101
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Ravi K, Abdelaziz OY, Nöbel M, García-Hidalgo J, Gorwa-Grauslund MF, Hulteberg CP, Lidén G. Bacterial conversion of depolymerized Kraft lignin. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:56. [PMID: 30923564 PMCID: PMC6420747 DOI: 10.1186/s13068-019-1397-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/08/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Lignin is a potential feedstock for microbial conversion into various chemicals. However, the microbial degradation rate of native or technical lignin is low, and chemical depolymerization is needed to obtain reasonable conversion rates. In the current study, nine bacterial strains belonging to the Pseudomonas and Rhodococcus genera were evaluated for their ability to grow on alkaline-treated softwood lignin as a sole carbon source. RESULTS Pseudomonas fluorescens DSM 50090 and Rhodococcus opacus DSM1069 showed the best growth of the tested species on plates with lignin. Further evaluation of P. fluorescens and R. opacus was made in liquid cultivations with depolymerized softwood Kraft lignin (DL) at a concentration of 1 g/L. Size-exclusion chromatography (SEC) showed that R. opacus consumed most of the available lower-molecular weight compounds (approximately 0.1-0.4 kDa) in the DL, but the weight distribution of larger fractions was almost unaffected. Importantly, the consumed compounds included guaiacol-one of the main monomers in the DL. SEC analysis of P. fluorescens culture broth, in contrast, did not show a large conversion of low-molecular weight compounds, and guaiacol remained unconsumed. However, a significant shift in molecular weight distribution towards lower average weights was seen after cultivation with P. fluorescens. CONCLUSIONS Rhodococcus opacus and P. fluorescens were identified as two potential microbial candidates for the conversion/consumption of base-catalyzed depolymerized lignin, acting on low- and high-molecular weight lignin fragments, respectively. These findings will be of relevance for designing bioconversion of softwood Kraft lignin.
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Affiliation(s)
- Krithika Ravi
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Omar Y. Abdelaziz
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Matthias Nöbel
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
- Present Address: Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
| | - Javier García-Hidalgo
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Marie F. Gorwa-Grauslund
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | | | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
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102
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García-Hidalgo J, Ravi K, Kuré LL, Lidén G, Gorwa-Grauslund M. Identification of the two-component guaiacol demethylase system from Rhodococcus rhodochrous and expression in Pseudomonas putida EM42 for guaiacol assimilation. AMB Express 2019; 9:34. [PMID: 30859469 PMCID: PMC6411806 DOI: 10.1186/s13568-019-0759-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/27/2019] [Indexed: 12/03/2022] Open
Abstract
A diversity of softwood lignin depolymerization processes yield guaiacol as the main low molecular weight product. This key aromatic compound can be utilized as a carbon source by several microbial species, most of which are Gram positive bacteria. Microbial degradation of guaiacol is known to proceed initially via demethylation to catechol, and this reaction is catalyzed by cytochrome P450 monooxygenases. These enzymes typically require a set of redox partner proteins, whose number and identities were not described until very recently in the case of guaiacol. In this work we identified two proteins involved in guaiacol demethylation by the actinomycete Rhodococcus rhodochrous. Additionally, we constructed four different polycistronic operons carrying combinations of putative redox partners of this guaiacol demethylation system in an inducible expression plasmid that was introduced into the Gram negative host Pseudomonas putida EM42, and the guaiacol consumption dynamics of each resulting strain were analyzed. All the polycistronic operons, expressing a cytochrome P450 together with a putative ferredoxin reductase from R. rhodochrous and putative ferredoxins from R. rhodochrous or Amycolatopsis ATCC 39116 enabled P. putida EM42 to metabolize and grow on guaiacol as the sole carbon source.
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103
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Kreis W, Munkert J. Exploiting enzyme promiscuity to shape plant specialized metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1435-1445. [PMID: 30715457 DOI: 10.1093/jxb/erz025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/11/2018] [Accepted: 01/11/2019] [Indexed: 05/23/2023]
Abstract
The amazing variability of plant metabolism and its rapid divergence during evolution pose fundamental questions as to the driving forces, mechanisms, and players in metabolic differentiation. This review examines concepts that help us understand adaptive pathway evolution, with a particular emphasis on plant specialized metabolism, previously often termed secondary metabolism. Following a general introduction to pathway and metabolite evolution, the focus is directed to enzyme promiscuity and its classification. Promiscuous enzymes (or substrates), 'silent' elements of the metabolome, and the 'underground metabolism' may be used and combined to evolve 'new' metabolic pathways. It appears that new pathways rarely appear from scratch, but instead emerge from 'floppy' enzymes and elements of a 'messy' metabolism, and in this way a range of metabolites is generated, some of which may provide benefits to the plant.
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Affiliation(s)
| | - Jennifer Munkert
- Friedrich-Alexander University Erlangen-Nürnberg, Department of Biology, Division of Pharmaceutical Biology, Erlangen, Germany
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104
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Cytochrome P450 Monooxygenases in Biotechnology and Synthetic Biology. Trends Biotechnol 2019; 37:882-897. [PMID: 30739814 DOI: 10.1016/j.tibtech.2019.01.001] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/28/2018] [Accepted: 01/03/2019] [Indexed: 12/14/2022]
Abstract
Cytochromes P450 (P450 or CYP) are heme-containing enzymes that catalyze the introduction of one atom of molecular oxygen into nonactivated C-H bonds, often in a regio- and stereoselective manner. This ability, combined with a tremendous number of accepted substrates, makes P450s powerful biocatalysts. Sixty years after their discovery, P450 systems are recognized as essential bio-bricks in synthetic biology approaches to enable production of high-value complex molecules in recombinant hosts. Recent impressive results in protein engineering led to P450s with tailored properties that are even able to catalyze abiotic reactions. The introduction of P450s in artificial multi-enzymatic cascades reactions and chemo-enzymatic processes offers exciting future perspectives to access novel compounds that cannot be synthesized by nature or by chemical routes.
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105
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Xu Z, Lei P, Zhai R, Wen Z, Jin M. Recent advances in lignin valorization with bacterial cultures: microorganisms, metabolic pathways, and bio-products. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:32. [PMID: 30815030 PMCID: PMC6376720 DOI: 10.1186/s13068-019-1376-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/08/2019] [Indexed: 05/09/2023]
Abstract
Lignin is the most abundant aromatic substrate on Earth and its valorization technologies are still under developed. Depolymerization and fragmentation are the predominant preparatory strategies for valorization of lignin to chemicals and fuels. However, due to the structural heterogeneity of lignin, depolymerization and fragmentation typically result in diverse product species, which require extensive separation and purification procedures to obtain target products. For lignin valorization, bacterial-based systems have attracted increasing attention because of their diverse metabolisms, which can be used to funnel multiple lignin-based compounds into specific target products. Here, recent advances in lignin valorization using bacteria are critically reviewed, including lignin-degrading bacteria that are able to degrade lignin and use lignin-associated aromatics, various associated metabolic pathways, and application of bacterial cultures for lignin valorization. This review will provide insight into the recent breakthroughs and future trends of lignin valorization based on bacterial systems.
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Affiliation(s)
- Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
| | - Peng Lei
- Nanjing Institute for Comprehensive Utilization of Wild Plants, Nanjing, 211111 China
| | - Rui Zhai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
| | - Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
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106
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Zhu D, Si H, Zhang P, Geng A, Zhang W, Yang B, Qian WJ, Gabriel M, Sun J. Genomics and biochemistry investigation on the metabolic pathway of milled wood and alkali lignin-derived aromatic metabolites of Comamonas serinivorans SP-35. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:338. [PMID: 30603046 PMCID: PMC6307125 DOI: 10.1186/s13068-018-1341-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 12/15/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND The efficient depolymerization and utilization of lignin are one of the most important goals for the renewable use of lignocelluloses. The degradation and complete mineralization of lignin by bacteria represent a key step for carbon recycling in land ecosystems as well. However, many aspects of this process remain unclear, for example, the complex network of metabolic pathways involved in the degradation of lignin and the catabolic pathway of intermediate aromatic metabolites. To address these subjects, we characterized the deconstruction and mineralization of lignin with milled wood lignin (MWL, the most representative molecule of lignin in its native state) and alkali lignin (AL), and elucidated metabolic pathways of their intermediate metabolites by a bacterium named Comamonas serinivorans SP-35. RESULTS The degradation rate of MWL reached 30.9%, and its particle size range was decreased from 6 to 30 µm to 2-4 µm-when cultured with C. serinivorans SP35 over 7 days. FTIR analysis showed that the C-C and C-O-C bonds between the phenyl propane structures of lignin were oxidized and cleaved and the side chain structure was modified. More than twenty intermediate aromatic metabolites were identified in the MWL and AL cultures based on GC-MS analysis. Through genome sequencing and annotation, and from GC-MS analysis, 93 genes encoding 33 enzymes and 5 regulatory factors that may be involved in lignin degradation were identified and more than nine metabolic pathways of lignin and its intermediates were predicted. Of particular note is that the metabolic pathway to form the powerful antioxidant 3,4-dihydroxyphenylglycol is described for the first time in bacteria. CONCLUSION Elucidation of the β-aryl ether cleavage pathway in the strain SP-35 indicates that the β-aryl ether catabolic system is not only present in the family of Sphingomonadaceae, but also other species of bacteria kingdom. These newly elucidated catabolic pathways of lignin in strain SP-35 and the enzymes responsible for them provide exciting biotechnological opportunities for lignin valorization in future.
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Affiliation(s)
- Daochen Zhu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu China
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Haibing Si
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu China
| | - Peipei Zhang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu China
| | - Alei Geng
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Bin Yang
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA 99354 USA
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Murillo Gabriel
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu China
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107
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Lanfranchi E, Trajković M, Barta K, de Vries JG, Janssen DB. Exploring the Selective Demethylation of Aryl Methyl Ethers with a
Pseudomonas
Rieske Monooxygenase. Chembiochem 2018; 20:118-125. [DOI: 10.1002/cbic.201800594] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Elisa Lanfranchi
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
- Present address: School of Food and Nutritional Science SciencesUniversity College Cork College Road Cork T12 YN60 Republic of Ireland
| | - Miloš Trajković
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
| | - Katalin Barta
- Synthetic Organic ChemistryStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
| | - Johannes G. de Vries
- Synthetic Organic ChemistryStratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
- Leibniz-Institut für Katalyse e.V. Albert-Einstein-Strasse 29a 18059 Rostock Germany
| | - Dick B. Janssen
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of Groningen Nijenborgh 4 9726 AG Groningen The Netherlands
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108
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Specificity and mechanism of carbohydrate demethylation by cytochrome P450 monooxygenases. Biochem J 2018; 475:3875-3886. [PMID: 30404923 PMCID: PMC6292453 DOI: 10.1042/bcj20180762] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/02/2018] [Accepted: 11/06/2018] [Indexed: 01/21/2023]
Abstract
Degradation of carbohydrates by bacteria represents a key step in energy metabolism that can be inhibited by methylated sugars. Removal of methyl groups, which is critical for further processing, poses a biocatalytic challenge because enzymes need to overcome a high energy barrier. Our structural and computational analysis revealed how a member of the cytochrome P450 family evolved to oxidize a carbohydrate ligand. Using structural biology, we ascertained the molecular determinants of substrate specificity and revealed a highly specialized active site complementary to the substrate chemistry. Invariance of the residues involved in substrate recognition across the subfamily suggests that they are critical for enzyme function and when mutated, the enzyme lost substrate recognition. The structure of a carbohydrate-active P450 adds mechanistic insight into monooxygenase action on a methylated monosaccharide and reveals the broad conservation of the active site machinery across the subfamily.
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109
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Arora NK, Fatima T, Mishra I, Verma M, Mishra J, Mishra V. Environmental sustainability: challenges and viable solutions. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s42398-018-00038-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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110
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Zhang R, Li C, Wang J, Yan Y. Microbial Ligninolysis: Toward a Bottom-Up Approach for Lignin Upgrading. Biochemistry 2018; 58:1501-1510. [DOI: 10.1021/acs.biochem.8b00920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ruihua Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Chenyi Li
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Jian Wang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
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111
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Tumen-Velasquez M, Johnson CW, Ahmed A, Dominick G, Fulk EM, Khanna P, Lee SA, Schmidt AL, Linger JG, Eiteman MA, Beckham GT, Neidle EL. Accelerating pathway evolution by increasing the gene dosage of chromosomal segments. Proc Natl Acad Sci U S A 2018; 115:7105-7110. [PMID: 29915086 PMCID: PMC6142232 DOI: 10.1073/pnas.1803745115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Experimental evolution is a critical tool in many disciplines, including metabolic engineering and synthetic biology. However, current methods rely on the chance occurrence of a key step that can dramatically accelerate evolution in natural systems, namely increased gene dosage. Our studies sought to induce the targeted amplification of chromosomal segments to facilitate rapid evolution. Since increased gene dosage confers novel phenotypes and genetic redundancy, we developed a method, Evolution by Amplification and Synthetic Biology (EASy), to create tandem arrays of chromosomal regions. In Acinetobacter baylyi, EASy was demonstrated on an important bioenergy problem, the catabolism of lignin-derived aromatic compounds. The initial focus on guaiacol (2-methoxyphenol), a common lignin degradation product, led to the discovery of Amycolatopsis genes (gcoAB) encoding a cytochrome P450 enzyme that converts guaiacol to catechol. However, chromosomal integration of gcoAB in Pseudomonas putida or A. baylyi did not enable guaiacol to be used as the sole carbon source despite catechol being a growth substrate. In ∼1,000 generations, EASy yielded alleles that in single chromosomal copy confer growth on guaiacol. Different variants emerged, including fusions between GcoA and CatA (catechol 1,2-dioxygenase). This study illustrates the power of harnessing chromosomal gene amplification to accelerate the evolution of desirable traits.
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Affiliation(s)
| | | | - Alaa Ahmed
- Department of Microbiology, University of Georgia, Athens, GA 30602
| | - Graham Dominick
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401
| | - Emily M Fulk
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401
| | - Payal Khanna
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401
| | - Sarah A Lee
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602
| | - Alicia L Schmidt
- Department of Microbiology, University of Georgia, Athens, GA 30602
| | - Jeffrey G Linger
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401
| | - Mark A Eiteman
- Department of Microbiology, University of Georgia, Athens, GA 30602
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602
| | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401;
| | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, GA 30602;
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