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Tramontina R, Ciancaglini I, Roman EKB, Chacón MG, Corrêa TLR, Dixon N, Bugg TDH, Squina FM. Sustainable biosynthetic pathways to value-added bioproducts from hydroxycinnamic acids. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12571-8. [PMID: 37212882 DOI: 10.1007/s00253-023-12571-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 05/23/2023]
Abstract
The biorefinery concept, in which biomass is utilized for the production of fuels and chemicals, emerges as an eco-friendly, cost-effective, and renewable alternative to petrochemical-based production. The hydroxycinnamic acid fraction of lignocellulosic biomass represents an untapped source of aromatic molecules that can be converted to numerous high-value products with industrial applications, including in the flavor and fragrance sector and pharmaceuticals. This review describes several biochemical pathways useful in the development of a biorefinery concept based on the biocatalytic conversion of the hydroxycinnamic acids ferulic, caffeic, and p-coumaric acid into high-value molecules. KEY POINTS: • The phenylpropanoids bioconversion pathways in the context of biorefineries • Description of pathways from hydroxycinnamic acids to high-value compounds • Metabolic engineering and synthetic biology advance hydroxycinnamic acid-based biorefineries.
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Affiliation(s)
- Robson Tramontina
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Programa de Processos Tecnológicos E Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, São Paulo, Brazil
| | - Iara Ciancaglini
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Ellen K B Roman
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Micaela G Chacón
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Thamy L R Corrêa
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Neil Dixon
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos E Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, São Paulo, Brazil.
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2
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Chaudhury D, Torkelson ER, Meyers KA, Acheson JF, Landucci L, Pu Y, Sun Z, Tonelli M, Bingman CA, Smith RA, Karlen SD, Mansfield SD, Ralph J, Fox BG. Rapid Biocatalytic Synthesis of Aromatic Acid CoA Thioesters by Using Microbial Aromatic Acid CoA Ligases. Chembiochem 2023; 24:e202300001. [PMID: 36821718 PMCID: PMC10467583 DOI: 10.1002/cbic.202300001] [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: 01/01/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 02/25/2023]
Abstract
Chemically labile ester linkages can be introduced into lignin by incorporation of monolignol conjugates, which are synthesized in planta by acyltransferases that use a coenzyme A (CoA) thioester donor and a nucleophilic monolignol alcohol acceptor. The presence of these esters facilitates processing and aids in the valorization of renewable biomass feedstocks. However, the effectiveness of this strategy is potentially limited by the low steady-state levels of aromatic acid thioester donors in plants. As part of an effort to overcome this, aromatic acid CoA ligases involved in microbial aromatic degradation were identified and screened against a broad panel of substituted cinnamic and benzoic acids involved in plant lignification. Functional fingerprinting of this ligase library identified four robust, highly active enzymes capable of facile, rapid, and high-yield synthesis of aromatic acid CoA thioesters under mild aqueous reaction conditions mimicking in planta activity.
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Affiliation(s)
- Debayan Chaudhury
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Ella R Torkelson
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Kaya A Meyers
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Justin F Acheson
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Leta Landucci
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Yucen Pu
- Department of Botany and Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Zimou Sun
- Department of Botany and Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Rebecca A Smith
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Steven D Karlen
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Shawn D Mansfield
- Department of Botany and Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - John Ralph
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Brian G Fox
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
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Vilela N, Tomazetto G, Gonçalves TA, Sodré V, Persinoti GF, Moraes EC, de Oliveira AHC, da Silva SN, Fill TP, Damasio A, Squina FM. Integrative omics analyses of the ligninolytic Rhodosporidium fluviale LM-2 disclose catabolic pathways for biobased chemical production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:5. [PMID: 36624471 PMCID: PMC9830802 DOI: 10.1186/s13068-022-02251-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/18/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Lignin is an attractive alternative for producing biobased chemicals. It is the second major component of the plant cell wall and is an abundant natural source of aromatic compounds. Lignin degradation using microbial oxidative enzymes that depolymerize lignin and catabolize aromatic compounds into central metabolic intermediates is a promising strategy for lignin valorization. However, the intrinsic heterogeneity and recalcitrance of lignin severely hinder its biocatalytic conversion. In this context, examining microbial degradation systems can provide a fundamental understanding of the pathways and enzymes that are useful for lignin conversion into biotechnologically relevant compounds. RESULTS Lignin-degrading catabolism of a novel Rhodosporidium fluviale strain LM-2 was characterized using multi-omic strategies. This strain was previously isolated from a ligninolytic microbial consortium and presents a set of enzymes related to lignin depolymerization and aromatic compound catabolism. Furthermore, two catabolic routes for producing 4-vinyl guaiacol and vanillin were identified in R. fluviale LM-2. CONCLUSIONS The multi-omic analysis of R. fluviale LM-2, the first for this species, elucidated a repertoire of genes, transcripts, and secreted proteins involved in lignin degradation. This study expands the understanding of ligninolytic metabolism in a non-conventional yeast, which has the potential for future genetic manipulation. Moreover, this work unveiled critical pathways and enzymes that can be exported to other systems, including model organisms, for lignin valorization.
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Affiliation(s)
- Nathália Vilela
- grid.442238.b0000 0001 1882 0259Programa de Processos Tecnológicos e Ambientais, University of Sorocaba (UNISO), Sorocaba, Brazil ,grid.411087.b0000 0001 0723 2494Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Geizecler Tomazetto
- grid.7048.b0000 0001 1956 2722Department of Biological and Chemical Engineering (BCE), Aarhus University, 8200 Aarhus, Denmark
| | - Thiago Augusto Gonçalves
- grid.4989.c0000 0001 2348 0746Photobiocatalysis Unit—CPBL, and Biomass Transformation Lab—BTL, École Interfacultaire de Bioingénieurs, Université Libre de Bruxelles, Brussels, Belgium
| | - Victoria Sodré
- grid.7372.10000 0000 8809 1613Department of Chemistry, University of Warwick, Coventry, UK
| | - Gabriela Felix Persinoti
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Eduardo Cruz Moraes
- grid.411087.b0000 0001 0723 2494Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Arthur Henrique Cavalcante de Oliveira
- grid.11899.380000 0004 1937 0722Department of Chemistry, Faculty of Philosophy Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Stephanie Nemesio da Silva
- grid.411087.b0000 0001 0723 2494Laboratory of Biology Chemical Microbial (LaBioQuiMi), Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - Taícia Pacheco Fill
- grid.411087.b0000 0001 0723 2494Laboratory of Biology Chemical Microbial (LaBioQuiMi), Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Brazil
| | - André Damasio
- grid.411087.b0000 0001 0723 2494Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fabio Marcio Squina
- grid.442238.b0000 0001 1882 0259Programa de Processos Tecnológicos e Ambientais, University of Sorocaba (UNISO), Sorocaba, Brazil
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Chen Q, Jiang Y, Kang Z, Cheng J, Xiong X, Hu CY, Meng Y. Engineering a Feruloyl-Coenzyme A Synthase for Bioconversion of Phenylpropanoid Acids into High-Value Aromatic Aldehydes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9948-9960. [PMID: 35917470 DOI: 10.1021/acs.jafc.2c02980] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Aromatic aldehydes find extensive applications in food, perfume, pharmaceutical, and chemical industries. However, a limited natural enzyme selectivity has become the bottleneck of bioconversion of aromatic aldehydes from natural phenylpropanoid acids. Here, based on the original structure of feruloyl-coenzyme A (CoA) synthetase (FCS) from Streptomyces sp. V-1, we engineered five substrate-binding domains to match specific phenylpropanoid acids. FcsCIAE407A/K483L, FcsMAE407R/I481R/K483R, FcsHAE407K/I481K/K483I, FcsCAE407R/I481R/K483T, and FcsFAE407R/I481K/K483R showed 9.96-, 10.58-, 4.25-, 6.49-, and 8.71-fold enhanced catalytic efficiency for degrading CoA thioesters of cinnamic acid, 4-methoxycinnamic acid, 4-hydroxycinnamic acid, caffeic acid, and ferulic acid, respectively. Molecular dynamics simulation illustrated that novel substrate-binding domains formed strong interaction forces with substrates' methoxy/hydroxyl group and provided hydrophobic/alkaline catalytic surfaces. Five recombinant E. coli with FCS mutants were constructed with the maximum benzaldehyde, p-anisaldehyde, p-hydroxybenzaldehyde, protocatechualdehyde, and vanillin productivity of 6.2 ± 0.3, 5.1 ± 0.23, 4.1 ± 0.25, 7.1 ± 0.3, and 8.7 ± 0.2 mM/h, respectively. Hence, our study provided novel and efficient enzymes for the bioconversion of phenylpropanoid acids into aromatic aldehydes.
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Affiliation(s)
- Qihang Chen
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian 710119, P.R. China
| | - Yaqin Jiang
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian 710119, P.R. China
| | - Zhengzhong Kang
- AutoDrug Biotech Co. Ltd, No. 58 XiangKe Rd, Pudong New Area, Shanghai 201210, China
| | - Jie Cheng
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, P.R. China
| | - Xiaochao Xiong
- Biological Systems Engineering, Washington State University, Pullman, Washington 99163, United States
| | - Ching Yuan Hu
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian 710119, P.R. China
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, 1955 East-West Road, AgSci. 415J, Honolulu, Hawaii 96822, United States
| | - Yonghong Meng
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian 710119, P.R. China
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5
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Recombinant expression, purification and characterization of an active bacterial feruloyl-CoA synthase with potential for application in vanillin production. Protein Expr Purif 2022; 197:106109. [DOI: 10.1016/j.pep.2022.106109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/25/2022] [Accepted: 05/03/2022] [Indexed: 11/23/2022]
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Applying biochemical and structural characterization of hydroxycinnamate catabolic enzymes from soil metagenome for lignin valorization strategies. Appl Microbiol Biotechnol 2022; 106:2503-2516. [PMID: 35352150 DOI: 10.1007/s00253-022-11885-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/15/2022] [Accepted: 03/06/2022] [Indexed: 11/02/2022]
Abstract
The biocatalytic production of fuels and chemicals from plant biomass represents an attractive alternative to fossil fuel-based refineries. In this context, the mining and characterization of novel biocatalysts can promote disruptive innovation opportunities in the field of lignocellulose conversion and valorization. In the present work, we conducted the biochemical and structural characterization of two novel hydroxycinnamic acid catabolic enzymes, isolated from a lignin-degrading microbial consortium, a feruloyl-CoA synthetase, and a feruloyl-CoA hydratase-lyase, named LM-FCS2 and LM-FCHL2, respectively. Besides establishing the homology model structures for novel FCS and FCHL members with unique characteristics, the enzymes presented interesting biochemical features: LM-FCS2 showed stability in alkaline pHs and was able to convert a wide array of p-hydroxycinnamic acids to their respective CoA-thioesters, including sinapic acid; LM-FCHL2 efficiently converted feruloyl-CoA and p-coumaroyl-CoA into vanillin and 4-hydroxybenzaldehyde, respectively, and could produce vanillin directly from ferulic acid. The coupled reaction of LM-FCS2 and LM-FCHL2 produced vanillin, not only from commercial ferulic acid but also from a crude lignocellulosic hydrolysate. Collectively, this work illuminates the structure and function of two critical enzymes involved in converting ferulic acid into high-value molecules, thus providing valuable concepts applied to the development of plant biomass biorefineries. KEY POINTS: • Comprehensive characterization of feruloyl-CoA synthetase from metagenomic origin. • Novel low-resolution structures of hydroxycinnamate catabolic enzymes. • Production of vanillin via enzymatic reaction using lignocellulosic hydrolysates.
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7
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Liberato MV, Araújo JN, Sodré V, Gonçalves TA, Vilela N, Moraes EC, Garcia W, Squina FM. The structure of a prokaryotic feruloyl-CoA hydratase-lyase from a lignin-degrading consortium with high oligomerization stability under extreme pHs. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140344. [PMID: 31841665 DOI: 10.1016/j.bbapap.2019.140344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 10/25/2022]
Abstract
In the context of increasing demand for renewable alternatives of fuels and chemicals, the valorization of lignin emerges as a value-adding strategy in biorefineries and an alternative to petroleum-derived molecules. One of the compounds derived from lignin is ferulic acid (FA), which can be converted into valuable molecules such as vanillin. In microorganisms, FA biotransformation into vanillin can occur via a two-step reaction catalyzed by the sequential activity of a feruloyl-CoA synthetase (FCS) and an feruloyl-CoA hydratase-lyase (FCHL), which could be exploited industrially. In this study, a prokaryotic FCHL derived from a lignin-degrading microbial consortium (named LM-FCHL) was cloned, successfully expressed in soluble form and purified. The crystal structure was solved and refined at 2.1 Å resolution. The LM-FCHL is a hexamer composed of a dimer of trimers, which showed to be quite stable under extreme pH conditions. Finally, small angle X-ray scattering corroborates the hexameric state in solution and indicates flexibility in the protein structure. The present study contributes to the field of lignin valorization to valuable molecules by establishing the biophysical and structural characterization for a novel FCHL member of unique characteristics.
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Affiliation(s)
- Marcelo Vizoná Liberato
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - Juscemácia N Araújo
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Victoria Sodré
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil; Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Thiago Augusto Gonçalves
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil; Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Nathalia Vilela
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil; Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Eduardo Cruz Moraes
- Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil.
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