1
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Willers VP, Beer B, Sieber V. Integrating Carbohydrate and C1 Utilization for Chemicals Production. CHEMSUSCHEM 2023; 16:e202202122. [PMID: 36520644 DOI: 10.1002/cssc.202202122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/14/2022] [Indexed: 06/17/2023]
Abstract
In the face of increasing mobility and energy demand, as well as the mitigation of climate change, the development of sustainable and environmentally friendly alternatives to fossil fuels will be one of the most important tasks facing humankind in the coming years. In order to initiate the transition from a petroleum-based economy to a new, greener future, biofuels and synthetic fuels have great potential as they can be adapted to already common processes. Thereby, especially synthetic fuels from CO2 and renewable energies are seen as the next big step for a sustainable and ecological life. In our study, we directly address the sustainable production of the most common biofuel, ethanol, and the highly interesting next-generation biofuel, isobutanol, from methanol and xylose, which are directly derivable from CO2 and lignocellulosic waste streams, respectively, such integrating synthetic fuel and biofuel production. After enzyme and reaction optimization, we succeeded in producing either 3 g L-1 ethanol or 2 g L-1 isobutanol from 7.5 g L-1 xylose and 1.6 g L-1 methanol. In our cell-free enzyme system, C1-compounds are efficiently combined and fixed by the key enzyme transketolase and converted to the intermediate pyruvate. This opens the way for a hybrid production of biofuels, platform chemicals and fine chemicals from CO2 and lignocellulosic waste streams as alternative to conventional routes depending solely either on CO2 or sugars.
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Affiliation(s)
- Vivian Pascal Willers
- Chair of Chemistry of Biogenic Resources, Technical University of Munich Campus Straubing, 94315, Straubing, Germany
| | - Barbara Beer
- Chair of Chemistry of Biogenic Resources, Technical University of Munich Campus Straubing, 94315, Straubing, Germany
- Current address: CASCAT GmbH, 94315, Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich Campus Straubing, 94315, Straubing, Germany
- Technical University of Munich, 94315, Straubing, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, 4072, Australia
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2
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Singh HB, Kang MK, Kwon M, Kim SW. Developing methylotrophic microbial platforms for a methanol-based bioindustry. Front Bioeng Biotechnol 2022; 10:1050740. [PMID: 36507257 PMCID: PMC9727194 DOI: 10.3389/fbioe.2022.1050740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022] Open
Abstract
Methanol, a relatively cheap and renewable single-carbon feedstock, has gained considerable attention as a substrate for the bio-production of commodity chemicals. Conventionally produced from syngas, along with emerging possibilities of generation from methane and CO2, this C1 substrate can serve as a pool for sequestering greenhouse gases while supporting a sustainable bio-economy. Methylotrophic organisms, with the inherent ability to use methanol as the sole carbon and energy source, are competent candidates as platform organisms. Accordingly, methanol bioconversion pathways have been an attractive target for biotechnological and bioengineering interventions in developing microbial cell factories. This review summarizes the recent advances in methanol-based production of various bulk and value-added chemicals exploiting the native and synthetic methylotrophic organisms. Finally, the current challenges and prospects of streamlining these methylotrophic platforms are discussed.
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Affiliation(s)
- Hawaibam Birla Singh
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, South Korea
| | - Min-Kyoung Kang
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, South Korea
| | - Moonhyuk Kwon
- Division of Life Science, ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, South Korea,*Correspondence: Moonhyuk Kwon, ; Seon-Won Kim,
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, South Korea,*Correspondence: Moonhyuk Kwon, ; Seon-Won Kim,
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3
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Johnston ML, Bonett EM, DeColli AA, Freel Meyers CL. Antibacterial Target DXP Synthase Catalyzes the Cleavage of d-Xylulose 5-Phosphate: a Study of Ketose Phosphate Binding and Ketol Transfer Reaction. Biochemistry 2022; 61:1810-1823. [PMID: 35998648 PMCID: PMC9531112 DOI: 10.1021/acs.biochem.2c00274] [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] [Indexed: 11/28/2022]
Abstract
The bacterial enzyme 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) catalyzes the formation of DXP from pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) in a thiamin diphosphate (ThDP)-dependent manner. In addition to its role in isoprenoid biosynthesis, DXP is required for ThDP and pyridoxal phosphate biosynthesis. Due to its function as a branch-point enzyme and its demonstrated substrate and catalytic promiscuity, we hypothesize that DXPS could be key for bacterial adaptation in the dynamic metabolic landscape during infection. Prior work in the Freel Meyers laboratory has illustrated that DXPS displays relaxed specificity toward donor and acceptor substrates and varies acceptor specificity according to the donor used. We have reported that DXPS forms dihydroxyethyl (DHE)ThDP from ketoacid or aldehyde donor substrates via decarboxylation and deprotonation, respectively. Here, we tested other DHE donors and found that DXPS cleaves d-xylulose 5-phosphate (X5P) at C2-C3, producing DHEThDP through a third mechanism involving d-GAP elimination. We interrogated DXPS-catalyzed reactions using X5P as a donor substrate and illustrated (1) production of a semi-stable enzyme-bound intermediate and (2) O2, H+, and d-erythrose 4-phosphate act as acceptor substrates, highlighting a new transketolase-like activity of DXPS. Furthermore, we examined X5P binding to DXPS and suggest that the d-GAP binding pocket plays a crucial role in X5P binding and turnover. Overall, this study reveals a ketose-cleavage reaction catalyzed by DXPS, highlighting the remarkable flexibility for donor substrate usage by DXPS compared to other C-C bond-forming enzymes.
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Affiliation(s)
- Melanie L. Johnston
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eucolona M. Bonett
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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4
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Zhan C, Li X, Yang Y, Nielsen J, Bai Z, Chen Y. Strategies and challenges with the microbial conversion of methanol to high-value chemicals. Biotechnol Bioeng 2021; 118:3655-3668. [PMID: 34133022 DOI: 10.1002/bit.27862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 05/25/2021] [Accepted: 06/10/2021] [Indexed: 01/03/2023]
Abstract
As alternatives to traditional fermentation substrates, methanol (CH3 OH), carbon dioxide (CO2 ) and methane (CH4 ) represent promising one-carbon (C1) sources that are readily available at low-cost and share similar metabolic pathway. Of these C1 compounds, methanol is used as a carbon and energy source by native methylotrophs, and can be obtained from CO2 and CH4 by chemical catalysis. Therefore, constructing and rewiring methanol utilization pathways may enable the use of one-carbon sources for microbial fermentations. Recent bioengineering efforts have shown that both native and nonnative methylotrophic organisms can be engineered to convert methanol, together with other carbon sources, into biofuels and other commodity chemicals. However, many challenges remain and must be overcome before industrial-scale bioprocessing can be established using these engineered cell refineries. Here, we provide a comprehensive summary and comparison of methanol metabolic pathways from different methylotrophs, followed by a review of recent progress in engineering methanol metabolic pathways in vitro and in vivo to produce chemicals. We discuss the major challenges associated with establishing efficient methanol metabolic pathways in microbial cells, and propose improved designs for future engineering.
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Affiliation(s)
- Chunjun Zhan
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Xiaowei Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.,BioInnovation Institute, Copenhagen N, Denmark
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
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5
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Nattermann M, Burgener S, Pfister P, Chou A, Schulz L, Lee SH, Paczia N, Zarzycki J, Gonzalez R, Erb TJ. Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism. ACS Catal 2021; 11:5396-5404. [PMID: 34484855 PMCID: PMC8411744 DOI: 10.1021/acscatal.1c01237] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/06/2021] [Indexed: 12/15/2022]
Abstract
![]()
One of the biggest
challenges to realize a circular carbon economy
is the synthesis of complex carbon compounds from one-carbon (C1)
building blocks. Since the natural solution space of C1–C1
condensations is limited to highly complex enzymes, the development
of more simple and robust biocatalysts may facilitate the engineering
of C1 assimilation routes. Thiamine diphosphate-dependent enzymes
harbor great potential for this task, due to their ability to create
C–C bonds. Here, we employed structure-guided iterative saturation
mutagenesis to convert oxalyl-CoA decarboxylase (OXC) from Methylobacterium extorquens into a glycolyl-CoA synthase
(GCS) that allows for the direct condensation of the two C1 units
formyl-CoA and formaldehyde. A quadruple variant MeOXC4 showed a 100 000-fold
switch between OXC and GCS activities, a 200-fold increase in the
GCS activity compared to the wild type, and formaldehyde affinity
that is comparable to natural formaldehyde-converting enzymes. Notably,
MeOCX4 outcompetes all other natural and engineered enzymes for C1–C1
condensations by more than 40-fold in catalytic efficiency and is
highly soluble in Escherichia coli.
In addition to the increased GCS activity, MeOXC4 showed up to 300-fold
higher activity than the wild type toward a broad range of carbonyl
acceptor substrates. When applied in vivo, MeOXC4 enables the production
of glycolate from formaldehyde, overcoming the current bottleneck
of C1–C1 condensation in whole-cell bioconversions and paving
the way toward synthetic C1 assimilation routes in vivo.
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Affiliation(s)
- Maren Nattermann
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Simon Burgener
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Pascal Pfister
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Alexander Chou
- Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, Florida 33620, United States
| | - Luca Schulz
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Seung Hwan Lee
- Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, Florida 33620, United States
| | - Nicole Paczia
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Jan Zarzycki
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Ramon Gonzalez
- Department of Chemical and Biomedical Engineering, University of South Florida, Tampa, Florida 33620, United States
| | - Tobias J. Erb
- Department of Biochemistry & Synthetic Metabolism, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), 35043 Marburg, Germany
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6
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Yang Q, Guo X, Liu Y, Jiang H. Biocatalytic C-C Bond Formation for One Carbon Resource Utilization. Int J Mol Sci 2021; 22:ijms22041890. [PMID: 33672882 PMCID: PMC7918591 DOI: 10.3390/ijms22041890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/31/2021] [Accepted: 02/05/2021] [Indexed: 12/22/2022] Open
Abstract
The carbon-carbon bond formation has always been one of the most important reactions in C1 resource utilization. Compared to traditional organic synthesis methods, biocatalytic C-C bond formation offers a green and potent alternative for C1 transformation. In recent years, with the development of synthetic biology, more and more carboxylases and C-C ligases have been mined and designed for the C1 transformation in vitro and C1 assimilation in vivo. This article presents an overview of C-C bond formation in biocatalytic C1 resource utilization is first provided. Sets of newly mined and designed carboxylases and ligases capable of catalyzing C-C bond formation for the transformation of CO2, formaldehyde, CO, and formate are then reviewed, and their catalytic mechanisms are discussed. Finally, the current advances and the future perspectives for the development of catalysts for C1 resource utilization are provided.
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Affiliation(s)
- Qiaoyu Yang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Q.Y.); (X.G.)
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxian Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Q.Y.); (X.G.)
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yuwan Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Q.Y.); (X.G.)
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Correspondence: (Y.L.); (H.J.)
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Q.Y.); (X.G.)
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Correspondence: (Y.L.); (H.J.)
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7
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De Simone A, Vicente CM, Peiro C, Gales L, Bellvert F, Enjalbert B, Heux S. Mixing and matching methylotrophic enzymes to design a novel methanol utilization pathway in E. coli. Metab Eng 2020; 61:315-325. [PMID: 32687991 DOI: 10.1016/j.ymben.2020.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 01/23/2023]
Abstract
One-carbon (C1) compounds, such as methanol, have recently gained attention as alternative low-cost and non-food feedstocks for microbial bioprocesses. Considerable research efforts are thus currently focused on the generation of synthetic methylotrophs by transferring methanol assimilation pathways into established bacterial production hosts. In this study, we used an iterative combination of dry and wet approaches to design, implement and optimize this metabolic trait in the most common chassis, E. coli. Through in silico modelling, we designed a new route that "mixed and matched" two methylotrophic enzymes: a bacterial methanol dehydrogenase (Mdh) and a dihydroxyacetone synthase (Das) from yeast. To identify the best combination of enzymes to introduce into E. coli, we built a library of 266 pathway variants containing different combinations of Mdh and Das homologues and screened it using high-throughput 13C-labeling experiments. The highest level of incorporation of methanol into central metabolism intermediates (e.g. 22% into the PEP), was obtained using a variant composed of a Mdh from A. gerneri and a codon-optimized version of P. angusta Das. Finally, the activity of this new synthetic pathway was further improved by engineering strategic metabolic targets identified using omics and modelling approaches. The final synthetic strain had 1.5 to 5.9 times higher methanol assimilation in intracellular metabolites and proteinogenic amino acids than the starting strain did. Broadening the repertoire of methanol assimilation pathways is one step further toward synthetic methylotrophy in E. coli.
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Affiliation(s)
- A De Simone
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - C M Vicente
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - C Peiro
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - L Gales
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France; MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France
| | - F Bellvert
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France; MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France
| | - B Enjalbert
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - S Heux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
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8
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Engineering unnatural methylotrophic cell factories for methanol-based biomanufacturing: Challenges and opportunities. Biotechnol Adv 2020; 39:107467. [DOI: 10.1016/j.biotechadv.2019.107467] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 12/14/2022]
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9
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Genome Sequence of
Rhodococcus
sp. Strain RD6.2 DSM 46800, a Methanesulfonate-Degrading Strain. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00730-15. [PMID: 26184930 PMCID: PMC4505118 DOI: 10.1128/genomea.00730-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The complete genome sequence of a methanesulfonate-degrading strain, Rhodococcus sp. strain RD6.2 DSM 46800, which was isolated from a brackish marsh sediment sample, is described here. This is the first reported genome of a nonproteobacterial strain using methanesulfonate (MSA) as a sole source of carbon and energy, which does not possess the conventional MSA-monooxygenase (MSAMO).
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10
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Markert B, Stolzenberger J, Brautaset T, Wendisch VF. Characterization of two transketolases encoded on the chromosome and the plasmid pBM19 of the facultative ribulose monophosphate cycle methylotroph Bacillus methanolicus. BMC Microbiol 2014; 14:7. [PMID: 24405865 PMCID: PMC3905653 DOI: 10.1186/1471-2180-14-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 01/07/2014] [Indexed: 11/19/2022] Open
Abstract
Background Transketolase (TKT) is a key enzyme of the pentose phosphate pathway (PPP), the Calvin cycle and the ribulose monophosphate (RuMP) cycle. Bacillus methanolicus is a facultative RuMP pathway methylotroph. B. methanolicus MGA3 harbors two genes putatively coding for TKTs; one located on the chromosome (tktC) and one located on the natural occurring plasmid pBM19 (tktP). Results Both enzymes were produced in recombinant Escherichia coli, purified and shown to share similar biochemical parameters in vitro. They were found to be active as homotetramers and require thiamine pyrophosphate for catalytic activity. The inactive apoform of the TKTs, yielded by dialysis against buffer containing 10 mM EDTA, could be reconstituted most efficiently with Mn2+ and Mg2+. Both TKTs were thermo stable at physiological temperature (up to 65°C) with the highest activity at neutral pH. Ni2+, ATP and ADP significantly inhibited activity of both TKTs. Unlike the recently characterized RuMP pathway enzymes fructose 1,6-bisphosphate aldolase (FBA) and fructose 1,6-bisphosphatase/sedoheptulose 1,7-bisphosphatase (FBPase/SBPase) from B. methanolicus MGA3, both TKTs exhibited similar kinetic parameters although they only share 76% identical amino acids. The kinetic parameters were determined for the reaction with the substrates xylulose 5-phosphate (TKTC: kcat/KM: 264 s-1 mM-1; TKTP: kcat/KM: 231 s-1 mM) and ribulose 5-phosphate (TKTC: kcat/KM: 109 s-1 mM; TKTP: kcat/KM: 84 s-1 mM) as well as for the reaction with the substrates glyceraldehyde 3-phosphate (TKTC: kcat/KM: 108 s-1 mM; TKTP: kcat/KM: 71 s-1 mM) and fructose 6-phosphate (TKTC kcat/KM: 115 s-1 mM; TKTP: kcat/KM: 448 s-1 mM). Conclusions Based on the kinetic parameters no major TKT of B. methanolicus could be determined. Increased expression of tktP, but not of tktC during growth with methanol [J Bacteriol 188:3063–3072, 2006] argues for TKTP being the major TKT relevant in the RuMP pathway. Neither TKT exhibited activity as dihydroxyacetone synthase, as found in methylotrophic yeast, or as the evolutionary related 1-deoxyxylulose-5-phosphate synthase. The biological significance of the two TKTs for B. methanolicus methylotrophy is discussed.
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Affiliation(s)
| | | | | | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr, 25, 33615 Bielefeld, Germany.
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11
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DeLorenzo S, Bräuer SL, Edgmont CA, Herfort L, Tebo BM, Zuber P. Ubiquitous dissolved inorganic carbon assimilation by marine bacteria in the Pacific Northwest coastal ocean as determined by stable isotope probing. PLoS One 2012; 7:e46695. [PMID: 23056406 PMCID: PMC3463544 DOI: 10.1371/journal.pone.0046695] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Accepted: 09/06/2012] [Indexed: 11/25/2022] Open
Abstract
In order to identify bacteria that assimilate dissolved inorganic carbon (DIC) in the northeast Pacific Ocean, stable isotope probing (SIP) experiments were conducted on water collected from 3 different sites off the Oregon and Washington coasts in May 2010, and one site off the Oregon Coast in September 2008 and March 2009. Samples were incubated in the dark with 2 mM (13)C-NaHCO(3), doubling the average concentration of DIC typically found in the ocean. Our results revealed a surprising diversity of marine bacteria actively assimilating DIC in the dark within the Pacific Northwest coastal waters, indicating that DIC fixation is relevant for the metabolism of different marine bacterial lineages, including putatively heterotrophic taxa. Furthermore, dark DIC-assimilating assemblages were widespread among diverse bacterial classes. Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes dominated the active DIC-assimilating communities across the samples. Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia were also implicated in DIC assimilation. Alteromonadales and Oceanospirillales contributed significantly to the DIC-assimilating Gammaproteobacteria within May 2010 clone libraries. 16S rRNA gene sequences related to the sulfur-oxidizing symbionts Arctic96BD-19 were observed in all active DIC assimilating clone libraries. Among the Alphaproteobacteria, clones related to the ubiquitous SAR11 clade were found actively assimilating DIC in all samples. Although not a dominant contributor to our active clone libraries, Betaproteobacteria, when identified, were predominantly comprised of Burkholderia. DIC-assimilating bacteria among Deltaproteobacteria included members of the SAR324 cluster. Our research suggests that DIC assimilation is ubiquitous among many bacterial groups in the coastal waters of the Pacific Northwest marine environment and may represent a significant metabolic process.
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Affiliation(s)
- Suzanne DeLorenzo
- Center for Coastal Margin Observation & Prediction and Division of Environmental & Biomolecular Systems, Oregon Health & Science University, Beaverton, Oregon, United States of America.
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12
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Kim YM, Park SW. Microbiology and genetics of CO utilization in mycobacteria. Antonie van Leeuwenhoek 2012; 101:685-700. [PMID: 22277984 DOI: 10.1007/s10482-012-9698-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 01/06/2012] [Indexed: 11/29/2022]
Abstract
Although extensive studies on the oxidation of carbon monoxide (CO) in aerobic carboxydotrophic bacteria have been carried out for over 30 years, utilization of CO as a source of carbon and energy by mycobacteria was recognized only recently. Studies on pathogenic and nonpathogenic mycobacteria have revealed that the basis for CO utilization in these bacteria is different in many aspects from that of other aerobic carboxydobacteria. We review the basis for CO utilization in mycobacterial carboxydobacteria, which is unique from physiological, biochemical, molecular, genetic and phylogenetic points of view.
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Affiliation(s)
- Young Min Kim
- Molecular Microbiology Laboratory, Department of Systems Biology, Yonsei University, Seoul, Korea.
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13
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Molecular cloning, purification, and characterization of a superoxide dismutase from a fast-growing Mycobacterium sp. Strain JC1 DSM 3803. J Microbiol 2011; 49:399-406. [DOI: 10.1007/s12275-011-1046-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 02/16/2011] [Indexed: 10/18/2022]
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15
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Park H, Lee H, Ro YT, Kim YM. Identification and functional characterization of a gene for the methanol : N,N'-dimethyl-4-nitrosoaniline oxidoreductase from Mycobacterium sp. strain JC1 (DSM 3803). MICROBIOLOGY-SGM 2009; 156:463-471. [PMID: 19875438 DOI: 10.1099/mic.0.034124-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mycobacterium sp. strain JC1 is able to grow on methanol as a sole source of carbon and energy using methanol : N,N'-dimethyl-4-nitrosoaniline oxidoreductase (MDO) as a key enzyme for primary methanol oxidation. Purified MDO oxidizes ethanol and formaldehyde as well as methanol. The Mycobacterium sp. strain JC1 gene for MDO (mdo) was cloned, sequenced, and determined to have an open reading frame of 1272 bp. Northern blot and promoter analysis revealed that mdo transcription was induced in cells grown in the presence of methanol. Northern blotting together with RT-PCR also showed that the mdo gene was transcribed as monocistronic mRNA. Primer extension analysis revealed that the transcriptional start site of the mdo gene is located 21 bp upstream of the mdo start codon. An mdo-deficient mutant of Mycobacterium sp. strain JC1 did not grow with methanol as a sole source of carbon and energy.
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Affiliation(s)
- Hyuk Park
- Molecular Microbiology Laboratory, Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Hyunil Lee
- Laboratory of Biochemistry, Graduate School of Medicine, Konkuk University, Seoul 143-701, Republic of Korea
| | - Young T Ro
- Laboratory of Biochemistry, Graduate School of Medicine, Konkuk University, Seoul 143-701, Republic of Korea
| | - Young M Kim
- Molecular Microbiology Laboratory, Department of Biology, Yonsei University, Seoul 120-749, Republic of Korea
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Zheng Y, Chen X, Shen Y. Commodity Chemicals Derived from Glycerol, an Important Biorefinery Feedstock. Chem Rev 2008; 108:5253-77. [DOI: 10.1021/cr068216s] [Citation(s) in RCA: 285] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yuguo Zheng
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou 310032, Peopleʼs Republic of China
| | - Xiaolong Chen
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou 310032, Peopleʼs Republic of China
| | - Yinchu Shen
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou 310032, Peopleʼs Republic of China
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17
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Seo JG, Park SW, Park H, Kim SY, Ro YT, Kim E, Cho JW, Kim YM. Cloning, characterization and expression of a gene encoding dihydroxyacetone synthase in Mycobacterium sp. strain JC1 DSM 3803. MICROBIOLOGY-SGM 2008; 153:4174-4182. [PMID: 18048931 DOI: 10.1099/mic.0.2007/011965-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dihydroxyacetone synthase (DHAS) is a key enzyme involved in the assimilation of methanol in Mycobacterium sp. strain JC1 DSM 3803. The structural gene encoding DHAS in Mycobacterium sp. strain JC1 was cloned using random-primed probes synthesized after PCR with synthetic primers based on the amino acid sequences conserved in two yeast DHASs and several transketolases. The cloned gene, dasS, had an ORF of 2193 nt, encoding a protein with a calculated molecular mass of 78,197 Da. The deduced amino acid sequence of dasS contained an internal sequence of Mycobacterium sp. strain JC1 DHAS and exhibited 29.2 and 27.3 % identity with those of Candida boidinii and Hansenula polymorpha enzymes, respectively. Escherichia coli transformed with the cloned gene produced a novel protein with a molecular mass of approximately 78 kDa, which cross-reacted with anti-DHAS antiserum and exhibited DHAS activity. Primer-extension analysis revealed that the transcriptional start site of the gene was the nucleotide A located 31 bp upstream from the dasS start codon. RT-PCR showed that dasS was transcribed as a monocistronic message. Northern hybridization and beta-galactosidase assay with the putative promoter region of dasS revealed that the gene was transcribed only in cells growing on methanol. The expression of dasS in Mycobacterium sp. strain JC1 was free from catabolite repression.
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Affiliation(s)
- Jae-Gu Seo
- Department of Biology, Yonsei University, Seoul 120-749, Korea
| | - Sae W Park
- Department of Biology, Yonsei University, Seoul 120-749, Korea
| | - Hyuk Park
- Department of Biology, Yonsei University, Seoul 120-749, Korea
| | - Seo Y Kim
- Department of Biology, Yonsei University, Seoul 120-749, Korea
| | - Young T Ro
- Laboratory of Biochemistry, Konkuk College of Medicine, Chungju 380-701, Korea
| | - Eungbin Kim
- Department of Biology, Yonsei University, Seoul 120-749, Korea
| | - Jin W Cho
- Department of Biology, Yonsei University, Seoul 120-749, Korea
| | - Young M Kim
- Department of Biology, Yonsei University, Seoul 120-749, Korea
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Park SW, Hwang EH, Park H, Kim JA, Heo J, Lee KH, Song T, Kim E, Ro YT, Kim SW, Kim YM. Growth of mycobacteria on carbon monoxide and methanol. J Bacteriol 2003; 185:142-7. [PMID: 12486050 PMCID: PMC141938 DOI: 10.1128/jb.185.1.142-147.2003] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several mycobacterial strains, such as Mycobacterium flavescens, Mycobacterium gastri, Mycobacterium neoaurum, Mycobacterium parafortuitum, Mycobacterium peregrinum, Mycobacterium phlei, Mycobacterium smegmatis, Mycobacterium tuberculosis, and Mycobacterium vaccae, were found to grow on carbon monoxide (CO) as the sole source of carbon and energy. These bacteria, except for M. tuberculosis, also utilized methanol as the sole carbon and energy source. A CO dehydrogenase (CO-DH) assay, staining by activity of CO-DH, and Western blot analysis using an antibody raised against CO-DH of Mycobacterium sp. strain JC1 (formerly Acinetobacter sp. strain JC1 [J. W. Cho, H. S. Yim, and Y. M. Kim, Kor. J. Microbiol. 23:1-8, 1985]) revealed that CO-DH is present in extracts of the bacteria prepared from cells grown on CO. Ribulose bisphosphate carboxylase/oxygenase (RubisCO) activity was also detected in extracts prepared from all cells, except M. tuberculosis, grown on CO. The mycobacteria grown on methanol, except for M. gastri, which showed hexulose phosphate synthase activity, did not exhibit activities of classic methanol dehydrogenase, hydroxypyruvate reductase, or hexulose phosphate synthase but exhibited N,N-dimethyl-4-nitrosoaniline-dependent methanol dehydrogenase and RuBisCO activities. Cells grown on methanol were also found to have dihydroxyacetone synthase. Double immunodiffusion revealed that the antigenic sites of CO-DHs, RuBisCOs, and dihydroxyacetone synthases in all mycobacteria tested are identical with those of the Mycobacterium sp. strain JC1 enzymes.
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Affiliation(s)
- Sae W Park
- Department of Biology, Yonsei University, Seoul 120-749, Korea
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Schenk G, Duggleby RG, Nixon PF. Properties and functions of the thiamin diphosphate dependent enzyme transketolase. Int J Biochem Cell Biol 1998; 30:1297-318. [PMID: 9924800 DOI: 10.1016/s1357-2725(98)00095-8] [Citation(s) in RCA: 166] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This review highlights recent research on the properties and functions of the enzyme transketolase, which requires thiamin diphosphate and a divalent metal ion for its activity. The transketolase-catalysed reaction is part of the pentose phosphate pathway, where transketolase appears to control the non-oxidative branch of this pathway, although the overall flux of labelled substrates remains controversial. Yeast transketolase is one of several thiamin diphosphate dependent enzymes whose three-dimensional structures have been determined. Together with mutational analysis these structural data have led to detailed understanding of thiamin diphosphate catalysed reactions. In the homodimer transketolase the two catalytic sites, where dihydroxyethyl groups are transferred from ketose donors to aldose acceptors, are formed at the interface between the two subunits, where the thiazole and pyrimidine rings of thiamin diphosphate are bound. Transketolase is ubiquitous and more than 30 full-length sequences are known. The encoded protein sequences contain two motifs of high homology; one common to all thiamin diphosphate-dependent enzymes and the other a unique transketolase motif. All characterised transketolases have similar kinetic and physical properties, but the mammalian enzymes are more selective in substrate utilisation than the nonmammalian representatives. Since products of the transketolase-catalysed reaction serve as precursors for a number of synthetic compounds this enzyme has been exploited for industrial applications. Putative mutant forms of transketolase, once believed to predispose to disease, have not stood up to scrutiny. However, a modification of transketolase is a marker for Alzheimer's disease, and transketolase activity in erythrocytes is a measure of thiamin nutrition. The cornea contains a particularly high transketolase concentration, consistent with the proposal that pentose phosphate pathway activity has a role in the removal of light-generated radicals.
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Affiliation(s)
- G Schenk
- Department of Biochemistry, University of Queensland, Brisbane, Australia
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Schörken U, Sprenger GA. Thiamin-dependent enzymes as catalysts in chemoenzymatic syntheses. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1385:229-43. [PMID: 9655911 DOI: 10.1016/s0167-4838(98)00071-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Enzymes are increasingly being used to perform regio- and enantioselective reactions in chemoenzymatic syntheses. To utilize enzymes for unphysiological reactions and to yield novel products, a broad substrate spectrum is desirable. Thiamin diphosphate (ThDP)-dependent enzymes vary in their substrate tolerance from rather strict substrate specificity (phosphoketolases, glyoxylate carboligase) to more permissive enzymes (transketolase, dihydroxyacetone synthase, pyruvate decarboxylase) and therefore differ in their potential to be used as biocatalysts. We give an overview of the known substrate spectra of ThDP-dependent enzymes and present examples of multi-enzyme or chemoenzymatic approaches which involve ThDP-dependent enzymes as biocatalysts to obtain pharmaceutical compounds as ephedrine and glycosidase inhibitors, sex pheromones as exo-brevicomin, 13C-labeled metabolites, and other intermediates as 1-deoxyxylulose 5-phosphate, a precursor of vitamins and isoprenoids.
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Affiliation(s)
- U Schörken
- Institut für Biotechnologie 1, Forschungszentrum Jülich GmbH, P.O. Box 1913, D-52425 Jülich, Germany
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