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Zhang J, Zhao Y, Peng Z, Yang M, Zou W, Wu X, Wang C, Si M, Chen C. The role of the transcriptional repressor CssR in Corynebacterium glutamicum in response to phenolic compounds. Heliyon 2024; 10:e27929. [PMID: 38509974 PMCID: PMC10950717 DOI: 10.1016/j.heliyon.2024.e27929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
The cssR gene (ncgl1578) of Corynebacterium glutamicum encodes a repressor of the TetR (tetracycline regulator) family. Its role in the stress response to antibiotics/heavy metals has been investigated, but how CssR functions in response to phenolic compounds in C. glutamicum has been rarely studied. In this study, we applied transcriptomic analysis, β-galactosidase analysis, qRT-PCR, and EMSAs to analyze the target genes and functions of CssR in response to phenolic compounds. Consistent with the upregulation of genes involved in the degradation of phenolic compounds, the ΔcssR mutant was more resistant to various phenolic compounds than was the wild-type strain. Furthermore, the addition of phenolic compounds induced the expression of corresponding genes (ncgl0283, ncgl1032, ncgl1111, ncgl2920, ncgl2923, and ncgl2952) in vivo. However, the DNA binding activity of CssR to the promoter of phenolic compound-degrading genes was undetected in vitro. Additionally, we also found that CssR indirectly negatively regulates the expression of cell wall/membrane/envelope biogenesis-related genes, which may enhance resistance to stress caused by phenolic compounds. Together, our findings demonstrate that CssR is a key regulator that copes with stress conditions induced by phenolic compounds, thus greatly expanding our understanding of the functions of TetR family transcription factors.
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Affiliation(s)
- Ju Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, Henan, China
- College of Horticulture, Agricultural University of Hebei/Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei/Collaborative Innovation Center of Vegetable Industry in Hebei, Baoding, 071001, China
| | - Yuying Zhao
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Zhaoxin Peng
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - MingFei Yang
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Wenyu Zou
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Xinyu Wu
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Chenghui Wang
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Meiru Si
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Can Chen
- Key Laboratory of Plant Genetics and Molecular Breeding, Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, Henan, China
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Jeong H, Kim Y, Lee HS. CdbC: a disulfide bond isomerase involved in the refolding of mycoloyltransferases in Corynebacterium glutamicum cells exposed to oxidative conditions. J Biochem 2024; 175:457-470. [PMID: 38227582 DOI: 10.1093/jb/mvae005] [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: 11/09/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 01/18/2024] Open
Abstract
In Corynebacterium glutamicum cells, cdbC, which encodes a protein containing the CysXXCys motif, is regulated by the global redox-responsive regulator OsnR. In this study, we assessed the role of the periplasmic protein CdbC in disulfide bond formation and its involvement in mycomembrane biosynthesis. Purified CdbC efficiently refolded scrambled RNaseA, exhibiting prominent disulfide bond isomerase activity. The transcription of cdbC was decreased in cells grown in the presence of the reductant dithiothreitol (DTT). Moreover, unlike wild-type and cdbC-deleted cells, cdbC-overexpressing (P180-cdbC) cells grown in the presence of DTT exhibited retarded growth, abnormal cell morphology, increased cell surface hydrophobicity and altered mycolic acid composition. P180-cdbC cells cultured in a reducing environment accumulated trehalose monocorynomycolate, indicating mycomembrane deformation. Similarly, a two-hybrid analysis demonstrated the interaction of CdbC with the mycoloyltransferases MytA and MytB. Collectively, our findings suggest that CdbC, a periplasmic disulfide bond isomerase, refolds misfolded MytA and MytB and thereby assists in mycomembrane biosynthesis in cells exposed to oxidative conditions.
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Affiliation(s)
- Haeri Jeong
- Department of Biotechnology and Bioinformatics, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
| | - Younhee Kim
- Department of Korean Medicine, Semyung University, Jecheon, 65, Semyeong-ro, Chungbuk 27136, Republic of Korea
| | - Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, 2511, Sejong-ro, Sejong 30019, Republic of Korea
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Jiang Z, Guan J, Liu T, Shangguan C, Xu M, Rao Z. The flavohaemoprotein hmp maintains redox homeostasis in response to reactive oxygen and nitrogen species in Corynebacterium glutamicum. Microb Cell Fact 2023; 22:158. [PMID: 37596674 PMCID: PMC10436651 DOI: 10.1186/s12934-023-02160-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND During the production of L-arginine through high dissolved oxygen and nitrogen supply fermentation, the industrial workhorse Corynebacterium glutamicum is exposed to oxidative stress. This generates reactive oxygen species (ROS) and reactive nitrogen species (RNS), which are harmful to the bacteria. To address the issue and to maintain redox homeostasis during fermentation, the flavohaemoprotein (Hmp) was employed. RESULTS The results showed that the overexpression of Hmp led to a decrease in ROS and RNS content by 9.4% and 22.7%, respectively, and improved the survivability of strains. When the strains were treated with H2O2 and NaNO2, the RT-qPCR analysis indicated an up-regulation of ammonium absorption and transporter genes amtB and glnD. Conversely, the deletion of hmp gives rise to the up-regulation of eight oxidative stress-related genes. These findings suggested that hmp is associated with oxidative stress and intracellular nitrogen metabolism genes. Finally, we released the inhibitory effect of ArnR on hmp. The Cc-ΔarnR-hmp strain produced 48.4 g/L L-arginine during batch-feeding fermentation, 34.3% higher than the original strain. CONCLUSIONS This report revealed the influence of dissolved oxygen and nitrogen concentration on reactive species of Corynebacterium glutamicum and the role of the Hmp in coping with oxidative stress. The Hmp first demonstrates related to redox homeostasis and nitrite metabolism, providing a feasible strategy for improving the robustness of strains.
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Affiliation(s)
- Ziqin Jiang
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jingyi Guan
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Tingting Liu
- Yantai Shinho Enterprise Foods Co., Ltd, Yantai, 265503, China
| | - Chunyu Shangguan
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
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Yu X, Li S, Feng H, Liao X, Xing XH, Bai Z, Liu X, Zhang C. CRISPRi-microfluidics screening enables genome-scale target identification for high-titer protein production and secretion. Metab Eng 2023; 75:192-204. [PMID: 36572334 DOI: 10.1016/j.ymben.2022.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/25/2022]
Abstract
Genome-scale target identification promises to guide microbial cell factory engineering for higher-titer production of biomolecules such as recombinant proteins (r-protein), but challenges remain due to the need not only for comprehensive genotypic perturbation but also in conjunction with high-throughput phenotypic screening strategies. Here, we developed a CRISPRi-microfluidics screening platform to systematically identify crucial gene targets that can be engineered to enhance r-protein secretion in Corynebacterium glutamicum. We created a CRISPR interference (CRISPRi) library containing 46,549 single-guide RNAs, where we aimed to unbiasedly target all genes for repression. Meanwhile, we developed a highly efficient droplet-based microfluidics system integrating the FlAsH-tetracysteine assay that enables screening of millions of strains to identify potential knockdowns conducive to nanobody VHH secretion. Among our highest-ranking candidates are a slew of previously unknown targets involved in transmembrane transport, amino-acid metabolism and redox regulation. Guided by these findings, we eventually constructed a hyperproducer for multiple proteins via combinatorial engineering of redox-response transcription factors. As the near-universal applicability of CRISPRi technology and the FlAsH-based screening platform, this procedure might be expanded to include a varied variety of microbial species and recombinant proteins.
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Affiliation(s)
- Xinyu Yu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Shuang Li
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Huibao Feng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xihao Liao
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, China
| | - Zhonghu Bai
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiuxia Liu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China.
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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Yang HD, Jeong H, Kim Y, Lee HS. The cysS gene (ncgl0127) of Corynebacterium glutamicum is required for sulfur assimilation and affects oxidative stress-responsive cysteine import. Res Microbiol 2022; 173:103983. [PMID: 35931248 DOI: 10.1016/j.resmic.2022.103983] [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: 04/25/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022]
Abstract
The OsnR protein functions as a transcriptional repressor of genes involved in redox-dependent stress responses. Here, we studied Corynebacterium glutamicum ORF ncgl0127 (referred to as cysS in this study), one of the target genes of OsnR, to reveal its role in osnR-mediated stress responses. The ΔcysS strain was found to be a cysteine auxotroph, and the transcription levels of the sulfur assimilatory genes and cysR, the master regulatory gene for sulfur assimilation, were low in this strain. Complementation of the strain with cysR transformed the strain into a cysteine prototroph. Cells challenged with oxidants or cysteine showed transcriptional stimulation of the cysS gene and decreased transcription of the ncgl2463 gene, which encodes a cysteine/cystine importer. The transcription of the ncgl2463 gene was increased in the ΔcysS strain and further stimulated by cysteine. Unlike the wild-type strain, ΔcysS cells grown with an excess amount of cysteine showed an oxidant- and alkylating agent-resistant phenotype, suggesting deregulated cysteine import. Collectively, our data suggest that the cysS gene plays a positive role in sulfur assimilation and a negative role in cysteine import, in particular in cells under oxidative stress.
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Affiliation(s)
- Han-Deul Yang
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, Republic of Korea.
| | - Haeri Jeong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea.
| | - Younhee Kim
- Department of Korean Medicine, Semyung University, Jecheon, Chungbuk 27136, Republic of Korea.
| | - Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, Republic of Korea.
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Jeong H, Kim Y, Lee HS. OsnR is an autoregulatory negative transcription factor controlling redox-dependent stress responses in Corynebacterium glutamicum. Microb Cell Fact 2021; 20:203. [PMID: 34663317 PMCID: PMC8524982 DOI: 10.1186/s12934-021-01693-1] [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: 06/17/2021] [Accepted: 10/07/2021] [Indexed: 01/11/2023] Open
Abstract
Background Corynebacterium glutamicum is used in the industrial production of amino acids and nucleotides. During the course of fermentation, C. glutamicum cells face various stresses and employ multiple regulatory genes to cope with the oxidative stress. The osnR gene plays a negative regulatory role in redox-dependent oxidative-stress responses, but the underlying mechanism is not known yet. Results Overexpression of the osnR gene in C. glutamicum affected the expression of genes involved in the mycothiol metabolism. ChIP-seq analysis revealed that OsnR binds to the promoter region of multiple genes, including osnR and cg0026, which seems to function in the membrane-associated redox metabolism. Studies on the role of the osnR gene involving in vitro assays employing purified OsnR proteins and in vivo physiological analyses have identified that OsnR inhibits the transcription of its own gene. Further, oxidant diamide stimulates OsnR-binding to the promoter region of the osnR gene. The genes affected by the overexpression of osnR have been found to be under the control of σH. In the osnR-overexpressing strain, the transcription of sigH is significantly decreased and the stimulation of sigH transcription by external stress is lost, suggesting that osnR and sigH form an intimate regulatory network. Conclusions Our study suggests that OsnR not only functions as a transcriptional repressor of its own gene and of those involved in redox-dependent stress responses but also participates in the global transcriptional regulation by controlling the transcription of other master regulators, such as sigH. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01693-1.
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Affiliation(s)
- Haeri Jeong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, Republic of Korea
| | - Younhee Kim
- Department of Korean Medicine, Semyung University, Jecheon, Chungbuk, Republic of Korea
| | - Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, Republic of Korea.
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Liu Y, Yang W, Su T, Che C, Li G, Chen C, Si M. The cssR gene of Corynebacterium glutamicum plays a negative regulatory role in stress responses. Microb Cell Fact 2021; 20:110. [PMID: 34082775 PMCID: PMC8176726 DOI: 10.1186/s12934-021-01600-8] [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: 04/08/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022] Open
Abstract
Background CssR, the product of the Corynebacterium glutamicum ncgl1578 gene cotranscribed with ncgl1579, is a TetR (tetracycline regulator) family repressor. Although many TetR-type regulators in C. glutamicum have been extensively described, members of the TetR family involved in the stress response remain unidentified. Results In this study, we found that CssR regulated the transcription of its own gene and the ncgl1576-ncgl1577 operon. The ncgl1576-ncgl1577 operon, which is located upstream of cssR in the orientation opposite that of the cssR operon, encodes an ATP-binding cassette (ABC), some of which are involved in the export of a wide range of antimicrobial compounds. The cssR-deletion (ΔcssR) mutant displayed increased resistance to various stresses. An imperfect palindromic motif (5′-TAA(G)TGN13CA(G)TTA-3′; 25 bp) located at the intergenic region between cssR and ncgl1577 was identified as the sole binding site for CssR. Expression of cssR and ncgl1577 was induced by antibiotics and heavy metals but not H2O2 or diamide, and the DNA-binding activity of CssR was impaired by antibiotics and heavy metals but not H2O2. Antibiotics and heavy metals caused CssR dissociation from target gene promoters, thus derepressing their transcription. Oxidant treatment neither altered the conformation of CssR nor modified its cysteine residues, indicating that the cysteine residues in CssR have no redox activity. In the ΔcssR mutant strain, genes involved in redox homeostasis also showed increased transcription levels, and the NADPH/NADP+ ratio was higher than that of the parental strain. Conclusion The stress response mechanism of CssR in C. glutamicum is realized via ligand-induced conformational changes of the protein, not via cysteine oxidation-based thiol modification. Moreover, the crucial role of CssR in the stress response was demonstrated by negatively controlling the expression of the ncgl1576-ncgl1577 operon, its structural gene, and/or redox homeostasis-related genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01600-8.
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Affiliation(s)
- Yang Liu
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Wenzhi Yang
- School of Food Science and Nutrition, University of Leeds, Leeds, LS2 9JT, UK
| | - Tao Su
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Chengchuan Che
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Guizhi Li
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Can Chen
- Key Laboratory of Plant Genetics and Molecular Breeding, Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, Henan, China.
| | - Meiru Si
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China.
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Jeong H, Lee JH, Kim Y, Lee HS. Thiol-specific oxidant diamide downregulates whiA gene of Corynebacterium glutamicum, thereby suppressing cell division and metabolism. Res Microbiol 2020; 171:331-340. [PMID: 32750493 DOI: 10.1016/j.resmic.2020.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 11/24/2022]
Abstract
The whiA (NCgl1527) gene from Corynebacterium glutamicum plays a crucial role during cell growth, and WhiA is recognized as the transcription factor for genes involved in cell division. In this study, we assessed the regulatory role of the gene in cell physiology. Transcription of the gene was specifically downregulated by the thiol-specific oxidant, diamide, and by heat stress. Cells exposed to diamide showed decreased transcription of genes involved in cell division and these effects were more profound in ΔwhiA cells. In addition, the ΔwhiA cells showed sensitivity to thiol-specific oxidants, DNA-damaging agents, and high temperature. Further, downregulation of sigH (NCgl0733), the central regulator in stress responses, along with master regulatory genes in cell metabolism, was observed in the ΔwhiA strain. Moreover, the amount of cAMP in the ΔwhiA cells in the early stationary phase was only at 30% level of that for the wild-type strain. Collectively, our data indicate that the role of whiA is to downregulate genes associated with cell division in response to heat or thiol-specific oxidative stress, and may suggest a role for the gene in downshifting cell metabolism by downregulating global regulatory genes when growth condition is not optimal for cells.
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Affiliation(s)
- Haeri Jeong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, Republic of Korea.
| | - Jae-Hyun Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, Republic of Korea.
| | - Younhee Kim
- Department of Korean Medicine, Semyung University, Jecheon, Chungbuk, Republic of Korea.
| | - Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, Republic of Korea.
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Lee JH, Jeong H, Kim Y, Lee HS. Corynebacterium glutamicum whiA plays roles in cell division, cell envelope formation, and general cell physiology. Antonie van Leeuwenhoek 2019; 113:629-641. [DOI: 10.1007/s10482-019-01370-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/30/2019] [Indexed: 10/25/2022]
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