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Diversity of gut methanogens and functional enzymes associated with methane metabolism in smallholder dairy cattle. Arch Microbiol 2022; 204:608. [PMID: 36075991 DOI: 10.1007/s00203-022-03187-z] [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: 11/27/2021] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/02/2022]
Abstract
Methane is a greenhouse gas with disastrous consequences when released to intolerable levels. Ruminants produce methane during gut fermentation releasing it through belching and/or flatulence. To better understand the diversity of methanogens and functional enzymes associated with methane metabolism in dairy cows, 48 samples; 6 rumen fluid and 42 dung samples were collected from Kenyan and Tanzanian farms and were analyzed using shotgun metagenomic approach. Statistical analysis for species frequency, relative abundance, percentages, and P values were undertaken using MS Excel and IBM SPSS statistics 20. The results showed archaea from 5 phyla, 9 classes, 16 orders, 25 families, 59 genera, and 87 species. Gut sites significantly contributed to the presence and distribution of various methanogens (P < 0.01). The class Methanomicrobia was abundant in the rumen samples (~ 39%) and dung (~ 44%). The most abundant (~ 17%) methanogen species identified was Methanocorpusculum labreanum. However, some taxonomic class data were unclassified (~ 6% in the rumen and ~ 4% in the dung). Five functional enzymes: Glycine/Serine hydroxymethyltransferase, Formylmethanofuran-tetrahydromethanopterin N-formyltransferase, Formate dehydrogenase, anaerobic carbon monoxide dehydrogenase, and catalase-peroxidase associated with methane metabolism were identified. KEGG functional metabolic analysis for the enzymes identified during this study was significant (P < 0.05) for five metabolism processes. The methanogen species abundances from this study in numbers/kind can be utilized exclusively or jointly as indirect selection criteria for methane mitigation. When targeting functional genes of the microbes/animal for better performance, the concern not to affect the host animal's functionality should be undertaken. Future studies should consider taxonomically categorizing unclassified species.
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l-Serine Biosensor-Controlled Fermentative Production of l-Tryptophan Derivatives by Corynebacterium glutamicum. BIOLOGY 2022; 11:biology11050744. [PMID: 35625472 PMCID: PMC9138238 DOI: 10.3390/biology11050744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary l-tryptophan is an amino acid found in proteins. Its derivatives, such as hydroxylated or halogenated l-tryptophans, find applications in the chemical and pharmaceutical industries, for example, in therapeutic peptides. Biotechnology provides a sustainable way for the production of l-tryptophan and its derivatives. In the final reaction of l-tryptophan biosynthesis in bacteria, such as Corynebacterium glutamicum, another amino acid, l-serine, is incorporated. Here, we show that C. glutamicum TrpB is able to convert indole derivatives, which were added to cells synthesizing l-serine, to the corresponding l-tryptophan derivatives. The gene trpB was expressed under the control of the l-serine-responsive transcriptional activator SerR in the C. glutamicum cells engineered for this fermentation process. Abstract l-Tryptophan derivatives, such as hydroxylated or halogenated l-tryptophans, are used in therapeutic peptides and agrochemicals and as precursors of bioactive compounds, such as serotonin. l-Tryptophan biosynthesis depends on another proteinogenic amino acid, l-serine, which is condensed with indole-3-glycerophosphate by tryptophan synthase. This enzyme is composed of the α-subunit TrpA, which catalyzes the retro-aldol cleavage of indole-3-glycerol phosphate, yielding glyceraldehyde-3-phosphate and indole, and the β-subunit TrpB that catalyzes the β-substitution reaction between indole and l-serine to water and l-tryptophan. TrpA is reported as an allosteric actuator, and its absence severely attenuates TrpB activity. In this study, however, we showed that Corynebacterium glutamicum TrpB is catalytically active in the absence of TrpA. Overexpression of C. glutamicumtrpB in a trpBA double deletion mutant supported growth in minimal medium only when exogenously added indole was taken up into the cell and condensed with intracellularly synthesized l-serine. The fluorescence reporter gene of an l-serine biosensor, which was based on the endogenous transcriptional activator SerR and its target promoter PserE, was replaced by trpB. This allowed for l-serine-dependent expression of trpB in an l-serine-producing strain lacking TrpA. Upon feeding of the respective indole derivatives, this strain produced the l-tryptophan derivatives 5-hydroxytryptophan, 7-bromotryptophan, and 5-fluorotryptophan.
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Li N, Wang M, Yu S, Zhou J. Optimization of CRISPR-Cas9 through promoter replacement and efficient production of L-homoserine in Corynebacterium glutamicum. Biotechnol J 2021; 16:e2100093. [PMID: 34018325 DOI: 10.1002/biot.202100093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Corynebacterium glutamicum is an important chassis for industrial applications. The low efficiency of commonly used genome editing methods for C. glutamicum limits the rapid multiple engineering of the bacterium. MAIN METHODS AND MAJOR RESULTS In this study, chromosome-borne expression of cas9 and recET from Escherichia coli K12-MG1655 was achieved to avoid toxicity to the strain, increase the probability of homologous recombination, and reduce loss of viability caused by double-strand breaks. Constitutive strong promoters, such as P45 , Ptrc , and PH36 , were used to replace PglyA and to expand the application of the CRISPR-Cas9 system. By using this system, a C. glutamicum strain producing L-homoserine to 22.1 g per L in a 5-L bioreactor after 96 h was obtained. CONCLUSIONS AND IMPLICATIONS Through the application of visualized fluorescent protein, the process of plasmid curing was optimized, obtain a continuous and rapid CRISPR-Cas9 genome editing system. The method described here could be useful to construct C. glutamicum mutant rapidly.
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Affiliation(s)
- Ning Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China.,State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Miao Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Shiqin Yu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
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The Iron Deficiency Response of Corynebacterium glutamicum and a Link to Thiamine Biosynthesis. Appl Environ Microbiol 2020; 86:AEM.00065-20. [PMID: 32144105 DOI: 10.1128/aem.00065-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 02/28/2020] [Indexed: 12/20/2022] Open
Abstract
The response to iron limitation of the Gram-positive soil bacterium Corynebacterium glutamicum was analyzed with respect to secreted metabolites, the transcriptome, and the proteome. During growth in glucose minimal medium, iron limitation caused a shift from lactate to pyruvate as the major secreted organic acid complemented by l-alanine and 2-oxoglutarate. Transcriptome and proteome analyses revealed that a pronounced iron starvation response governed by the transcriptional regulators DtxR and RipA was detectable in the late, but not in the early, exponential-growth phase. A link between iron starvation and thiamine pyrophosphate (TPP) biosynthesis was uncovered by the strong upregulation of thiC As phosphomethylpyrimidine synthase (ThiC) contains an iron-sulfur cluster, limiting activities of the TPP-dependent pyruvate-2-oxoglutarate dehydrogenase supercomplex probably cause the excretion of pyruvate and 2-oxoglutarate. In line with this explanation, thiamine supplementation could strongly diminish the secretion of these acids. The upregulation of thiC and other genes involved in thiamine biosynthesis and transport is presumably due to TPP riboswitches present at the 5' end of the corresponding operons. The results obtained in this study provide new insights into iron homeostasis in C. glutamicum and demonstrate that the metabolic consequences of iron limitation can be due to the iron dependency of coenzyme biosynthesis.IMPORTANCE Iron is an essential element for most organisms but causes problems due to poor solubility under oxic conditions and due to toxicity by catalyzing the formation of reactive oxygen species (ROS). Therefore, bacteria have evolved complex regulatory networks for iron homeostasis aiming at a sufficient iron supply while minimizing ROS formation. In our study, the responses of the actinobacterium Corynebacterium glutamicum to iron limitation were analyzed, resulting in a detailed view on the processes involved in iron homeostasis in this model organism. In particular, we provide evidence that iron limitation causes TPP deficiency, presumably due to insufficient activity of the iron-dependent phosphomethylpyrimidine synthase (ThiC). TPP deficiency was deduced from the upregulation of genes controlled by a TPP riboswitch and secretion of metabolites caused by insufficient activity of the TPP-dependent enzymes pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase. To our knowledge, the link between iron starvation and thiamine synthesis has not been elaborated previously.
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Liu W, Tang D, Wang H, Lian J, Huang L, Xu Z. Combined genome editing and transcriptional repression for metabolic pathway engineering in Corynebacterium glutamicum using a catalytically active Cas12a. Appl Microbiol Biotechnol 2019; 103:8911-8922. [PMID: 31583448 DOI: 10.1007/s00253-019-10118-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/20/2019] [Accepted: 09/03/2019] [Indexed: 10/25/2022]
Abstract
Corynebacterium glutamicum is a versatile workhorse for producing industrially important commodities. The design of an optimal strain often requires the manipulation of metabolic and regulatory genes to different levels, such as overexpression, downregulation, and deletion. Unfortunately, few tools to achieve multiple functions simultaneously have been reported. Here, a dual-functional clustered regularly interspaced short palindromic repeats (CRISPR) (RE-CRISPR) system that combined genome editing and transcriptional repression was designed using a catalytically active Cas12a (a.k.a. Cpf1) in C. glutamicum. Firstly, gene deletion was achieved using Cas12a under a constitutive promoter. Then, via engineering of the guide RNA sequences, transcriptional repression was successfully achieved using a catalytically active Cas12a with crRNAs containing 15 or 16 bp spacer sequences, whose gene repression efficiency was comparable to that of the canonical system (deactivated Cas12a with full-length crRNAs). Finally, RE-CRISPR was developed to achieve genome editing and transcriptional repression simultaneously by transforming a single crRNA plasmid and Cas12a plasmid. The application of RE-CRISPR was demonstrated to increase the production of cysteine and serine for ~ 3.7-fold and 2.5-fold, respectively, in a single step. This study expands the application of CRISPR/Cas12a-based genome engineering and provides a powerful synthetic biology tool for multiplex metabolic engineering of C. glutamicum.
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Affiliation(s)
- Wei Liu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Dandan Tang
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- State Key Laboratory of Clean Energy Utilization, College of Energy Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Haijiao Wang
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Lei Huang
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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Zhang X, Lai L, Xu G, Zhang X, Shi J, Koffas MAG, Xu Z. Rewiring the Central Metabolic Pathway for High‐Yieldl‐Serine Production inCorynebacterium glutamicumby Using Glucose. Biotechnol J 2019; 14:e1800497. [DOI: 10.1002/biot.201800497] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/14/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Xiaomei Zhang
- Laboratory of Pharmaceutical EngineeringSchool of Pharmaceutics Science, Jiangnan UniversityWuxi 214122 China
- The Key Laboratory of Industrial BiotechnologyMinistry of Education, School of Biotechnology, Jiangnan UniversityWuxi 214122 China
| | - Lianhe Lai
- Laboratory of Pharmaceutical EngineeringSchool of Pharmaceutics Science, Jiangnan UniversityWuxi 214122 China
- The Key Laboratory of Industrial BiotechnologyMinistry of Education, School of Biotechnology, Jiangnan UniversityWuxi 214122 China
| | - Guoqiang Xu
- The Key Laboratory of Industrial BiotechnologyMinistry of Education, School of Biotechnology, Jiangnan UniversityWuxi 214122 China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan UniversityNo. 1800, Lihu Avenue Wuxi 214122 China
| | - Xiaojuan Zhang
- The Key Laboratory of Industrial BiotechnologyMinistry of Education, School of Biotechnology, Jiangnan UniversityWuxi 214122 China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan UniversityNo. 1800, Lihu Avenue Wuxi 214122 China
| | - Jinsong Shi
- Laboratory of Pharmaceutical EngineeringSchool of Pharmaceutics Science, Jiangnan UniversityWuxi 214122 China
- The Key Laboratory of Industrial BiotechnologyMinistry of Education, School of Biotechnology, Jiangnan UniversityWuxi 214122 China
| | - Mattheos A. G. Koffas
- Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic InstituteTroy 12180 NY USA
- Department of Chemical and Biological EngineeringRensselaer Polytechnic InstituteTroy 12180 NY USA
| | - Zhenghong Xu
- The Key Laboratory of Industrial BiotechnologyMinistry of Education, School of Biotechnology, Jiangnan UniversityWuxi 214122 China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan UniversityNo. 1800, Lihu Avenue Wuxi 214122 China
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Schwentner A, Feith A, Münch E, Stiefelmaier J, Lauer I, Favilli L, Massner C, Öhrlein J, Grund B, Hüser A, Takors R, Blombach B. Modular systems metabolic engineering enables balancing of relevant pathways for l-histidine production with Corynebacterium glutamicum. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:65. [PMID: 30962820 PMCID: PMC6432763 DOI: 10.1186/s13068-019-1410-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/14/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND l-Histidine biosynthesis is embedded in an intertwined metabolic network which renders microbial overproduction of this amino acid challenging. This is reflected in the few available examples of histidine producers in literature. Since knowledge about the metabolic interplay is limited, we systematically perturbed the metabolism of Corynebacterium glutamicum to gain a holistic understanding in the metabolic limitations for l-histidine production. We, therefore, constructed C. glutamicum strains in a modularized metabolic engineering approach and analyzed them with LC/MS-QToF-based systems metabolic profiling (SMP) supported by flux balance analysis (FBA). RESULTS The engineered strains produced l-histidine, equimolar amounts of glycine, and possessed heavily decreased intracellular adenylate concentrations, despite a stable adenylate energy charge. FBA identified regeneration of ATP from 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) as crucial step for l-histidine production and SMP identified strong intracellular accumulation of inosine monophosphate (IMP) in the engineered strains. Energy engineering readjusted the intracellular IMP and ATP levels to wild-type niveau and reinforced the intrinsic low ATP regeneration capacity to maintain a balanced energy state of the cell. SMP further indicated limitations in the C1 supply which was overcome by expression of the glycine cleavage system from C. jeikeium. Finally, we rerouted the carbon flux towards the oxidative pentose phosphate pathway thereby further increasing product yield to 0.093 ± 0.003 mol l-histidine per mol glucose. CONCLUSION By applying the modularized metabolic engineering approach combined with SMP and FBA, we identified an intrinsically low ATP regeneration capacity, which prevents to maintain a balanced energy state of the cell in an l-histidine overproduction scenario and an insufficient supply of C1 units. To overcome these limitations, we provide a metabolic engineering strategy which constitutes a general approach to improve the production of ATP and/or C1 intensive products.
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Affiliation(s)
- Andreas Schwentner
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - André Feith
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Eugenia Münch
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Judith Stiefelmaier
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Ira Lauer
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Lorenzo Favilli
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Christoph Massner
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | | | - Bastian Grund
- Evonik Creavis GmbH, Paul-Baumann-Straße 1, 45772 Marl, Germany
| | - Andrea Hüser
- Evonik Nutrition & Care GmbH, Kantstraße 2, 33790 Halle, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Bastian Blombach
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany
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Wei L, Wang H, Xu N, Zhou W, Ju J, Liu J, Ma Y. Metabolic engineering of Corynebacterium glutamicum for l-cysteine production. Appl Microbiol Biotechnol 2018; 103:1325-1338. [DOI: 10.1007/s00253-018-9547-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/26/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
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Kumar A, Wu G, Wu Z, Kumar N, Liu Z. Improved catalytic properties of a serine hydroxymethyl transferase from Idiomarina loihiensis by site directed mutagenesis. Int J Biol Macromol 2018; 117:1216-1223. [PMID: 29727646 DOI: 10.1016/j.ijbiomac.2018.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 04/05/2018] [Accepted: 05/01/2018] [Indexed: 11/17/2022]
Abstract
A novel glyA gene was screened from a marine bacterium, Idiomarina loihiensis encoding a thermo-stable serine hydroxymethyl transferase (SHMT; 418 AA; 45.4 kDa). The activities of wild type (WT) and mutants were analyzed against d-phenylserine using pyrodoxal-5-phosphate (PLP) as cofactor under optimized conditions. Based on homology modelling and molecular docking, several residues were found that may be able to improve the activity of WT-SHMT. Site directed mutagenesis was conducted. The activity and thermostability of the wild type SHMT was improved by two variants H61G and G132P, which showed a noteworthy change in the thermo-stability and activity as compared to WT. To investigate the mechanism of activity of mutants, we combined two residues into one mutant DUAL. WT showed the optimum activity at 50 °C, whereas H61G, G132P and DUAL had the temperature optima of 55, 60 and 60 °C, respectively. These mutants G132P, H61G and DUAL were quite stable at 45 and 55 °C as compared to WT. Dual mutant was relatively more stable at all tested pH(s) while WT loses its activity in alkaline pH(s). Kinetics studies indicated the 1.52, 2.42 and 4.54 folds increase in the kcat value of H61G, G132P and Dual mutants as compared to WT respectively. The molecular docking indicated that hydrophobic interactions are more prominent than hydrogen-bonding and had more influence on ligand binding and active site cavity. The molecular dynamics showed the changed RMSD values for ligand and formation of new hydrogen bonds, hydrophobic interaction which considerably increased the activity and thermo-stability of the mutant proteins as compared to WT. Thus, increased stabilities at higher temperatures and activities can be attributed to new hydrogen bonding, altered active site geometry and increased ligand interactions.
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Affiliation(s)
- Ashok Kumar
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430 070, China; Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 172 234, Himachal Pradesh, India
| | - Gaobing Wu
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430 070, China
| | - Zuo Wu
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430 070, China
| | - Narendra Kumar
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 172 234, Himachal Pradesh, India
| | - Ziduo Liu
- College of Life Science and Technology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430 070, China.
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Zhang Y, Shang X, Lai S, Zhang Y, Hu Q, Chai X, Wang B, Liu S, Wen T. Reprogramming One-Carbon Metabolic Pathways To Decouple l-Serine Catabolism from Cell Growth in Corynebacterium glutamicum. ACS Synth Biol 2018; 7:635-646. [PMID: 29316787 DOI: 10.1021/acssynbio.7b00373] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
l-Serine, the principal one-carbon source for DNA biosynthesis, is difficult for microorganisms to accumulate due to the coupling of l-serine catabolism and microbial growth. Here, we reprogrammed the one-carbon unit metabolic pathways in Corynebacterium glutamicum to decouple l-serine catabolism from cell growth. In silico model-based simulation showed a negative influence on glyA-encoding serine hydroxymethyltransferase flux with l-serine productivity. Attenuation of glyA transcription resulted in increased l-serine accumulation, and a decrease in purine pools, poor growth and longer cell shapes. The gcvTHP-encoded glycine cleavage (Gcv) system from Escherichia coli was introduced into C. glutamicum, allowing glycine-derived 13CH2 to be assimilated into intracellular purine synthesis, which resulted in an increased amount of one-carbon units. Gcv introduction not only restored cell viability and morphology but also increased l-serine accumulation. Moreover, comparative proteomic analysis indicated that abundance changes of the enzymes involved in one-carbon unit cycles might be responsible for maintaining one-carbon unit homeostasis. Reprogramming of the one-carbon metabolic pathways allowed cells to reach a comparable growth rate to accumulate 13.21 g/L l-serine by fed-batch fermentation in minimal medium. This novel strategy provides new insights into the regulation of cellular properties and essential metabolite accumulation by introducing an extrinsic pathway.
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Affiliation(s)
- Yun Zhang
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiuling Shang
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shujuan Lai
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Zhang
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qitiao Hu
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Chai
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Wang
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuwen Liu
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tingyi Wen
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid
Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
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Lee JH, Wendisch VF. Production of amino acids - Genetic and metabolic engineering approaches. BIORESOURCE TECHNOLOGY 2017; 245:1575-1587. [PMID: 28552565 DOI: 10.1016/j.biortech.2017.05.065] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 05/22/2023]
Abstract
The biotechnological production of amino acids occurs at the million-ton scale and annually about 6milliontons of l-glutamate and l-lysine are produced by Escherichia coli and Corynebacterium glutamicum strains. l-glutamate and l-lysine production from starch hydrolysates and molasses is very efficient and access to alternative carbon sources and new products has been enabled by metabolic engineering. This review focusses on genetic and metabolic engineering of amino acid producing strains. In particular, rational approaches involving modulation of transcriptional regulators, regulons, and attenuators will be discussed. To address current limitations of metabolic engineering, this article gives insights on recent systems metabolic engineering approaches based on functional tools and method such as genome reduction, amino acid sensors based on transcriptional regulators and riboswitches, CRISPR interference, small regulatory RNAs, DNA scaffolding, and optogenetic control, and discusses future prospects.
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Affiliation(s)
- Jin-Ho Lee
- Major in Food Science & Biotechnology, School of Food Biotechnology & Nutrition, Kyungsung University, 309, Suyeong-ro, Nam-gu, Busan 48434, Republic of Korea
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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Shang X, Chai X, Lu X, Li Y, Zhang Y, Wang G, Zhang C, Liu S, Zhang Y, Ma J, Wen T. Native promoters of Corynebacterium glutamicum and its application in L-lysine production. Biotechnol Lett 2017; 40:383-391. [PMID: 29164417 DOI: 10.1007/s10529-017-2479-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/09/2017] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To identify useful native promoters of Corynebacterium glutamicum for fine-tuning of gene expression in metabolic engineering. RESULTS Sixteen native promoters of C. glutamicum were characterized. These promoters covered a strength range of 31-fold with small increments and exhibited relatively stable activity during the whole growth phase using β-galactosidase as the reporter. The mRNA level and enzymatic activity of the lacZ reporter gene exhibited high correlation (R 2 = 0.96) under the control of these promoters. Sequence analysis found that strong promoters had high similarity of the -10 hexamer to the consensus sequence and preference of the AT-rich UP element upstream the -35 region. To test the utility of the promoter library, the characterized native promoters were applied to modulate the sucCD-encoded succinyl-CoA synthetase expression for L-lysine overproduction. CONCLUSIONS The native promoters with various strengths realize the efficient and precise regulation of gene expression in metabolic engineering of C. glutamicum.
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Affiliation(s)
- Xiuling Shang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Xin Chai
- Beijing Zhongke EPPEN Biotechnology Co., Ltd, Beijing, 100085, China.,Ningxia EPPEN Biotechnology Co., Ltd, Yongning, 750100, Ningxia, China
| | - Xuemei Lu
- Beijing Zhongke EPPEN Biotechnology Co., Ltd, Beijing, 100085, China.,Ningxia EPPEN Biotechnology Co., Ltd, Yongning, 750100, Ningxia, China
| | - Yuan Li
- Beijing Zhongke EPPEN Biotechnology Co., Ltd, Beijing, 100085, China.,Ningxia EPPEN Biotechnology Co., Ltd, Yongning, 750100, Ningxia, China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Guoqiang Wang
- Beijing Zhongke EPPEN Biotechnology Co., Ltd, Beijing, 100085, China.,Ningxia EPPEN Biotechnology Co., Ltd, Yongning, 750100, Ningxia, China
| | - Chen Zhang
- Beijing Zhongke EPPEN Biotechnology Co., Ltd, Beijing, 100085, China.,Ningxia EPPEN Biotechnology Co., Ltd, Yongning, 750100, Ningxia, China
| | - Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Yu Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Jiyin Ma
- Beijing Zhongke EPPEN Biotechnology Co., Ltd, Beijing, 100085, China.,Ningxia EPPEN Biotechnology Co., Ltd, Yongning, 750100, Ningxia, China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China. .,Beijing Zhongke EPPEN Biotechnology Co., Ltd, Beijing, 100085, China. .,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Zou Y, Chen T, Feng L, Zhang S, Xing D, Wang Z. Enhancement of 5-aminolevulinic acid production by metabolic engineering of the glycine biosynthesis pathway in Corynebacterium glutamicum. Biotechnol Lett 2017; 39:1369-1374. [DOI: 10.1007/s10529-017-2362-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/18/2017] [Indexed: 11/30/2022]
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14
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Guo W, Chen Z, Zhang X, Xu G, Zhang X, Shi J, Xu Z. A novel aceE mutation leading to a better growth profile and a higher l-serine production in a high-yield l-serine-producing Corynebacterium glutamicum strain. ACTA ACUST UNITED AC 2016; 43:1293-301. [DOI: 10.1007/s10295-016-1801-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/20/2016] [Indexed: 10/21/2022]
Abstract
Abstract
A comparative genomic analysis was performed to study the genetic variations between the l-serine-producing strain Corynebacterium glutamicum SYPS-062 and the mutant strain SYPS-062-33a, which was derived from SYPS-062 by random mutagenesis with enhanced l-serine production. Some variant genes between the two strains were reversely mutated or deleted in the genome of SYPS-062-33a to verify the influences of the gene mutations introduced by random mutagenesis. It was found that a His-594 → Tyr mutation in aceE was responsible for the more accumulation of by-products, such as l-alanine and l-valine, in SYPS-062-33a. Furthermore, the influence of this point mutation on the l-serine production was investigated, and the results suggested that this point mutation led to a better growth profile and a higher l-serine production in the high-yield strain 33a∆SSAAI, which was derived from SYPS-062-33a by metabolic engineering with the highest l-serine production to date.
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Affiliation(s)
- Wen Guo
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
- grid.258151.a 0000000107081323 The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 214122 Wuxi People’s Republic of China
| | - Ziwei Chen
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
- grid.258151.a 0000000107081323 The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 214122 Wuxi People’s Republic of China
| | - Xiaomei Zhang
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
- grid.258151.a 0000000107081323 The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 214122 Wuxi People’s Republic of China
| | - Guoqiang Xu
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
- grid.258151.a 0000000107081323 National Engineering Laboratory for Cereal Fermentation Technology Jiangnan University 214122 Wuxi People’s Republic of China
| | - Xiaojuan Zhang
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
| | - Jinsong Shi
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
- grid.258151.a 0000000107081323 The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 214122 Wuxi People’s Republic of China
| | - Zhenghong Xu
- grid.258151.a 0000000107081323 Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science Jiangnan University 214122 Wuxi People’s Republic of China
- grid.258151.a 0000000107081323 The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology Jiangnan University 214122 Wuxi People’s Republic of China
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15
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Characterization, modification, and overexpression of 3-phosphoglycerate dehydrogenase in Corynebacterium glutamicum for enhancing l-serine production. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0936-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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16
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Pátek M, Nešvera J. Promoters and Plasmid Vectors of Corynebacterium glutamicum. CORYNEBACTERIUM GLUTAMICUM 2013. [DOI: 10.1007/978-3-642-29857-8_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Metabolic engineering and flux analysis of Corynebacterium glutamicum for L-serine production. SCIENCE CHINA-LIFE SCIENCES 2012; 55:283-90. [DOI: 10.1007/s11427-012-4304-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 03/19/2012] [Indexed: 12/14/2022]
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18
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Development and application of an arabinose-inducible expression system by facilitating inducer uptake in Corynebacterium glutamicum. Appl Environ Microbiol 2012; 78:5831-8. [PMID: 22685153 DOI: 10.1128/aem.01147-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Corynebacterium glutamicum is currently used for the industrial production of a variety of biological materials. Many available inducible expression systems in this species use lac-derived promoters from Escherichia coli that exhibit much lower levels of inducible expression and leaky basal expression. We developed an arabinose-inducible expression system that contains the L-arabinose regulator AraC, the P(BAD) promoter from the araBAD operon, and the L-arabinose transporter AraE, all of which are derived from E. coli. The level of inducible P(BAD)-based expression could be modulated over a wide concentration range from 0.001 to 0.4% L-arabinose. This system tightly controlled the expression of the uracil phosphoribosyltransferase without leaky expression. When the gene encoding green fluorescent protein (GFP) was under the control of P(BAD) promoter, flow cytometry analysis showed that GFP was expressed in a highly homogeneous profile throughout the cell population. In contrast to the case in E. coli, P(BAD) induction was not significantly affected in the presence of different carbon sources in C. glutamicum, which makes it useful in fermentation applications. We used this system to regulate the expression of the odhI gene from C. glutamicum, which encodes an inhibitor of α-oxoglutarate dehydrogenase, resulting in high levels of glutamate production (up to 13.7 mM) under biotin nonlimiting conditions. This system provides an efficient tool available for molecular biology and metabolic engineering of C. glutamicum.
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Sigma factors and promoters in Corynebacterium glutamicum. J Biotechnol 2011; 154:101-13. [DOI: 10.1016/j.jbiotec.2011.01.017] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 01/05/2011] [Accepted: 01/18/2011] [Indexed: 11/19/2022]
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20
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Tools for genetic manipulations in Corynebacterium glutamicum and their applications. Appl Microbiol Biotechnol 2011; 90:1641-54. [DOI: 10.1007/s00253-011-3272-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 03/21/2011] [Accepted: 03/23/2011] [Indexed: 01/26/2023]
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21
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Frunzke J, Gätgens C, Brocker M, Bott M. Control of heme homeostasis in Corynebacterium glutamicum by the two-component system HrrSA. J Bacteriol 2011; 193:1212-21. [PMID: 21217007 PMCID: PMC3067591 DOI: 10.1128/jb.01130-10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 12/22/2010] [Indexed: 12/16/2022] Open
Abstract
The response regulator HrrA of the HrrSA two-component system (previously named CgtSR11) was recently found to be repressed by the global iron-dependent regulator DtxR in Corynebacterium glutamicum. Here, we provide evidence that HrrA mediates heme-dependent gene regulation in this nonpathogenic soil bacterium. Growth experiments and DNA microarray analysis revealed that C. glutamicum is able to use hemin as an alternative iron source and emphasize the involvement of the putative hemin ABC transporter HmuTUV and heme oxygenase (HmuO) in heme utilization. As a central part of this study, we investigated the regulon of the response regulator HrrA via comparative transcriptome analysis of an hrrA deletion mutant and C. glutamicum wild-type strain in combination with DNA-protein interaction studies with purified HrrA protein. Our data provide evidence for a heme-dependent transcriptional activation of heme oxygenase. Based on our results, it can be furthermore deduced that HrrA activates the expression of heme-containing components of the respiratory chain, namely, ctaD and the ctaE-qcrCAB operon encoding subunits I and III of cytochrome aa(3) oxidase and three subunits of the cytochrome bc(1) complex. In addition, HrrA was found to repress almost all genes involved in heme biosynthesis, including those for glutamyl-tRNA reductase (hemA), uroporphyrinogen decarboxylase (hemE), and ferrochelatase (hemH). Growth experiments with an hrrA deletion mutant showed that this strain is significantly impaired in heme utilization. In summary, our results provide evidence for a central role of the HrrSA system in the control of heme homeostasis in C. glutamicum.
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Affiliation(s)
- Julia Frunzke
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany.
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Schröder J, Tauch A. Transcriptional regulation of gene expression inCorynebacterium glutamicum: the role of global, master and local regulators in the modular and hierarchical gene regulatory network. FEMS Microbiol Rev 2010; 34:685-737. [DOI: 10.1111/j.1574-6976.2010.00228.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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