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Park J, Lim S. Review of the Proteomics and Metabolic Properties of Corynebacterium glutamicum. Microorganisms 2024; 12:1681. [PMID: 39203523 PMCID: PMC11356982 DOI: 10.3390/microorganisms12081681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Corynebacterium glutamicum (C. glutamicum) has become industrially important in producing glutamic acid and lysine since its discovery and has been the subject of proteomics and central carbon metabolism studies. The proteome changes depending on environmental conditions, nutrient availability, and stressors. Post-translational modification (PTMs), such as phosphorylation, methylation, and glycosylation, alter the function and activity of proteins, allowing them to respond quickly to environmental changes. Proteomics techniques, such as mass spectrometry and two-dimensional gel electrophoresis, have enabled the study of proteomes, identification of proteins, and quantification of the expression levels. Understanding proteomes and central carbon metabolism in microorganisms provides insight into their physiology, ecology, and biotechnological applications, such as biofuels, pharmaceuticals, and industrial enzyme production. Several attempts have been made to create efficient production strains to increase productivity in several research fields, such as genomics and proteomics. In addition to amino acids, C. glutamicum is used to produce vitamins, nucleotides, organic acids, and alcohols, expanding its industrial applications. Considerable information has been accumulated, but recent research has focused on proteomes and central carbon metabolism. The development of genetic engineering technologies, such as CRISPR-Cas9, has improved production efficiency by allowing precise manipulation of the metabolic pathways of C. glutamicum. In addition, methods for designing new metabolic pathways and developing customized strains using synthetic biology technology are gradually expanding. This review is expected to enhance the understanding of C. glutamicum and its industrial potential and help researchers identify research topics and design studies.
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Affiliation(s)
| | - Sooa Lim
- Department of Pharmaceutical Engineering, Hoseo University, Asan-si 31499, Chungnam, Republic of Korea
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Cai N, Chen J, Gao N, Ni X, Lei Y, Pu W, Wang L, Che B, Fan L, Zhou W, Feng J, Wang Y, Zheng P, Sun J. Engineering of the DNA replication and repair machinery to develop binary mutators for rapid genome evolution of Corynebacterium glutamicum. Nucleic Acids Res 2023; 51:8623-8642. [PMID: 37449409 PMCID: PMC10484736 DOI: 10.1093/nar/gkad602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Corynebacterium glutamicum is an important industrial workhorse for production of amino acids and chemicals. Although recently developed genome editing technologies have advanced the rational genetic engineering of C. glutamicum, continuous genome evolution based on genetic mutators is still unavailable. To address this issue, the DNA replication and repair machinery of C. glutamicum was targeted in this study. DnaQ, the homolog of ϵ subunit of DNA polymerase III responsible for proofreading in Escherichia coli, was proven irrelevant to DNA replication fidelity in C. glutamicum. However, the histidinol phosphatase (PHP) domain of DnaE1, the α subunit of DNA polymerase III, was characterized as the key proofreading element and certain variants with PHP mutations allowed elevated spontaneous mutagenesis. Repression of the NucS-mediated post-replicative mismatch repair pathway or overexpression of newly screened NucS variants also impaired the DNA replication fidelity. Simultaneous interference with the DNA replication and repair machinery generated a binary genetic mutator capable of increasing the mutation rate by up to 2352-fold. The mutators facilitated rapid evolutionary engineering of C. glutamicum to acquire stress tolerance and protein overproduction phenotypes. This study provides efficient tools for evolutionary engineering of C. glutamicum and could inspire the development of mutagenesis strategy for other microbial hosts.
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Affiliation(s)
- Ningyun Cai
- Tianjin University of Science and Technology, Tianjin 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jiuzhou Chen
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ning Gao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomeng Ni
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yu Lei
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wei Pu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Lixian Wang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Bin Che
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Liwen Fan
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wenjuan Zhou
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jinhui Feng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yu Wang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| | - Ping Zheng
- Tianjin University of Science and Technology, Tianjin 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Jibin Sun
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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Busche T, Dostálová H, Rucká L, Holátko J, Barvík I, Štěpánek V, Pátek M, Kalinowski J. Overlapping SigH and SigE sigma factor regulons in Corynebacterium glutamicum. Front Microbiol 2023; 13:1059649. [PMID: 36925999 PMCID: PMC10012870 DOI: 10.3389/fmicb.2022.1059649] [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: 10/01/2022] [Accepted: 11/15/2022] [Indexed: 03/06/2023] Open
Abstract
The sigma H (σΗ) and sigma E (σE) subunits of Corynebacterium glutamicum RNA polymerase belong to Group 4 of sigma factors, also called extracytoplasmic function (ECF) sigma factors. Genes of the C. glutamicum σΗ regulon that are involved in heat and oxidative stress response have already been defined, whereas the genes of the σE regulon, which is involved in cell surface stress response, have not been explored until now. Using the C. glutamicum RES167 strain and its derivative C. glutamicum ΔcseE with a deletion in the anti-σΕ gene, differential gene expression was analyzed by RNA sequencing. We found 296 upregulated and 398 downregulated genes in C. glutamicum ΔcseE compared to C. glutamicum RES167. To confirm the functional link between σΕ and the corresponding promoters, we tested selected promoters using the in vivo two-plasmid system with gfpuv as a reporter gene and by in vitro transcription. Analyses with RNAP+σΗ and RNAP+σΕ, which were previously shown to recognize similar promoters, proved that the σΗ and σE regulons significantly overlap. The σE-controlled genes were found to be involved for example in protein quality control (dnaK, dnaJ2, clpB, and clpC), the regulation of Clp proteases (clgR), and membrane integrity maintenance. The single-promoter analyses with σΗ and σΕ revealed that there are two groups of promoters: those which are exclusively σΗ-specific, and the other group of promoters, which are σΗ/σE-dependent. No exclusively σE-dependent promoter was detected. We defined the consensus sequences of exclusively σΗ-regulated promotors to be -35 GGAAt and - 10 GTT and σΗ/σE-regulated promoters to be -35 GGAAC and - 10 cGTT. Fifteen genes were found to belong to the σΗ/σΕ regulon. Homology modeling showed that there is a specific interaction between Met170 in σΗ and the nucleotides -31 and - 30 within the non-coding strand (AT or CT) of the σΗ-dependent promoters. In σE, Arg185 was found to interact with the nucleotides GA at the same positions in the σE-dependent promoters.
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Affiliation(s)
- Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Medical School East Westphalia-Lippe, Bielefeld University, Bielefeld, Germany
| | - Hana Dostálová
- Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), Prague, Czechia
| | - Lenka Rucká
- Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), Prague, Czechia
| | - Jiří Holátko
- Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), Prague, Czechia
| | - Ivan Barvík
- Faculty of Mathematics and Physics, Institute of Physics, Charles University, Prague, Czechia
| | - Václav Štěpánek
- Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), Prague, Czechia
| | - Miroslav Pátek
- Institute of Microbiology, Academy of Sciences of the Czech Republic (ASCR), Prague, Czechia
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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Rigas Y, Treat BR, Shane J, Shanks RMQ, St. Leger AJ. Genetic Manipulation of Corynebacterium mastitidis to Better Understand the Ocular Microbiome. Invest Ophthalmol Vis Sci 2023; 64:19. [PMID: 36799874 PMCID: PMC9942783 DOI: 10.1167/iovs.64.2.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/24/2023] [Indexed: 02/18/2023] Open
Abstract
Purpose Corynebacterium spp. are Gram-positive bacteria commonly associated with the ocular surface. Corynebacterium mastitidis was isolated from mouse eyes and was demonstrated to induce a beneficial immune response that can protect the eye from pathogenic infection. Because eye-relevant Corynebacterium spp. are not well described, we generated a C. mast transposon (Tn) mutant library to gain a better understanding of the nature of eye-colonizing bacteria. Methods Tn mutagenesis was performed with a custom Tn5-based transposon that incorporated a promoterless gene for the fluorescent protein mCherry. We screened our library using flow cytometry and enzymatic assays to identify useful mutants that demonstrate the utility of our approach. Results Fluorescence-activated cell sorting (FACS) of mCherry+ bacteria allowed us to identify a highly fluorescent mutant that was detectable on the murine ocular surface using microscopy. We also identified a functional knockout that was unable to hydrolyze urea, UreaseKO. Although uric acid is an antimicrobial factor produced in tears, UreaseKO bacterium maintained an ability to colonize the eye, suggesting that urea hydrolysis is not required for colonization. In vitro and in vivo, both mutants maintained the potential to stimulate protective immunity as compared to wild-type C. mast. Conclusions In sum, we describe a method to genetically modify an eye-colonizing microbe, C. mast. Furthermore, the procedures outlined here will allow for the continued development of genetic tools for modifying ocular Corynebacterium spp., which will lead to a more complete understanding of the interactions between the microbiome and host immunity at the ocular surface.
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Affiliation(s)
- Yannis Rigas
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh Pennsylvania, United States
| | - Benjamin R. Treat
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh Pennsylvania, United States
| | - Jackie Shane
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh Pennsylvania, United States
| | - Robert M. Q. Shanks
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh Pennsylvania, United States
| | - Anthony J. St. Leger
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh Pennsylvania, United States
- Department of Immunology, University of Pittsburgh, Pittsburgh Pennsylvania, United States
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Development of a novel platform for recombinant protein production in Corynebacterium glutamicum on ethanol. Synth Syst Biotechnol 2022; 7:765-774. [PMID: 35387228 PMCID: PMC8942793 DOI: 10.1016/j.synbio.2022.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 03/04/2022] [Accepted: 03/15/2022] [Indexed: 02/03/2023] Open
Abstract
Corynebacterium glutamicum represents an emerging recombinant protein expression factory due to its ideal features for protein secretion, but its applicability is harmed by the lack of an autoinduction system with tight regulation and high yield. Here, we propose a new recombinant protein manufacturing platform that leverages ethanol as both a delayed carbon source and an inducer. First, we reanalysed the native inducible promoter PICL from the acetate uptake operon and found that its limited capacity is the result of the inadequate translation initial architecture. The two strategies of bicistronic design and ribozyme-based insulator can ensure the high activity of this promoter. Next, through transcriptional engineering that alters transcription factor binding sites (TFBSs) and the first transcribed sequence, the truncated promoter PA256 with a dramatically higher transcription level was generated. When producing the superfolder green fluorescent protein (sfGFP) under 1% ethanol conditions, PA256 exhibited substantially lower protein accumulation in prophase but an approximately 2.5-fold greater final yield than the strong promoter PH36. This superior expression mode was further validated using two secreted proteins, camelid antibody fragment (VHH) and endoxylanase (XynA). Furthermore, utilizing CRISPRi technology, ethanol utilization blocking strains were created, and PA256 was shown to be impaired in the phosphotransacetylase (PTA) knockdown strains, indicating that ethanol metabolism into the tricarboxylic acid cycle is required for PA256 upregulation. Finally, this platform was applied to produce the “de novo design” protein NEO-2/15, and by introducing the N-propeptide of CspB, NEO-2/15 was effectively secreted with the accumulation 281 mg/L obtained after 24 h of shake-flask fermentation. To the best of our knowledge, this is the first report of NEO-2/15 secretory overexpression.
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OUP accepted manuscript. FEMS Microbiol Lett 2022; 369:6528914. [DOI: 10.1093/femsle/fnac014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/13/2022] [Accepted: 02/13/2022] [Indexed: 11/14/2022] Open
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Liu H, Shi F, Tan S, Yu X, Lai W, Li Y. Engineering a Bifunctional ComQXPA-P srfA Quorum-Sensing Circuit for Dynamic Control of Gene Expression in Corynebacterium glutamicum. ACS Synth Biol 2021; 10:1761-1774. [PMID: 34165971 DOI: 10.1021/acssynbio.1c00149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Corynebacterium glutamicum is an important industrial workhorse for the production of amino acids and other chemicals. However, the engineering of C. glutamicum is inflexible due to the lack of dynamic regulation tools. In this study, a quorum sensing (QS) circuit and its modulated hfq-sRNA cassette were constructed, and the dynamic control of gene expression by these bifunctional circuits was researched. First, the ComQXPA-PsrfA QS system of Bacillus subtilis was harnessed and modified to create an upregulating QS circuit, in which the transcription of genes controlled by the PsrfA promoter may be promoted at high cell density. This QS circuit successfully activated the expression of green fluorescent protein (GFP) to 6.35-fold in a cell density-dependent manner in C. glutamicum. Next, the hfq-sRNA-mediated downregulating circuit under the control of the ComQXPA-PsrfA QS system was established, and the expression of GFP was autonomously repressed by 96.1%. Next, to fine-tune these two QS circuits, a library of synthetic PsrfA based promoters was constructed, and a series of mutant PsrfAM promoters with 0.4-1.5-fold strength of native PsrfA were selected. Subsequently, the ComQXPA-PsrfAM QS circuit was utilized to upregulate the expression of red fluorescent protein, and the same QS-based hfq-sRNA system was utilized to downregulate the expression of GFP simultaneously. Last, this bifunctional ComQXPA-PsrfAM QS circuit was verified again by fine-tuning the expression of α-amylase. Therefore, the engineered ComQXPA-PsrfAM QS cassette can be applied as a novel bifunctional QS circuit to flexibly control gene expression in C. glutamicum.
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Affiliation(s)
- Haiyan Liu
- 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
| | - Feng Shi
- 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
| | - Shuyu Tan
- 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
| | - Xinping Yu
- 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
| | - Wenmei Lai
- 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
| | - Yongfu Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
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Wang Q, Zhang J, Al Makishah NH, Sun X, Wen Z, Jiang Y, Yang S. Advances and Perspectives for Genome Editing Tools of Corynebacterium glutamicum. Front Microbiol 2021; 12:654058. [PMID: 33897668 PMCID: PMC8058222 DOI: 10.3389/fmicb.2021.654058] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/01/2021] [Indexed: 12/17/2022] Open
Abstract
Corynebacterium glutamicum has been considered a promising synthetic biological platform for biomanufacturing and bioremediation. However, there are still some challenges in genetic manipulation of C. glutamicum. Recently, more and more genetic parts or elements (replicons, promoters, reporter genes, and selectable markers) have been mined, characterized, and applied. In addition, continuous improvement of classic molecular genetic manipulation techniques, such as allelic exchange via single/double-crossover, nuclease-mediated site-specific recombination, RecT-mediated single-chain recombination, actinophages integrase-mediated integration, and transposition mutation, has accelerated the molecular study of C. glutamicum. More importantly, emerging gene editing tools based on the CRISPR/Cas system is revolutionarily rewriting the pattern of genetic manipulation technology development for C. glutamicum, which made gene reprogramming, such as insertion, deletion, replacement, and point mutation, much more efficient and simpler. This review summarized the recent progress in molecular genetic manipulation technology development of C. glutamicum and discussed the bottlenecks and perspectives for future research of C. glutamicum as a distinctive microbial chassis.
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Affiliation(s)
- Qingzhuo Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Jiao Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Naief H. Al Makishah
- Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhiqiang Wen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Shemyakina AO, Grechishnikova EG, Novikov AD, Asachenko AF, Kalinina TI, Lavrov KV, Yanenko AS. A Set of Active Promoters with Different Activity Profiles for Superexpressing Rhodococcus Strain. ACS Synth Biol 2021; 10:515-530. [PMID: 33605147 DOI: 10.1021/acssynbio.0c00508] [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] [Indexed: 02/02/2023]
Abstract
Rhodococcus bacteria are a promising platform for biodegradation, biocatalysis, and biosynthesis, but the use of rhodococci is hampered by the insufficient number of both platform strains for expression and promoters that are functional and thoroughly studied in these strains. To expand the list of such strains and promoters, we studied the expression capability of the Rhodococcus rhodochrous M33 strain, and the functioning of a set of recombinant promoters in it. We showed that the strain supports superexpression of the target enzyme (nitrile hydratase) using alternative inexpensive feedings-acetate and urea-without growth factor supplementation, thus being a suitable expression platform. The promoter set included Ptuf (elongation factor Tu) and Psod (superoxide dismutase) from Corynebacterium glutamicum ATCC13032, Pcpi (isocitrate lyase) from Rhodococcus erythropolis PR4, and Pnh (nitrile hydratase) from R. rhodochrous M8. Activity levels, regulation possibilities, and growth-phase-dependent activity profiles of these promoters were studied in derivatives of the M33 strain. The activities of the promoters were significantly different (Pcpi < Psod ≪ Ptuf < Pnh), covering 103-fold range, and the most active Pnh and Ptuf produced up to a 30-50% portion of target protein in soluble intracellular proteins. On the basis of the mRNA quantification and amount of target protein, the production level of Pnh was positioned close to the theoretical upper limit of expression in a bacterial cell. A selection method for the laboratory evolution of such active promoters directly in Rhodococcus was also proposed. Concerning regulation, Ptuf could not be regulated (2-fold change), while others were tunable (6-fold for Psod, 79-fold for Pnh, and 44-fold for Pcpi). The promoters possessed four different activity profiles, including three with peak of activity at different growth phases and one with constant activity throughout the growth phases. Ptuf and Pcpi did not change their activity profile under different growth conditions, whereas the Psod and Pnh profiles changed depending on the growth media. The results allow flexible construction of Rhodococcus strains using the studied promoters, and demonstrate a valuable approach for complex characterization of promoters intended for biotechnological strain construction.
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Affiliation(s)
- Anna O. Shemyakina
- NRC Kurchatov Institute-Gosniigenetika, Kurchatov Genomic Center, 1st Dorojny pr. 1, Moscow, 117545, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 123182, Russia
| | - Elena G. Grechishnikova
- NRC Kurchatov Institute-Gosniigenetika, Kurchatov Genomic Center, 1st Dorojny pr. 1, Moscow, 117545, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 123182, Russia
| | - Andrey D. Novikov
- NRC Kurchatov Institute-Gosniigenetika, Kurchatov Genomic Center, 1st Dorojny pr. 1, Moscow, 117545, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 123182, Russia
| | - Andrey F. Asachenko
- A. V. Topchiev Institute of Petrochemical Synthesis of Russian Academy of Sciences, Leninsky prospect 29, Moscow, 119991, Russia
| | - Tatyana I. Kalinina
- NRC Kurchatov Institute-Gosniigenetika, Kurchatov Genomic Center, 1st Dorojny pr. 1, Moscow, 117545, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 123182, Russia
| | - Konstantin V. Lavrov
- NRC Kurchatov Institute-Gosniigenetika, Kurchatov Genomic Center, 1st Dorojny pr. 1, Moscow, 117545, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 123182, Russia
| | - Alexander S. Yanenko
- NRC Kurchatov Institute-Gosniigenetika, Kurchatov Genomic Center, 1st Dorojny pr. 1, Moscow, 117545, Russia
- NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 123182, Russia
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Henke NA, Krahn I, Wendisch VF. Improved Plasmid-Based Inducible and Constitutive Gene Expression in Corynebacterium glutamicum. Microorganisms 2021; 9:204. [PMID: 33478126 PMCID: PMC7835838 DOI: 10.3390/microorganisms9010204] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/18/2023] Open
Abstract
Corynebacterium glutamicum has been safely used in white biotechnology for the last 60 years and the portfolio of new pathways and products is increasing rapidly. Hence, expression vectors play a central role in discovering endogenous gene functions and in establishing heterologous gene expression. In this work, new expression vectors were designed based on two strategies: (i) a library screening of constitutive native and synthetic promoters and (ii) an increase of the plasmid copy number. Both strategies were combined and resulted in a very strong expression and overproduction of the fluorescence protein GfpUV. As a second test case, the improved vector for constitutive expression was used to overexpress the endogenous xylulokinase gene xylB in a synthetic operon with xylose isomerase gene xylA from Xanthomonas campestris. The xylose isomerase activity in crude extracts was increased by about three-fold as compared to that of the parental vector. In terms of application, the improved vector for constitutive xylA and xylB expression was used for production of the N-methylated amino acid sarcosine from monomethylamine, acetate, and xylose. As a consequence, the volumetric productivity of sarcosine production was 50% higher as compared to that of the strain carrying the parental vector.
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Affiliation(s)
| | | | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; (N.A.H.); (I.K.)
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Duan Y, Zhai W, Liu W, Zhang X, Shi JS, Zhang X, Xu Z. Fine-Tuning Multi-Gene Clusters via Well-Characterized Gene Expression Regulatory Elements: Case Study of the Arginine Synthesis Pathway in C. glutamicum. ACS Synth Biol 2021; 10:38-48. [PMID: 33382575 DOI: 10.1021/acssynbio.0c00405] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Promoters and ribosome binding sites (RBSs) are routinely applied in gene expression regulation, but their orthogonality and combinatorial effects have not yet been systematically studied in Corynebacterium glutamicum. Here, 17 core promoters and 29 RBSs in C. glutamicum were characterized, which exhibited 470-fold and 430-fold in transcriptional and translational activity, respectively. By comparing the expression of two reporter genes regulated by multiple RBSs, the RBS efficacy showed significant dependence on the gene context, besides the RBSs' strength, reflecting the poor orthogonality of RBSs. Bicistron-modified RBS (referred as bc-RBS) was adapted to C. glutamicum, which improved RBS reliability. By coupling a series of promoters with RBSs/bc-RBSs, a much broader regulation range that spanned 4 orders of magnitude was observed compared with that of a sole element, and the contribution to gene expression of RBS was more than that of promoter. Finally, promoters and RBSs were applied as built-in elements to fine-tune the gene cluster in the arginine synthesis pathway in C. glutamicum. Compared with the original strain, more arginine (1.61-fold) or citrulline (2.35-fold) was accumulated in a 7 L bioreactor by strains with the gene expression regulation system rationally engineered. We demonstrated that, via combination of well-characterized gene elements, and overall consideration for both transcription and translation, the biosynthesis pathway can be effectively balanced, and the yield of a target metabolite can be further improved.
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Affiliation(s)
- Yanting Duan
- National Engineering Laboratory for Cereal Fermentation Technology, Key Laboratory of Industrial Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Weiji Zhai
- National Engineering Laboratory for Cereal Fermentation Technology, Key Laboratory of Industrial Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Weijia Liu
- Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Xiaomei Zhang
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Jin-Song Shi
- School of Pharmaceutical Science, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Engineering Research Center for Bioactive Products Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Xiaojuan Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Key Laboratory of Industrial Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhenghong Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Key Laboratory of Industrial Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
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12
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Wiechert J, Gätgens C, Wirtz A, Frunzke J. Inducible Expression Systems Based on Xenogeneic Silencing and Counter-Silencing and Design of a Metabolic Toggle Switch. ACS Synth Biol 2020; 9:2023-2038. [PMID: 32649183 DOI: 10.1021/acssynbio.0c00111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inducible expression systems represent key modules in regulatory circuit design and metabolic engineering approaches. However, established systems are often limited in terms of applications due to high background expression levels and inducer toxicity. In bacteria, xenogeneic silencing (XS) proteins are involved in the tight control of horizontally acquired, AT-rich DNA. The action of XS proteins may be opposed by interference with a specific transcription factor, resulting in the phenomenon of counter-silencing, thereby activating gene expression. In this study, we harnessed this principle for the construction of a synthetic promoter library consisting of phage promoters targeted by the Lsr2-like XS protein CgpS of Corynebacterium glutamicum. Counter-silencing was achieved by inserting the operator sequence of the gluconate-responsive transcription factor GntR. The GntR-dependent promoter library is comprised of 28 activated and 16 repressed regulatory elements featuring effector-dependent tunability. For selected candidates, background expression levels were confirmed to be significantly reduced in comparison to established heterologous expression systems. Finally, a GntR-dependent metabolic toggle switch was implemented in a C. glutamicum l-valine production strain allowing the dynamic redirection of carbon flux between biomass and product formation.
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Affiliation(s)
- Johanna Wiechert
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Cornelia Gätgens
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Astrid Wirtz
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Julia Frunzke
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, 52425 Jülich, Germany
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13
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Zhou Q, Ning S, Luo Y. Coordinated regulation for nature products discovery and overproduction in Streptomyces. Synth Syst Biotechnol 2020; 5:49-58. [PMID: 32346621 PMCID: PMC7176746 DOI: 10.1016/j.synbio.2020.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/04/2020] [Accepted: 04/08/2020] [Indexed: 12/19/2022] Open
Abstract
Streptomyces is an important treasure trove for natural products discovery. In recent years, many scientists focused on the genetic modification and metabolic regulation of Streptomyces to obtain diverse bioactive compounds with high yields. This review summarized the commonly used regulatory strategies for natural products discovery and overproduction in Streptomyces from three main aspects, including regulator-related strategies, promoter engineering, as well as other strategies employing transposons, signal factors, or feedback regulations. It is expected that the metabolic regulation network of Streptomyces will be elucidated more comprehensively to shed light on natural products research in the future.
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Affiliation(s)
- Qun Zhou
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Shuqing Ning
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yunzi Luo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China
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14
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Andriiash GS, Sekan OS, Tigunova OO, Blume YB, Shulga SM. Metabolic Engineering of Lysine Producing Corynebacterium glutamicum Strains. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720020024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Nelkner J, Tejerizo GT, Hassa J, Lin TW, Witte J, Verwaaijen B, Winkler A, Bunk B, Spröer C, Overmann J, Grosch R, Pühler A, Schlüter AA. Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics. Genes (Basel) 2019; 10:E601. [PMID: 31405015 PMCID: PMC6722718 DOI: 10.3390/genes10080601] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/02/2019] [Accepted: 08/06/2019] [Indexed: 01/17/2023] Open
Abstract
The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.
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Affiliation(s)
- Johanna Nelkner
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Gonzalo Torres Tejerizo
- Facultad de Ciencias Exactas, Departamento de Ciencias Biologicas, IBBM, Universidad Nacional de La Plata, Calle 115 y 47, 1900 La Plata, Argentina
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Timo Wentong Lin
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Julian Witte
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Bart Verwaaijen
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Anika Winkler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Boyke Bunk
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Rita Grosch
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - And Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
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16
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Li X, Xu S, Zhang X, Xu M, Yang T, Wang L, Zhang H, Fang H, Osire T, Yang S, Rao Z. Design of a high-efficiency synthetic system for l-asparaginase production in Bacillus subtilis. Eng Life Sci 2019; 19:229-239. [PMID: 32625005 DOI: 10.1002/elsc.201800166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/07/2018] [Accepted: 01/17/2019] [Indexed: 12/28/2022] Open
Abstract
l-asparaginase has high application value in medicine and food industry, but the low yield limits its application. In this study, we designed a synthetic system in Bacillus subtilis to produce l-asparaginase by improving gene expression and optimizing the fermentation agitation speed. Gene expression was improved by respectively increasing transcription levels and translation speeds through screening promoters and RBS sequences. With the optimal promoter, P43, and the synthetic RBS sequence, the yield obtained in a shake flask was 371.87 U/mL, which was 2.09 times that with the original strain. To further enhance production in a 5-L fermenter, a multistage agitation speed control strategy was adopted, involving agitation at 600 rpm for the first 12 h, followed by a gradual increase in speed to 900 rpm, which resulted in the highest yield of l-asparaginase, 5321 U/mL, after 42 h of fermentation.
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Affiliation(s)
- Xu Li
- The Key Laboratory of Industrial Biotechnology Ministry of Education School of Biotechnology Jiangnan University Wuxi P. R. China
| | - Shuqin Xu
- The Key Laboratory of Industrial Biotechnology Ministry of Education School of Biotechnology Jiangnan University Wuxi P. R. China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology Ministry of Education School of Biotechnology Jiangnan University Wuxi P. R. China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology Ministry of Education School of Biotechnology Jiangnan University Wuxi P. R. China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology Ministry of Education School of Biotechnology Jiangnan University Wuxi P. R. China
| | - Li Wang
- School of Food Science and Technology Jiangnan University Wuxi P. R. China
| | - Huiling Zhang
- School of Agriculture Ningxia University Yinchuan P. R. China
| | - Haitian Fang
- School of Agriculture Ningxia University Yinchuan P. R. China
| | - Tolbert Osire
- The Key Laboratory of Industrial Biotechnology Ministry of Education School of Biotechnology Jiangnan University Wuxi P. R. China
| | - Shangtian Yang
- Department of Chemical and Biomolecular Engineering The Ohio State University Columbus OH USA
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology Ministry of Education School of Biotechnology Jiangnan University Wuxi P. R. China
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17
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Xu N, Wei L, Liu J. Recent advances in the applications of promoter engineering for the optimization of metabolite biosynthesis. World J Microbiol Biotechnol 2019; 35:33. [DOI: 10.1007/s11274-019-2606-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/23/2019] [Indexed: 01/24/2023]
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18
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Metabolically engineered Corynebacterium glutamicum for bio-based production of chemicals, fuels, materials, and healthcare products. Metab Eng 2018; 50:122-141. [DOI: 10.1016/j.ymben.2018.07.008] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 01/15/2023]
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19
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One-step process for production of N-methylated amino acids from sugars and methylamine using recombinant Corynebacterium glutamicum as biocatalyst. Sci Rep 2018; 8:12895. [PMID: 30150644 PMCID: PMC6110843 DOI: 10.1038/s41598-018-31309-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/02/2018] [Indexed: 02/07/2023] Open
Abstract
N-methylated amino acids are found in Nature in various biological compounds. N-methylation of amino acids has been shown to improve pharmacokinetic properties of peptide drugs due to conformational changes, improved proteolytic stability and/or higher lipophilicity. Due to these characteristics N-methylated amino acids received increasing interest by the pharmaceutical industry. Syntheses of N-methylated amino acids by chemical and biocatalytic approaches are known, but often show incomplete stereoselectivity, low yields or expensive co-factor regeneration. So far a one-step fermentative process from sugars has not yet been described. Here, a one-step conversion of sugars and methylamine to the N-methylated amino acid N-methyl-l-alanine was developed. A whole-cell biocatalyst was derived from a pyruvate overproducing C. glutamicum strain by heterologous expression of the N-methyl-l-amino acid dehydrogenase gene from Pseudomonas putida. As proof-of-concept, N-methyl-l-alanine titers of 31.7 g L−1 with a yield of 0.71 g per g glucose were achieved in fed-batch cultivation. The C. glutamicum strain producing this imine reductase enzyme was engineered further to extend this green chemistry route to production of N-methyl-l-alanine from alternative feed stocks such as starch or the lignocellulosic sugars xylose and arabinose.
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20
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Shi F, Luan M, Li Y. Ribosomal binding site sequences and promoters for expressing glutamate decarboxylase and producing γ-aminobutyrate in Corynebacterium glutamicum. AMB Express 2018; 8:61. [PMID: 29671147 PMCID: PMC5906420 DOI: 10.1186/s13568-018-0595-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 04/13/2018] [Indexed: 12/14/2022] Open
Abstract
Glutamate decarboxylase (GAD) converts l-glutamate (Glu) into γ-aminobutyric acid (GABA). Corynebacterium glutamicum that expresses exogenous GAD gene, gadB2 or gadB1, can synthesize GABA from its own produced Glu. To enhance GABA production in C. glutamicum, ribosomal binding site (RBS) sequence and promoter were searched and optimized for increasing the expression efficiency of gadB2. R4 exhibited the highest strength among RBS sequences tested, with 6 nt the optimal aligned spacing (AS) between RBS and start codon. This combination of RBS sequence and AS contributed to gadB2 expression, increased GAD activity by 156% and GABA production by 82% compared to normal strong RBS and AS combination. Then, a series of native promoters were selected for transcribing gadB2 under optimal RBS and AS combination. PdnaK, PdtsR, PodhI and PclgR expressed gadB2 and produced GABA as effectively as widely applied Ptuf and PcspB promoters and more effectively than Psod promoter. However, each native promoter did not work as well as the synthetic strong promoter PtacM, which produced 20.2 ± 0.3 g/L GABA. Even with prolonged length and bicistronic architecture, the strength of PdnaK did not enhance. Finally, gadB2 and mutant gadB1 were co-expressed under the optimal promoter and RBS combination, thus converted Glu into GABA completely and improved GABA production to more than 25 g/L. This study provides useful promoters and RBS sequences for gene expression in C. glutamicum.
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21
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Promoter library-based module combination (PLMC) technology for optimization of threonine biosynthesis in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2018; 102:4117-4130. [DOI: 10.1007/s00253-018-8911-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 02/24/2018] [Accepted: 03/03/2018] [Indexed: 12/20/2022]
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22
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Investigation of specific interactions between T7 promoter and T7 RNA polymerase by force spectroscopy using atomic force microscope. Biochem J 2018; 475:319-328. [DOI: 10.1042/bcj20170616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/23/2017] [Accepted: 11/29/2017] [Indexed: 12/30/2022]
Abstract
The specific recognition and binding of promoter and RNA polymerase is the first step of transcription initiation in bacteria and largely determines transcription activity. Therefore, direct analysis of the interaction between promoter and RNA polymerase in vitro may be a new strategy for promoter characterization, to avoid interference due to the cell's biophysical condition and other regulatory elements. In the present study, the specific interaction between T7 promoter and T7 RNA polymerase was studied as a model system using force spectroscopy based on atomic force microscope (AFM). The specific interaction between T7 promoter and T7 RNA polymerase was verified by control experiments, and the rupture force in this system was measured as 307.2 ± 6.7 pN. The binding between T7 promoter mutants with various promoter activities and T7 RNA polymerase was analyzed. Interaction information including rupture force, rupture distance and binding percentage were obtained in vitro, and reporter gene expression regulated by these promoters was also measured according to a traditional promoter activity characterization method in vivo. Using correlation analysis, it was found that the promoter strength characterized by reporter gene expression was closely correlated with rupture force and the binding percentage by force spectroscopy. These results indicated that the analysis of the interaction between promoter and RNA polymerase using AFM-based force spectroscopy was an effective and valid approach for the quantitative characterization of promoters.
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23
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Dostálová H, Holátko J, Busche T, Rucká L, Rapoport A, Halada P, Nešvera J, Kalinowski J, Pátek M. Assignment of sigma factors of RNA polymerase to promoters in Corynebacterium glutamicum. AMB Express 2017. [PMID: 28651382 PMCID: PMC5483222 DOI: 10.1186/s13568-017-0436-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Corynebacterium glutamicum is an important industrial producer of various amino acids and other metabolites. The C. glutamicum genome encodes seven sigma subunits (factors) of RNA polymerase: the primary sigma factor SigA (σA), the primary-like σB and five alternative sigma factors (σC, σD, σE, σH and σM). We have developed in vitro and in vivo methods to assign particular sigma factors to individual promoters of different classes. In vitro transcription assays and measurements of promoter activity using the overexpression of a single sigma factor gene and the transcriptional fusion of the promoter to the gfpuv reporter gene enabled us to reliably define the sigma factor dependency of promoters. To document the strengths of these methods, we tested examples of respective promoters for each C. glutamicum sigma factor. Promoters of the rshA (anti-sigma for σH) and trxB1 (thioredoxin) genes were found to be σH-dependent, whereas the promoter of the sigB gene (sigma factor σB) was σE- and σH-dependent. It was confirmed that the promoter of the cg2556 gene (iron-regulated membrane protein) is σC-dependent as suggested recently by other authors. The promoter of cmt1 (trehalose corynemycolyl transferase) was found to be clearly σD-dependent. No σM-dependent promoter was identified. The typical housekeeping promoter P2sigA (sigma factor σA) was proven to be σA-dependent but also recognized by σB. Similarly, the promoter of fba (fructose-1,6-bisphosphate aldolase) was confirmed to be σB-dependent but also functional with σA. The study provided demonstrations of the broad applicability of the developed methods and produced original data on the analyzed promoters.
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24
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Albersmeier A, Pfeifer-Sancar K, Rückert C, Kalinowski J. Genome-wide determination of transcription start sites reveals new insights into promoter structures in the actinomycete Corynebacterium glutamicum. J Biotechnol 2017; 257:99-109. [PMID: 28412515 DOI: 10.1016/j.jbiotec.2017.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/06/2017] [Accepted: 04/11/2017] [Indexed: 12/21/2022]
Abstract
The genome-wide identification of transcription start sites, enabled by high-throughput sequencing of a cDNA library enriched for native 5' transcript ends, is ideally suited for the analysis of promoters. Here, the transcriptome of Corynebacterium glutamicum, a non-pathogenic soil bacterium from the actinomycetes branch that is used in industry for the production of amino acids, was analysed by transcriptome sequencing of the 5'-ends of native transcripts. Total RNA samples were harvested from the exponential phase of growth, therefore the study mainly addressed promoters recognized by the main house-keeping sigma factor σA. The identification of 2454 transcription start sites (TSS) allowed the detailed analysis of most promoters recognized by σA and furthermore enabled us to form different promoter groups according to their location relative to protein-coding regions. These groups included leaderless transcripts (546 promoters), short-leadered (<500 bases) transcripts (917), and long-leadered (>500 bases) transcripts (173) as well as intragenic (557) and antisense transcripts (261). All promoters and the individual groups were searched for information, e.g. conserved residues and promoter motifs, and general design features as well as group-specific preferences were identified. A purine was found highly favored as TSS, whereas the -1 position was dominated by pyrimidines. The spacer between TSS and -10 region were consistently 6-7 bases and the -10 promoter motif was generally visible, whereas a recognizable -35 region was only occurring in a smaller fraction of promoters (7.5%) and enriched for leadered and antisense transcripts but depleted for leaderless transcripts. Promoters showing an extended -10 region were especially frequent in case of non-canonical -10 motifs (45.5%). Two bases downstream of the -10 core region, a G was conserved, exceeding 40% abundance in most groups. This fraction reached 74.6% for a group of putative σB-dependent promoters, thus giving a hint to a specific property of these promoters. In addition, the high number of promoters analysed allowed finding of subtle signals only showing up significantly with this large set. This included the observation of a periodically changing A+T-content with maxima spaced by a full turn of the DNA helix. This periodic structure includes the A+T-rich UP-element of bacterial promoters known before but was found to extend up to -100, indicating hitherto unknown constraints influencing promoter architecture and possibly also promoter function.
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Affiliation(s)
- Andreas Albersmeier
- Microbial Genomics Biotechnology, Centrum für Biotechnologie Universität Bielefeld, Sequenz 1, 33615 Bielefeld, Germany
| | - Katharina Pfeifer-Sancar
- Microbial Genomics Biotechnology, Centrum für Biotechnologie Universität Bielefeld, Sequenz 1, 33615 Bielefeld, Germany
| | - Christian Rückert
- Microbial Genomics Biotechnology, Centrum für Biotechnologie Universität Bielefeld, Sequenz 1, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics Biotechnology, Centrum für Biotechnologie Universität Bielefeld, Sequenz 1, 33615 Bielefeld, Germany.
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25
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A novel genetic tool for metabolic optimization of Corynebacterium glutamicum: efficient and repetitive chromosomal integration of synthetic promoter-driven expression libraries. Appl Microbiol Biotechnol 2017; 101:4737-4746. [DOI: 10.1007/s00253-017-8222-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/26/2017] [Accepted: 03/04/2017] [Indexed: 10/19/2022]
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26
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Kallscheuer N, Vogt M, Marienhagen J. A Novel Synthetic Pathway Enables Microbial Production of Polyphenols Independent from the Endogenous Aromatic Amino Acid Metabolism. ACS Synth Biol 2017; 6:410-415. [PMID: 27936616 DOI: 10.1021/acssynbio.6b00291] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Numerous plant polyphenols have potential applications as pharmaceuticals or nutraceuticals. Stilbenes and flavonoids as most abundant polyphenols are synthesized from phenylpropanoids, which are exclusively derived from aromatic amino acids in nature. Several microorganisms were engineered for the synthesis of biotechnologically interesting plant polyphenols; however, low activity of heterologous ammonia lyases, linking endogenous microbial aromatic amino acid biosynthesis to phenylpropanoid synthesis, turned out to be the limiting step during microbial synthesis. We here developed an alternative strategy for polyphenol production from cheap benzoic acids by reversal of a β-oxidative phenylpropanoid degradation pathway avoiding any ammonia lyase activity. The synthetic pathway running in the non-natural direction is feasible with respect to thermodynamics and involved reaction mechanisms. Instantly, product titers of 5 mg/L resveratrol could be achieved in recombinant Corynebacterium glutamicum strains indicating that phenylpropanoid synthesis from 4-hydroxybenzoic acid can in principle be implemented independently from aromatic amino acids and ammonia lyase activity.
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Affiliation(s)
- Nicolai Kallscheuer
- Institute of Bio- and Geosciences,
IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Michael Vogt
- Institute of Bio- and Geosciences,
IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences,
IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
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Becker J, Wittmann C. Industrial Microorganisms: Corynebacterium glutamicum. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Judith Becker
- Saarland University; Institute of Systems Biotechnology; Campus A 15 66123 Saarbrücken Germany
| | - Christoph Wittmann
- Saarland University; Institute of Systems Biotechnology; Campus A 15 66123 Saarbrücken Germany
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Toyoda K, Inui M. Regulons of global transcription factors in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2015; 100:45-60. [DOI: 10.1007/s00253-015-7074-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 10/03/2015] [Accepted: 10/07/2015] [Indexed: 10/22/2022]
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29
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Ruan Y, Zhu L, Li Q. Improving the electro-transformation efficiency of Corynebacterium glutamicum by weakening its cell wall and increasing the cytoplasmic membrane fluidity. Biotechnol Lett 2015; 37:2445-52. [DOI: 10.1007/s10529-015-1934-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/04/2015] [Indexed: 10/23/2022]
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30
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Heider SAE, Wendisch VF. Engineering microbial cell factories: Metabolic engineering ofCorynebacterium glutamicumwith a focus on non-natural products. Biotechnol J 2015. [DOI: 10.1002/biot.201400590] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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31
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Enhanced production of l-sorbose in an industrial Gluconobacter oxydans strain by identification of a strong promoter based on proteomics analysis. ACTA ACUST UNITED AC 2015; 42:1039-47. [DOI: 10.1007/s10295-015-1624-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/25/2015] [Indexed: 10/23/2022]
Abstract
Abstract
Gluconobacter oxydans is capable of rapidly incomplete oxidation of many sugars and alcohols, which means the strain has great potential for industrial purposes. Strong promoters are one of the essential factors that can improve strain performance by overexpression of specific genes. In this study, a pipeline for screening strong promoters by proteomics analysis was established. Based on the procedure, a new strong promoter designated as PB932_2000 was identified in G. oxydans WSH-003. The promoter region was characterized based on known genome sequence information using BPROM. The strength of PB932_2000 was further assessed by analysis of enhanced green fluorescent protein (egfp) expression and comparison with egfp expression by two commonly used strong promoters, PE. coli_tufB and PG. oxydans_tufB. Both quantitative real-time PCR and fluorescence intensities for egfp gene expression showed that PB932_2000 promoter is stronger than the other two. Overexpression of d-sorbitol dehydrogenase (sldh) by PB932_2000 in G. oxydans WSH-003 enhanced the titer and productivity of l-sorbose synthesis from d-sorbitol by 12.0 % and 33.3 %, respectively. These results showed that proteomics analysis is an efficient way to identify strong promoters. The isolated promoter PB932_2000 could further facilitate the metabolic engineering of G. oxydans.
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Ribosome binding site libraries and pathway modules for shikimic acid synthesis with Corynebacterium glutamicum. Microb Cell Fact 2015; 14:71. [PMID: 25981633 PMCID: PMC4453273 DOI: 10.1186/s12934-015-0254-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/06/2015] [Indexed: 11/15/2022] Open
Abstract
Background The shikimic acid (SA) pathway is a fundamental route to synthesize aromatic building blocks for cell growth and metabolic processes, as well as for fermentative production of various aromatic compounds. Genes encoding enzymes of SA pathway are not continuous on genome and they are differently regulated. Results In this study, efforts were made to construct continuous genetic modules of SA pathway that are regulated by a same Ptac promoter. Firstly, aro genes [aroG (NCgl2098), aroB (NCgl1559), aroD (NCgl0408) and aroE (NCgl1567)] from Corynebacterium glutamicum and ribosome binding site (RBS) libraries that were tailored for the above genes were obtained, and the strength of each RBS in the 4 libraries was quantified. Secondly, 9 genetic modules were built up from the RBS libraries, a previously characterized ribozyme insulator (RiboJ) and transcriptional promoter (Ptac) and terminator, and aroG, aroB, aroD and aroE. The functionality and efficiency of the constructed genetic modules were evaluated in C. glutamicum by determination of SA synthesis. Results showed that C. glutamicum RES167ΔaroK carrying a genetic module produced 4.3 g/L of SA, which was 54 folds higher compared to that of strain RES167ΔaroK (80 mg/L, without the genetic module) during fermentation in 250-mL flasks. The same strain produced 7.4, and 11.3 g/L of SA during 5-L batch and fed-batch fermentations, respectively, which corresponding to SA molar yields of 0.39 and 0.24 per mole sucrose consumption. Conclusion These results demonstrated that the constructed SA pathway modules are effective in increasing SA synthesis in C. glutamicum, and they might be useful for fermentative production of aromatic compounds derived from SA pathway.
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Liu X, Yang Y, Zhang W, Sun Y, Peng F, Jeffrey L, Harvey L, McNeil B, Bai Z. Expression of recombinant protein using Corynebacterium Glutamicum: progress, challenges and applications. Crit Rev Biotechnol 2015; 36:652-64. [PMID: 25714007 DOI: 10.3109/07388551.2015.1004519] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Corynebacterium glutamicum (C. glutamicum) is a highly promising alternative prokaryotic host for recombinant protein expression, as it possesses several significant advantages over Escherichia coli (E. coli), the currently leading bacterial protein expression system. During the past decades, several experimental techniques and vector components for genetic manipulation of C. glutamicum have been developed and validated, including strong promoters for tightly regulating target gene expression, various types of plasmid vectors, protein secretion systems and methods of genetically modifying the host strain genome to improve protein production potential. This review critically discusses current progress in establishing C. glutamicum as a host for recombinant protein expression, and examines, in depth, some successful case studies of actual application of this expression system. The established "expression tool box" for developing novel constructs based on C. glutamicum as a host are also evaluated. Finally, the existing issues and solutions in process development with C. glutamicum as a host are specifically addressed.
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Affiliation(s)
- Xiuxia Liu
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Yankun Yang
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Wei Zhang
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Yang Sun
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Feng Peng
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Laura Jeffrey
- b Institute of Pharmacy & Biomedical Sciences, Strathclyde University , Glasgow , UK
| | - Linda Harvey
- b Institute of Pharmacy & Biomedical Sciences, Strathclyde University , Glasgow , UK
| | - Brian McNeil
- b Institute of Pharmacy & Biomedical Sciences, Strathclyde University , Glasgow , UK
| | - Zhonghu Bai
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
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Choi JW, Yim SS, Lee SH, Kang TJ, Park SJ, Jeong KJ. Enhanced production of gamma-aminobutyrate (GABA) in recombinant Corynebacterium glutamicum by expressing glutamate decarboxylase active in expanded pH range. Microb Cell Fact 2015; 14:21. [PMID: 25886194 PMCID: PMC4335662 DOI: 10.1186/s12934-015-0205-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/05/2015] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Gamma-aminobutylate (GABA) is an important chemical in pharmacetucal field and chemical industry. GABA has mostly been produced in lactic acid bacteria by adding L-glutamate to the culture medium since L-glutamate can be converted into GABA by inherent L-glutamate decarboxylase. Recently, GABA has gained much attention for the application as a major building block for the synthesis of 2-pyrrolidone and biodegradable polyamide nylon 4, which opens its application area in the industrial biotechnology. Therefore, Corynebacterium glutamicum, the major L-glutamate producing microorganism, has been engineered to achieve direct fermentative production of GABA from glucose, but their productivity was rather low. RESULTS Recombinant C. glutamicum strains were developed for enhanced production of GABA from glucose by expressing Escherichia coli glutamate decarboxylase (GAD) mutant, which is active in expanded pH range. Synthetic PH36, PI16, and PL26 promoters, which have different promoter strengths in C. glutamicum, were examined for the expression of E. coli GAD mutant. C. glutamicum expressing E. coli GAD mutant under the strong PH36 promoter could produce GABA to the concentration of 5.89±0.35 g/L in GP1 medium at pH 7.0, which is 17-fold higher than that obtained by C. glutamicum expressing wild-type E. coli GAD in the same condition (0.34±0.26 g/L). Fed-bath culture of C. glutamicum expressing E. coli GAD mutant in GP1 medium containing 50 μg/L of biotin at pH 6, culture condition of which was optimized in flask cultures, resulted in the highest GABA concentration of 38.6±0.85 g/L with the productivity of 0.536 g/L/h. CONCLUSION Recombinant C. glutamicum strains developed in this study should be useful for the direct fermentative production of GABA from glucose, which allows us to achieve enhanced production of GABA suitable for its application area in the industrial biotechnology.
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Affiliation(s)
- Jae Woong Choi
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), KAIST, 335 Gwahagno, Yuseong-gu, Daejeon, 305-701, Republic of Korea.
| | - Sung Sun Yim
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), KAIST, 335 Gwahagno, Yuseong-gu, Daejeon, 305-701, Republic of Korea.
| | - Seung Hwan Lee
- Department of Biotechnology and Bioengineering, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 500-757, Republic of Korea.
| | - Taek Jin Kang
- Department of Chemical and Biochemical Engineering, Dongguk University-Seoul, 30 Pildong-ro 1-gil, Jung-gu, Seoul, 100-715, Republic of Korea.
| | - Si Jae Park
- Department of Environmental Engineering and Energy, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin, Gyeonggido, 449-728, Republic of Korea.
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), KAIST, 335 Gwahagno, Yuseong-gu, Daejeon, 305-701, Republic of Korea.
- Institute for the BioCentury, KAIST, 335 Gwahagno, Yuseong-gu, Daejeon, 305-701, Republic of Korea.
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Becker J, Wittmann C. Advanced Biotechnology: Metabolically Engineered Cells for the Bio-Based Production of Chemicals and Fuels, Materials, and Health-Care Products. Angew Chem Int Ed Engl 2015; 54:3328-50. [DOI: 10.1002/anie.201409033] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Indexed: 12/16/2022]
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36
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Biotechnologie von Morgen: metabolisch optimierte Zellen für die bio-basierte Produktion von Chemikalien und Treibstoffen, Materialien und Gesundheitsprodukten. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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37
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Kortmann M, Kuhl V, Klaffl S, Bott M. A chromosomally encoded T7 RNA polymerase-dependent gene expression system for Corynebacterium glutamicum: construction and comparative evaluation at the single-cell level. Microb Biotechnol 2014; 8:253-65. [PMID: 25488698 PMCID: PMC4353339 DOI: 10.1111/1751-7915.12236] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 01/09/2023] Open
Abstract
Corynebacterium glutamicum has become a favourite model organism in white biotechnology. Nevertheless, only few systems for the regulatable (over)expression of homologous and heterologous genes are currently available, all of which are based on the endogenous RNA polymerase. In this study, we developed an isopropyl-β-d-1-thiogalactopyranosid (IPTG)-inducible T7 expression system in the prophage-free strain C. glutamicum MB001. For this purpose, part of the DE3 region of Escherichia coli BL21(DE3) including the T7 RNA polymerase gene 1 under control of the lacUV5 promoter was integrated into the chromosome, resulting in strain MB001(DE3). Furthermore, the expression vector pMKEx2 was constructed allowing cloning of target genes under the control of the T7lac promoter. The properties of the system were evaluated using eyfp as heterologous target gene. Without induction, the system was tightly repressed, resulting in a very low specific eYFP fluorescence (= fluorescence per cell density). After maximal induction with IPTG, the specific fluorescence increased 450-fold compared with the uninduced state and was about 3.5 times higher than in control strains expressing eyfp under control of the IPTG-induced tac promoter with the endogenous RNA polymerase. Flow cytometry revealed that T7-based eyfp expression resulted in a highly uniform population, with 99% of all cells showing high fluorescence. Besides eyfp, the functionality of the corynebacterial T7 expression system was also successfully demonstrated by overexpression of the C. glutamicum pyk gene for pyruvate kinase, which led to an increase of the specific activity from 2.6 to 135 U mg−1. It thus presents an efficient new tool for protein overproduction, metabolic engineering and synthetic biology approaches with C. glutamicum.
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Affiliation(s)
- Maike Kortmann
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, D-52425, Germany
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38
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Wang G, Li Q, Xu D, Cui M, Sun X, Xu Y, Wang W. Construction of a host-independent T7 expression system with small RNA regulation. J Biotechnol 2014; 189:72-5. [DOI: 10.1016/j.jbiotec.2014.08.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/22/2014] [Accepted: 08/26/2014] [Indexed: 01/15/2023]
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The contest for precursors: channelling l-isoleucine synthesis in Corynebacterium glutamicum without byproduct formation. Appl Microbiol Biotechnol 2014; 99:791-800. [DOI: 10.1007/s00253-014-6109-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 09/22/2014] [Indexed: 10/24/2022]
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40
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Souza BM, Castro TLDP, Carvalho RDDO, Seyffert N, Silva A, Miyoshi A, Azevedo V. σ(ECF) factors of gram-positive bacteria: a focus on Bacillus subtilis and the CMNR group. Virulence 2014; 5:587-600. [PMID: 24921931 PMCID: PMC4105308 DOI: 10.4161/viru.29514] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The survival of bacteria to different environmental conditions depends on the activation of adaptive mechanisms, which are intricately driven through gene regulation. Because transcriptional initiation is considered to be the major step in the control of bacterial genes, we discuss the characteristics and roles of the sigma factors, addressing (1) their structural, functional and phylogenetic classification; (2) how their activity is regulated; and (3) the promoters recognized by these factors. Finally, we focus on a specific group of alternative sigma factors, the so-called σ(ECF) factors, in Bacillus subtilis and some of the main species that comprise the CMNR group, providing information on the roles they play in the microorganisms' physiology and indicating some of the genes whose transcription they regulate.
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Affiliation(s)
- Bianca Mendes Souza
- Laboratório de Genética Celular e Molecular; Instituto de Ciências Biológicas; Departamento de Biologia Geral; Universidade Federal de Minas Gerais; Belo Horizonte, MG Brazil
| | - Thiago Luiz de Paula Castro
- Laboratório de Genética Celular e Molecular; Instituto de Ciências Biológicas; Departamento de Biologia Geral; Universidade Federal de Minas Gerais; Belo Horizonte, MG Brazil
| | - Rodrigo Dias de Oliveira Carvalho
- Laboratório de Genética Celular e Molecular; Instituto de Ciências Biológicas; Departamento de Biologia Geral; Universidade Federal de Minas Gerais; Belo Horizonte, MG Brazil
| | - Nubia Seyffert
- Laboratório de Genética Celular e Molecular; Instituto de Ciências Biológicas; Departamento de Biologia Geral; Universidade Federal de Minas Gerais; Belo Horizonte, MG Brazil
| | - Artur Silva
- Laboratório de Polimorfismo de DNA; Instituto de Ciências Biológicas; Departamento de Genética; Universidade Federal do Pará; Belém, PA Brazil
| | - Anderson Miyoshi
- Laboratório de Genética Celular e Molecular; Instituto de Ciências Biológicas; Departamento de Biologia Geral; Universidade Federal de Minas Gerais; Belo Horizonte, MG Brazil
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular; Instituto de Ciências Biológicas; Departamento de Biologia Geral; Universidade Federal de Minas Gerais; Belo Horizonte, MG Brazil
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Woo HM, Park JB. Recent progress in development of synthetic biology platforms and metabolic engineering of Corynebacterium glutamicum. J Biotechnol 2014; 180:43-51. [DOI: 10.1016/j.jbiotec.2014.03.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/08/2014] [Accepted: 03/03/2014] [Indexed: 01/21/2023]
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42
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Rytter JV, Helmark S, Chen J, Lezyk MJ, Solem C, Jensen PR. Synthetic promoter libraries for Corynebacterium glutamicum. Appl Microbiol Biotechnol 2014; 98:2617-23. [DOI: 10.1007/s00253-013-5481-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 12/17/2013] [Indexed: 02/01/2023]
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