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Gao Y, Zhang X, Xu G, Zhang X, Li H, Shi J, Xu Z. Enhanced L-serine production by Corynebacterium glutamicum based on novel insights into L-serine exporters. Biotechnol J 2024; 19:e2300136. [PMID: 37971189 DOI: 10.1002/biot.202300136] [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: 03/25/2023] [Revised: 10/11/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
The L-serine exporters ThrE and SerE play important roles in L-serine production by Corynebacterium glutamicum. Deletion of both thrE and serE decreased L-serine titer by 60%, suggesting the existence of other L-serine exporters. A comparative transcriptomics identified NCgl0254 and NCgl0255 as novel L-serine exporters. Further analysis of the contributions of ThrE, SerE, NCgl0254, and NCgl0255 found that SerE was the major L-serine exporter in C. glutamicum and these four L-serine exporters were responsible for 79.7% of L-serine export. Deletion of one L-serine exporter upregulated the transcription levels of the other three, which might be coursed by increased intracellular concentrations of L-serine. Overexpression of NCgl0254 and NCgl0255 increased L-serine titer by 20.8% in C. glutamicum A36, while overexpression of the four L-serine exporters increased L-serine production by 31.9% (41.1 g·L-1 ) in C. glutamicum A36. The identification of novel L-serine exporters in C. glutamicum will help to improve industrial production of L-serine.
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Affiliation(s)
- Yujie Gao
- Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
| | - Xiaomei Zhang
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Wuxi, China
| | - Guoqiang Xu
- Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
| | - Xiaojuan Zhang
- Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
| | - Hui Li
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Wuxi, China
| | - Jinsong Shi
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Wuxi, China
| | - Zhenghong Xu
- Biotechnology of Ministry of Education, Jiangnan University, Wuxi, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, China
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2
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Wang Y, Bai Y, Zeng Q, Jiang Z, Liu Y, Wang X, Liu X, Liu C, Min W. Recent advances in the metabolic engineering and physiological opportunities for microbial synthesis of L-aspartic acid family amino acids: A review. Int J Biol Macromol 2023; 253:126916. [PMID: 37716660 DOI: 10.1016/j.ijbiomac.2023.126916] [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: 07/24/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Abstract
L-aspartic acid, L-threonine, L-isoleucine, l-lysine, and L-methionine constitute the l-aspartate amino acids (AFAAs). Except for L-aspartic acid, these are essential amino acids that cannot be synthesized by humans or animals themselves. E. coli and C. glutamicum are the main model organisms for AFAA production. It is necessary to reconstitute microbial cell factories and the physiological state of industrial fermentation cells for in-depth research into strains with higher AFAA production levels and optimal growth states. Considering that the anabolic pathways of the AFAAs and engineering modifications have rarely been reviewed in the latest progress, this work reviews the central metabolic pathways of two strains and strategies for the metabolic engineering of AFAA synthetic pathways. The challenges posed by microbial physiology in AFAA production and possible strategies to address them, as well as future research directions for constructing strains with high AFAA production levels, are discussed in this review article.
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Affiliation(s)
- Yusheng Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Yunlong Bai
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Qi Zeng
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Zeyuan Jiang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Yuzhe Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Xiyan Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Xiaoting Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Chunlei Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China.
| | - Weihong Min
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China.
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3
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Wang L, Yang H, Wu M, Zhang J, Zhang H, Mao Z, Chen X. Integrative transcriptome and proteome revealed high-yielding mechanisms of epsilon-poly-L-lysine by Streptomyces albulus. Front Microbiol 2023; 14:1123050. [PMID: 37152744 PMCID: PMC10157215 DOI: 10.3389/fmicb.2023.1123050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction ε-poly-L-lysine (ε-PL) is a high value, widely used natural antimicrobial peptide additive for foods and cosmetic products that is mainly produced by Streptomyces albulus. In previous work, we developed the high-yield industrial strain S. albulus WG-608 through successive rounds of engineering. Methods Here, we use integrated physiological, transcriptomic, and proteomics association analysis to resolve the complex mechanisms underlying high ε-PL production by comparing WG-608 with the progenitor strain M-Z18. Results Our results show that key genes in the glycolysis, pentose phosphate pathway, glyoxylate pathway, oxidative phosphorylation, and L-lysine biosynthesis pathways are differentially upregulated in WG-608, while genes in the biosynthetic pathways for fatty acids, various branched amino acids, and secondary metabolite by-products are downregulated. This regulatory pattern results in the introduction of more carbon atoms into L-lysine biosynthesis and ε-PL production. In addition, significant changes in the regulation of DNA replication, transcription, and translation, two component systems, and quorum sensing may facilitate the adaptability to environmental pressure and the biosynthesis of ε-PL. Overexpression of ppk gene and addition of polyP6 further enhanced the ε-PL production. Discussion This study enables comprehensive understanding of the biosynthetic mechanisms of ε-PL in S. albulus WG-608, while providing some genetic modification and fermentation strategies to further improve the ε-PL production.
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Sheremetieva M, Anufriev K, Khlebodarova T, Kolchanov N, Yanenko A. Rational metabolic engineering of Corynebacterium glutamicum to create a producer of L-valine. Vavilovskii Zhurnal Genet Selektsii 2022; 26:743-757. [PMID: 36694718 PMCID: PMC9834717 DOI: 10.18699/vjgb-22-90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 01/06/2023] Open
Abstract
L-Valine is one of the nine amino acids that cannot be synthesized de novo by higher organisms and must come from food. This amino acid not only serves as a building block for proteins, but also regulates protein and energy metabolism and participates in neurotransmission. L-Valine is used in the food and pharmaceutical industries, medicine and cosmetics, but primarily as an animal feed additive. Adding L-valine to feed, alone or mixed with other essential amino acids, allows for feeds with lower crude protein content, increases the quality and quantity of pig meat and broiler chicken meat, as well as improves reproductive functions of farm animals. Despite the fact that the market for L-valine is constantly growing, this amino acid is not yet produced in our country. In modern conditions, the creation of strains-producers and organization of L-valine production are especially relevant for Russia. One of the basic microorganisms most commonly used for the creation of amino acid producers, along with Escherichia coli, is the soil bacterium Corynebacterium glutamicum. This review is devoted to the analysis of the main strategies for the development of L- valine producers based on C. glutamicum. Various aspects of L-valine biosynthesis in C. glutamicum are reviewed: process biochemistry, stoichiometry and regulation, enzymes and their corresponding genes, export and import systems, and the relationship of L-valine biosynthesis with central cell metabolism. Key genetic elements for the creation of C. glutamicum-based strains-producers are identified. The use of metabolic engineering to enhance L-valine biosynthesis reactions and to reduce the formation of byproducts is described. The prospects for improving strains in terms of their productivity and technological characteristics are shown. The information presented in the review can be used in the production of producers of other amino acids with a branched side chain, namely L-leucine and L-isoleucine, as well as D-pantothenate.
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Affiliation(s)
| | - K.E. Anufriev
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, Moscow, Russia
| | - T.M. Khlebodarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - N.A. Kolchanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A.S. Yanenko
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, Moscow, Russia
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5
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Golubyatnikov V, Akinshin A, Ayupova N, Minushkina L. Stratifications and foliations in phase portraits of gene network models. Vavilovskii Zhurnal Genet Selektsii 2022; 26:758-764. [PMID: 36694713 PMCID: PMC9837163 DOI: 10.18699/vjgb-22-91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 01/06/2023] Open
Abstract
Periodic processes of gene network functioning are described with good precision by periodic trajectories (limit cycles) of multidimensional systems of kinetic-type differential equations. In the literature, such systems are often called dynamical, they are composed according to schemes of positive and negative feedback between components of these networks. The variables in these equations describe concentrations of these components as functions of time. In the preparation of numerical experiments with such mathematical models, it is useful to start with studies of qualitative behavior of ensembles of trajectories of the corresponding dynamical systems, in particular, to estimate the highest likelihood domain of the initial data, to solve inverse problems of parameter identification, to list the equilibrium points and their characteristics, to localize cycles in the phase portraits, to construct stratification of the phase portraits to subdomains with different qualities of trajectory behavior, etc. Such an à priori geometric analysis of the dynamical systems is quite analogous to the basic section "Investigation of functions and plot of their graphs" of Calculus, where the methods of qualitative studies of shapes of curves determined by equations are exposed. In the present paper, we construct ensembles of trajectories in phase portraits of some dynamical systems. These ensembles are 2-dimensional surfaces invariant with respect to shifts along the trajectories. This is analogous to classical construction in analytic mechanics, i. e. the level surfaces of motion integrals (energy, kinetic moment, etc.). Such surfaces compose foliations in phase portraits of dynamical systems of Hamiltonian mechanics. In contrast with this classical mechanical case, the foliations considered in this paper have singularities: all their leaves have a non-empty intersection, they contain limit cycles on their boundaries. Description of the phase portraits of these systems at the level of their stratifications, and that of ensembles of trajectories allows one to construct more realistic gene network models on the basis of methods of statistical physics and the theory of stochastic differential equations.
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Affiliation(s)
- V.P. Golubyatnikov
- Sobolev Institute of Mathematics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
| | - A.A. Akinshin
- Huawei Russian Research Institute, St. Petersburg, Russia
| | - N.B. Ayupova
- Sobolev Institute of Mathematics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
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The role of trehalose biosynthesis on mycolate composition and L-glutamate production in Corynebacterium glutamicum. Microbiol Res 2022; 267:127260. [PMID: 36463830 DOI: 10.1016/j.micres.2022.127260] [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: 06/15/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/21/2022]
Abstract
Corynebacterium glutamicum has been widely utilized for the industrial production of various amino acids. Trehalose is a prerequisite for the biosynthesis of mycolates which are structurally important constituents of the cell envelope in C. glutamicum. In this study, C. glutamicum mutant ΔSYA, which is unable to synthesize trehalose was constructed by deleting genes treS, treY and otsA in the three pathways of trehalose biosynthesis. In the fermentation medium, ΔSYA grew as well as the control C. glutamicum ATCC13869, synthesized similar levels of glucose monocorynomycolate, trehalose dicorynomycolate, and phospholipids to ATCC13869, but produced 12.5 times more L-glutamate than ATCC13869. Transcriptional levels of the genes relevant to L-arginine biosynthesis, encoding ODHC and relevant to the biosynthesis of sulfur-containing amino acids were down-regulated in ΔSYA. In minimal medium with different concentrations of glucose, ΔSYA grew worse than ATCC13869 but excreted more L-glutamate. When grown in minimal medium, phospholipids are the major lipid in ΔSYA, while glucose monocorynomycolate, trehalose dicorynomycolate, and phospholipids are the major lipid in ATCC13869. The transcriptional levels of mscCG in ΔSYA was significantly up-regulated when grown in minimal medium.
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Rasmussen C, Hoffman DW. Novel Nuclear Magnetic Resonance Method for Position-Specific Carbon Isotope Analysis of Organic Molecules with Significant Impurities. Anal Chem 2022; 94:15124-15131. [PMID: 36265131 DOI: 10.1021/acs.analchem.2c03356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We introduce a novel nuclear magnetic resonance (NMR) tool for determining position-specific carbon (13C/12C) isotope ratios within complex organic molecules. This analytical advancement allows us to measure position-specific isotope ratios of samples that contain impurities with NMR peaks that overlap with the signals of interest. The method involves collecting a series of alternating 13C-coupled and 13C-decoupled 1H NMR spectra using an NMR pulse sequence designed to optimize temperature stability, followed by a data reduction scheme that allows the signals of interest to be isolated from signals of impurities. The method was validated using glycine reference materials with known 13C/12C ratios from the US Geological Survey (USGS) into which impurities typically found in amino acid samples were intentionally introduced. Following validation, the method was used to determine position-specific 13C/12C ratios in a set of USGS l-valine materials (USGS73, -74, -75) that contain significant impurities associated with their biological origin. The l-valines were found to contain distinct intramolecular isotope variability, and the 13Cα isotope spikes in USGS74 and USGS75 were clearly detected, where they preserve carbon isotope ratios of -4.8 ± 0.9‰ and +11.5 ± 0.8‰, respectively. Carbon isotope abundance at the beta and gamma positions indicates that the USGS73 l-valine was obtained from a different source than USGS74 and -75. This analytical approach is a significant step forward in the field of position-specific isotope analysis at natural abundance via NMR because it enables the investigation of samples that contain impurities which are typically present in samples derived from natural sources.
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Affiliation(s)
- Cornelia Rasmussen
- University of Texas Institute for Geophysics, Jackson School of Geosciences, University of Texas at Austin, 10601 Exploration Way, Austin, Texas78758, United States
| | - David W Hoffman
- Department of Molecular Biosciences, College of Natural Science, University of Texas at Austin, 100 E 24th Street, Austin, Texas78712, United States
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8
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Ray D, Anand U, Jha NK, Korzeniewska E, Bontempi E, Proćków J, Dey A. The soil bacterium, Corynebacterium glutamicum, from biosynthesis of value-added products to bioremediation: A master of many trades. ENVIRONMENTAL RESEARCH 2022; 213:113622. [PMID: 35710026 DOI: 10.1016/j.envres.2022.113622] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/05/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Ever since its discovery in 1957, Corynebacterium glutamicum has become a well-established industrial strain and is known for its massive capability of producing various amino acids (like L-lysine and L-glutamate) and other value-added chemicals. With the rising demand for these bio-based products, the revelation of the whole genome sequences of the wild type strains, and the astounding advancements made in the fields of metabolic engineering and systems biology, our perspective of C. glutamicum has been revolutionized and has expanded our understanding of its strain development. With these advancements, a new era for C. glutamicum supremacy in the field of industrial biotechnology began. This led to remarkable progress in the enhancement of tailor-made over-producing strains and further development of the substrate spectrum of the bacterium, to easily accessible, economical, and renewable resources. C. glutamicum has also been metabolically engineered and used in the degradation/assimilation of highly toxic and ubiquitous environmental contaminant, arsenic, present in water or soil. Here, we review the history, current knowledge, progress, achievements, and future trends relating to the versatile metabolic factory, C. glutamicum. This review paper is devoted to C. glutamicum which is one of the leading industrial microbes, and one of the most promising and versatile candidates to be developed. It can be used not only as a platform microorganism to produce different value-added chemicals and recombinant proteins, but also as a tool for bioremediation, allowing to enhance specific properties, for example in situ bioremediation.
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Affiliation(s)
- Durga Ray
- Department of Microbiology, St. Aloysius' College, Jabalpur, Madhya Pradesh, 482001, India.
| | - Uttpal Anand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida, 201310, Uttar Pradesh, India; Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, 140413, Punjab, India; Department of Biotechnology, School of Applied & Life Sciences, Uttaranchal University, Dehradun 248007, Uttarakhand, India
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-719, Olsztyn, Poland
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123, Brescia, Italy
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631, Wrocław, Poland.
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, West Bengal, India.
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Li H, Xu D, Liu Y, Tan X, Qiao J, Li Z, Qi B, Hu X, Wang X. Preventing mycolic acid reduction in Corynebacterium glutamicum can efficiently increase L-glutamate production. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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10
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Banerjee D, Eng T, Sasaki Y, Srinivasan A, Oka A, Herbert RA, Trinh J, Singan VR, Sun N, Putnam D, Scown CD, Simmons B, Mukhopadhyay A. Genomics Characterization of an Engineered Corynebacterium glutamicum in Bioreactor Cultivation Under Ionic Liquid Stress. Front Bioeng Biotechnol 2021; 9:766674. [PMID: 34869279 PMCID: PMC8637627 DOI: 10.3389/fbioe.2021.766674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/27/2021] [Indexed: 12/04/2022] Open
Abstract
Corynebacterium glutamicum is an ideal microbial chassis for production of valuable bioproducts including amino acids and next generation biofuels. Here we resequence engineered isopentenol (IP) producing C. glutamicum BRC-JBEI 1.1.2 strain and assess differential transcriptional profiles using RNA sequencing under industrially relevant conditions including scale transition and compare the presence vs absence of an ionic liquid, cholinium lysinate ([Ch][Lys]). Analysis of the scale transition from shake flask to bioreactor with transcriptomics identified a distinct pattern of metabolic and regulatory responses needed for growth in this industrial format. These differential changes in gene expression corroborate altered accumulation of organic acids and bioproducts, including succinate, acetate, and acetoin that occur when cells are grown in the presence of 50 mM [Ch][Lys] in the stirred-tank reactor. This new genome assembly and differential expression analysis of cells grown in a stirred tank bioreactor clarify the cell response of an C. glutamicum strain engineered to produce IP.
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Affiliation(s)
- Deepanwita Banerjee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Thomas Eng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yusuke Sasaki
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Aparajitha Srinivasan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Asun Oka
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, United States
| | - Robin A Herbert
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jessica Trinh
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Vasanth R Singan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ning Sun
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, United States
| | - Dan Putnam
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Corinne D Scown
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Energy Analysis and Environmental Impacts Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Blake Simmons
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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11
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Wang J, Wang X, Liang Q, Li D, Li D, Guo Q. Transcriptome analysis of L-leucine-producing Corynebacterium glutamicum under the addition of trimethylglycine. Amino Acids 2021; 54:229-240. [PMID: 34837555 DOI: 10.1007/s00726-021-03105-5] [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: 05/07/2021] [Accepted: 11/14/2021] [Indexed: 11/30/2022]
Abstract
It has been widely reported that the addition of trimethylglycine (betaine) decreases osmotic pressure inhibition for cell growth, leading to increased production of amino acids. However, the underlying mechanism is unclear. To determine the global metabolic differences that occur under the addition of trimethylglycine, transcriptome analysis was performed. Transcriptome analysis of Corynebacterium glutamicum JL1211 revealed that 272 genes exhibited significant changes under trimethylglycine addition. We performed Gene Ontology (GO) and KEGG enrichment pathway analyses on these differentially expressed genes (DEGs). Significantly upregulated genes were mainly involved in the regulation of ABC transporters, especially phosphate transporters and sulfur metabolism. The three phosphate transporter genes pstC, pstA and pstB were upregulated by 13.06-fold, 29.80-fold and 30.49-fold, respectively. Notably, the transcriptional levels of the cysD, cysN, cysH and sir genes were upregulated by 81.5-fold, 57.3-fold, 77.6-fold and 125.4-fold, respectively, consistent with assimilatory sulfate reduction under the addition of trimethylglycine. The upregulation of ilvBN and leuD genes might result in increased L-leucine formation. The data indicated changes in the transcriptome of C. glutamicum with trimethylglycine treatment, thus providing a mechanism supporting the application of trimethylglycine in the production of L-leucine and other amino acids by C. glutamicum strains.
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Affiliation(s)
- Jian Wang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China.
| | - Xuesong Wang
- College of Life Sciences, Jilin University, Changchun, China
| | - Qing Liang
- College of Life Sciences, Jilin University, Changchun, China
| | - Deheng Li
- Xinjiang Fufeng Biotechnologies Co., Urumqi, China
| | - Dawei Li
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Qunqun Guo
- Tianjin Dexiang Biotechnology Co., Ltd, Tianjin, China
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12
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Gao H, Tuyishime P, Zhang X, Yang T, Xu M, Rao Z. Engineering of microbial cells for L-valine production: challenges and opportunities. Microb Cell Fact 2021; 20:172. [PMID: 34461907 PMCID: PMC8406616 DOI: 10.1186/s12934-021-01665-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/24/2021] [Indexed: 11/10/2022] Open
Abstract
L-valine is an essential amino acid that has wide and expanding applications with a suspected growing market demand. Its applicability ranges from animal feed additive, ingredient in cosmetic and special nutrients in pharmaceutical and agriculture fields. Currently, fermentation with the aid of model organisms, is a major method for the production of L-valine. However, achieving the optimal production has often been limited because of the metabolic imbalance in recombinant strains. In this review, the constrains in L-valine biosynthesis are discussed first. Then, we summarize the current advances in engineering of microbial cell factories that have been developed to address and overcome major challenges in the L-valine production process. Future prospects for enhancing the current L-valine production strategies are also discussed.
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Affiliation(s)
- Hui Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Philibert Tuyishime
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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L-valine production in Corynebacterium glutamicum based on systematic metabolic engineering: progress and prospects. Amino Acids 2021; 53:1301-1312. [PMID: 34401958 DOI: 10.1007/s00726-021-03066-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
L-valine is an essential branched-chain amino acid that cannot be synthesized by the human body and has a wide range of applications in food, medicine and feed. Market demand has stimulated people's interest in the industrial production of L-valine. At present, the mutagenized or engineered Corynebacterium glutamicum is an effective microbial cell factory for producing L-valine. Because the biosynthetic pathway and metabolic network of L-valine are intricate and strictly regulated by a variety of key enzymes and genes, highly targeted metabolic engineering can no longer meet the demand for efficient biosynthesis of L-valine. In recent years, the development of omics technology has promoted the upgrading of traditional metabolic engineering to systematic metabolic engineering. This whole-cell-scale transformation strategy has become a productive method for developing L-valine producing strains. This review provides an overview of the biosynthesis and regulation mechanism of L-valine, and summarizes the current metabolic engineering techniques and strategies for constructing L-valine high-producing strains. Finally, the opinion of constructing a cell factory for efficiently biosynthesizing L-valine was proposed.
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14
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Advances in metabolic engineering of Corynebacterium glutamicum to produce high-value active ingredients for food, feed, human health, and well-being. Essays Biochem 2021; 65:197-212. [PMID: 34096577 PMCID: PMC8313993 DOI: 10.1042/ebc20200134] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022]
Abstract
The soil microbe Corynebacterium glutamicum is a leading workhorse in industrial biotechnology and has become famous for its power to synthetise amino acids and a range of bulk chemicals at high titre and yield. The product portfolio of the microbe is continuously expanding. Moreover, metabolically engineered strains of C. glutamicum produce more than 30 high value active ingredients, including signature molecules of raspberry, savoury, and orange flavours, sun blockers, anti-ageing sugars, and polymers for regenerative medicine. Herein, we highlight recent advances in engineering of the microbe into novel cell factories that overproduce these precious molecules from pioneering proofs-of-concept up to industrial productivity.
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15
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Borah K, Mendum TA, Hawkins ND, Ward JL, Beale MH, Larrouy‐Maumus G, Bhatt A, Moulin M, Haertlein M, Strohmeier G, Pichler H, Forsyth VT, Noack S, Goulding CW, McFadden J, Beste DJV. Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis. Mol Syst Biol 2021; 17:e10280. [PMID: 33943004 PMCID: PMC8094261 DOI: 10.15252/msb.202110280] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022] Open
Abstract
The co-catabolism of multiple host-derived carbon substrates is required by Mycobacterium tuberculosis (Mtb) to successfully sustain a tuberculosis infection. However, the metabolic plasticity of this pathogen and the complexity of the metabolic networks present a major obstacle in identifying those nodes most amenable to therapeutic interventions. It is therefore critical that we define the metabolic phenotypes of Mtb in different conditions. We applied metabolic flux analysis using stable isotopes and lipid fingerprinting to investigate the metabolic network of Mtb growing slowly in our steady-state chemostat system. We demonstrate that Mtb efficiently co-metabolises either cholesterol or glycerol, in combination with two-carbon generating substrates without any compartmentalisation of metabolism. We discovered that partitioning of flux between the TCA cycle and the glyoxylate shunt combined with a reversible methyl citrate cycle is the critical metabolic nodes which underlie the nutritional flexibility of Mtb. These findings provide novel insights into the metabolic architecture that affords adaptability of bacteria to divergent carbon substrates and expand our fundamental knowledge about the methyl citrate cycle and the glyoxylate shunt.
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Affiliation(s)
- Khushboo Borah
- Department of Microbial and Cellular SciencesFaculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
| | - Tom A Mendum
- Department of Microbial and Cellular SciencesFaculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
| | - Nathaniel D Hawkins
- Department of Computational and Analytical SciencesRothamsted ResearchHarpendenUK
| | - Jane L Ward
- Department of Computational and Analytical SciencesRothamsted ResearchHarpendenUK
| | - Michael H Beale
- Department of Computational and Analytical SciencesRothamsted ResearchHarpendenUK
| | - Gerald Larrouy‐Maumus
- MRC Centre for Molecular Bacteriology and InfectionDepartment of Life SciencesFaculty of Natural SciencesImperial College LondonLondonUK
| | - Apoorva Bhatt
- School of BiosciencesUniversity of BirminghamEdgbastonUK
| | - Martine Moulin
- Life Sciences GroupInstitut Laue‐LangevinGrenoble Cedex 9France
- Partnership for Structural BiologyGrenoble Cedex 9France
| | - Michael Haertlein
- Life Sciences GroupInstitut Laue‐LangevinGrenoble Cedex 9France
- Partnership for Structural BiologyGrenoble Cedex 9France
| | - Gernot Strohmeier
- Austrian Centre of Industrial BiotechnologyGrazAustria
- Institute of Organic ChemistryNAWI GrazGraz University of TechnologyGrazAustria
| | - Harald Pichler
- Austrian Centre of Industrial BiotechnologyGrazAustria
- Institute of Organic ChemistryNAWI GrazGraz University of TechnologyGrazAustria
- Institute of Molecular BiotechnologyNAWI GrazBioTechMed GrazGraz University of TechnologyGrazAustria
| | - V Trevor Forsyth
- Life Sciences GroupInstitut Laue‐LangevinGrenoble Cedex 9France
- Partnership for Structural BiologyGrenoble Cedex 9France
- Faculty of Natural SciencesKeele UniversityStaffordshireUK
| | - Stephan Noack
- Institute of Bio‐ and Geosciences 1: Biotechnology 2Forschungszentrum Jülich GmbHJülichGermany
| | - Celia W Goulding
- Department of Pharmaceutical Sciences & Molecular Biology & BiochemistryUniversity of California IrvineIrvineCAUSA
| | - Johnjoe McFadden
- Department of Microbial and Cellular SciencesFaculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
| | - Dany J V Beste
- Department of Microbial and Cellular SciencesFaculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
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16
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Li Z, Shen J, Xu Y, Zhu W. Metagenomic analysis reveals significant differences in microbiome and metabolic profiles in the rumen of sheep fed low N diet with increased urea supplementation. FEMS Microbiol Ecol 2021; 96:5861934. [PMID: 32578861 DOI: 10.1093/femsec/fiaa117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 06/23/2020] [Indexed: 11/13/2022] Open
Abstract
Urea is a cost-effective replacement for feed proteins in ruminant diets. However, its metabolism by the rumen microbiome is not fully understood. Here, rumen contents were collected from 18 male sheep fed one of the following three treatments: a low N basal diet with no urea (UC, 0 g/kg dry matter (DM)), low urea (LU, 10 g/kg DM) and high urea (HU, 30 g/kg DM). Principal coordinate analysis showed that the microbial composition and functional profiles of the LU treatment significantly differed from the UC and HU treatments. The genera Prevotella, Succinivibrio, Succinatimonas and Megasphaera were higher in the LU rumen, while the genera Clostridium, Ruminococcus and Butyrivibrio were enriched in the UC and HU rumen. The aspartate-glutamate and arginine-proline metabolic pathways and valine, leucine and isoleucine biosynthesis were higher in the LU rumen. The cysteine and methionine metabolism, lysine degradation and fructose and pentose phosphate metabolism pathways were higher in the UC and HU rumen. The protozoa population in the HU treatment was higher than in the UC and LU treatments. These findings suggest that the rumen microbiome of sheep fed low N diet with different urea supplementation are significantly different.
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Affiliation(s)
- Zhipeng Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China.,Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, Jilin Province, China
| | - Junshi Shen
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China
| | - Yixuan Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China
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17
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Jiang Y, Sheng Q, Wu XY, Ye BC, Zhang B. l-arginine production in Corynebacterium glutamicum: manipulation and optimization of the metabolic process. Crit Rev Biotechnol 2020; 41:172-185. [PMID: 33153325 DOI: 10.1080/07388551.2020.1844625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
As an important semi-essential amino acid, l-arginine is extensively used in the food and pharmaceutical fields. At present, l-arginine production depends on cost-effective, green, and sustainable microbial fermentation by using a renewable carbon source. To enhance its fermentative production, various metabolic engineering strategies have been employed, which provide valid paths for reducing the cost of l-arginine production. This review summarizes recent advances in molecular biology strategies for the optimization of l-arginine-producing strains, including manipulating the principal metabolic pathway, modulating the carbon metabolic pathway, improving the intracellular biosynthesis of cofactors and energy usage, manipulating the assimilation of ammonia, improving the transportation and membrane permeability, and performing biosensor-assisted high throughput screening, providing useful insight into the current state of l-arginine production.
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Affiliation(s)
- Yan Jiang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
| | - Qi Sheng
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China.,College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiao-Yu Wu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China.,College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bin Zhang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China.,College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
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18
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Hua J, Jia X, Zhang L, Li Y. The Characterization of Two-Component System PmrA/PmrB in Cronobacter sakazakii. Front Microbiol 2020; 11:903. [PMID: 32655500 PMCID: PMC7326031 DOI: 10.3389/fmicb.2020.00903] [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] [Received: 12/17/2019] [Accepted: 04/16/2020] [Indexed: 01/12/2023] Open
Abstract
Cronobacter sakazakii is an opportunistic Gram-negative pathogen that could cause meningitis and necrotizing enterocolitis. Several Gram-negative bacteria use the PmrA/PmrB system to sense and adapt to environmental change by resistance to cationic antimicrobial peptides of host immune systems. The PmrA/PmrB two-component system regulates several genes to modify LPS structure in the bacterial outer membrane. The role of PmrA/PmrB of C. sakazakii has been studied within the current study. The results suggest that PmrA/PmrB plays a crucial role in modifying LPS structure, cationic antimicrobial peptide susceptibility, cell membrane permeability and hydrophobicity, and invading macrophage.
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Affiliation(s)
- Jingjing Hua
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Xiangyin Jia
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Liang Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Yanyan Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
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19
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Zhang Y, Liu Y, Zhang S, Ma W, Wang J, Yin L, Wang X. Metabolic engineering of Corynebacterium glutamicum WM001 to improve l-isoleucine production. Biotechnol Appl Biochem 2020; 68:568-584. [PMID: 32474971 DOI: 10.1002/bab.1963] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/29/2020] [Indexed: 01/02/2023]
Abstract
In this study, l-isoleucine production in Corynebacterium glutamicum WM001 was improved by deleting three genes in the genome, replacing the native promoter of ilvA in the genome, and overexpression of five genes in an alr-based auxotrophic complementation expression system. The three genes deleted in the genome are alaT, brnQ, and alr. Deletion of alaT improved l-isoleucine production by increasing the supply of pyruvate, whereas deletion of brnQ improved l-isoleucine production by blocking the uptake of extracellular l-isoleucine. Exchange of the native promoter of ilvA with promoter tac or tacM could contribute to l-isoleucine production by increasing 2-ketobutyric acid; tac is better than tacM for improving l-isoleucine yield. Different combinations of the genes ilvBN, ppnK, lrp, and brnFE were overexpressed in an alr-based auxotrophic complementation expression system to further improve l-isoleucine production, and the best yield after 72-H flask fermentation was obtained from the strain WM005/pYCW-1-ilvBN2-ppnK1. Without addition of any antibiotics, WM005/pYCW-1-ilvBN2-ppnK1 could produce 32.1 g/L l-isoleucine after 72-H fed-batch fermentation, which is 34.3% increase compared with the original strain WM001.
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Affiliation(s)
- Yanchao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Yadi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Shuyan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Lianghong Yin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, People's Republic of China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, People's Republic of China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, People's Republic of China
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20
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Zhao L, Zhang H, Wang X, Han G, Ma W, Hu X, Li Y. Transcriptomic analysis of an l-threonine-producing Escherichia coli TWF001. Biotechnol Appl Biochem 2020; 67:414-429. [PMID: 31976571 DOI: 10.1002/bab.1890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/21/2020] [Indexed: 01/10/2023]
Abstract
Wild-type Escherichia coli usually does not accumulate l-threonine, but E. coli strain TWF001 could produce 30.35 g/L l-threonine after 23-H fed-batch fermentation. To understand the mechanism for the high yield of l-threonine production in TWF001, transcriptomic analyses of the TWF001 cell samples collected at the logarithmic and stationary phases were performed, using the wild-type E. coli strain W3110 as the control. Compared with W3110, 1739 and 2361 genes were differentially transcribed in the logarithmic and stationary phases, respectively. Most genes related to the biosynthesis of l-threonine were significantly upregulated. Some key genes related to the NAD(P)H regeneration were upregulated. Many genes relevant to glycolysis and TCA cycle were downregulated. The key genes involved in the l-threonine degradation were downregulated. The gene rhtA encoding the l-threonine exporter was upregulated, whereas the genes sstT and tdcC encoding the l-threonine importer were downregulated. The upregulated genes in the glutamate pathway might form an amino-providing loop, which is beneficial for the high yield of l-threonine production. Many genes encoding the 30S and 50S subunits of ribosomes were also upregulated. The findings are useful for gene engineering to increase l-threonine production in E. coli.
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Affiliation(s)
- Lei Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Hailing Zhang
- Department of Biological Engineering, College of Life Science, Yantai University, Shandong, 408100, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Guoqiang Han
- College of Modern Agriculture and Biological Engineering, Yangtze Normal University, Chongqing, 264005, China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Xiaoqing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Ye Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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21
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Wu XY, Guo XY, Zhang B, Jiang Y, Ye BC. Recent Advances of L-ornithine Biosynthesis in Metabolically Engineered Corynebacterium glutamicum. Front Bioeng Biotechnol 2020; 7:440. [PMID: 31998705 PMCID: PMC6962107 DOI: 10.3389/fbioe.2019.00440] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/11/2019] [Indexed: 12/31/2022] Open
Abstract
L-ornithine, a valuable non-protein amino acid, has a wide range of applications in the pharmaceutical and food industries. Currently, microbial fermentation is a promising, sustainable, and environment-friendly method to produce L-ornithine. However, the industrial production capacity of L-ornithine by microbial fermentation is low and rarely meets the market demands. Various strategies have been employed to improve the L-ornithine production titers in the model strain, Corynebacterium glutamicum, which serves as a major indicator for improving the cost-effectiveness of L-ornithine production by microbial fermentation. This review focuses on the development of high L-ornithine-producing strains by metabolic engineering and reviews the recent advances in breeding strategies, such as reducing by-product formation, improving the supplementation of precursor glutamate, releasing negative regulation and negative feedback inhibition, increasing the supply of intracellular cofactors, modulating the central metabolic pathway, enhancing the transport system, and adaptive evolution for improving L-ornithine production.
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Affiliation(s)
- Xiao-Yu Wu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiao-Yan Guo
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Bin Zhang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Yan Jiang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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22
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Liu Y, Wang X, Zhan J, Hu J. The 138th residue of acetohydroxyacid synthase in Corynebacterium glutamicum is important for the substrate binding specificity. Enzyme Microb Technol 2019; 129:109357. [DOI: 10.1016/j.enzmictec.2019.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/12/2019] [Accepted: 06/01/2019] [Indexed: 11/28/2022]
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23
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Strategy for improving L-isoleucine production efficiency in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2019; 103:2101-2111. [DOI: 10.1007/s00253-019-09632-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 01/25/2023]
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24
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Ma Y, Ma Q, Cui Y, Du L, Xie X, Chen N. Transcriptomic and metabolomics analyses reveal metabolic characteristics of L-leucine- and L-valine-producing Corynebacterium glutamicum mutants. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-018-1431-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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25
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Enhancement of Bacitracin Production by NADPH Generation via Overexpressing Glucose-6-Phosphate Dehydrogenase Zwf in Bacillus licheniformis. Appl Biochem Biotechnol 2018; 187:1502-1514. [PMID: 30267286 DOI: 10.1007/s12010-018-2894-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/10/2018] [Indexed: 12/14/2022]
Abstract
Bacitracin, a kind of cyclic peptide antibiotic mainly produced by Bacillus, has wide ranges of applications. NADPH generation plays an important role in amino acid synthesis, which might influence precursor amino acid supply for bacitracin production. In this study, we want to improve bacitracin yield by enhancing intracellular precursor amino acids via strengthening NAPDH generation pathways in the bacitracin industrial production strain Bacillus licheniformis DW2. Based on our results, strengthening of NADPH pathway genes (zwf, gnd, ppnk, pntAB, and udhA) could all improve bacitracin yields in DW2, and the glucose-6-phosphate dehydrogenase Zwf overexpression strain DW2::Zwf displayed the best performance, the yield of which (886.43 U/mL) was increased by 12.43% compared to DW2 (788.40 U/mL). Then, the zwf transcriptional level and Zwf activity of DW2::Zwf were increased by 12.24-fold and 1.57-fold; NADPH and NADPH/NADH were enhanced by 61.24% and 90.63%, compared with those of DW2, respectively. Moreover, the concentrations of intracellular precursor amino acids (isoleucine, leucine, cysteine, ornithine, lysine, glutamic acid) were all enhanced obviously for bacitracin production in DW2::Zwf. Collectively, this research constructed a promising B. licheniformis strain for industrial production of bacitracin, more importantly, which revealed that strengthening of NADPH generation is an efficient strategy to improve precursor amino acid supplies for bacitracin production.
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Wang X, Zhang H, Quinn PJ. Production of l-valine from metabolically engineered Corynebacterium glutamicum. Appl Microbiol Biotechnol 2018; 102:4319-4330. [DOI: 10.1007/s00253-018-8952-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 01/25/2023]
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