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Jallet D, Soldan V, Shayan R, Stella A, Ismail N, Zenati R, Cahoreau E, Burlet-Schiltz O, Balor S, Millard P, Heux S. Integrative in vivo analysis of the ethanolamine utilization bacterial microcompartment in Escherichia coli. mSystems 2024; 9:e0075024. [PMID: 39023255 PMCID: PMC11334477 DOI: 10.1128/msystems.00750-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
Bacterial microcompartments (BMCs) are self-assembling protein megacomplexes that encapsulate metabolic pathways. Although approximately 20% of sequenced bacterial genomes contain operons encoding putative BMCs, few have been thoroughly characterized, nor any in the most studied Escherichia coli strains. We used an interdisciplinary approach to gain deep molecular and functional insights into the ethanolamine utilization (Eut) BMC system encoded by the eut operon in E. coli K-12. The eut genotype was linked with the ethanolamine utilization phenotype using deletion and overexpression mutants. The subcellular dynamics and morphology of the E. coli Eut BMCs were characterized in cellula by fluorescence microscopy and electron (cryo)microscopy. The minimal proteome reorganization required for ethanolamine utilization and the in vivo stoichiometric composition of the Eut BMC were determined by quantitative proteomics. Finally, the first flux map connecting the Eut BMC with central metabolism in cellula was obtained by genome-scale modeling and 13C-fluxomics. Our results reveal that contrary to previous suggestions, ethanolamine serves both as a nitrogen and a carbon source in E. coli K-12, while also contributing to significant metabolic overflow. Overall, this study provides a quantitative molecular and functional understanding of the BMCs involved in ethanolamine assimilation by E. coli.IMPORTANCEThe properties of bacterial microcompartments make them an ideal tool for building orthogonal network structures with minimal interactions with native metabolic and regulatory networks. However, this requires an understanding of how BMCs work natively. In this study, we combined genetic manipulation, multi-omics, modeling, and microscopy to address this issue for Eut BMCs. We show that the Eut BMC in Escherichia coli turns ethanolamine into usable carbon and nitrogen substrates to sustain growth. These results improve our understanding of compartmentalization in a widely used bacterial chassis.
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Affiliation(s)
- Denis Jallet
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Vanessa Soldan
- Plateforme de Microscopie Electronique Intégrative, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Toulouse, France
| | - Ramteen Shayan
- Plateforme de Microscopie Electronique Intégrative, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Toulouse, France
| | - Alexandre Stella
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UT3), Toulouse, France
- Infrastructure nationale de protéomique, ProFI, Toulouse, France
| | - Nour Ismail
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Rania Zenati
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Edern Cahoreau
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- MetaToul-MetaboHUB, National infrastructure of metabolomics and fluxomics, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III—Paul Sabatier (UT3), Toulouse, France
- Infrastructure nationale de protéomique, ProFI, Toulouse, France
| | - Stéphanie Balor
- Plateforme de Microscopie Electronique Intégrative, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Toulouse, France
| | - Pierre Millard
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- MetaToul-MetaboHUB, National infrastructure of metabolomics and fluxomics, Toulouse, France
| | - Stéphanie Heux
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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2
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Liang SY, Li LH, Ling MX, Mo L, Huang LM, Ruan LR, Shang CH. Combined effects of nitrogen limitation and overexpression of malic enzyme gene on lipid accumulation in Dunaliella parva. BIORESOURCE TECHNOLOGY 2024; 410:131291. [PMID: 39153698 DOI: 10.1016/j.biortech.2024.131291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/08/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
Overexpression of Dunaliella parva (D. parva) malic enzyme (ME) gene (DpME) significantly increased DpME expression and ME enzyme activity in transgenic D. parva. Nitrogen limitation had an inhibitory effect on protein content, and DpME overexpression could improve protein content. Nitrogen limitation increased carbohydrate content, and Dunaliella parva overexpressing malic enzyme gene under nitrogen limitation (DpME-N-) group showed the lowest starch content among all groups. Dunaliella parva overexpressing malic enzyme gene under nitrogen sufficient condition (DpME) and DpME-N- groups showed considerably high mRNA levels of DpME. ME activity was significantly enhanced by DpME overexpression, and nitrogen limitation caused a smaller increase. DpME overexpression and nitrogen limitation obviously enhanced lipid accumulation, and DpME overexpression had more obvious effect. Compared with control (wild type), lipid content (68.97%) obviously increased in DpME-N- group. This study indicated that the combination of DpME overexpression and nitrogen limitation was favorable to the production of microalgae biodiesel.
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Affiliation(s)
- Shi-Yu Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin (Guangxi Normal University), Guilin, Guangxi 541006, China
| | - Li-Hua Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin (Guangxi Normal University), Guilin, Guangxi 541006, China
| | - Meng-Xiang Ling
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin (Guangxi Normal University), Guilin, Guangxi 541006, China
| | - Lei Mo
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin (Guangxi Normal University), Guilin, Guangxi 541006, China
| | - Li-Mei Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin (Guangxi Normal University), Guilin, Guangxi 541006, China
| | - Ling-Ru Ruan
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin (Guangxi Normal University), Guilin, Guangxi 541006, China
| | - Chang-Hua Shang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin (Guangxi Normal University), Guilin, Guangxi 541006, China.
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3
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Afzal AR, Jeon J, Jung CH. Fumarase activity in NAD-dependent malic enzyme, MaeA, from Escherichia coli. Biochem Biophys Res Commun 2023; 678:144-147. [PMID: 37634412 DOI: 10.1016/j.bbrc.2023.08.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/21/2023] [Indexed: 08/29/2023]
Abstract
NAD-dependent malic enzymes catalyze NAD reduction to NADH while converting malate to pyruvate and CO2. In this study, NAD was reduced to NADH by MaeA, NAD-dependent malic enzyme from Escherichia coli, when fumarate was used as substrate. This suggested that MaeA catalyzed the conversion of fumarate to malate and then malate to pyruvate. The K0.5 value for fumarate was determined as 13 mM, different from previously characterized fumarases in Escherichia coli. Fumarate inhibited the malic enzyme activity of MaeA where NAD reduction to NADH was examined in the presence of malate as substrate. Human ME2, an NAD-dependent malic enzyme, also converted NAD to NADH in the presence of fumarate, suggesting that the duplex activity as fumarase and malic enzyme might be conserved in various NAD-dependent malic enzymes. MaeB, NADP-dependent malic enzyme from Escherichia coli, did not reduce NADP to NADPH in the presence of fumarate, suggesting the fumarase activities of MaeA and ME2 were specific.
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Affiliation(s)
- Aqeel Rana Afzal
- Department of Medical Science, Chonam National University, Gwangju, 61186, South Korea
| | - Jinyoung Jeon
- Department of Medical Science, Chonam National University, Gwangju, 61186, South Korea
| | - Che-Hun Jung
- Department of Medical Science, Chonam National University, Gwangju, 61186, South Korea; Department of Chemistry, Chonnam National University, Gwangju, 61186, South Korea.
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4
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Chung H, Kim J, Lee YJ, Choi KR, Jeong KJ, Kim GJ, Lee SY. Enhanced production of difficult-to-express proteins through knocking down rnpA gene expression. Biotechnol J 2023; 18:e2200641. [PMID: 37285237 DOI: 10.1002/biot.202200641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 05/21/2023] [Accepted: 06/02/2023] [Indexed: 06/09/2023]
Abstract
Escherichia coli has been employed as a workhorse for the efficient production of recombinant proteins. However, some proteins were found to be difficult to produce in E. coli. The stability of mRNA has been considered as one of the important factors affecting recombinant protein production. Here we report a generally applicable and simple strategy for enhancing mRNA stability, and consequently improving recombinant protein production in E. coli. RNase P, a ribozyme comprising an RNA subunit (RnpB) and a protein subunit (RnpA), is involved in tRNA maturation. Based on the finding that purified RnpA can digest rRNA and mRNA in vitro, it was reasoned that knocking down the level of RnpA might enhance recombinant protein production. For this, the synthetic small regulatory RNA-based knockdown system was applied to reduce the expression level of RnpA. The developed RnpA knockdown system allowed successful overexpression of 23 different recombinant proteins of various origins and sizes, including Cas9 protein, antibody fragment, and spider silk protein. Notably, a 284.9-kDa ultra-high molecular weight, highly repetitive glycine-rich spider silk protein, which is one of the most difficult proteins to produce, could be produced to 1.38 g L-1 , about two-fold higher than the highest value previously achieved, by a fed-batch culture of recombinant E. coli strain employing the RnpA knockdown system. The RnpA-knockdown strategy reported here will be generally useful for the production of recombinant proteins including those that have been difficult to produce.
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Affiliation(s)
- Hannah Chung
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- MedicosBiotech Inc, Daejeon, Republic of Korea
| | - Jiyong Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- MedicosBiotech Inc, Daejeon, Republic of Korea
| | - Yong Jae Lee
- Protein Engineering Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Kyeong Rok Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Ki Jun Jeong
- Protein Engineering Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- MedicosBiotech Inc, Daejeon, Republic of Korea
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5
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Gu P, Zhao S, Niu H, Li C, Jiang S, Zhou H, Li Q. Synthesis of isobutanol using acetate as sole carbon source in Escherichia coli. Microb Cell Fact 2023; 22:196. [PMID: 37759284 PMCID: PMC10537434 DOI: 10.1186/s12934-023-02197-w] [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: 03/26/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND With concerns about depletion of fossil fuel and environmental pollution, synthesis of biofuels such as isobutanol from low-cost substrate by microbial cell factories has attracted more and more attention. As one of the most promising carbon sources instead of food resources, acetate can be utilized by versatile microbes and converted into numerous valuable chemicals. RESULTS An isobutanol synthetic pathway using acetate as sole carbon source was constructed in E. coli. Pyruvate was designed to be generated via acetyl-CoA by pyruvate-ferredoxin oxidoreductase YdbK or anaplerotic pathway. Overexpression of transhydrogenase and NAD kinase increased the isobutanol titer of recombinant E. coli from 121.21 mg/L to 131.5 mg/L under batch cultivation. Further optimization of acetate supplement concentration achieved 157.05 mg/L isobutanol accumulation in WY002, representing the highest isobutanol titer by using acetate as sole carbon source. CONCLUSIONS The utilization of acetate as carbon source for microbial production of valuable chemicals such as isobutanol could reduce the consumption of food-based substrates and save production cost. Engineering strategies applied in this study will provide a useful reference for microbial production of pyruvate derived chemical compounds from acetate.
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Affiliation(s)
- Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
| | - Shuo Zhao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Hao Niu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Chengwei Li
- RZBC GROUP CO., LTD, Rizhao, 276800, Shandong, China
| | | | - Hao Zhou
- RZBC GROUP CO., LTD, Rizhao, 276800, Shandong, China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
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6
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Bekiaris PS, Klamt S. Network-wide thermodynamic constraints shape NAD(P)H cofactor specificity of biochemical reactions. Nat Commun 2023; 14:4660. [PMID: 37537166 PMCID: PMC10400544 DOI: 10.1038/s41467-023-40297-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023] Open
Abstract
The ubiquitous coexistence of the redox cofactors NADH and NADPH is widely considered to facilitate an efficient operation of cellular redox metabolism. However, it remains unclear what shapes the NAD(P)H specificity of specific redox reactions. Here, we present a computational framework to analyze the effect of redox cofactor swaps on the maximal thermodynamic potential of a metabolic network and use it to investigate key aspects of redox cofactor redundancy in Escherichia coli. As one major result, our analysis suggests that evolved NAD(P)H specificities are largely shaped by metabolic network structure and associated thermodynamic constraints enabling thermodynamic driving forces that are close or even identical to the theoretical optimum and significantly higher compared to random specificities. Furthermore, while redundancy of NAD(P)H is clearly beneficial for thermodynamic driving forces, a third redox cofactor would require a low standard redox potential to be advantageous. Our approach also predicts trends of redox-cofactor concentration ratios and could facilitate the design of optimal redox cofactor specificities.
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Affiliation(s)
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, Magdeburg, Germany.
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7
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Jiang K, Bai R, Gao T, Lu P, Zhang J, Zhang S, Xu F, Wang S, Zhao H. Optimization of hydrogen production in Enterobacter aerogenes by Complex I peripheral fragments destruction and maeA overexpression. Microb Cell Fact 2023; 22:137. [PMID: 37496040 PMCID: PMC10373349 DOI: 10.1186/s12934-023-02155-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
As a concentrated energy source with high added value, hydrogen has great development prospects, with special emphasis on sustainable microbial production as a replacement for traditional fossil fuels. In this study, λ-Red recombination was used to alter the activity of Complex I by single and combined knockout of nuoE, nuoF and nuoG. In addition, the conversion of malic to pyruvic acid was promoted by overexpressing the maeA gene, which could increase the content of NADH and formic acid in the bacterial cells. Compared to the original strain, hydrogen production was 65% higher in the optimized strain IAM1183-EFG/M, in which the flux of the formic acid pathway was increased by 257%, the flux of the NADH pathway was increased by 13%, and the content of metabolites also changed significantly. In further bioreactor, the total hydrogen production of the scale-up IAM1183-EFG/M after 44 h of fermentation was 4.76 L, which increased by 18% compared with the starting strain. This study provides a new direction for future exploration of microbial hydrogen production by combinatorial modification of multiple genes.
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Affiliation(s)
- Ke Jiang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ruoxuan Bai
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ting Gao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ping Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jingya Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Shuting Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Fangxu Xu
- Shenyang Functional Cordyceps militaris Industrial Technology Research Institute, Shenyang, 110034, China
- Liaoning Province Key Laboratory of Cordyceps Militaris with Functional Value, Experimental Teaching Center, Shenyang Normal University, Shenyang, 110034, China
| | - Shenghou Wang
- Shenyang Functional Cordyceps militaris Industrial Technology Research Institute, Shenyang, 110034, China
- Liaoning Province Key Laboratory of Cordyceps Militaris with Functional Value, Experimental Teaching Center, Shenyang Normal University, Shenyang, 110034, China
| | - Hongxin Zhao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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8
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de Leeuw M, Matos MRA, Nielsen LK. Omics data for sampling thermodynamically feasible kinetic models. Metab Eng 2023; 78:41-47. [PMID: 37209863 DOI: 10.1016/j.ymben.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
Abstract
Kinetic models are key to understanding and predicting the dynamic behaviour of metabolic systems. Traditional models require kinetic parameters which are not always available and are often estimated in vitro. Ensemble models overcome this challenge by sampling thermodynamically feasible models around a measured reference point. However, it is unclear if the convenient distributions used to generate the ensemble produce a natural distribution of model parameters and hence if the model predictions are reasonable. In this paper, we produced a detailed kinetic model for the central carbon metabolism of Escherichia coli. The model consists of 82 reactions (including 13 reactions with allosteric regulation) and 79 metabolites. To sample the model, we used metabolomic and fluxomic data from a single steady-state time point for E. coli K-12 MG1655 growing on glucose minimal M9 medium (average sampling time for 1000 models: 11.21 ± 0.14 min). Afterwards, in order to examine whether our sampled models are biologically sound, we calculated Km, Vmax and kcat for the reactions and compared them to previously published values. Finally, we used metabolic control analysis to identify enzymes with high control over the fluxes in the central carbon metabolism. Our analyses demonstrate that our platform samples thermodynamically feasible kinetic models, which are in agreement with previously published experimental results and can be used to investigate metabolic control patterns within cells. This renders it a valuable tool for the study of cellular metabolism and the design of metabolic pathways.
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Affiliation(s)
- Marina de Leeuw
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Marta R A Matos
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Lars Keld Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark; Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072, Brisbane QLD, Australia.
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9
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Wilkes RA, Waldbauer J, Carroll A, Nieto-Domínguez M, Parker DJ, Zhang L, Guss AM, Aristilde L. Complex regulation in a Comamonas platform for diverse aromatic carbon metabolism. Nat Chem Biol 2023; 19:651-662. [PMID: 36747056 PMCID: PMC10154247 DOI: 10.1038/s41589-022-01237-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 11/29/2022] [Indexed: 02/08/2023]
Abstract
Critical to a sustainable energy future are microbial platforms that can process aromatic carbons from the largely untapped reservoir of lignin and plastic feedstocks. Comamonas species present promising bacterial candidates for such platforms because they can use a range of natural and xenobiotic aromatic compounds and often possess innate genetic constraints that avoid competition with sugars. However, the metabolic reactions of these species are underexplored, and the regulatory mechanisms are unknown. Here we identify multilevel regulation in the conversion of lignin-related natural aromatic compounds, 4-hydroxybenzoate and vanillate, and the plastics-related xenobiotic aromatic compound, terephthalate, in Comamonas testosteroni KF-1. Transcription-level regulation controls initial catabolism and cleavage, but metabolite-level thermodynamic regulation governs fluxes in central carbon metabolism. Quantitative 13C mapping of tricarboxylic acid cycle and cataplerotic reactions elucidates key carbon routing not evident from enzyme abundance changes. This scheme of transcriptional activation coupled with metabolic fine-tuning challenges outcome predictions during metabolic manipulations.
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Affiliation(s)
- Rebecca A Wilkes
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Austin Carroll
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Darren J Parker
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Lichun Zhang
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA.
- Northwestern Center for Synthetic Biology, Evanston, IL, USA.
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10
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Sugiki S, Niide T, Toya Y, Shimizu H. Logistic Regression-Guided Identification of Cofactor Specificity-Contributing Residues in Enzyme with Sequence Datasets Partitioned by Catalytic Properties. ACS Synth Biol 2022; 11:3973-3985. [PMID: 36321539 PMCID: PMC9764414 DOI: 10.1021/acssynbio.2c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Changing the substrate/cofactor specificity of an enzyme requires multiple mutations at spatially adjacent positions around the substrate pocket. However, this is challenging when solely based on crystal structure information because enzymes undergo dynamic conformational changes during the reaction process. Herein, we proposed a method for estimating the contribution of each amino acid residue to substrate specificity by deploying a phylogenetic analysis with logistic regression. Since this method can estimate the candidate amino acids for mutation by ranking, it is readable and can be used in protein engineering. We demonstrated our concept using redox cofactor conversion of the Escherichia coli malic enzyme as a model, which still lacks crystal structure elucidation. The use of logistic regression with amino acid sequences classified by cofactor specificity showed that the NADP+-dependent malic enzyme completely switched cofactor specificity to NAD+ dependence without the need for a practical screening step. The model showed that surrounding residues made a greater contribution to cofactor specificity than those in the interior of the substrate pocket. These residues might be difficult to identify from crystal structure observations. We show that a highly accurate and inferential machine learning model was obtained using amino acid sequences of structurally homologous and functionally distinct enzymes as input data.
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11
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Engineering Escherichia coli for Efficient Aerobic Conversion of Glucose to Malic Acid through the Modified Oxidative TCA Cycle. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8120738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Malic acid is a versatile building-block chemical that can serve as a precursor of numerous valuable products, including food additives, pharmaceuticals, and biodegradable plastics. Despite the present petrochemical synthesis, malic acid, being an intermediate of the TCA cycle of a variety of living organisms, can also be produced from renewable carbon sources using wild-type and engineered microbial strains. In the current study, Escherichia coli was engineered for efficient aerobic conversion of glucose to malic acid through the modified oxidative TCA cycle resembling that of myco- and cyanobacteria and implying channelling of 2-ketoglutarate towards succinic acid via succinate semialdehyde formation. The formation of succinate semialdehyde was enabled in the core strain MAL 0 (∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆ptsG, PL-glk, Ptac-galP, ∆aceBAK, ∆glcB) by the expression of Mycobacterium tuberculosis kgd gene. The secretion of malic acid by the strain was ensured, resulting from the deletion of the mdh, maeA, maeB, and mqo genes. The Bacillus subtilis pycA gene was expressed in the strain to allow pyruvate to oxaloacetate conversion. The corresponding recombinant was able to synthesise malic acid from glucose aerobically with a yield of 0.65 mol/mol. The yield was improved by the derepression in the strain of the electron transfer chain and succinate dehydrogenase due to the enforcement of ATP hydrolysis and reached 0.94 mol/mol, amounting to 94% of the theoretical maximum. The implemented strategy offers the potential for the development of highly efficient strains and processes of bio-based malic acid production.
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Keller P, Reiter MA, Kiefer P, Gassler T, Hemmerle L, Christen P, Noor E, Vorholt JA. Generation of an Escherichia coli strain growing on methanol via the ribulose monophosphate cycle. Nat Commun 2022; 13:5243. [PMID: 36068201 PMCID: PMC9448777 DOI: 10.1038/s41467-022-32744-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Methanol is a liquid with high energy storage capacity that holds promise as an alternative substrate to replace sugars in the biotechnology industry. It can be produced from CO2 or methane and its use does not compete with food and animal feed production. However, there are currently only limited biotechnological options for the valorization of methanol, which hinders its widespread adoption. Here, we report the conversion of the industrial platform organism Escherichia coli into a synthetic methylotroph that assimilates methanol via the energy efficient ribulose monophosphate cycle. Methylotrophy is achieved after evolution of a methanol-dependent E. coli strain over 250 generations in continuous chemostat culture. We demonstrate growth on methanol and biomass formation exclusively from the one-carbon source by 13C isotopic tracer analysis. In line with computational modeling, the methylotrophic E. coli strain optimizes methanol oxidation by upregulation of an improved methanol dehydrogenase, increasing ribulose monophosphate cycle activity, channeling carbon flux through the Entner-Doudoroff pathway and downregulating tricarboxylic acid cycle enzymes. En route towards sustainable bioproduction processes, our work lays the foundation for the efficient utilization of methanol as the dominant carbon and energy resource. Using one carbon compounds as feedstock is a promising approach in abating climate change. Here, the authors report the conversion of E. coli into a synthetic methylotroph that assimilates methanol via the ribulose monophosphate cycle and a set of distinctive mutations.
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Affiliation(s)
- Philipp Keller
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Michael A Reiter
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Patrick Kiefer
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Thomas Gassler
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Lucas Hemmerle
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland.,Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Philipp Christen
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093, Zurich, Switzerland.
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13
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Abstract
Trichomonas vaginalis can host the endosymbiont Mycoplasma hominis, an opportunistic pathogenic bacterium capable of modulating T. vaginalis pathobiology. Recently, a new noncultivable mycoplasma, "Candidatus Mycoplasma girerdii," has been shown to be closely associated with women affected by trichomoniasis, suggesting a biological association. Although several features of "Ca. M. girerdii" have been investigated through genomic analysis, the nature of the potential T. vaginalis-"Ca. M. girerdii" consortium and its impact on the biology and pathogenesis of both microorganisms have not yet been explored. Here, we investigate the association between "Ca. M. girerdii" and T. vaginalis isolated from patients affected by trichomoniasis, demonstrating their intracellular localization. By using an in vitro model system based on single- and double-Mycoplasma infection of Mycoplasma-free isogenic T. vaginalis, we investigated the ability of the protist to establish a relationship with the bacteria and impact T. vaginalis growth. Our data indicate likely competition between M. hominis and "Ca. M. girerdii" while infecting trichomonad cells. Comparative dual-transcriptomics data showed major shifts in parasite gene expression in response to the presence of Mycoplasma, including genes associated with energy metabolism and pathogenesis. Consistent with the transcriptomics data, both parasite-mediated hemolysis and binding to host epithelial cells were significantly upregulated in the presence of either Mycoplasma species. Taken together, these results support a model in which this microbial association could modulate the virulence of T. vaginalis. IMPORTANCE T. vaginalis and M. hominis form a unique case of endosymbiosis that modulates the parasite's pathobiology. Recently, a new nonculturable mycoplasma species ("Candidatus Mycoplasma girerdii") has been described as closely associated with the protozoon. Here, we report the characterization of this endosymbiotic relationship. Clinical isolates of the parasite demonstrate that mycoplasmas are common among trichomoniasis patients. The relationships are studied by devising an in vitro system of single and/or double infections in isogenic protozoan recipients. Comparative growth experiments and transcriptomics data demonstrate that the composition of different microbial consortia influences the growth of the parasite and significantly modulates its transcriptomic profile, including metabolic enzymes and virulence genes such as adhesins and pore-forming proteins. The data on modulation from RNA sequencing (RNA-Seq) correlated closely with those of the cytopathic effect and adhesion to human target cells. We propose the hypothesis that the presence and the quantitative ratios of endosymbionts may contribute to modulating protozoan virulence. Our data highlight the importance of considering pathogenic entities as microbial ecosystems, reinforcing the importance of the development of integrated diagnostic and therapeutic strategies.
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14
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Skorokhodova AY, Gulevich AY, Debabov VG. Engineering Escherichia coli for efficient aerobic conversion of glucose to fumaric acid. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2022; 33:e00703. [PMID: 35145886 PMCID: PMC8801760 DOI: 10.1016/j.btre.2022.e00703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/09/2022] [Accepted: 01/16/2022] [Indexed: 12/16/2022]
Abstract
Escherichia coli was engineered for efficient aerobic conversion of glucose to fumaric acid. A novel design for biosynthesis of the target product through the modified TCA cycle rather than via glyoxylate shunt, implying oxaloacetate formation from pyruvate and artificial channelling of 2-ketoglutarate towards succinic acid via succinate semialdehyde formation, was implemented. The main fumarases were inactivated in the core strain MSG1.0 (∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆ptsG, PL-glk, Ptac-galP) by the deletion of the fumA, fumB, and fumC genes. The Bacillus subtilis pycA gene was expressed in the strain to ensure pyruvate to oxaloacetate conversion. The Mycobacterium tuberculosis kgd gene was expressed to enable succinate semialdehyde formation. The resulting strain was able to convert glucose to fumaric acid with a yield of 0.86 mol/mol, amounting to 86% of the theoretical maximum. The results demonstrated the high potential of the implemented strategy for development of efficient strains for bio-based fumaric acid production.
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Affiliation(s)
- Alexandra Yu. Skorokhodova
- Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2. Leninsky Ave., Moscow 119071, Russia
| | - Andrey Yu. Gulevich
- Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2. Leninsky Ave., Moscow 119071, Russia
| | - Vladimir G. Debabov
- Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2. Leninsky Ave., Moscow 119071, Russia
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15
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Calace P, Tonetti T, Margarit E, Figueroa CM, Lobertti C, Andreo CS, Gerrard Wheeler MC, Saigo M. The C4 cycle and beyond: diverse metabolic adaptations accompany dual-cell photosynthetic functions in Setaria. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7876-7890. [PMID: 34402880 DOI: 10.1093/jxb/erab381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
C4 photosynthesis is typically characterized by the spatial compartmentalization of the photosynthetic reactions into mesophyll (M) and bundle sheath (BS) cells. Initial carbon fixation within M cells gives rise to C4 acids, which are transported to the BS cells. There, C4 acids are decarboxylated so that the resulting CO2 is incorporated into the Calvin cycle. This work is focused on the study of Setaria viridis, a C4 model plant, closely related to several major feed and bioenergy grasses. First, we performed the heterologous expression and biochemical characterization of Setaria isoforms for chloroplastic NADP-malic enzyme (NADP-ME) and mitochondrial NAD-malic enzyme (NAD-ME). The kinetic parameters obtained agree with a major role for NADP-ME in the decarboxylation of the C4 acid malate in the chloroplasts of BS cells. In addition, mitochondria-located NAD-ME showed regulatory properties that could be important in the context of the operation of the C4 carbon shuttle. Secondly, we compared the proteomes of M and BS compartments and found 825 differentially accumulated proteins that could support different metabolic scenarios. Most interestingly, we found evidence of metabolic strategies to insulate the C4 core avoiding the leakage of intermediates by either up-regulation or down-regulation of chloroplastic, mitochondrial, and peroxisomal proteins. Overall, the results presented in this work provide novel data concerning the complexity of C4 metabolism, uncovering future lines of research that will undoubtedly contribute to the expansion of knowledge on this topic.
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Affiliation(s)
- Paula Calace
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Tomás Tonetti
- Instituto de Agrobiotecnología del Litoral (IAL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Ezequiel Margarit
- Grupo de Calidad de Frutos Cítricos, Bayas y Mejoramiento Forestal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral (IAL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Carlos Lobertti
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Laboratorio de Patogénesis Bacteriana, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Centro Científico Tecnológico Rosario, Rosario, Argentina
| | - Carlos S Andreo
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Mariel C Gerrard Wheeler
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Mariana Saigo
- Grupo de Metabolismo del Carbono y Producción Vegetal, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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16
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Gelsinger DR, Reddy R, Whittington K, Debic S, DiRuggiero J. Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea. RNA Biol 2021; 18:1867-1881. [PMID: 33522404 PMCID: PMC8583180 DOI: 10.1080/15476286.2021.1874717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
While haloarchaea are highly resistant to oxidative stress, a comprehensive understanding of the processes regulating this remarkable response is lacking. Oxidative stress-responsive small non-coding RNAs (sRNAs) have been reported in the model archaeon, Haloferax volc anii, but targets and mechanisms have not been elucidated. Using a combination of high throughput and reverse molecular genetic approaches, we elucidated the functional role of the most up-regulated intergenic sRNA during oxidative stress in H. volcanii, named Small RNA in Haloferax Oxidative Stress (SHOxi). SHOxi was predicted to form a stable secondary structure with a conserved stem-loop region as the potential binding site for trans-targets. NAD-dependent malic enzyme mRNA, identified as a putative target of SHOxi, interacted directly with a putative 'seed' region within the predicted stem loop of SHOxi. Malic enzyme catalyzes the oxidative decarboxylation of malate into pyruvate using NAD+ as a cofactor. The destabilization of malic enzyme mRNA, and the decrease in the NAD+/NADH ratio, resulting from the direct RNA-RNA interaction between SHOxi and its trans-target was essential for the survival of H. volcanii to oxidative stress. These findings indicate that SHOxi likely regulates redox homoeostasis during oxidative stress by the post-transcriptional destabilization of malic enzyme mRNA. SHOxi-mediated regulation provides evidence that the fine-tuning of metabolic cofactors could be a core strategy to mitigate damage from oxidative stress and confer resistance. This study is the first to establish the regulatory effects of sRNAs on mRNAs during the oxidative stress response in Archaea.
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Affiliation(s)
| | - Rahul Reddy
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Sara Debic
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Jocelyne DiRuggiero
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA
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17
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Luo G, Fujii S, Koda T, Tajima T, Sambongi Y, Hida A, Kato J. Unexpectedly high thermostability of an NADP-dependent malic enzyme from a psychrophilic bacterium, Shewanella livingstonensis Ac10. J Biosci Bioeng 2021; 132:445-450. [PMID: 34380602 DOI: 10.1016/j.jbiosc.2021.07.005] [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: 06/02/2021] [Revised: 07/10/2021] [Accepted: 07/17/2021] [Indexed: 10/20/2022]
Abstract
Psychrophilic enzymes are generally active at low temperatures, and their functions have attracted much interest in food processing, biochemical research, and chemical industry. However, their activities are usually lost above their growth temperature because of their flexible and unstable structure. Here, we unexpectedly found that a homodimeric NADP-dependent malic enzyme from a psychrophilic bacterium, Shewanella livingstonensis Ac10 (SL-ME) showed sufficient activity with 60°C treatment, similar to its counterpart from mesophilic Escherichia coli (MaeB). Consistently, SL-ME and MaeB irreversibly denatured at 71.9°C and 64.5°C, respectively. Therefore, SL-ME shows robust catalytic activity, which appears to be advantageous for its application in the bioconversion of NADP to NADPH, an essential ingredient for membrane phospholipid synthesis.
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Affiliation(s)
- Gonglinfeng Luo
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Sotaro Fujii
- Unit of Food and AgriLife Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takumi Koda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takahisa Tajima
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.
| | - Yoshihiro Sambongi
- Unit of Food and AgriLife Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Akiko Hida
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Junichi Kato
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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18
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Bat-Erdene U, Billingsley JM, Turner WC, Lichman BR, Ippoliti FM, Garg NK, O'Connor SE, Tang Y. Cell-Free Total Biosynthesis of Plant Terpene Natural Products using an Orthogonal Cofactor Regeneration System. ACS Catal 2021; 11:9898-9903. [PMID: 35355836 DOI: 10.1021/acscatal.1c02267] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here we report the one-pot, cell-free enzymatic synthesis of the plant monoterpene nepetalactol starting from the readily available geraniol. A pair of orthogonal cofactor regeneration systems permitted NAD+-dependent geraniol oxidation followed by NADPH-dependent reductive cyclization without isolation of intermediates. The orthogonal cofactor regeneration system maintained a high ratio of NAD+ to NADH and a low ratio of NADP+ to NADPH. The overall reaction contains four biosynthetic enzymes, including a soluble P450; and five accessory and cofactor regeneration enzymes. Furthermore, addition of a NAD+-dependent dehydrogenase to the one-pot mixture led to ~1 g/L of nepetalactone, the active cat- attractant in catnip.
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Affiliation(s)
- Undramaa Bat-Erdene
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - John M Billingsley
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - William C Turner
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Benjamin R Lichman
- Centre for Agricultural Products, Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Francesca M Ippoliti
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Neil K Garg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
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19
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Koendjbiharie JG, van Kranenburg R, Kengen SWM. The PEP-pyruvate-oxaloacetate node: variation at the heart of metabolism. FEMS Microbiol Rev 2021; 45:fuaa061. [PMID: 33289792 PMCID: PMC8100219 DOI: 10.1093/femsre/fuaa061] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
At the junction between the glycolysis and the tricarboxylic acid cycle-as well as various other metabolic pathways-lies the phosphoenolpyruvate (PEP)-pyruvate-oxaloacetate node (PPO-node). These three metabolites form the core of a network involving at least eleven different types of enzymes, each with numerous subtypes. Obviously, no single organism maintains each of these eleven enzymes; instead, different organisms possess different subsets in their PPO-node, which results in a remarkable degree of variation, despite connecting such deeply conserved metabolic pathways as the glycolysis and the tricarboxylic acid cycle. The PPO-node enzymes play a crucial role in cellular energetics, with most of them involved in (de)phosphorylation of nucleotide phosphates, while those responsible for malate conversion are important redox enzymes. Variations in PPO-node therefore reflect the different energetic niches that organisms can occupy. In this review, we give an overview of the biochemistry of these eleven PPO-node enzymes. We attempt to highlight the variation that exists, both in PPO-node compositions, as well as in the roles that the enzymes can have within those different settings, through various recent discoveries in both bacteria and archaea that reveal deviations from canonical functions.
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Affiliation(s)
- Jeroen G Koendjbiharie
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
- Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University, Stippeneng4, 6708 WE Wageningen, The Netherlands
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20
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Bifunctional Malic/Malolactic Enzyme Provides a Novel Mechanism for NADPH-Balancing in Bacillus subtilis. mBio 2021; 12:mBio.03438-20. [PMID: 33824210 PMCID: PMC8092299 DOI: 10.1128/mbio.03438-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new mechanism for NADPH balancing was discovered in Bacillus subtilis. It pivots on the bifunctional enzyme YtsJ, which is known to catalyze NADP-dependent malate decarboxylation. We found that in the presence of excessive NADPH, the same enzyme switches to malolactic activity and creates a transhydrogenation cycle that ultimately converts NADPH to NADH. This provides a regulated mechanism to immediately adjust NADPH/NADP+ in response to instantaneous needs. The redox cofactor NADPH is required as a reducing equivalent in about 100 anabolic reactions throughout metabolism. To ensure fitness under all conditions, the demand is fulfilled by a few dehydrogenases in central carbon metabolism that reduce NADP+ with electrons derived from the catabolism of nutrients. In the case of Bacillus subtilis growing on glucose, quantitative flux analyses indicate that NADPH production largely exceeds biosynthetic needs, suggesting a hitherto unknown mechanism for NADPH balancing. We investigated the role of the four malic enzymes present in B. subtilis that could bring about a metabolic cycle for transhydrogenation of NADPH into NADH. Using quantitative 13C metabolic flux analysis, we found that isoform YtsJ alone contributes to NADPH balancing in vivo and demonstrated relevant NADPH-oxidizing activity by YtsJ in vitro. To our surprise, we discovered that depending on NADPH, YtsJ switches activity from a pyruvate-producing malic enzyme to a lactate-generating malolactic enzyme. This switch in activity allows YtsJ to adaptively compensate for cellular NADPH over- and underproduction upon demand. Finally, NADPH-dependent bifunctional activity was also detected in the YtsJ homolog in Escherichia coli MaeB. Overall, our study extends the known redox cofactor balancing mechanisms by providing first-time evidence that the type of catalyzed reaction by an enzyme depends on metabolite abundance.
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21
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Harding CJ, Cadby IT, Moynihan PJ, Lovering AL. A rotary mechanism for allostery in bacterial hybrid malic enzymes. Nat Commun 2021; 12:1228. [PMID: 33623032 PMCID: PMC7902834 DOI: 10.1038/s41467-021-21528-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 02/01/2021] [Indexed: 01/31/2023] Open
Abstract
Bacterial hybrid malic enzymes (MaeB grouping, multidomain) catalyse the transformation of malate to pyruvate, and are a major contributor to cellular reducing power and carbon flux. Distinct from other malic enzyme subtypes, the hybrid enzymes are regulated by acetyl-CoA, a molecular indicator of the metabolic state of the cell. Here we solve the structure of a MaeB protein, which reveals hybrid enzymes use the appended phosphotransacetylase (PTA) domain to form a hexameric sensor that communicates acetyl-CoA occupancy to the malic enzyme active site, 60 Å away. We demonstrate that allostery is governed by a large-scale rearrangement that rotates the catalytic subunits 70° between the two states, identifying MaeB as a new model enzyme for the study of ligand-induced conformational change. Our work provides the mechanistic basis for metabolic control of hybrid malic enzymes, and identifies inhibition-insensitive variants that may find utility in synthetic biology.
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Affiliation(s)
- Christopher John Harding
- grid.6572.60000 0004 1936 7486Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Ian Thomas Cadby
- grid.6572.60000 0004 1936 7486Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Patrick Joseph Moynihan
- grid.6572.60000 0004 1936 7486Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Andrew Lee Lovering
- grid.6572.60000 0004 1936 7486Department of Biosciences, University of Birmingham, Birmingham, UK
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22
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Nan J, Zhang S, Jiang L. Antibacterial Potential of Bacillus amyloliquefaciens GJ1 against Citrus Huanglongbing. PLANTS 2021; 10:plants10020261. [PMID: 33572917 PMCID: PMC7910844 DOI: 10.3390/plants10020261] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 01/13/2023]
Abstract
Citrus huanglongbing (HLB) is a destructive disease caused by Candidatus Liberibacter species and is a serious global concern for the citrus industry. To date, there is no established strategy for control of this disease. Previously, Bacillus amyloliquefaciens GJ1 was screened as the biocontrol agent against HLB. In this study, two-year-old citrus infected by Ca. L. asiaticus were treated with B. amyloliquefaciens GJ1 solution via root irrigation. In these plants, after seven irrigation treatments, the results indicated that the photosynthetic parameters, chlorophyll content, resistance-associated enzyme content and the expression of defense-related genes were significantly higher than for the plants treated with the same volume water. The content of starch and soluble sugar were significantly lower, compared to the control treatment. The parallel reaction monitoring (PRM) results revealed that treatment with B. amyloliquefaciens GJ1 solution, the expression levels of 3 proteins with photosynthetic function were upregulated in citrus leaves. The accumulation of reactive oxygen species (ROS) in citrus leaves treated with B. amyloliquefaciens GJ1 flag22 was significantly higher than untreated plants and induced the defense-related gene expression in citrus. Finally, surfactin was identified from the fermentation broth of B. amyloliquefaciens GJ1 by high-performance liquid chromatography. These results indicate that B. amyloliquefaciens GJ1 may improve the immunity of citrus by increasing the photosynthesis and enhancing the expression of the resistance-related genes.
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Affiliation(s)
- Jing Nan
- College of Horticulture and Forestry, Ministry of Education Key Laboratory of Plant Biology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Shaoran Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Ling Jiang
- College of Horticulture and Forestry, Ministry of Education Key Laboratory of Plant Biology, Huazhong Agricultural University, Wuhan 430070, China;
- Correspondence:
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23
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Burley KH, Cuthbert BJ, Basu P, Newcombe J, Irimpan EM, Quechol R, Foik IP, Mobley DL, Beste DJV, Goulding CW. Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target. ACS Infect Dis 2021; 7:174-188. [PMID: 33356117 DOI: 10.1021/acsinfecdis.0c00735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Tuberculosis (TB) is the most lethal bacterial infectious disease worldwide. It is notoriously difficult to treat, requiring a cocktail of antibiotics administered over many months. The dense, waxy outer membrane of the TB-causing agent, Mycobacterium tuberculosis (Mtb), acts as a formidable barrier against uptake of antibiotics. Subsequently, enzymes involved in maintaining the integrity of the Mtb cell wall are promising drug targets. Recently, we demonstrated that Mtb lacking malic enzyme (MEZ) has altered cell wall lipid composition and attenuated uptake by macrophages. These results suggest that MEZ contributes to lipid biosynthesis by providing reductants in the form of NAD(P)H. Here, we present the X-ray crystal structure of MEZ to 3.6 Å. We use biochemical assays to demonstrate MEZ is dimeric in solution and to evaluate the effects of pH and allosteric regulators on its kinetics and thermal stability. To assess the interactions between MEZ and its substrate malate and cofactors, Mn2+ and NAD(P)+, we ran a series of molecular dynamics (MD) simulations. First, the MD analysis corroborates our empirical observations that MEZ is unusually flexible, which persists even with the addition of substrate and cofactors. Second, the MD simulations reveal that dimeric MEZ subunits alternate between open and closed states, and that MEZ can stably bind its NAD(P)+ cofactor in multiple conformations, including an inactive, compact NAD+ form. Together the structure of MEZ and insights from its dynamics can be harnessed to inform the design of MEZ inhibitors that target Mtb and not human malic enzyme homologues.
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Affiliation(s)
| | | | - Piyali Basu
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom
| | - Jane Newcombe
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom
| | | | | | | | | | - Dany J. V. Beste
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom
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Kuprat T, Johnsen U, Ortjohann M, Schönheit P. Acetate Metabolism in Archaea: Characterization of an Acetate Transporter and of Enzymes Involved in Acetate Activation and Gluconeogenesis in Haloferax volcanii. Front Microbiol 2020; 11:604926. [PMID: 33343547 PMCID: PMC7746861 DOI: 10.3389/fmicb.2020.604926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/13/2020] [Indexed: 02/01/2023] Open
Abstract
The haloarchaeon Haloferax volcanii grows on acetate as sole carbon and energy source. The genes and proteins involved in uptake and activation of acetate and in gluconeogenesis were identified and analyzed by characterization of enzymes and by growth experiments with the respective deletion mutants. (i) An acetate transporter of the sodium: solute-symporter family (SSF) was characterized by kinetic analyses of acetate uptake into H. volcanii cells. The functional involvement of the transporter was proven with a Δssf mutant. (ii) Four paralogous AMP-forming acetyl-CoA synthetases that belong to different phylogenetic clades were shown to be functionally involved in acetate activation. (iii) The essential involvement of the glyoxylate cycle as an anaplerotic sequence was concluded from growth experiments with an isocitrate lyase knock-out mutant excluding the operation of the methylaspartate cycle reported for Haloarcula species. (iv) Enzymes involved in phosphoenolpyruvate synthesis from acetate, namely two malic enzymes and a phosphoenolpyruvate synthetase, were identified and characterized. Phylogenetic analyses of haloarchaeal malic enzymes indicate a separate evolutionary line distinct from other archaeal homologs. The exclusive function of phosphoenolpyruvate synthetase in gluconeogenesis was proven by the respective knock-out mutant. Together, this is a comprehensive study of acetate metabolism in archaea.
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Affiliation(s)
- Tom Kuprat
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| | - Ulrike Johnsen
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| | - Marius Ortjohann
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
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Zhu F, San KY, Bennett GN. Metabolic engineering of Escherichia coli for malate production with a temperature sensitive malate dehydrogenase. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Revealing the Metabolic Flexibility of " Candidatus Accumulibacter phosphatis" through Redox Cofactor Analysis and Metabolic Network Modeling. Appl Environ Microbiol 2020; 86:AEM.00808-20. [PMID: 33008826 DOI: 10.1128/aem.00808-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/21/2020] [Indexed: 12/27/2022] Open
Abstract
Environmental fluctuations in the availability of nutrients lead to intricate metabolic strategies. "Candidatus Accumulibacter phosphatis," a polyphosphate-accumulating organism (PAO) responsible for enhanced biological phosphorus removal (EBPR) from wastewater treatment systems, is prevalent in aerobic/anaerobic environments. While the overall metabolic traits of these bacteria are well described, the nonavailability of isolates has led to controversial conclusions on the metabolic pathways used. In this study, we experimentally determined the redox cofactor preferences of different oxidoreductases in the central carbon metabolism of a highly enriched "Ca Accumulibacter phosphatis" culture. Remarkably, we observed that the acetoacetyl coenzyme A reductase engaged in polyhydroxyalkanoate (PHA) synthesis is NADH preferring instead of showing the generally assumed NADPH dependency. This allows rethinking of the ecological role of PHA accumulation as a fermentation product under anaerobic conditions and not just a stress response. Based on previously published metaomics data and the results of enzymatic assays, a reduced central carbon metabolic network was constructed and used for simulating different metabolic operating modes. In particular, scenarios with different acetate-to-glycogen consumption ratios were simulated, which demonstrated optima using different combinations of glycolysis, glyoxylate shunt, or branches of the tricarboxylic acid (TCA) cycle. Thus, optimal metabolic flux strategies will depend on the environment (acetate uptake) and on intracellular storage compound availability (polyphosphate/glycogen). This NADH-related metabolic flexibility is enabled by the NADH-driven PHA synthesis. It allows for maintaining metabolic activity under various environmental substrate conditions, with high carbon conservation and lower energetic costs than for NADPH-dependent PHA synthesis. Such (flexible) metabolic redox coupling can explain the competitiveness of PAOs under oxygen-fluctuating environments.IMPORTANCE Here, we demonstrate how microbial storage metabolism can adjust to a wide range of environmental conditions. Such flexibility generates a selective advantage under fluctuating environmental conditions. It can also explain the different observations reported in PAO literature, including the capacity of "Ca Accumulibacter phosphatis" to act like glycogen-accumulating organisms (GAOs). These observations stem from slightly different experimental conditions, and controversy arises only when one assumes that metabolism can operate only in a single mode. Furthermore, we also show how the study of metabolic strategies is possible when combining omics data with functional cofactor assays and modeling. Genomic information can only provide the potential of a microorganism. The environmental context and other complementary approaches are still needed to study and predict the functional expression of such metabolic potential.
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The Protein-Protein Interaction Network Reveals a Novel Role of the Signal Transduction Protein PII in the Control of c-di-GMP Homeostasis in Azospirillum brasilense. mSystems 2020; 5:5/6/e00817-20. [PMID: 33144311 PMCID: PMC7646526 DOI: 10.1128/msystems.00817-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The PII proteins sense and integrate important metabolic signals which reflect the cellular nutrition and energy status. Such extraordinary ability was capitalized by nature in such a way that the various PII proteins regulate different facets of metabolism by controlling the activity of a range of target proteins by protein-protein interactions. Here, we determined the PII protein interaction network in the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense. The interactome data along with metabolome analysis suggest that PII functions as a master metabolic regulator hub. We provide evidence that PII proteins act to regulate c-di-GMP levels in vivo and cell motility and adherence behaviors. The PII family comprises a group of widely distributed signal transduction proteins ubiquitous in prokaryotes and in the chloroplasts of plants. PII proteins sense the levels of key metabolites ATP, ADP, and 2-oxoglutarate, which affect the PII protein structure and thereby the ability of PII to interact with a range of target proteins. Here, we performed multiple ligand fishing assays with the PII protein orthologue GlnZ from the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense to identify 37 proteins that are likely to be part of the PII protein-protein interaction network. Among the PII targets identified were enzymes related to nitrogen and fatty acid metabolism, signaling, coenzyme synthesis, RNA catabolism, and transcription. Direct binary PII-target complex was confirmed for 15 protein complexes using pulldown assays with recombinant proteins. Untargeted metabolome analysis showed that PII is required for proper homeostasis of important metabolites. Two enzymes involved in c-di-GMP metabolism were among the identified PII targets. A PII-deficient strain showed reduced c-di-GMP levels and altered aerotaxis and flocculation behavior. These data support that PII acts as a major metabolic hub controlling important enzymes and the homeostasis of key metabolites such as c-di-GMP in response to the prevailing nutritional status. IMPORTANCE The PII proteins sense and integrate important metabolic signals which reflect the cellular nutrition and energy status. Such extraordinary ability was capitalized by nature in such a way that the various PII proteins regulate different facets of metabolism by controlling the activity of a range of target proteins by protein-protein interactions. Here, we determined the PII protein interaction network in the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense. The interactome data along with metabolome analysis suggest that PII functions as a master metabolic regulator hub. We provide evidence that PII proteins act to regulate c-di-GMP levels in vivo and cell motility and adherence behaviors.
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Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks. mSystems 2020; 5:5/3/e00057-20. [PMID: 32487739 PMCID: PMC8534726 DOI: 10.1128/msystems.00057-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Small noncoding RNAs (sRNAs) are key regulators of bacterial gene expression. Through complementary base pairing, sRNAs affect mRNA stability and translation efficiency. Here, we describe a network inference approach designed to identify sRNA-mediated regulation of transcript levels. We use existing transcriptional data sets and prior knowledge to infer sRNA regulons using our network inference tool, the Inferelator. This approach produces genome-wide gene regulatory networks that include contributions by both transcription factors and sRNAs. We show the benefits of estimating and incorporating sRNA activities into network inference pipelines using available experimental data. We also demonstrate how these estimated sRNA regulatory activities can be mined to identify the experimental conditions where sRNAs are most active. We uncover 45 novel experimentally supported sRNA-mRNA interactions in Escherichia coli, outperforming previous network-based efforts. Additionally, our pipeline complements sequence-based sRNA-mRNA interaction prediction methods by adding a data-driven filtering step. Finally, we show the general applicability of our approach by identifying 24 novel, experimentally supported, sRNA-mRNA interactions in Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus subtilis. Overall, our strategy generates novel insights into the functional context of sRNA regulation in multiple bacterial species. IMPORTANCE Individual bacterial genomes can have dozens of small noncoding RNAs with largely unexplored regulatory functions. Although bacterial sRNAs influence a wide range of biological processes, including antibiotic resistance and pathogenicity, our current understanding of sRNA-mediated regulation is far from complete. Most of the available information is restricted to a few well-studied bacterial species; and even in those species, only partial sets of sRNA targets have been characterized in detail. To close this information gap, we developed a computational strategy that takes advantage of available transcriptional data and knowledge about validated and putative sRNA-mRNA interactions for inferring expanded sRNA regulons. Our approach facilitates the identification of experimentally supported novel interactions while filtering out false-positive results. Due to its data-driven nature, our method prioritizes biologically relevant interactions among lists of candidate sRNA-target pairs predicted in silico from sequence analysis or derived from sRNA-mRNA binding experiments.
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The NADP-dependent malic enzyme MaeB is a central metabolic hub controlled by the acetyl-CoA to CoASH ratio. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140462. [PMID: 32485238 DOI: 10.1016/j.bbapap.2020.140462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 11/20/2022]
Abstract
Malic enzymes participate in key metabolic processes, the MaeB-like malic enzymes carry a catalytic inactive phosphotransacetylase domain whose function remains elusive. Here we show that acetyl-CoA directly binds and inhibits MaeB-like enzymes with a saturable profile under physiological relevant acetyl-CoA concentrations. A MaeB-like enzyme from the nitrogen-fixing bacterium Azospirillum brasilense, namely AbMaeB1, binds both acetyl-CoA and unesterified CoASH in a way that inhibition of AbMaeB1 by acetyl-CoA is relieved by increasing CoASH concentrations. Hence, AbMaeB1 senses the acetyl-CoA/CoASH ratio. We revisited E. coli MaeB regulation to determine the inhibitory constant for acetyl-CoA. Our data support that the phosphotransacetylase domain of MaeB-like enzymes senses acetyl-CoA to dictate the fate of carbon distribution at the phosphoenol-pyruvate / pyruvate / oxaloacetate metabolic node.
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Rozova ON, Mustakhimov II, But SY, Reshetnikov AS, Khmelenina VN. Role of the malic enzyme in metabolism of the halotolerant methanotroph Methylotuvimicrobium alcaliphilum 20Z. PLoS One 2019; 14:e0225054. [PMID: 31738793 PMCID: PMC6860931 DOI: 10.1371/journal.pone.0225054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 10/28/2019] [Indexed: 01/10/2023] Open
Abstract
The bacteria utilizing methane as a growth substrate (methanotrophs) are important constituents of the biosphere. Methanotrophs mitigate the emission of anthropogenic and natural greenhouse gas methane to the environment and are the promising agents for future biotechnologies. Many aspects of CH4 bioconversion by methanotrophs require further clarification. This study was aimed at characterizing the biochemical properties of the malic enzyme (Mae) from the halotolerant obligate methanotroph Methylotuvimicrobium alcaliphilum 20Z. The His6-tagged Mae was obtained by heterologous expression in Escherichia coli BL21 (DE3) and purified by affinity metal chelating chromatography. As determined by gel filtration and non-denaturating gradient gel electrophoresis, the molecular mass of the native enzyme is 260 kDa. The homotetrameric Mae (65x4 kDa) catalyzed an irreversible NAD+-dependent reaction of L-malate decarboxylation into pyruvate with a specific activity of 32 ± 2 units mg-1 and Km value of 5.5 ± 0.8 mM for malate and 57 ± 5 μM for NAD+. The disruption of the mae gene by insertion mutagenesis resulted in a 20-fold increase in intracellular malate level in the mutant compared to the wild type strain. Based on both enzyme and mutant properties, we conclude that the malic enzyme is involved in the control of intracellular L-malate level in Mtm. alcaliphilum 20Z. Genomic analysis has revealed that Maes present in methanotrophs fall into two different clades in the amino acid-based phylogenetic tree, but no correlation of the division with taxonomic affiliations of the host bacteria was observed.
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Affiliation(s)
- Olga N. Rozova
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Ildar I. Mustakhimov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Sergei Y. But
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Aleksandr S. Reshetnikov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Valentina N. Khmelenina
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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31
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Morello G, Siritanaratkul B, Megarity CF, Armstrong FA. Efficient Electrocatalytic CO2 Fixation by Nanoconfined Enzymes via a C3-to-C4 Reaction That Is Favored over H2 Production. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03532] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Giorgio Morello
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford 0X13QR, U.K
| | - Bhavin Siritanaratkul
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford 0X13QR, U.K
| | - Clare F. Megarity
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford 0X13QR, U.K
| | - Fraser A. Armstrong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford 0X13QR, U.K
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32
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Zampieri M, Hörl M, Hotz F, Müller NF, Sauer U. Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli. Nat Commun 2019; 10:3354. [PMID: 31350417 PMCID: PMC6659692 DOI: 10.1038/s41467-019-11331-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 07/05/2019] [Indexed: 02/06/2023] Open
Abstract
How microbes dynamically coordinate uptake and simultaneous utilization of nutrients in complex nutritional ecosystems is still an open question. Here, we develop a constraint-based modeling approach that exploits non-targeted exo-metabolomics data to unravel adaptive decision-making processes in dynamic nutritional environments. We thereby investigate metabolic adaptation of Escherichia coli to continuously changing conditions during batch growth in complex medium. Unexpectedly, model-based analysis of time resolved exo-metabolome data revealed that fastest growth coincides with preferred catabolism of amino acids, which, in turn, reduces glucose uptake and increases acetate overflow. We show that high intracellular levels of the amino acid degradation metabolites pyruvate and oxaloacetate can directly inhibit the phosphotransferase system (PTS), and reveal their functional role in mediating regulatory decisions for uptake and catabolism of alternative carbon sources. Overall, the proposed methodology expands the spectrum of possible applications of flux balance analysis to decipher metabolic adaptation mechanisms in naturally occurring habitats and diverse organisms.
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Affiliation(s)
- Mattia Zampieri
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, 8093, Switzerland.
| | - Manuel Hörl
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, 8093, Switzerland
| | - Florian Hotz
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, 8093, Switzerland
| | - Nicola F Müller
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, 8093, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, 8093, Switzerland.
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Tian D, Guo R, Li Y, Chen P, Zi B, Wang J, Liu R, Min Y, Wang Z, Niu Z, Liu F. Effects of lysine deficiency or excess on growth and the expression of lipid metabolism genes in slow-growing broilers. Poult Sci 2019; 98:2927-2932. [DOI: 10.3382/ps/pez041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 01/24/2019] [Indexed: 01/16/2023] Open
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Rozova ON, Khmelenina VN, Mustakhimov II, But SY, Trotsenko YA. Properties of Malic Enzyme from the Aerobic Methanotroph Methylosinus trichosporium. BIOCHEMISTRY (MOSCOW) 2019; 84:390-397. [PMID: 31228930 DOI: 10.1134/s0006297919040060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recombinant malic enzyme from the aerobic methanotroph Methylosinus trichosporium was obtained by heterologous expression in Escherichia coli and purified by affinity metal-chelating chromatography. The homohexameric enzyme of 6×80 kDa catalyzed the reversible reaction of oxidative decarboxylation of malate to pyruvate in the presence of mono- and divalent cations and NADP+ as a cofactor. The kcat/Km ratio indicated much higher catalytic efficiency of the malate decarboxylation reaction as compared with the pyruvate carboxylation reaction. Analysis of the protein sequence revealed that the C-region of the enzyme contains a large domain homologous to phosphoacetyltransferase, but no phosphoacetyltransferase activity was detected either for a full chimeric malic enzyme or for the C-end fragment obtained as a separate protein. This C-end domain promoted activity of the malic enzyme.
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Affiliation(s)
- O N Rozova
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia
| | - V N Khmelenina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia.
| | - I I Mustakhimov
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia
| | - S Y But
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia
| | - Yu A Trotsenko
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, 142290, Russia
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Christensen DG, Baumgartner JT, Xie X, Jew KM, Basisty N, Schilling B, Kuhn ML, Wolfe AJ. Mechanisms, Detection, and Relevance of Protein Acetylation in Prokaryotes. mBio 2019; 10:e02708-18. [PMID: 30967470 PMCID: PMC6456759 DOI: 10.1128/mbio.02708-18] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Posttranslational modification of a protein, either alone or in combination with other modifications, can control properties of that protein, such as enzymatic activity, localization, stability, or interactions with other molecules. N-ε-Lysine acetylation is one such modification that has gained attention in recent years, with a prevalence and significance that rival those of phosphorylation. This review will discuss the current state of the field in bacteria and some of the work in archaea, focusing on both mechanisms of N-ε-lysine acetylation and methods to identify, quantify, and characterize specific acetyllysines. Bacterial N-ε-lysine acetylation depends on both enzymatic and nonenzymatic mechanisms of acetylation, and recent work has shed light into the regulation of both mechanisms. Technological advances in mass spectrometry have allowed researchers to gain insight with greater biological context by both (i) analyzing samples either with stable isotope labeling workflows or using label-free protocols and (ii) determining the true extent of acetylation on a protein population through stoichiometry measurements. Identification of acetylated lysines through these methods has led to studies that probe the biological significance of acetylation. General and diverse approaches used to determine the effect of acetylation on a specific lysine will be covered.
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Affiliation(s)
- D G Christensen
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
| | - J T Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - X Xie
- Buck Institute for Research on Aging, Novato, California, USA
| | - K M Jew
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - N Basisty
- Buck Institute for Research on Aging, Novato, California, USA
| | - B Schilling
- Buck Institute for Research on Aging, Novato, California, USA
| | - M L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - A J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
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Keasey SL, Suh MJ, Das S, Blancett CD, Zeng X, Andresson T, Sun MG, Ulrich RG. Decreased Antibiotic Susceptibility Driven by Global Remodeling of the Klebsiella pneumoniae Proteome. Mol Cell Proteomics 2019; 18:657-668. [PMID: 30617156 PMCID: PMC6442359 DOI: 10.1074/mcp.ra118.000739] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 01/04/2019] [Indexed: 12/04/2022] Open
Abstract
Bacteria can circumvent the effect of antibiotics by transitioning to a poorly understood physiological state that does not involve conventional genetic elements of resistance. Here we examine antibiotic susceptibility with a Class A β-lactamase+ invasive strain of Klebsiella pneumoniae that was isolated from a lethal outbreak within laboratory colonies of Chlorocebus aethiops sabaeus monkeys. Bacterial responses to the ribosomal synthesis inhibitors streptomycin and doxycycline resulted in distinct proteomic adjustments that facilitated decreased susceptibility to each antibiotic. Drug-specific changes to proteomes included proteins for receptor-mediated membrane transport and sugar utilization, central metabolism, and capsule production, whereas mechanisms common to both antibiotics included elevated scavenging of reactive oxygen species and turnover of misfolded proteins. Resistance to combined antibiotics presented integrated adjustments to protein levels as well as unique drug-specific proteomic features. Our results demonstrate that dampening of Klebsiella pneumoniae susceptibility involves global remodeling of the bacterial proteome to counter the effects of antibiotics and stabilize growth.
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Affiliation(s)
- Sarah L Keasey
- From the ‡Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland;; Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland
| | - Moo-Jin Suh
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland
| | - Sudipto Das
- Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, NCI-Frederick, Frederick, Maryland
| | - Candace D Blancett
- Pathology Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland
| | - Xiankun Zeng
- Pathology Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland
| | - Thorkell Andresson
- Laboratory of Proteomics and Analytical Technologies, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, NCI-Frederick, Frederick, Maryland
| | - Mei G Sun
- Pathology Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland
| | - Robert G Ulrich
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland;.
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Skorokhodova AY, Gulevich AY, Debabov VG. Inactivation of Malic Enzymes Improves the Anaerobic Production of Four-Carbon Dicarboxylic Acids by Recombinant Escherichia coli Strains Expressing Pyruvate Carboxylase. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683818090065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Megarity CF, Siritanaratkul B, Heath RS, Wan L, Morello G, FitzPatrick SR, Booth RL, Sills AJ, Robertson AW, Warner JH, Turner NJ, Armstrong FA. Electrocatalytic Volleyball: Rapid Nanoconfined Nicotinamide Cycling for Organic Synthesis in Electrode Pores. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Clare F. Megarity
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QR UK
| | | | - Rachel S. Heath
- Manchester Institute of BiotechnologySchool of ChemistryUniversity of Manchester Manchester M1 7DN UK
| | - Lei Wan
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QR UK
| | - Giorgio Morello
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QR UK
| | | | - Rosalind L. Booth
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QR UK
| | - Adam J. Sills
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QR UK
| | | | - Jamie H. Warner
- Department of MaterialsUniversity of Oxford Parks Road Oxford OX1 3PH UK
| | - Nicholas J. Turner
- Manchester Institute of BiotechnologySchool of ChemistryUniversity of Manchester Manchester M1 7DN UK
| | - Fraser A. Armstrong
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QR UK
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Megarity CF, Siritanaratkul B, Heath RS, Wan L, Morello G, FitzPatrick SR, Booth RL, Sills AJ, Robertson AW, Warner JH, Turner NJ, Armstrong FA. Electrocatalytic Volleyball: Rapid Nanoconfined Nicotinamide Cycling for Organic Synthesis in Electrode Pores. Angew Chem Int Ed Engl 2019; 58:4948-4952. [PMID: 30633837 PMCID: PMC6491978 DOI: 10.1002/anie.201814370] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 11/05/2022]
Abstract
In living cells, redox chains rely on nanoconfinement using tiny enclosures, such as the mitochondrial matrix or chloroplast stroma, to concentrate enzymes and limit distances that nicotinamide cofactors and other metabolites must diffuse. In a chemical analogue exploiting this principle, nicotinamide adenine dinucleotide phosphate (NADPH) and NADP+ are cycled rapidly between ferredoxin–NADP+ reductase and a second enzyme—the pairs being juxtaposed within the 5–100 nm scale pores of an indium tin oxide electrode. The resulting electrode material, denoted (FNR+E2)@ITO/support, can drive and exploit a potentially large number of enzyme‐catalysed reactions.
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Affiliation(s)
- Clare F Megarity
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| | - Bhavin Siritanaratkul
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| | - Rachel S Heath
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | - Lei Wan
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| | - Giorgio Morello
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| | - Sarah R FitzPatrick
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| | - Rosalind L Booth
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| | - Adam J Sills
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| | | | - Jamie H Warner
- Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, UK
| | - Nicholas J Turner
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | - Fraser A Armstrong
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
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Azarian B, Azimi A, Sepehri M, Samimi Fam V, Rezaie F, Talebkhan Y, Khalaj V, Davami F. Proteomics investigation of molecular mechanisms affected by EnBase culture system in anti-VEGF fab fragment producing E. coli BL21 (DE3). Prep Biochem Biotechnol 2019; 49:48-57. [PMID: 30735089 DOI: 10.1080/10826068.2018.1508037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Aggregation of recombinant proteins, a major problem in E. coli expression system, is improved by using EnBase culture system based on slow release of glucose. In the present study, to understand the intracellular mechanisms involved in increased solubility of the target recombinant protein through EnBase system, the effect of this system was investigated on E. coli cells proteome profile. The proteome profile of E. coli cells cultured in EnBase and conventional batch mode was analyzed by two-dimensional gel electrophoresis. The proteins with significant expressional changes were identified through MALDI-TOF/TOF mass spectrometry. In EnBase system, the expressions of carbon metabolism-related proteins, sugar transport system-related proteins, and amino acids metabolism-related proteins were significantly altered. Furthermore, the expression of Thioredoxin 1 as the facilitator of protein folding was up-regulated in EnBase system that could be related to the increased solubility of recombinant protein. The proteomics analysis of E. coli cells cultured in EnBase system revealed that Thioredoxin 1 can be a potential candidate for future studies aiming at increased anti-VEGF fab fragment solubility. Studying proteomics is a valuable tool for revealing the target proteins that play the central role in EnBase culture system for increasing the solubility.
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Affiliation(s)
- Bahareh Azarian
- a Protein Chemistry Unit, Biotechnology Research Centre , Pasteur Institute of Iran , Tehran , Iran
| | - Amin Azimi
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran.,c Department of Biotechnology , College of Science, University of Tehran , Tehran , Iran
| | - Mahboubeh Sepehri
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran.,d Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences & Technology , Pharmaceutical sciences Branch, Islamic Azad University , Tehran , Iran
| | - Vahideh Samimi Fam
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran.,e Department of Microbiology , Islamic Azad University Rasht Branch , Rasht , Guilan , Iran
| | - Faegheh Rezaie
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran
| | - Yeganeh Talebkhan
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran
| | - Vahid Khalaj
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran
| | - Fatemeh Davami
- b Medical Biotechnology Department , Biotechnology Research Centre, Pasteur Institute of Iran , Tehran , Iran
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41
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Cabulong RB, Valdehuesa KNG, Bañares AB, Ramos KRM, Nisola GM, Lee WK, Chung WJ. Improved cell growth and biosynthesis of glycolic acid by overexpression of membrane-bound pyridine nucleotide transhydrogenase. J Ind Microbiol Biotechnol 2018; 46:159-169. [PMID: 30554290 DOI: 10.1007/s10295-018-2117-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/27/2018] [Indexed: 01/07/2023]
Abstract
The non-conventional D-xylose metabolism called the Dahms pathway which only requires the expression of at least three enzymes to produce pyruvate and glycolaldehyde has been previously engineered in Escherichia coli. Strains that rely on this pathway exhibit lower growth rates which were initially attributed to the perturbed redox homeostasis as evidenced by the lower intracellular NADPH concentrations during exponential growth phase. NADPH-regenerating systems were then tested to restore the redox homeostasis. The membrane-bound pyridine nucleotide transhydrogenase, PntAB, was overexpressed and resulted to a significant increase in biomass and glycolic acid titer and yield. Furthermore, expression of PntAB in an optimized glycolic acid-producing strain improved the growth and product titer significantly. This work demonstrated that compensating for the NADPH demand can be achieved by overexpression of PntAB in E. coli strains assimilating D-xylose through the Dahms pathway. Consequently, increase in biomass accumulation and product concentration was also observed.
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Affiliation(s)
- Rhudith B Cabulong
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Kris Niño G Valdehuesa
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Angelo B Bañares
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Kristine Rose M Ramos
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Grace M Nisola
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea.
| | - Wook-Jin Chung
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, Gyeonggi-do, 170-58, South Korea.
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42
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Fedor JG, Hirst J. Mitochondrial Supercomplexes Do Not Enhance Catalysis by Quinone Channeling. Cell Metab 2018; 28:525-531.e4. [PMID: 29937372 PMCID: PMC6125145 DOI: 10.1016/j.cmet.2018.05.024] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/14/2018] [Accepted: 05/24/2018] [Indexed: 12/12/2022]
Abstract
Mitochondrial respiratory supercomplexes, comprising complexes I, III, and IV, are the minimal functional units of the electron transport chain. Assembling the individual complexes into supercomplexes may stabilize them, provide greater spatiotemporal control of respiration, or, controversially, confer kinetic advantages through the sequestration of local quinone and cytochrome c pools (substrate channeling). Here, we have incorporated an alternative quinol oxidase (AOX) into mammalian heart mitochondrial membranes to introduce a competing pathway for quinol oxidation and test for channeling. AOX substantially increases the rate of NADH oxidation by O2 without affecting the membrane integrity, the supercomplexes, or NADH-linked oxidative phosphorylation. Therefore, the quinol generated in supercomplexes by complex I is reoxidized more rapidly outside the supercomplex by AOX than inside the supercomplex by complex III. Our results demonstrate that quinone and quinol diffuse freely in and out of supercomplexes: substrate channeling does not occur and is not required to support respiration.
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Affiliation(s)
- Justin G Fedor
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
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Guo Y, Song Y, Zheng H, Zhang Y, Guo J, Sui N. NADP-Malate Dehydrogenase of Sweet Sorghum Improves Salt Tolerance of Arabidopsis thaliana. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:5992-6002. [PMID: 29847118 DOI: 10.1021/acs.jafc.8b02159] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Sweet sorghum is a C4 crop that shows high salt tolerance and high yield. NADP-malate dehydrogenase ( NADP-ME) is a crucial enzyme of the C4 pathway. The regulatory mechanism of NADP-ME remains unclear. In this study, we isolated SbNADP-ME from sweet sorghum. The open reading frame of SbNADP-ME is 1911 bp and 637 amino acid residues. Quantitative real-time PCR analysis showed that SbNADP-ME transcription in sweet sorghum was enhanced by salt stress. The SbNADP-ME transcript level was highest under exposure to 150 mM NaCl. Arabidopsis overexpressing SbNADP-ME showed increased germination rate and root length under NaCl treatments. At the seedling stage, physiological photosynthesis parameters, chlorophyll content, PSII photochemical efficiency, and PSI oxidoreductive activity in the wild type decreased more severely than in the overexpression lines but less than in T-DNA insertion mutants under salt stress. Overexpression of SbNADP-ME in Arabidopsis may also increase osmotic adjustment and scavenging activity on DPPH and decrease membrane peroxidation. These results suggest that SbNADP-ME overexpression in Arabidopsis increases salt tolerance and alleviates PSII and PSI photoinhibition under salt stress by improving photosynthetic capacity.
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Affiliation(s)
- Yuanyuan Guo
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science , Shandong Normal University , Jinan 250014 , China
| | - Yushuang Song
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science , Shandong Normal University , Jinan 250014 , China
| | - Hongxiang Zheng
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science , Shandong Normal University , Jinan 250014 , China
| | - Yi Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science , Shandong Normal University , Jinan 250014 , China
| | - Jianrong Guo
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science , Shandong Normal University , Jinan 250014 , China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science , Shandong Normal University , Jinan 250014 , China
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Dai Z, Zhou H, Zhang S, Gu H, Yang Q, Zhang W, Dong W, Ma J, Fang Y, Jiang M, Xin F. Current advance in biological production of malic acid using wild type and metabolic engineered strains. BIORESOURCE TECHNOLOGY 2018; 258:345-353. [PMID: 29550171 DOI: 10.1016/j.biortech.2018.03.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 06/08/2023]
Abstract
Malic acid (2-hydroxybutanedioic acid) is a four-carbon dicarboxylic acid, which has attracted great interest due to its wide usage as a precursor of many industrially important chemicals in the food, chemicals, and pharmaceutical industries. Several mature routes for malic acid production have been developed, such as chemical synthesis, enzymatic conversion and biological fermentation. With depletion of fossil fuels and concerns regarding environmental issues, biological production of malic acid has attracted more attention, which mainly consists of three pathways, namely non-oxidative pathway, oxidative pathway and glyoxylate cycle. In recent decades, metabolic engineering of model strains, and process optimization for malic acid production have been rapidly developed. Hence, this review comprehensively introduces an overview of malic acid producers and highlight some of the successful metabolic engineering approaches.
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Affiliation(s)
- Zhongxue Dai
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Huiyuan Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Shangjie Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Honglian Gu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Qiao Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| | - Yan Fang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
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45
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Yu H, Li X, Duchoud F, Chuang DS, Liao JC. Augmenting the Calvin-Benson-Bassham cycle by a synthetic malyl-CoA-glycerate carbon fixation pathway. Nat Commun 2018; 9:2008. [PMID: 29789614 PMCID: PMC5964204 DOI: 10.1038/s41467-018-04417-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/19/2018] [Indexed: 11/21/2022] Open
Abstract
The Calvin–Benson–Bassham (CBB) cycle is presumably evolved for optimal synthesis of C3 sugars, but not for the production of C2 metabolite acetyl-CoA. The carbon loss in producing acetyl-CoA from decarboxylation of C3 sugar limits the maximum carbon yield of photosynthesis. Here we design a synthetic malyl-CoA-glycerate (MCG) pathway to augment the CBB cycle for efficient acetyl-CoA synthesis. This pathway converts a C3 metabolite to two acetyl-CoA by fixation of one additional CO2 equivalent, or assimilates glyoxylate, a photorespiration intermediate, to produce acetyl-CoA without net carbon loss. We first functionally demonstrate the design of the MCG pathway in vitro and in Escherichia coli. We then implement the pathway in a photosynthetic organism Synechococcus elongates PCC7942, and show that it increases the intracellular acetyl-CoA pool and enhances bicarbonate assimilation by roughly 2-fold. This work provides a strategy to improve carbon fixation efficiency in photosynthetic organisms. Improving carbon fixation efficiency and reducing carbon loss have been long term goals for people working on photosynthetic organism improvement. Here, the authors design a synthetic malyl-CoA-glycerate pathway for efficient acetyl-CoA synthesis and verify its function in vitro, in E. coli and in cyanobacterium.
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Affiliation(s)
- Hong Yu
- UCLA-DOE Institute of Genomics and Proteomics, 420 Westwood Plaza, Los Angeles, CA, 90095, USA.,Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, USA
| | - Xiaoqian Li
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, USA
| | - Fabienne Duchoud
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, USA
| | - Derrick S Chuang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, USA
| | - James C Liao
- Academia Sinica, 128 Academia Road, Section 2, 115, Taipei, Taiwan.
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Song HS, Seo HM, Jeon JM, Moon YM, Hong JW, Hong YG, Bhatia SK, Ahn J, Lee H, Kim W, Park YC, Choi KY, Kim YG, Yang YH. Enhanced isobutanol production from acetate by combinatorial overexpression of acetyl-CoA synthetase and anaplerotic enzymes in engineered Escherichia coli. Biotechnol Bioeng 2018; 115:1971-1978. [DOI: 10.1002/bit.26710] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 03/03/2018] [Accepted: 04/05/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Hun-Suk Song
- Department of Biological Engineering; College of Engineering; Konkuk University; Seoul Korea
| | - Hyung-Min Seo
- Department of Biological Engineering; College of Engineering; Konkuk University; Seoul Korea
| | - Jong-Min Jeon
- Department of Biological Engineering; College of Engineering; Konkuk University; Seoul Korea
| | - Yu-Mi Moon
- Department of Biological Engineering; College of Engineering; Konkuk University; Seoul Korea
| | - Ju Won Hong
- Department of Biological Engineering; College of Engineering; Konkuk University; Seoul Korea
| | - Yoon Gi Hong
- Department of Biological Engineering; College of Engineering; Konkuk University; Seoul Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering; College of Engineering; Konkuk University; Seoul Korea
- Institute for Ubiquitous Information Technology and Applications (CBRU); Konkuk University; Seoul South Korea
| | - Jungoh Ahn
- Biotechnology Process Engineering Center; Korea Research Institute Bioscience Biotechnology (KRIBB); Daejeon Korea
| | - Hongweon Lee
- Biotechnology Process Engineering Center; Korea Research Institute Bioscience Biotechnology (KRIBB); Daejeon Korea
| | - Wooseong Kim
- Division of Infectious Diseases; Rhode Island Hospital; Alpert Medical School of Brown University; Providence Rhode Island
| | - Yong-Cheol Park
- Department of Bio and Fermentation Convergence Technology; Kookmin University; Seoul Republic of Korea
| | - Kwon-Young Choi
- Department of Environmental Engineering; Ajou University; Suwon Gyeonggi-do Republic of Korea
| | - Yun-Gon Kim
- Department of Chemical Engineering; Soongsil University; Seoul Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering; College of Engineering; Konkuk University; Seoul Korea
- Institute for Ubiquitous Information Technology and Applications (CBRU); Konkuk University; Seoul South Korea
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47
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Alvarez CE, Trajtenberg F, Larrieux N, Saigo M, Golic A, Andreo CS, Hogenhout SA, Mussi MA, Drincovich MF, Buschiazzo A. The crystal structure of the malic enzyme from Candidatus Phytoplasma reveals the minimal structural determinants for a malic enzyme. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:332-340. [PMID: 29652260 DOI: 10.1107/s2059798318002759] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 02/15/2018] [Indexed: 11/10/2022]
Abstract
Phytoplasmas are wall-less phytopathogenic bacteria that produce devastating effects in a wide variety of plants. Reductive evolution has shaped their genome, with the loss of many genes, limiting their metabolic capacities. Owing to the high concentration of C4 compounds in plants, and the presence of malic enzyme (ME) in all phytoplasma genomes so far sequenced, the oxidative decarboxylation of L-malate might represent an adaptation to generate energy. Aster yellows witches'-broom (Candidatus Phytoplasma) ME (AYWB-ME) is one of the smallest of all characterized MEs, yet retains full enzymatic activity. Here, the crystal structure of AYWB-ME is reported, revealing a unique fold that differs from those of `canonical' MEs. AYWB-ME is organized as a dimeric species formed by intertwining of the N-terminal domains of the protomers. As a consequence of such structural differences, key catalytic residues such as Tyr36 are positioned in the active site of each protomer but are provided by the other protomer of the dimer. A Tyr36Ala mutation abolishes the catalytic activity, indicating the key importance of this residue in the catalytic process but not in the dimeric assembly. Phylogenetic analyses suggest that larger MEs (large-subunit or chimeric MEs) might have evolved from this type of smaller scaffold by gaining small sequence cassettes or an entire functional domain. The Candidatus Phytoplasma AYWB-ME structure showcases a novel minimal structure design comprising a fully functional active site, making this enzyme an attractive starting point for rational genetic design.
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Affiliation(s)
- C E Alvarez
- CEFOBI, Suipacha 531, Rosario, S2000LRJ Santa Fe, Argentina
| | - F Trajtenberg
- Institute Pasteur, Mataojo 2020, Montevideo, Uruguay
| | - N Larrieux
- Institute Pasteur, Mataojo 2020, Montevideo, Uruguay
| | - M Saigo
- CEFOBI, Suipacha 531, Rosario, S2000LRJ Santa Fe, Argentina
| | - A Golic
- CEFOBI, Suipacha 531, Rosario, S2000LRJ Santa Fe, Argentina
| | - C S Andreo
- CEFOBI, Suipacha 531, Rosario, S2000LRJ Santa Fe, Argentina
| | - S A Hogenhout
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England
| | - M A Mussi
- CEFOBI, Suipacha 531, Rosario, S2000LRJ Santa Fe, Argentina
| | - M F Drincovich
- CEFOBI, Suipacha 531, Rosario, S2000LRJ Santa Fe, Argentina
| | - A Buschiazzo
- Institute Pasteur, Mataojo 2020, Montevideo, Uruguay
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48
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Skorokhodova AY, Stasenko AA, Gulevich AY, Debabov VG. Effect of Anaplerotic Pathways Activation on CO2-dependent Anaerobic Glucose Utilization by Escherichia coli Strains Deficient in the Main Pathways of Mixed Acid Fermentation. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818020102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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49
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Tronconi MA, Andreo CS, Drincovich MF. Chimeric Structure of Plant Malic Enzyme Family: Different Evolutionary Scenarios for NAD- and NADP-Dependent Isoforms. FRONTIERS IN PLANT SCIENCE 2018; 9:565. [PMID: 29868045 PMCID: PMC5958461 DOI: 10.3389/fpls.2018.00565] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/10/2018] [Indexed: 05/15/2023]
Abstract
Malic enzyme (ME) comprises a family of proteins with multiple isoforms located in different compartments of eukaryotic cells. In plants, cytosolic and plastidic enzymes share several characteristics such as NADP specificity (NADP-ME), oxaloacetate decarboxylase (OAD) activity, and homo-oligomeric assembly. However, mitochondrial counterparts are NAD-dependent proteins (mNAD-ME) lacking OAD activity, which can be structured as homo- and hetero-oligomers of two different subunits. In this study, we examined the molecular basis of these differences using multiple sequence analysis, structural modeling, and phylogenetic approaches. Plant mNAD-MEs show the lowest identity values when compared with other eukaryotic MEs with major differences including short amino acid insertions distributed throughout the primary sequence. Some residues in these exclusive segments are co-evolutionarily connected, suggesting that they could be important for enzymatic functionality. Phylogenetic analysis indicates that eukaryotes from different kingdoms used different strategies for acquiring the current set of NAD(P)-ME isoforms. In this sense, while the full gene family of vertebrates derives from the same ancestral gene, plant NADP-ME and NAD-ME isoforms have a distinct evolutionary history. Plant NADP-ME genes may have arisen from the α-protobacterial-like mitochondrial ancestor, a characteristic shared with major eukaryotic taxa. On the other hand, plant mNAD-ME genes were probably gained through an independent process involving the Archaeplastida ancestor. Finally, several residue signatures unique to all plant mNAD-MEs could be identified, some of which might be functionally connected to their exclusive biochemical properties. In light of these results, molecular evolutionary scenarios for these widely distributed enzymes in plants are discussed.
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Golyshina OV, Toshchakov SV, Makarova KS, Gavrilov SN, Korzhenkov AA, La Cono V, Arcadi E, Nechitaylo TY, Ferrer M, Kublanov IV, Wolf YI, Yakimov MM, Golyshin PN. 'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ. Nat Commun 2017; 8:60. [PMID: 28680072 PMCID: PMC5498576 DOI: 10.1038/s41467-017-00104-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/31/2017] [Indexed: 11/09/2022] Open
Abstract
Intriguing, yet uncultured ‘ARMAN’-like archaea are metabolically dependent on other members of the microbial community. It remains uncertain though which hosts they rely upon, and, because of the lack of complete genomes, to what extent. Here, we report the co-culturing of ARMAN-2-related organism, Mia14, with Cuniculiplasma divulgatum PM4 during the isolation of this strain from acidic streamer in Parys Mountain (Isle of Anglesey, UK). Mia14 is highly enriched in the binary culture (ca. 10% genomic reads) and its ungapped 0.95 Mbp genome points at severe voids in central metabolic pathways, indicating dependence on the host, C. divulgatum PM4. Analysis of C. divulgatum isolates from different sites and shotgun sequence data of Parys Mountain samples suggests an extensive genetic exchange between Mia14 and hosts in situ. Within the subset of organisms with high-quality genomic assemblies representing the ‘DPANN’ superphylum, the Mia14 lineage has had the largest gene flux, with dozens of genes gained that are implicated in the host interaction. In the absence of complete genomes, the metabolic capabilities of uncultured ARMAN-like archaea have been uncertain. Here, Golyshina et al. apply an enrichment culture technique and find that the ungapped genome of the ARMAN-like archaeon Mia14 has lost key metabolic pathways, suggesting dependence on the host archaeon Cuniculiplasma divulgatum.
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Affiliation(s)
- Olga V Golyshina
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK.
| | | | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine-National Institutes of Health, Bethesda, MD, 20894, USA
| | - Sergey N Gavrilov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow, 117312, Russia
| | | | - Violetta La Cono
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Erika Arcadi
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Taras Y Nechitaylo
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, Jena, 07745, Germany
| | - Manuel Ferrer
- Institute of Catalysis CSIC, Campus Cantoblanco, 28049, Madrid, Spain
| | - Ilya V Kublanov
- Immanuel Kant Baltic Federal University, Kaliningrad, 236040, Russia.,Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow, 117312, Russia
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine-National Institutes of Health, Bethesda, MD, 20894, USA
| | - Michail M Yakimov
- Immanuel Kant Baltic Federal University, Kaliningrad, 236040, Russia.,Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
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