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 07/14/2023] [Indexed: 09/21/2023] Open
Abstract
Pseudomonas putida have emerged as promising biocatalysts for the conversion of sugars and aromatic compounds obtained from lignocellulosic biomass. Understanding the role of carbon catabolite repression (CCR) in these strains is critical to optimize biomass conversion to fuels and chemicals. The CCR functioning in P. putida M2, a strain capable of consuming both hexose and pentose sugars as well as aromatic compounds, was investigated by cultivation experiments, proteomics, and CRISPRi-based gene repression. Strain M2 co-utilized sugars and aromatic compounds simultaneously; however, during cultivation with glucose and aromatic compounds (p-coumarate and ferulate) mixture, intermediates (4-hydroxybenzoate and vanillate) accumulated, and substrate consumption was incomplete. In contrast, xylose-aromatic consumption resulted in transient intermediate accumulation and complete aromatic consumption, while xylose was incompletely consumed. Proteomics analysis revealed that glucose exerted stronger repression than xylose on the aromatic catabolic proteins. Key glucose (Eda) and xylose (XylX) catabolic proteins were also identified at lower abundance during cultivation with aromatic compounds implying simultaneous catabolite repression by sugars and aromatic compounds. Reduction of crc expression via CRISPRi led to faster growth and glucose and p-coumarate uptake in the CRISPRi strains compared to the control, while no difference was observed on xylose+p-coumarate. The increased abundances of Eda and amino acid biosynthesis proteins in the CRISPRi strain further supported these observations. Lastly, small RNAs (sRNAs) sequencing results showed that CrcY and CrcZ homologues levels in M2, previously identified in P. putida strains, were lower under strong CCR (glucose+p-coumarate) condition compared to when repression was absent (p-coumarate or glucose only).IMPORTANCEA newly isolated Pseudomonas putida strain, P. putida M2, can utilize both hexose and pentose sugars as well as aromatic compounds making it a promising host for the valorization of lignocellulosic biomass. Pseudomonads have developed a regulatory strategy, carbon catabolite repression, to control the assimilation of carbon sources in the environment. Carbon catabolite repression may impede the simultaneous and complete metabolism of sugars and aromatic compounds present in lignocellulosic biomass and hinder the development of an efficient industrial biocatalyst. This study provides insight into the cellular physiology and proteome during mixed-substrate utilization in P. putida M2. The phenotypic and proteomics results demonstrated simultaneous catabolite repression in the sugar-aromatic mixtures, while the CRISPRi and sRNA sequencing demonstrated the potential role of the crc gene and small RNAs in carbon catabolite repression.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jennifer Gin
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher J. Petzold
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, California, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Blake A. Simmons
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven W. Singer
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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40
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Tang H, Li YQ, Wang MJ, Wang Y, Luo CB. Valorization of lignin-derived compounds into poly(3-hydroxybutyrate-co-3-hydroxyvalerate) by engineered Halomonas sp. Y3. Int J Biol Macromol 2023; 249:126079. [PMID: 37536413 DOI: 10.1016/j.ijbiomac.2023.126079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/25/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) is a biopolyester with great potential, but its high production cost via the propionate-dependent pathway has hindered its development. Herein, we engineer Halomonas sp. Y3 to achieve efficient conversion of various LDCs into PHBV without propionate supplement. Initially, we successfully achieve PHBV production without propionate supplement by overexpressing threonine synthesis. The resulting biopolyester exhibits a 3 HV proportion of up to 7.89 mol%, comparable to commercial PHBV (8 mol%) available from Sigma Aldrich (403105). To further enhance PHBV production, we rationally design the reconstruction of aromatic compound catabolism. The engineered strain Y3_18 efficiently assimilates all LDCs containing syringyl (S), guaiacyl (G), and p-hydroxyphenyl-type (H) units. From 1 g/L of S-, G-, and H-type LDCs, Y3_18 produces PHBV at levels of 449 mg/L, 488 mg/L, and 716 mg/L, respectively, with yields of 44.9 % (g/g), 48.8 % (g/g), and 71.6 % (g/g). Moreover, to improve PHBV yield from lignin, we integrate laccase-secretion and PHBV production modules. This integration leads to the accumulation of 425.84 mg/L of PHBV with a yield of 21.29 % (g/g) and a 3 HV proportion of 6.38 mol%. By harnessing the capabilities of Halomonas sp. Y3, we demonstrate an efficient and sustainable approach for PHBV production from a variety of LDCs.
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Affiliation(s)
- Hao Tang
- College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Yuan-Qiu Li
- College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Ming-Jun Wang
- College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Yan Wang
- College of Life Science, Leshan Normal University, Leshan 614000, China.
| | - Chao-Bing Luo
- College of Life Science, Leshan Normal University, Leshan 614000, China.
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41
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Eng T, Banerjee D, Menasalvas J, Chen Y, Gin J, Choudhary H, Baidoo E, Chen JH, Ekman A, Kakumanu R, Diercks YL, Codik A, Larabell C, Gladden J, Simmons BA, Keasling JD, Petzold CJ, Mukhopadhyay A. Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering. Cell Rep 2023; 42:113087. [PMID: 37665664 DOI: 10.1016/j.celrep.2023.113087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/10/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023] Open
Abstract
Maximizing the production of heterologous biomolecules is a complex problem that can be addressed with a systems-level understanding of cellular metabolism and regulation. Specifically, growth-coupling approaches can increase product titers and yields and also enhance production rates. However, implementing these methods for non-canonical carbon streams is challenging due to gaps in metabolic models. Over four design-build-test-learn cycles, we rewire Pseudomonas putida KT2440 for growth-coupled production of indigoidine from para-coumarate. We explore 4,114 potential growth-coupling solutions and refine one design through laboratory evolution and ensemble data-driven methods. The final growth-coupled strain produces 7.3 g/L indigoidine at 77% maximum theoretical yield in para-coumarate minimal medium. The iterative use of growth-coupling designs and functional genomics with experimental validation was highly effective and agnostic to specific hosts, carbon streams, and final products and thus generalizable across many systems.
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Affiliation(s)
- Thomas Eng
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Deepanwita Banerjee
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Javier Menasalvas
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yan Chen
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer Gin
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hemant Choudhary
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA
| | - Edward Baidoo
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian Hua Chen
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Axel Ekman
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ramu Kakumanu
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuzhong Liu Diercks
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alex Codik
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John Gladden
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA
| | - Blake A Simmons
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay D Keasling
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; QB3 Institute, University of California, Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA 94608, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, 2970 Horsholm, Denmark; Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Christopher J Petzold
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- The Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Werner AZ, Cordell WT, Lahive CW, Klein BC, Singer CA, Tan EC, Ingraham MA, Ramirez KJ, Kim DH, Pedersen JN, Johnson CW, Pfleger BF, Beckham GT, Salvachúa D. Lignin conversion to β-ketoadipic acid by Pseudomonas putida via metabolic engineering and bioprocess development. SCIENCE ADVANCES 2023; 9:eadj0053. [PMID: 37672573 PMCID: PMC10482344 DOI: 10.1126/sciadv.adj0053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023]
Abstract
Bioconversion of a heterogeneous mixture of lignin-related aromatic compounds (LRCs) to a single product via microbial biocatalysts is a promising approach to valorize lignin. Here, Pseudomonas putida KT2440 was engineered to convert mixed p-coumaroyl- and coniferyl-type LRCs to β-ketoadipic acid, a precursor for performance-advantaged polymers. Expression of enzymes mediating aromatic O-demethylation, hydroxylation, and ring-opening steps was tuned, and a global regulator was deleted. β-ketoadipate titers of 44.5 and 25 grams per liter and productivities of 1.15 and 0.66 grams per liter per hour were achieved from model LRCs and corn stover-derived LRCs, respectively, the latter representing an overall yield of 0.10 grams per gram corn stover-derived lignin. Technoeconomic analysis of the bioprocess and downstream processing predicted a β-ketoadipate minimum selling price of $2.01 per kilogram, which is cost competitive with fossil carbon-derived adipic acid ($1.10 to 1.80 per kilogram). Overall, this work achieved bioproduction metrics with economic relevance for conversion of lignin-derived streams into a performance-advantaged bioproduct.
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Affiliation(s)
- Allison Z. Werner
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - William T. Cordell
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Ciaran W. Lahive
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Bruno C. Klein
- Catalytic Carbon Transformation and Scale-Up Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Christine A. Singer
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Eric C. D. Tan
- Catalytic Carbon Transformation and Scale-Up Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Morgan A. Ingraham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Kelsey J. Ramirez
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Dong Hyun Kim
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Jacob Nedergaard Pedersen
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Christopher W. Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Brian F. Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Davinia Salvachúa
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
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43
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He S, Wang W, Wang W, Hu H, Xu P, Tang H. Microbial production of cis,cis-muconic acid from aromatic compounds in engineered Pseudomonas. Synth Syst Biotechnol 2023; 8:536-545. [PMID: 37637202 PMCID: PMC10448021 DOI: 10.1016/j.synbio.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 08/29/2023] Open
Abstract
Industrial expansion has led to environmental pollution by xenobiotic compounds like polycyclic aromatic hydrocarbons and monoaromatic hydrocarbons. Pseudomonas spp. have broad metabolic potential for degrading aromatic compounds. The objective of this study was to develop a "biological funneling" strategy based on genetic modification to convert complex aromatic compounds into cis,cis-muconate (ccMA) using Pseudomonas putida B6-2 and P. brassicacearum MPDS as biocatalysts. The engineered strains B6-2 (B6-2ΔcatBΔsalC) and MPDS (MPDSΔsalC(pUCP18k-catA)) thrived with biphenyl or naphthalene as the sole carbon source and produced ccMA, attaining molar conversions of 95.3% (ccMA/biphenyl) and 100% (ccMA/naphthalene). Under mixed substrates, B6-2ΔcatBΔsalC grew on biphenyl as a carbon source and transformed ccMA from non-growth substrates benzoate or salicylate to obtain higher product concentration. Inserting exogenous clusters like bedDC1C2AB and xylCMAB allowed B6-2 recombinant strains to convert benzene and toluene to ccMA. In mixed substrates, constructed consortia of engineered strains B6-2 and MPDS specialized in catabolism of biphenyl and naphthalene; the highest molar conversion rate of ccMA from mixed substrates was 85.2% when B6-2ΔcatBΔsalC was added after 24 h of MPDSΔsalC(pUCP18k-catA) incubation with biphenyl and naphthalene. This study provides worthwhile insights into efficient production of ccMA from aromatic hydrocarbons by reusing complex pollutants.
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Affiliation(s)
- Siyang He
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Weidong Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
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44
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Goswami L, Kushwaha A, Napathorn SC, Kim BS. Valorization of organic wastes using bioreactors for polyhydroxyalkanoate production: Recent advancement, sustainable approaches, challenges, and future perspectives. Int J Biol Macromol 2023; 247:125743. [PMID: 37423435 DOI: 10.1016/j.ijbiomac.2023.125743] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Microbial polyhydroxyalkanoates (PHA) are encouraging biodegradable polymers, which may ease the environmental problems caused by petroleum-derived plastics. However, there is a growing waste removal problem and the high price of pure feedstocks for PHA biosynthesis. This has directed to the forthcoming requirement to upgrade waste streams from various industries as feedstocks for PHA production. This review covers the state-of-the-art progress in utilizing low-cost carbon substrates, effective upstream and downstream processes, and waste stream recycling to sustain entire process circularity. This review also enlightens the use of various batch, fed-batch, continuous, and semi-continuous bioreactor systems with flexible results to enhance the productivity and simultaneously cost reduction. The life-cycle and techno-economic analyses, advanced tools and strategies for microbial PHA biosynthesis, and numerous factors affecting PHA commercialization were also covered. The review includes the ongoing and upcoming strategies viz. metabolic engineering, synthetic biology, morphology engineering, and automation to expand PHA diversity, diminish production costs, and improve PHA production with an objective of "zero-waste" and "circular bioeconomy" for a sustainable future.
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Affiliation(s)
- Lalit Goswami
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Anamika Kushwaha
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | | | - Beom Soo Kim
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea.
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45
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Bleem A, Kato R, Kellermyer ZA, Katahira R, Miyamoto M, Niinuma K, Kamimura N, Masai E, Beckham GT. Multiplexed fitness profiling by RB-TnSeq elucidates pathways for lignin-related aromatic catabolism in Sphingobium sp. SYK-6. Cell Rep 2023; 42:112847. [PMID: 37515767 DOI: 10.1016/j.celrep.2023.112847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/21/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023] Open
Abstract
Bioconversion of lignin-related aromatic compounds relies on robust catabolic pathways in microbes. Sphingobium sp. SYK-6 (SYK-6) is a well-characterized aromatic catabolic organism that has served as a model for microbial lignin conversion, and its utility as a biocatalyst could potentially be further improved by genome-wide metabolic analyses. To this end, we generate a randomly barcoded transposon insertion mutant (RB-TnSeq) library to study gene function in SYK-6. The library is enriched under dozens of enrichment conditions to quantify gene fitness. Several known aromatic catabolic pathways are confirmed, and RB-TnSeq affords additional detail on the genome-wide effects of each enrichment condition. Selected genes are further examined in SYK-6 or Pseudomonas putida KT2440, leading to the identification of new gene functions. The findings from this study further elucidate the metabolism of SYK-6, while also providing targets for future metabolic engineering in this organism or other hosts for the biological valorization of lignin.
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Affiliation(s)
- Alissa Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Ryo Kato
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Zoe A Kellermyer
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Rui Katahira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Masahiro Miyamoto
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Koh Niinuma
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Naofumi Kamimura
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Eiji Masai
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
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46
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Biggs BW, Tyo KEJ. Aromatic natural products synthesis from aromatic lignin monomers using Acinetobacter baylyi ADP1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554694. [PMID: 37662333 PMCID: PMC10473687 DOI: 10.1101/2023.08.24.554694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Achieving sustainable chemical synthesis and a circular economy will require process innovation to minimize or recover existing waste streams. Valorization of lignin biomass has the ability to advance this goal. While lignin has proved a recalcitrant feedstock for upgrading, biological approaches can leverage native microbial metabolism to simplify complex and heterogeneous feedstocks to tractable starting points for biochemical upgrading. Recently, we demonstrated that one microbe with lignin relevant metabolism, Acinetobacter baylyi ADP1, is both highly engineerable and capable of undergoing rapid design-build-test-learn cycles, making it an ideal candidate for these applications. Here, we utilize these genetic traits and ADP1's native β-ketoadipate metabolism to convert mock alkali pretreated liquor lignin (APL) to two valuable natural products, vanillin-glucoside and resveratrol. En route, we create strains with up to 22 genetic modifications, including up to 8 heterologously expressed enzymes. Our approach takes advantage of preexisting aromatic species in APL (vanillate, ferulate, and p-coumarate) to create shortened biochemical routes to end products. Together, this work demonstrates ADP1's potential as a platform for upgrading lignin waste streams and highlights the potential for biosynthetic methods to maximize the existing chemical potential of lignin aromatic monomers.
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Affiliation(s)
- Bradley W. Biggs
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Keith E. J. Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
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47
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Wu X, De Bruyn M, Barta K. Deriving high value products from depolymerized lignin oil, aided by (bio)catalytic funneling strategies. Chem Commun (Camb) 2023; 59:9929-9951. [PMID: 37526604 DOI: 10.1039/d3cc01555f] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Lignin holds tremendous and versatile possibilities to produce value-added chemicals and high performing polymeric materials. Over the years, different cutting-edge lignin depolymerization methodologies have been developed, mainly focusing on achieving excellent yields of mono-phenolic products, some even approaching the theoretical maximum. However, due to lignin's inherent heterogeneity and recalcitrance, its depolymerization leads to relatively complex product streams, also containing dimers, and higher molecular weight fragments in substantial quantities. The subsequent chemo-catalytic valorization of these higher molecular weight streams, containing difficult-to-break, mainly C-C covalent bonds, is tremendously challenging, and has consequently received much less attention. In this minireview, we present an overview of recent advances on the development of sustainable biorefinery strategies aimed at the production of well-defined chemicals and polymeric materials, the prime focus being on depolymerized lignin oils, containing high molecular weight fractions. The key central unit operation to achieve this is (bio)catalytic funneling, which holds great potential to overcome separation and purification challenges.
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Affiliation(s)
- Xianyuan Wu
- University of Groningen, Stratingh Institute for Chemistry, Nijenborgh 4, Groningen, The Netherlands
| | - Mario De Bruyn
- University of Graz, Department of Chemistry, Organic and Bioorganic Chemistry, Heinrichstrasse 28/II, 8010 Graz, Austria.
| | - Katalin Barta
- University of Groningen, Stratingh Institute for Chemistry, Nijenborgh 4, Groningen, The Netherlands
- University of Graz, Department of Chemistry, Organic and Bioorganic Chemistry, Heinrichstrasse 28/II, 8010 Graz, Austria.
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48
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Chen M, Li Y, Lu F, Luterbacher JS, Ralph J. Lignin Hydrogenolysis: Phenolic Monomers from Lignin and Associated Phenolates across Plant Clades. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2023; 11:10001-10017. [PMID: 37448721 PMCID: PMC10337261 DOI: 10.1021/acssuschemeng.3c01320] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/13/2023] [Indexed: 07/15/2023]
Abstract
The chemical complexity of lignin remains a major challenge for lignin valorization into commodity and fine chemicals. A knowledge of the lignin features that favor its valorization and which plants produce such lignins can be used in plant selection or to engineer them to produce lignins that are more ideally suited for conversion. Sixteen biomass samples were compositionally surveyed by NMR and analytical degradative methods, and the yields of phenolic monomers following hydrogenolytic depolymerization were assessed to elucidate the key determinants controlling the depolymerization. Hardwoods, including those incorporating monolignol p-hydroxybenzoates into their syringyl/guaiacyl copolymeric lignins, produced high monomer yields by hydrogenolysis, whereas grasses incorporating monolignol p-coumarates and ferulates gave lower yields, on a lignin basis. Softwoods, with their more condensed guaiacyl lignins, gave the lowest yields. Lignins with a high syringyl unit content released elevated monomer levels, with a high-syringyl polar transgenic being particularly striking. Herein, we distinguish phenolic monomers resulting from the core lignin vs those from pendent phenolate esters associated with the biomass cell wall, acylating either polysaccharides or lignins. The basis for these observations is rationalized as a means to select or engineer biomass for optimal conversion to worthy phenolic monomers.
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Affiliation(s)
- Mingjie Chen
- Department
of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, Wisconsin 53726, United States
| | - Yanding Li
- Department
of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, Wisconsin 53726, United States
| | - Fachuang Lu
- Department
of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, Wisconsin 53726, United States
| | - Jeremy S. Luterbacher
- Institute
of Chemical Sciences and Engineering, École
Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - John Ralph
- Department
of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, Wisconsin 53726, United States
- Department
of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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Ashoor S, Khang TU, Lee YH, Hyung JS, Choi SY, Lim SE, Lee J, Park SJ, Na JG. Bioupgrading of the aqueous phase of pyrolysis oil from lignocellulosic biomass: a platform for renewable chemicals and fuels from the whole fraction of biomass. BIORESOUR BIOPROCESS 2023; 10:34. [PMID: 38647900 PMCID: PMC10992256 DOI: 10.1186/s40643-023-00654-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/19/2023] [Indexed: 04/25/2024] Open
Abstract
Pyrolysis, a thermal decomposition without oxygen, is a promising technology for transportable liquids from whole fractions of lignocellulosic biomass. However, due to the hydrophilic products of pyrolysis, the liquid oils have undesirable physicochemical characteristics, thus requiring an additional upgrading process. Biological upgrading methods could address the drawbacks of pyrolysis by utilizing various hydrophilic compounds as carbon sources under mild conditions with low carbon footprints. Versatile chemicals, such as lipids, ethanol, and organic acids, could be produced through microbial assimilation of anhydrous sugars, organic acids, aldehydes, and phenolics in the hydrophilic fractions. The presence of various toxic compounds and the complex composition of the aqueous phase are the main challenges. In this review, the potential of bioconversion routes for upgrading the aqueous phase of pyrolysis oil is investigated with critical challenges and perspectives.
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Affiliation(s)
- Selim Ashoor
- Department of Agricultural Microbiology, Faculty of Agriculture, Ain Shams University, Hadayek Shoubra, Cairo, 11241, Egypt
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Tae Uk Khang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Young Hoon Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Ji Sung Hyung
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Seo Young Choi
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Sang Eun Lim
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Jinwon Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jeong-Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, Republic of Korea.
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Vigh M. A trashed treasure: Lignin could become a large and renewable source of organic compounds for the chemical industry to replace fossil fuel-based chemicals: Lignin could become a large and renewable source of organic compounds for the chemical industry to replace fossil fuel-based chemicals. EMBO Rep 2023; 24:e57103. [PMID: 36947364 PMCID: PMC10157301 DOI: 10.15252/embr.202357103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/08/2023] [Indexed: 03/23/2023] Open
Abstract
Plant-based industries generate huge amounts of lignin waste that could be converted to useful bioproducts. Efforts to recycle lignin include GM plants, microbial cell factories and "lignin-first" approaches.
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Affiliation(s)
- Maria Vigh
- University of CopenhagenCopenhagenDenmark
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