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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:e0171824. [PMID: 39012147 DOI: 10.1128/mbio.01718-24] [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: 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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2
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García-Romero I, de Dios R, Reyes-Ramírez F. An improved genome editing system for Sphingomonadaceae. Access Microbiol 2024; 6:000755.v3. [PMID: 38868378 PMCID: PMC11165598 DOI: 10.1099/acmi.0.000755.v3] [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: 12/14/2023] [Accepted: 04/05/2024] [Indexed: 06/14/2024] Open
Abstract
The sphingomonads encompass a diverse group of bacteria within the family Sphingomonadaceae, with the presence of sphingolipids on their cell surface instead of lipopolysaccharide as their main common feature. They are particularly interesting for bioremediation purposes due to their ability to degrade or metabolise a variety of recalcitrant organic pollutants. However, research and development on their full bioremediation potential has been hampered because of the limited number of tools available to investigate and modify their genome. Here, we present a markerless genome editing method for Sphingopyxis granuli TFA, which can be further optimised for other sphingomonads. This procedure is based on a double recombination triggered by a DNA double-strand break in the chromosome. The strength of this protocol lies in forcing the second recombination rather than favouring it by pressing a counterselection marker, thus avoiding laborious restreaking or passaging screenings. Additionally, we introduce a modification with respect to the original protocol to increase the efficiency of the screening after the first recombination event. We show this procedure step by step and compare our modified method with respect to the original one by deleting ecfG2, the master regulator of the general stress response in S. granuli TFA. This adds to the genetic tool repertoire that can be applied to sphingomonads and stands as an efficient option for fast genome editing of this bacterial group.
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Affiliation(s)
- Inmaculada García-Romero
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, 41013 Sevilla, Spain
| | - Rubén de Dios
- Division of Biosciences, Department of Life Sciences, Centre of Inflammation Research and Translational Medicine, College of Health, Medicine and Life Sciences,, Brunel University London, Uxbridge, UK
| | - Francisca Reyes-Ramírez
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, 41013 Sevilla, Spain
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Rashid GMM, Rivière GN, Cottyn-Boitte B, Majira A, Cézard L, Sodré V, Lam R, Fairbairn JA, Baumberger S, Bugg TDH. Ether Bond Cleavage of a Phenylcoumaran β-5 Lignin Model Compound and Polymeric Lignin Catalysed by a LigE-type Etherase from Agrobacterium sp. Chembiochem 2024; 25:e202400132. [PMID: 38416537 DOI: 10.1002/cbic.202400132] [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: 02/12/2024] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 02/29/2024]
Abstract
A LigE-type beta-etherase enzyme from lignin-degrading Agrobacterium sp. has been identified, which assists degradation of polymeric lignins. Testing against lignin dimer model compounds revealed that it does not catalyse the previously reported reaction of Sphingobium SYK-6 LigE, but instead shows activity for a β-5 phenylcoumaran lignin dimer. The reaction products did not contain glutathione, indicating a catalytic role for reduced glutathione in this enzyme. Three reaction products were identified: the major product was a cis-stilbene arising from C-C fragmentation involving loss of formaldehyde; two minor products were an alkene arising from elimination of glutathione, and an oxidised ketone, proposed to arise from reaction of an intermediate with molecular oxygen. Testing of the recombinant enzyme against a soda lignin revealed the formation of new signals by two-dimensional NMR analysis, whose chemical shifts are consistent with the formation of a stilbene unit in polymeric lignin.
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Affiliation(s)
- Goran M M Rashid
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Guillaume N Rivière
- Université Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Betty Cottyn-Boitte
- Université Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Amel Majira
- Université Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Laurent Cézard
- Université Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Victoria Sodré
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Richard Lam
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Julia A Fairbairn
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Stéphanie Baumberger
- Université Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
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4
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Vilbert AC, Kontur WS, Gille D, Noguera DR, Donohue TJ. Engineering Novosphingobium aromaticivorans to produce cis,cis-muconic acid from biomass aromatics. Appl Environ Microbiol 2024; 90:e0166023. [PMID: 38117061 PMCID: PMC10807440 DOI: 10.1128/aem.01660-23] [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: 09/20/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
The platform chemical cis,cis-muconic acid (ccMA) provides facile access to a number of monomers used in the synthesis of commercial plastics. It is also a metabolic intermediate in the β-ketoadipic acid pathway of many bacteria and, therefore, a current target for microbial production from abundant renewable resources via metabolic engineering. This study investigates Novosphingobium aromaticivorans DSM12444 as a chassis for the production of ccMA from biomass aromatics. The N. aromaticivorans genome predicts that it encodes a previously uncharacterized protocatechuic acid (PCA) decarboxylase and a catechol 1,2-dioxygenase, which would be necessary for the conversion of aromatic metabolic intermediates to ccMA. This study confirmed the activity of these two enzymes in vitro and compared their activity to ones that have been previously characterized and used in ccMA production. From these results, we generated one strain that is completely derived from native genes and a second that contains genes previously used in microbial engineering synthesis of this compound. Both of these strains exhibited stoichiometric production of ccMA from PCA and produced greater than 100% yield of ccMA from the aromatic monomers that were identified in liquor derived from alkaline pretreated biomass. Our results show that a strain completely derived from native genes and one containing homologs from other hosts are both capable of stoichiometric production of ccMA from biomass aromatics. Overall, this work combines previously unknown aspects of aromatic metabolism in N. aromaticivorans and the genetic tractability of this organism to generate strains that produce ccMA from deconstructed biomass.IMPORTANCEThe production of commodity chemicals from renewable resources is an important goal toward increasing the environmental and economic sustainability of industrial processes. The aromatics in plant biomass are an underutilized and abundant renewable resource for the production of valuable chemicals. However, due to the chemical composition of plant biomass, many deconstruction methods generate a heterogeneous mixture of aromatics, thus making it difficult to extract valuable chemicals using current methods. Therefore, recent efforts have focused on harnessing the pathways of microorganisms to convert a diverse set of aromatics into a single product. Novosphingobium aromaticivorans DSM12444 has the native ability to metabolize a wide range of aromatics and, thus, is a potential chassis for conversion of these abundant compounds to commodity chemicals. This study reports on new features of N. aromaticivorans that can be used to produce the commodity chemical cis,cis-muconic acid from renewable and abundant biomass aromatics.
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Affiliation(s)
- Avery C. Vilbert
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Wayne S. Kontur
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Derek Gille
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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5
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Bugg TDH. The chemical logic of enzymatic lignin degradation. Chem Commun (Camb) 2024; 60:804-814. [PMID: 38165282 PMCID: PMC10795516 DOI: 10.1039/d3cc05298b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
Lignin is an aromatic heteropolymer, found in plant cell walls as 20-30% of lignocellulose. It represents the most abundant source of renewable aromatic carbon in the biosphere, hence, if it could be depolymerised efficiently, then it would be a highly valuable source of renewable aromatic chemicals. However, lignin presents a number of difficulties for biocatalytic or chemocatalytic breakdown. Research over the last 10 years has led to the identification of new bacterial enzymes for lignin degradation, and the use of metabolic engineering to generate useful bioproducts from microbial lignin degradation. The aim of this article is to discuss the chemical mechanisms used by lignin-degrading enzymes and microbes to break down lignin, and to describe current methods for generating aromatic bioproducts from lignin using enzymes and engineered microbes.
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Affiliation(s)
- Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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6
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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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7
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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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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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9
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Kato R, Maekawa K, Kobayashi S, Hishiyama S, Katahira R, Nambo M, Higuchi Y, Kuatsjah E, Beckham GT, Kamimura N, Masai E. Stereoinversion via Alcohol Dehydrogenases Enables Complete Catabolism of β-1-Type Lignin-Derived Aromatic Isomers. Appl Environ Microbiol 2023; 89:e0017123. [PMID: 37184397 PMCID: PMC10304671 DOI: 10.1128/aem.00171-23] [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: 02/06/2023] [Accepted: 04/24/2023] [Indexed: 05/16/2023] Open
Abstract
Sphingobium sp. strain SYK-6 is an efficient aromatic catabolic bacterium that can consume all four stereoisomers of 1,2-diguaiacylpropane-1,3-diol (DGPD), which is a ring-opened β-1-type dimer. Recently, LdpA-mediated catabolism of erythro-DGPD was reported in SYK-6, but the catabolic pathway for threo-DGPD was as yet unknown. Here, we elucidated the catabolism of threo-DGPD, which proceeds through conversion to erythro-DGPD. When threo-DGPD was incubated with SYK-6, the Cα hydroxy groups of threo-DGPD (DGPD I and II) were initially oxidized to produce the Cα carbonyl form (DGPD-keto I and II). This initial oxidation step is catalyzed by Cα-dehydrogenases, which belong to the short-chain dehydrogenase/reductase (SDR) family and are involved in the catabolism of β-O-4-type dimers. Analysis of seven candidate genes revealed that NAD+-dependent LigD and LigL are mainly involved in the conversion of DGPD I and II, respectively. Next, we found that DGPD-keto I and II were reduced to erythro-DGPD (DGPD III and IV) in the presence of NADPH. Genes involved in this reduction were sought from Cα-dehydrogenase and ldpA-neighboring SDR genes. The gene products of SLG_12690 (ldpC) and SLG_12640 (ldpB) catalyzed the NADPH-dependent conversion of DGPD-keto I to DGPD III and DGPD-keto II to DGPD IV, respectively. Mutational analysis further indicated that ldpC and ldpB are predominantly involved in the reduction of DGPD-keto. Together, these results demonstrate that SYK-6 harbors a comprehensive catabolic enzyme system to utilize all four β-1-type stereoisomers through successive oxidation and reduction reactions of the Cα hydroxy group of threo-DGPD with a net stereoinversion using multiple dehydrogenases. IMPORTANCE In many catalytic depolymerization processes of lignin polymers, aryl-ether bonds are selectively cleaved, leaving carbon-carbon bonds between aromatic units intact, including dimers and oligomers with β-1 linkages. Therefore, elucidating the catabolic system of β-1-type lignin-derived compounds will aid in the establishment of biological funneling of heterologous lignin-derived aromatic compounds to value-added products. Here, we found that threo-DGPD was converted by successive stereoselective oxidation and reduction at the Cα position by multiple alcohol dehydrogenases to erythro-DGPD, which is further catabolized. This system is very similar to that developed to obtain enantiopure alcohols from racemic alcohols by artificially combining two enantiocomplementary alcohol dehydrogenases. The results presented here demonstrate that SYK-6 has evolved to catabolize all four stereoisomers of DGPD by incorporating this stereoinversion system into its native β-1-type dimer catabolic system.
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Affiliation(s)
- Ryo Kato
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Kodai Maekawa
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Shota Kobayashi
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Shojiro Hishiyama
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Rui Katahira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Miki Nambo
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Yudai Higuchi
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Eugene Kuatsjah
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Gregg T. Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Naofumi Kamimura
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Eiji Masai
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
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10
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Alruwaili A, Rashid GMM, Sodré V, Mason J, Rehman Z, Menakath AK, Cheung D, Brown SP, Bugg TDH. Elucidation of microbial lignin degradation pathways using synthetic isotope-labelled lignin. RSC Chem Biol 2023; 4:47-55. [PMID: 36685258 PMCID: PMC9811514 DOI: 10.1039/d2cb00173j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
Abstract
Pathways by which the biopolymer lignin is broken down by soil microbes could be used to engineer new biocatalytic routes from lignin to renewable chemicals, but are currently not fully understood. In order to probe these pathways, we have prepared synthetic lignins containing 13C at the sidechain β-carbon. Feeding of [β-13C]-labelled DHP lignin to Rhodococcus jostii RHA1 has led to the incorporation of 13C label into metabolites oxalic acid, 4-hydroxyphenylacetic acid, and 4-hydroxy-3-methoxyphenylacetic acid, confirming that they are derived from lignin breakdown. We have identified a glycolate oxidase enzyme in Rhodococcus jostii RHA1 which is able to oxidise glycolaldehyde via glycolic acid to oxalic acid, thereby identifying a pathway for the formation of oxalic acid. R. jostii glycolate oxidase also catalyses the conversion of 4-hydroxyphenylacetic acid to 4-hydroxybenzoylformic acid, identifying another possible pathway to 4-hydroxybenzoylformic acid. Formation of labelled oxalic acid was also observed from [β-13C]-polyferulic acid, which provides experimental evidence in favour of a radical mechanism for α,β-bond cleavage of β-aryl ether units.
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Affiliation(s)
- Awatif Alruwaili
- Department of Chemistry, University of WarwickCoventryCV4 7ALUK+44(0)-2476-573018
| | - Goran M. M. Rashid
- Department of Chemistry, University of WarwickCoventryCV4 7ALUK+44(0)-2476-573018
| | - Victoria Sodré
- Department of Chemistry, University of WarwickCoventryCV4 7ALUK+44(0)-2476-573018
| | - James Mason
- Department of Chemistry, University of WarwickCoventryCV4 7ALUK+44(0)-2476-573018
| | - Zainab Rehman
- Department of Physics, University of WarwickCoventryCV4 7ALUK
| | | | - David Cheung
- Department of Physics, University of WarwickCoventryCV4 7ALUK
| | - Steven P. Brown
- Department of Physics, University of WarwickCoventryCV4 7ALUK
| | - Timothy D. H. Bugg
- Department of Chemistry, University of WarwickCoventryCV4 7ALUK+44(0)-2476-573018
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11
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Liu ZH, Li BZ, Yuan JS, Yuan YJ. Creative biological lignin conversion routes toward lignin valorization. Trends Biotechnol 2022; 40:1550-1566. [PMID: 36270902 DOI: 10.1016/j.tibtech.2022.09.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/18/2022] [Accepted: 09/22/2022] [Indexed: 11/05/2022]
Abstract
Lignin, the largest renewable aromatic resource, is a promising alternative feedstock for the sustainable production of various chemicals, fuels, and materials. Despite this potential, lignin is characterized by heterogeneous and macromolecular structures that must be addressed. In this review, we present biological lignin conversion routes (BLCRs) that offer opportunities for overcoming these challenges, making lignin valorization feasible. Funneling heterogeneous aromatics via a 'biological funnel' offers a high-specificity bioconversion route for aromatic platform chemicals. The inherent aromaticity of lignin drives atom-economic functionalization routes toward aromatic natural product generation. By harnessing the ligninolytic capacities of specific microbial systems, powerful aromatic ring-opening routes can be developed to generate various value-added products. Thus, BLCRs hold the promise to make lignin valorization feasible and enable a lignocellulose-based bioeconomy.
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Affiliation(s)
- Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China.
| | - Joshua S Yuan
- Department of Energy, Environmental, and Chemical Engineering, The McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
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12
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Xu Z, Peng B, Kitata RB, Nicora CD, Weitz KK, Pu Y, Shi T, Cort JR, Ragauskas AJ, Yang B. Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:117. [PMID: 36316752 PMCID: PMC9620641 DOI: 10.1186/s13068-022-02214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Bacterial lignin degradation is believed to be primarily achieved by a secreted enzyme system. Effects of such extracellular enzyme systems on lignin structural changes and degradation pathways are still not clearly understood, which remains as a bottleneck in the bacterial lignin bioconversion process. RESULTS This study investigated lignin degradation using an isolated secretome secreted by Pseudomonas putida KT2440 that grew on glucose as the only carbon source. Enzyme assays revealed that the secretome harbored oxidase and peroxidase/Mn2+-peroxidase capacity and reached the highest activity at 120 h of the fermentation time. The degradation rate of alkali lignin was found to be only 8.1% by oxidases, but increased to 14.5% with the activation of peroxidase/Mn2+-peroxidase. Gas chromatography-mass spectrometry (GC-MS) and two-dimensional 1H-13C heteronuclear single-quantum coherence (HSQC) NMR analysis revealed that the oxidases exhibited strong C-C bond (β-β, β-5, and β-1) cleavage. The activation of peroxidases enhanced lignin degradation by stimulating C-O bond (β-O-4) cleavage, resulting in increased yields of aromatic monomers and dimers. Further mass spectrometry-based quantitative proteomics measurements comprehensively identified different groups of enzymes particularly oxidoreductases in P. putida secretome, including reductases, peroxidases, monooxygenases, dioxygenases, oxidases, and dehydrogenases, potentially contributed to the lignin degradation process. CONCLUSIONS Overall, we discovered that bacterial extracellular degradation of alkali lignin to vanillin, vanillic acid, and other lignin-derived aromatics involved a series of oxidative cleavage, catalyzed by active DyP-type peroxidase, multicopper oxidase, and other accessory enzymes. These results will guide further metabolic engineering design to improve the efficiency of lignin bioconversion.
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Affiliation(s)
- Zhangyang Xu
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA
| | - Bo Peng
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA
| | - Reta Birhanu Kitata
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Carrie D. Nicora
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Karl K. Weitz
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Yunqiao Pu
- grid.135519.a0000 0004 0446 2659Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Tujin Shi
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - John R. Cort
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Arthur J. Ragauskas
- grid.135519.a0000 0004 0446 2659Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA ,grid.411461.70000 0001 2315 1184Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA ,grid.411461.70000 0001 2315 1184Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN 37996 USA
| | - Bin Yang
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA ,grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
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13
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Increasing the Thermodynamic Driving Force of the Phosphofructokinase Reaction in
Clostridium thermocellum. Appl Environ Microbiol 2022; 88:e0125822. [PMID: 36286488 PMCID: PMC9680637 DOI: 10.1128/aem.01258-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability to control the distribution of thermodynamic driving force throughout a metabolic pathway is likely to be an important tool for metabolic engineering. The phosphofructokinase reaction is a key enzyme in Embden-Mayerhof-Parnas glycolysis and therefore improving the thermodynamic driving force of this reaction in
C. thermocellum
is believed to enable higher product titers.
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14
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Cai C, Xu Z, Li J, Zhou H, Jin M. Developing
Rhodococcus opacus
and
Sphingobium
sp. co‐culture systems for valorization of lignin‐derived dimers. Biotechnol Bioeng 2022; 119:3162-3177. [DOI: 10.1002/bit.28215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Chenggu Cai
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Zhaoxian Xu
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Jie Li
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Huarong Zhou
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Mingjie Jin
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
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15
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Debottlenecking 4-hydroxybenzoate hydroxylation in Pseudomonas putida KT2440 improves muconate productivity from p-coumarate. Metab Eng 2022; 70:31-42. [PMID: 34982998 DOI: 10.1016/j.ymben.2021.12.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/15/2021] [Accepted: 12/29/2021] [Indexed: 12/31/2022]
Abstract
The transformation of 4-hydroxybenzoate (4-HBA) to protocatechuate (PCA) is catalyzed by flavoprotein oxygenases known as para-hydroxybenzoate-3-hydroxylases (PHBHs). In Pseudomonas putida KT2440 (P. putida) strains engineered to convert lignin-related aromatic compounds to muconic acid (MA), PHBH activity is rate-limiting, as indicated by the accumulation of 4-HBA, which ultimately limits MA productivity. Here, we hypothesized that replacement of PobA, the native P. putida PHBH, with PraI, a PHBH from Paenibacillus sp. JJ-1b with a broader nicotinamide cofactor preference, could alleviate this bottleneck. Biochemical assays confirmed the strict preference of NADPH for PobA, while PraI can utilize either NADH or NADPH. Kinetic assays demonstrated that both PobA and PraI can utilize NADPH with comparable catalytic efficiency and that PraI also efficiently utilizes NADH at roughly half the catalytic efficiency. The X-ray crystal structure of PraI was solved and revealed absolute conservation of the active site architecture to other PHBH structures despite their differing cofactor preferences. To understand the effect in vivo, we compared three P. putida strains engineered to produce MA from p-coumarate (pCA), showing that expression of praI leads to lower 4-HBA accumulation and decreased NADP+/NADPH ratios relative to strains harboring pobA, indicative of a relieved 4-HBA bottleneck due to increased NADPH availability. In bioreactor cultivations, a strain exclusively expressing praI achieved a titer of 40 g/L MA at 100% molar yield and a productivity of 0.5 g/L/h. Overall, this study demonstrates the benefit of sampling readily available natural enzyme diversity for debottlenecking metabolic flux in an engineered strain for microbial conversion of lignin-derived compounds to value-added products.
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16
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Azubuike CC, Allemann MN, Michener JK. Microbial assimilation of lignin-derived aromatic compounds and conversion to value-added products. Curr Opin Microbiol 2021; 65:64-72. [PMID: 34775172 DOI: 10.1016/j.mib.2021.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 11/03/2022]
Abstract
Lignin is an abundant and sustainable source of aromatic compounds that can be converted to value-added products. However, lignin is underutilized, since depolymerization produces a complex mixture of aromatic compounds that is difficult to convert to a single product. Microbial conversion of mixed aromatic substrates provides a potential solution to this conversion challenge. Recent advances have expanded the range of lignin-derived aromatic substrates that can be assimilated and demonstrated efficient conversion via central metabolism to new potential products. The development of additional non-model microbial hosts and genetic tools for these hosts have accelerated engineering efforts. However, yields with real depolymerized lignin are still low, and additional work will be required to achieve viable conversion processes.
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Affiliation(s)
| | - Marco N Allemann
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Joshua K Michener
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
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17
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Kuatsjah E, Chan ACK, Katahira R, Haugen SJ, Beckham GT, Murphy MEP, Eltis LD. Structural and functional analysis of lignostilbene dioxygenases from Sphingobium sp. SYK-6. J Biol Chem 2021; 296:100758. [PMID: 33965373 PMCID: PMC8191317 DOI: 10.1016/j.jbc.2021.100758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 11/27/2022] Open
Abstract
Lignostilbene-α,β-dioxygenases (LSDs) are iron-dependent oxygenases involved in the catabolism of lignin-derived stilbenes. Sphingobium sp. SYK-6 contains eight LSD homologs with undetermined physiological roles. To investigate which homologs are involved in the catabolism of dehydrodiconiferyl alcohol (DCA), derived from β-5 linked lignin subunits, we heterologously produced the enzymes and screened their activities in lysates. The seven soluble enzymes all cleaved lignostilbene, but only LSD2, LSD3, and LSD4 exhibited high specific activity for 3-(4-hydroxy-3-(4-hydroxy-3-methoxystyryl)-5-methoxyphenyl) acrylate (DCA-S) relative to lignostilbene. LSD4 catalyzed the cleavage of DCA-S to 5-formylferulate and vanillin and cleaved lignostilbene and DCA-S (∼106 M−1 s−1) with tenfold greater specificity than pterostilbene and resveratrol. X-ray crystal structures of native LSD4 and the catalytically inactive cobalt-substituted Co-LSD4 at 1.45 Å resolution revealed the same fold, metal ion coordination, and edge-to-edge dimeric structure as observed in related enzymes. Key catalytic residues, Phe-59, Tyr-101, and Lys-134, were also conserved. Structures of Co-LSD4·vanillin, Co-LSD4·lignostilbene, and Co-LSD4·DCA-S complexes revealed that Ser-283 forms a hydrogen bond with the hydroxyl group of the ferulyl portion of DCA-S. This residue is conserved in LSD2 and LSD4 but is alanine in LSD3. Substitution of Ser-283 with Ala minimally affected the specificity of LSD4 for either lignostilbene or DCA-S. By contrast, substitution with phenylalanine, as occurs in LSD5 and LSD6, reduced the specificity of the enzyme for both substrates by an order of magnitude. This study expands our understanding of an LSD critical to DCA catabolism as well as the physiological roles of other LSDs and their determinants of substrate specificity.
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Affiliation(s)
- Eugene Kuatsjah
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada; 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
| | - Anson C K Chan
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Rui Katahira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Stefan J Haugen
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, 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
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada; BioProducts Institute, The University of British Columbia, Vancouver, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada; BioProducts Institute, The University of British Columbia, Vancouver, Canada.
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