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Lorenzo JP, Molla L, Amro EM, Ibarra IL, Ruf S, Neber C, Gkougkousis C, Ridani J, Subramani PG, Boulais J, Harjanto D, Vonica A, Di Noia JM, Dieterich C, Zaugg JB, Papavasiliou FN. APOBEC2 safeguards skeletal muscle cell fate through binding chromatin and regulating transcription of non-muscle genes during myoblast differentiation. Proc Natl Acad Sci U S A 2024; 121:e2312330121. [PMID: 38625936 PMCID: PMC11047093 DOI: 10.1073/pnas.2312330121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 03/07/2024] [Indexed: 04/18/2024] Open
Abstract
The apolipoprotein B messenger RNA editing enzyme, catalytic polypeptide (APOBEC) family is composed of nucleic acid editors with roles ranging from antibody diversification to RNA editing. APOBEC2, a member of this family with an evolutionarily conserved nucleic acid-binding cytidine deaminase domain, has neither an established substrate nor function. Using a cellular model of muscle differentiation where APOBEC2 is inducibly expressed, we confirmed that APOBEC2 does not have the attributed molecular functions of the APOBEC family, such as RNA editing, DNA demethylation, and DNA mutation. Instead, we found that during muscle differentiation APOBEC2 occupied a specific motif within promoter regions; its removal from those regions resulted in transcriptional changes. Mechanistically, these changes reflect the direct interaction of APOBEC2 with histone deacetylase (HDAC) transcriptional corepressor complexes. We also found that APOBEC2 could bind DNA directly, in a sequence-specific fashion, suggesting that it functions as a recruiter of HDAC to specific genes whose promoters it occupies. These genes are normally suppressed during muscle cell differentiation, and their suppression may contribute to the safeguarding of muscle cell fate. Altogether, our results reveal a unique role for APOBEC2 within the APOBEC family.
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Affiliation(s)
- J. Paulo Lorenzo
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg69120, Germany
| | - Linda Molla
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY10065
| | - Elias Moris Amro
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
| | - Ignacio L. Ibarra
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Sandra Ruf
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
| | - Cedrik Neber
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
| | - Christos Gkougkousis
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
| | - Jana Ridani
- Institut de Recherches Cliniques de Montréal, Montréal, QCH2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QCH4A 3J1, Canada
| | - Poorani Ganesh Subramani
- Institut de Recherches Cliniques de Montréal, Montréal, QCH2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QCH4A 3J1, Canada
| | - Jonathan Boulais
- Institut de Recherches Cliniques de Montréal, Montréal, QCH2W 1R7, Canada
| | - Dewi Harjanto
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY10065
| | - Alin Vonica
- Department of Biology, Nazareth University, Rochester, NY14618
| | - Javier M. Di Noia
- Institut de Recherches Cliniques de Montréal, Montréal, QCH2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QCH4A 3J1, Canada
- Department of Medicine, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg69120, Germany
- German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim, Heidelberg69120, Germany
| | - Judith B. Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
| | - F. Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg69120, Germany
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY10065
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Zheng Y, Sun H, Wang Y, Jin C, Li X, Pang Y, Ge Q, Wang L, Liu B. CsiR-mediated signal transduction pathway in response to low iron conditions promotes Escherichia coli K1 invasion and penetration of the blood-brain barrier. J Infect Dis 2024:jiae157. [PMID: 38531686 DOI: 10.1093/infdis/jiae157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 03/16/2024] [Accepted: 03/24/2024] [Indexed: 03/28/2024] Open
Abstract
Escherichia coli K1 is the leading cause of neonatal Gram-negative bacterial meningitis, but the pathogenesis of E. coli K1 meningitis remains unclear. Blood-brain barrier (BBB) penetration is a crucial step in E. coli meningitis development. Here, we uncovered the crucial role of CsiR, a GntR family regulator, in E. coli K1 virulence. During infection, csiR expression was induced due to the derepression by Fur in the blood and human brain microvascular endothelial cells (HBMECs). CsiR positively regulated ilvB expression, which is associated with branched chain amino acid synthesis. Furthermore, we revealed that IlvB activated the FAK/PI3 K pathway of HBMECs to induce actin cytoskeleton rearrangements, thereby promoting the bacterial invasion and penetration of the BBB. Overall, this study reveals a CsiR-mediated virulence regulation pathway in E. coli K1, which may provide a useful target for the prevention or therapy of E. coli meningitis.
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Affiliation(s)
- Yangyang Zheng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hao Sun
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Yanling Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Chen Jin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Xiaoya Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Yu Pang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Qianwen Ge
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Lei Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Bin Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
- Nankai International Advanced Research Institute, Shenzhen, China
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3
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Baugh AC, Defalco JB, Duscent-Maitland CV, Tumen-Velasquez MP, Laniohan NS, Figatner K, Hoover TR, Karls AC, Elliott KT, Neidle EL. Regulation of tricarboxylate transport and metabolism in Acinetobacter baylyi ADP1. Appl Environ Microbiol 2024; 90:e0211123. [PMID: 38289138 PMCID: PMC10880598 DOI: 10.1128/aem.02111-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 02/22/2024] Open
Abstract
Despite the significant presence of plant-derived tricarboxylic acids in some environments, few studies detail the bacterial metabolism of trans-aconitic acid (Taa) and tricarballylic acid (Tcb). In a soil bacterium, Acinetobacter baylyi ADP1, we discovered interrelated pathways for the consumption of Taa and Tcb. An intricate regulatory scheme tightly controls the transport and catabolism of both compounds and may reflect that they can be toxic inhibitors of the tricarboxylic acid cycle. The genes encoding two similar LysR-type transcriptional regulators, TcuR and TclR, were clustered on the chromosome with tcuA and tcuB, genes required for Tcb consumption. The genetic organization differed from that in Salmonella enterica serovar Typhimurium, in which tcuA and tcuB form an operon with a transporter gene, tcuC. In A. baylyi, tcuC was not cotranscribed with tcuAB. Rather, tcuC was cotranscribed with a gene, designated pacI, encoding an isomerase needed for Taa consumption. TcuC appears to transport Tcb and cis-aconitic acid (Caa), the presumed product of PacI-mediated periplasmic isomerization of Taa. Two operons, tcuC-pacI and tcuAB, were transcriptionally controlled by both TcuR and TclR, which have overlapping functions. We investigated the roles of the two regulators in activating transcription of both operons in response to multiple effector compounds, including Taa, Tcb, and Caa.IMPORTANCEIngestion of Taa and Tcb by grazing livestock can cause a serious metabolic disorder called grass tetany. The disorder, which results from Tcb absorption by ruminants, focuses attention on the metabolism of tricarboxylic acids. Additional interest stems from efforts to produce tricarboxylic acids as commodity chemicals. Improved understanding of bacterial enzymes and pathways for tricarboxylic acid metabolism may contribute to new biomanufacturing strategies.
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Affiliation(s)
- Alyssa C. Baugh
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Justin B. Defalco
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | | | | | | | - Kayla Figatner
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Timothy R. Hoover
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Anna C. Karls
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | | | - Ellen L. Neidle
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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Mallorson R, Miyagi E, Kao S, Sukegawa S, Saito H, Fabryova H, Morellatto Ruggieri L, Mediouni S, Valente ST, Strebel K. Transcriptional regulation of the HIV-1 inhibitory factor human mannose receptor 1 by the myeloid-specific transcription factor PU.1. J Virol 2024; 98:e0170223. [PMID: 38078733 PMCID: PMC10804955 DOI: 10.1128/jvi.01702-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 11/17/2023] [Indexed: 01/04/2024] Open
Abstract
HIV-1 infection of human macrophages leads to the downmodulation of human mannose receptor 1 (hMRC1), a cell-surface glycoprotein that is involved in the host innate immune response. We previously reported that downmodulation of hMRC1 involves the transactivator of transcription (Tat)-dependent transcriptional silencing of the hMRC1 promoter. However, the inhibitory effect of Tat on hMRC1 transcription was indirect and involved inhibition of the transcriptional activator PU.1, which normally upregulates hMRC1 expression in macrophages and other myeloid cells. We cloned a 284-bp fragment of the hMRC1 promoter, and within it, we identified four PU.1 box elements. We assessed the relative contribution of each of the four PU.1 boxes to PU.1-dependent transcriptional regulation and, surprisingly, found that only one of the four PU.1 boxes [PU.1(b)] was critically required for PU.1-mediated upregulation of luciferase expression. Transfer of this PU.1 box to a heterologous promoter conferred PU.1 responsiveness to an otherwise PU.1 insensitive promoter. Electrophoretic mobility shift assays identified this PU.1 box as a direct binding site for PU.1 both in the context of the hMRC1 promoter and the heterologous promoter. Furthermore, mutational analysis of the PU.1 protein identified the C-terminal DNA-binding domain in PU.1 as the region responsible for interaction with the PU.1 box. Recombinant HIV-1 Tat protein did not bind to the hMRC1 promoter element but efficiently interfered with the binding of PU.1 protein to the hMRC1 promoter. Thus, Tat is likely to inhibit the formation of active PU.1 transcription complexes, presumably by binding to and depleting common transcriptional cofactors.IMPORTANCEHIV-1 infection of cells results in the modulation of cellular gene expression by virus-encoded proteins in a manner that benefits the virus. We reported that HIV-1 transactivator of transcription (Tat) dysregulates the expression of the human mannose receptor 1 (hMRC1). hMRC1 is involved in the innate immune response of macrophages to foreign pathogens. Tat does not act directly on the hMRC1 promoter but instead inhibits PU.1, a cellular transcription factor regulating hMRC1 gene expression. Here, we characterize the PU.1-dependent regulation of hMRC1 expression. We identified four potential PU.1 binding sites in the hMRC1 promoter region but found that only one, PU.1(b), functioned as a true binding site for PU.1. Transfer of the PU.1(b) box to a heterologous promoter did not activate this promoter per se but rendered it responsive to PU.1. Our results support the view that PU.1 acts as a transcriptional co-factor whose activity can be regulated by HIV-1 Tat.
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Affiliation(s)
- Rosa Mallorson
- Viral Biochemistry Section, Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, Maryland, USA
| | - Eri Miyagi
- Viral Biochemistry Section, Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, Maryland, USA
| | - Sandra Kao
- Viral Biochemistry Section, Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, Maryland, USA
| | - Sayaka Sukegawa
- Department of Molecular Virology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hideki Saito
- Viral Biochemistry Section, Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, Maryland, USA
| | - Helena Fabryova
- Viral Biochemistry Section, Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, Maryland, USA
| | | | - Sonia Mediouni
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, Florida, USA
| | - Susana T. Valente
- Department of Immunology and Microbiology, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, Florida, USA
| | - Klaus Strebel
- Viral Biochemistry Section, Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, Maryland, USA
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5
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Wang Q, Wei Y, Huang Y, Qin J, Liu B, Liu R, Chen X, Li D, Wang Q, Li X, Yang X, Li Y, Sun H. Z3495, a LysR-Type Transcriptional Regulator Encoded in O Island 97, Regulates Virulence Gene Expression in Enterohemorrhagic Escherichia coli O157:H7. Microorganisms 2024; 12:140. [PMID: 38257967 PMCID: PMC10819331 DOI: 10.3390/microorganisms12010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is an important foodborne pathogen that infects humans by colonizing the large intestine. The genome of EHEC O157:H7 contains 177 unique O islands (OIs). Certain OIs significantly contribute to the heightened virulence and pathogenicity exhibited by EHEC O157:H7. However, the function of most OI genes remains unknown. We demonstrated here that EHEC O157:H7 adherence to and colonization of the mouse large intestine are both dependent on OI-97. Z3495, which is annotated as a LysR-type transcriptional regulator and encoded in OI-97, contributes to this phenotype. Z3495 activated the locus of enterocyte effacement (LEE) gene expression, promoting bacterial adherence. Deletion of z3495 significantly decreased the transcription of ler and other LEE genes, the ability to adhere to the host cells, and colonization in the mouse large intestine. Furthermore, the ChIP-seq results confirmed that Z3495 can directly bind to the promoter region of rcsF, which is a well-known activator of Ler, and increase LEE gene expression. Finally, phylogenetic analysis revealed that Z3495 is a widespread transcriptional regulator in enterohemorrhagic and enteropathogenic Escherichia coli. As a result of this study, we have gained a deeper understanding of how bacteria control their virulence and provide another example of a laterally acquired regulator that regulates LEE gene expression in bacteria.
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Affiliation(s)
- Qian Wang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (Q.W.); (Y.H.); (X.L.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Yi Wei
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (Q.W.); (Y.H.); (X.L.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Yu Huang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (Q.W.); (Y.H.); (X.L.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Jingliang Qin
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (Q.W.); (Y.H.); (X.L.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Bin Liu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (Q.W.); (Y.H.); (X.L.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
- Nankai International Advanced Research Institute, Shenzhen 518045, China
| | - Ruiying Liu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (Q.W.); (Y.H.); (X.L.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Xintong Chen
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (Q.W.); (Y.H.); (X.L.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Dan Li
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (Q.W.); (Y.H.); (X.L.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Qiushi Wang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (Q.W.); (Y.H.); (X.L.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Xiaoya Li
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (Q.W.); (Y.H.); (X.L.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Xinyuan Yang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (Q.W.); (Y.H.); (X.L.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Yuanke Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Hao Sun
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China; (Q.W.); (Y.H.); (X.L.)
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
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Chen C, Huang Z, Ge C, Yu H, Yuan H, Tian H. Regulation of the pleiotropic transcriptional regulator CodY on the conversion of branched-chain amino acids into branched-chain aldehydes in Lactococcus lactis. Appl Environ Microbiol 2023; 89:e0149323. [PMID: 37943058 PMCID: PMC10686057 DOI: 10.1128/aem.01493-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Branched-chain aldehydes are the primary compounds that contribute to the nutty flavor in cheddar cheese. Lactococcus lactis, which is often applied as primary starter culture, is a significant contributor to the nutty flavor of cheddar cheese due to its ability of conversion of BCAAs into branched-chain aldehydes. In the present study, we found that the regulatory role of CodY is crucial for the conversion. CodY acts as a pleiotropic transcriptional regulator via binding to various regulatory regions of key genes. The results presented valuable knowledge into the role of CodY on the regulation and biosynthetic pathway of branched-chain amino acids and the related aldehydes. Furthermore, it provided new insight for increasing the nutty flavor produced during the manufacture and ripening of cheese.
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Affiliation(s)
- Chen Chen
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
| | - Zhiyang Huang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
| | - Chang Ge
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
| | - Haiyan Yu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
| | - Haibin Yuan
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
| | - Huaixiang Tian
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
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7
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Stöckl R, Nißl L, Reichelt R, Rachel R, Grohmann D, Grünberger F. The transcriptional regulator EarA and intergenic terminator sequences modulate archaellation in Pyrococcus furiosus. Front Microbiol 2023; 14:1241399. [PMID: 38029142 PMCID: PMC10665913 DOI: 10.3389/fmicb.2023.1241399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The regulation of archaellation, the formation of archaeal-specific cell appendages called archaella, is crucial for the motility, adhesion, and survival of archaeal organisms. Although the heavily archaellated and highly motile Pyrococcus furiosus is a key model organism for understanding the production and function of archaella in Euryarchaea, the transcriptional regulation of archaellum assembly is so far unknown. Here we show that the transcription factor EarA is the master regulator of the archaellum (arl) operon transcription, which is further modulated by intergenic transcription termination signals. EarA deletion or overexpression strains demonstrate that EarA is essential for archaellation in P. furiosus and governs the degree of archaellation. Providing a single-molecule update on the transcriptional landscape of the arl operon in P. furiosus, we identify sequence motifs for EarA binding upstream of the arl operon and intergenic terminator sequences as critical elements for fine-tuning the expression of the multicistronic arl cluster. Furthermore, transcriptome re-analysis across different Thermococcales species demonstrated a heterogeneous production of major archaellins, suggesting a more diverse composition of archaella than previously recognized. Overall, our study provides novel insights into the transcriptional regulation of archaellation and highlights the essential role of EarA in Pyrococcus furiosus. These findings advance our understanding of the mechanisms governing archaellation and have implications for the functional diversity of archaella.
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Affiliation(s)
- Richard Stöckl
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Laura Nißl
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Robert Reichelt
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Reinhard Rachel
- Centre for Electron Microscopy, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Felix Grünberger
- Institute of Microbiology and Archaea Centre, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
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8
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Lu P, Wang K, Wang J, Xia C, Yang S, Ma L, Shi H. A novel zinc finger transcription factor, BcMsn2, is involved in growth, development, and virulence in Botrytis cinerea. Front Microbiol 2023; 14:1247072. [PMID: 37915851 PMCID: PMC10616473 DOI: 10.3389/fmicb.2023.1247072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/20/2023] [Indexed: 11/03/2023] Open
Abstract
Reactive oxygen species (ROS) are important for plant defense against fungal attack. As a necrotrophic fungus, Botrytis cinerea can exploit ROS that originated from both sides of the host and pathogen during interaction to facilitate its infestation. Meanwhile, B. cinerea needs to exert an efficient oxidative stress responsive system to balance the intracellular redox state when encountering deleterious ROS levels. However, the machinery applied by B. cinerea to cope with ROS remains obscure. Herein, we investigated the role of the transcription factor BcMsn2 in regulating B. cinerea redox homeostasis. Disruption of the BcMsn2 gene severely impaired vegetative growth, sclerotium formation, conidial yield, and fungal virulence. The intracellular oxidative homeostasis of the ∆bcmsn2 mutant was disrupted, leading to significantly elevated levels of ROS and reduced activities of enzymes closely associated with oxygen stress, such as catalase (CAT) and superoxide dismutase (SOD). RNA-Seq and qRT-PCR analyses showed remarkable downregulation of the expression of several genes encoding ROS scavenging factors involved in maintaining the redox homeostasis in ∆bcmsn2, suggesting that BcMsn2 functions as a transcriptional regulator of these genes. Our findings indicated that BcMsn2 plays an indispensable role in maintaining the equilibrium of the redox state in B. cinerea, and intracellular ROS serve as signaling molecules that regulate the growth, asexual reproduction, and virulence of this pathogen.
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Affiliation(s)
- Ping Lu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Ke Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Jiaqi Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Chunbo Xia
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Shu Yang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Liang Ma
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
| | - Haojie Shi
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
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Ahmed SM, Ragunathan P, Shin J, Peter S, Kleissle S, Neuenschwander M, Schäfer R, Kries JPV, Grüber G, Dröge P. The FGFR inhibitor PD173074 binds to the C-terminus of oncofetal HMGA2 and modulates its DNA-binding and transcriptional activation functions. FEBS Lett 2023; 597:1977-1988. [PMID: 37259564 DOI: 10.1002/1873-3468.14675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/20/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
The architectural chromatin factor high-mobility group AT-hook 2 (HMGA2) is causally involved in several human malignancies and pathologies. HMGA2 is not expressed in most normal adult somatic cells, which renders the protein an attractive drug target. An established cell-based compound library screen identified the fibroblast growth factor receptor (FGFR) inhibitor PD173074 as an antagonist of HMGA2-mediated transcriptional reporter gene activation. We determined that PD173074 binds the C-terminus of HMGA2 and interferes with functional coordination of the three AT-hook DNA-binding domains mediated by the C-terminus. The HMGA2-antagonistic effect of PD173074 on transcriptional activation may therefore result from an induced altered DNA-binding mode of HMGA2. PD173074 as a novel HMGA2-specific antagonist could trigger the development of derivates with enhanced attributes and clinical potential.
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Affiliation(s)
- Syed Moiz Ahmed
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Priya Ragunathan
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Joon Shin
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Sabrina Peter
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Sabrina Kleissle
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft, Berlin, Germany
| | | | - Reinhold Schäfer
- Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Jens Peter V Kries
- Leibniz-Forschungsinstitut fűr Molekulare Pharmakologie, Berlin, Germany
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
- LambdaGen Pte Ltd, Singapore City, Singapore
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10
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Guo Y, Cen XF, Li D, Qiu HL, Chen YJ, Zhang M, Huang SH, Xia H, Xu M. Identify Tcea3 as a novel anti-cardiomyocyte hypertrophy gene involved in fatty acid oxidation and oxidative stress. Front Cardiovasc Med 2023; 10:1137429. [PMID: 37404738 PMCID: PMC10315901 DOI: 10.3389/fcvm.2023.1137429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/07/2023] [Indexed: 07/06/2023] Open
Abstract
Background Chronic pressure overload triggers pathological cardiac hypertrophy that eventually leads to heart failure. Effective biomarkers and therapeutic targets for heart failure remain to be defined. The aim of this study is to identify key genes associated with pathological cardiac hypertrophy by combining bioinformatics analyses with molecular biology experiments. Methods Comprehensive bioinformatics tools were used to screen genes related to pressure overload-induced cardiac hypertrophy. We identified differentially expressed genes (DEGs) by overlapping three Gene Expression Omnibus (GEO) datasets (GSE5500, GSE1621, and GSE36074). Correlation analysis and BioGPS online tool were used to detect the genes of interest. A mouse model of cardiac remodeling induced by transverse aortic constriction (TAC) was established to verify the expression of the interest gene during cardiac remodeling by RT-PCR and western blot. By using RNA interference technology, the effect of transcription elongation factor A3 (Tcea3) silencing on PE-induced hypertrophy of neonatal rat ventricular myocytes (NRVMs) was detected. Next, gene set enrichment analysis (GSEA) and the online tool ARCHS4 were used to predict the possible signaling pathways, and the fatty acid oxidation relevant pathways were enriched and then verified in NRVMs. Furthermore, the changes of long-chain fatty acid respiration in NRVMs were detected using the Seahorse XFe24 Analyzer. Finally, MitoSOX staining was used to detect the effect of Tcea3 on mitochondrial oxidative stress, and the contents of NADP(H) and GSH/GSSG were detected by relevant kits. Results A total of 95 DEGs were identified and Tcea3 was negatively correlated with Nppa, Nppb and Myh7. The expression level of Tcea3 was downregulated during cardiac remodeling both in vivo and in vitro. Knockdown of Tcea3 aggravated cardiomyocyte hypertrophy induced by PE in NRVMs. GSEA and online tool ARCHS4 predict Tcea3 involved in fatty acid oxidation (FAO). Subsequently, RT-PCR results showed that knockdown of Tcea3 up-regulated Ces1d and Pla2g5 mRNA expression levels. In PE induced cardiomyocyte hypertrophy, Tcea3 silencing results in decreased fatty acid utilization, decreased ATP synthesis and increased mitochondrial oxidative stress. Conclusion Our study identifies Tcea3 as a novel anti-cardiac remodeling target by regulating FAO and governing mitochondrial oxidative stress.
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Affiliation(s)
- Yingying Guo
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xian-feng Cen
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Renmin Hospital of Wuhan University, Wuhan, China
| | - Dan Li
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hong-liang Qiu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ya-jie Chen
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Renmin Hospital of Wuhan University, Wuhan, China
| | - Meng Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Renmin Hospital of Wuhan University, Wuhan, China
| | - Si-hui Huang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hao Xia
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Cardiovascular Research Institute, Wuhan University, Wuhan, China
| | - Man Xu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Renmin Hospital of Wuhan University, Wuhan, China
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11
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Kubota S, Nakata M, Hirose Y, Yamaguchi M, Kreikemeyer B, Uzawa N, Sumitomo T, Kawabata S. Involvement of ribonuclease Y in pilus production by M49 Streptococcus pyogenes strain via modulation of messenger RNA level of transcriptional regulator. Microbiol Immunol 2023. [PMID: 37138376 DOI: 10.1111/1348-0421.13069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 05/05/2023]
Abstract
Streptococcus pyogenes displays a wide variety of pili, which is largely dependent on serotype. A distinct subset of S. pyogenes strains that possess the Nra transcriptional regulator demonstrates thermoregulated pilus production. Findings obtained in the present study of an Nra-positive serotype M49 strain revealed involvement of conserved virulence factor A (CvfA), also referred to as ribonuclease Y (RNase Y), in virulence factor expression and pilus production, while a cvfA deletion strain showed reduced pilus production and adherence to human keratinocytes as compared with wild-type and revertant strains. Furthermore, transcript levels of pilus subunits and srtC2 genes were decreased by cvfA deletion, which was remarkable at 25°C. Likewise, both messenger RNA (mRNA) and protein levels of Nra were remarkably decreased by cvfA deletion. Whether the expression of other pilus-related regulators, including fasX and CovR, was subject to thermoregulation was also examined. While the mRNA level of fasX, which inhibits cpa and fctA translation, was decreased by cvfA deletion at both 37°C and 25°C, CovR mRNA and protein levels, as well as its phosphorylation level were not significantly changed, suggesting that neither fasX nor CovR is necessarily involved in thermosensitive pilus production. Phenotypic analysis of the mutant strains revealed that culture temperature and cvfA deletion had varied effects on streptolysin S and SpeB activities. Furthermore, bactericidal assay data showed that cvfA deletion decreased the rate of survival in human blood. Together, the present findings indicate that CvfA is involved in regulation of pilus production and virulence-related phenotypes of the serotype M49 strain of S. pyogenes.
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Affiliation(s)
- Seiko Kubota
- Department of Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
- Department of Oral and Maxillofacial Surgery II, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Masanobu Nakata
- Department of Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
- Department of Oral Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yujiro Hirose
- Department of Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Masaya Yamaguchi
- Department of Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
- Bioinformatics Research Unit, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Narikazu Uzawa
- Department of Oral and Maxillofacial Surgery II, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Tomoko Sumitomo
- Department of Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
- Department of Oral Microbiology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Shigetada Kawabata
- Department of Microbiology, Osaka University Graduate School of Dentistry, Osaka, Japan
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12
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Hanko EKR, Joosab Noor Mahomed TA, Stoney RA, Breitling R. TFBMiner: A User-Friendly Command Line Tool for the Rapid Mining of Transcription Factor-Based Biosensors. ACS Synth Biol 2023; 12:1497-1507. [PMID: 37053505 DOI: 10.1021/acssynbio.2c00679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Transcription factors responsive to small molecules are essential elements in synthetic biology designs. They are often used as genetically encoded biosensors with applications ranging from the detection of environmental contaminants and biomarkers to microbial strain engineering. Despite our efforts to expand the space of compounds that can be detected using biosensors, the identification and characterization of transcription factors and their corresponding inducer molecules remain labor- and time-intensive tasks. Here, we introduce TFBMiner, a new data mining and analysis pipeline that enables the automated and rapid identification of putative metabolite-responsive transcription factor-based biosensors (TFBs). This user-friendly command line tool harnesses a heuristic rule-based model of gene organization to identify both gene clusters involved in the catabolism of user-defined molecules and their associated transcriptional regulators. Ultimately, biosensors are scored based on how well they fit the model, providing wet-lab scientists with a ranked list of candidates that can be experimentally tested. We validated the pipeline using a set of molecules for which TFBs have been reported previously, including sensors responding to sugars, amino acids, and aromatic compounds, among others. We further demonstrated the utility of TFBMiner by identifying a biosensor for S-mandelic acid, an aromatic compound for which a responsive transcription factor had not been found previously. Using a combinatorial library of mandelate-producing microbial strains, the newly identified biosensor was able to distinguish between low- and high-producing strain candidates. This work will aid in the unraveling of metabolite-responsive microbial gene regulatory networks and expand the synthetic biology toolbox to allow for the construction of more sophisticated self-regulating biosynthetic pathways.
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Affiliation(s)
- Erik K R Hanko
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Tariq A Joosab Noor Mahomed
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Ruth A Stoney
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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13
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Schoof M, O'Callaghan M, Hefer C, Glare TR, Paulson AR, Hurst MRH. Lysis Cassette-Mediated Exoprotein Release in Yersinia entomophaga Is Controlled by a PhoB-Like Regulator. Microbiol Spectr 2023:e0036423. [PMID: 36951587 PMCID: PMC10101115 DOI: 10.1128/spectrum.00364-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Secretion of exoproteins is a key component of bacterial virulence, and is tightly regulated in response to environmental stimuli and host-dependent signals. The entomopathogenic bacterium Yersinia entomophaga MH96 produces a wide range of exoproteins including its main virulence factor, the 2.46 MDa insecticidal Yen-Tc toxin complex. Previously, a high-throughput transposon-based screening assay identified the region of exoprotein release (YeRER) as essential to exoprotein release in MH96. This study defines the role of the YeRER associated ambiguous holin/endolysin-based lysis cluster (ALC) and the novel RoeA regulator in the regulation and release of exoproteins in MH96. A mutation in the ambiguous lysis cassette (ALC) region abolished exoprotein release and caused cell elongation, a phenotype able to be restored through trans-complementation with an intact ALC region. Endogenous ALC did not impact cell growth of the wild type, while artificial expression of an optimized ALC caused cell lysis. Using HolA-sfGFP and Rz1-sfGFP reporters, Rz1 expression was observed in all cells while HolA expression was limited to a small proportion of cells, which increased over time. Transcriptomic assessments found expression of the genes encoding the prominent exoproteins, including the Yen-Tc, was reduced in the roeA mutant and identified a 220 ncRNA of the YeRER intergenic region that, when trans complemented in the wildtype, abolished exoprotein release. A model for Y. entomophaga mediated exoprotein regulation and release is proposed. IMPORTANCE While theoretical models exist, there is not yet any empirical data that links ALC phage-like lysis cassettes with the release of large macro-molecular toxin complexes, such as Yen-Tc in Gram-negative bacteria. In this study, we demonstrate that the novel Y. entomophaga RoeA activates the production of exoproteins (including Yen-Tc) and the ALC at the transcriptional level. The translation of the ALC holin is confined to a subpopulation of cells that then lyse over time, indicative of a complex hierarchical regulatory network. The presence of an orthologous RoeA and a HolA like holin 5' of an eCIS Afp element in Pseudomonas chlororaphis, combined with the presented data, suggests a shared mechanism is required for the release of some large macromolecular protein assemblies, such as the Yen-Tc, and further supports classification of phage-like lysis clusters as type 10 secretion systems.
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Affiliation(s)
- Marion Schoof
- AgResearch, Resilient Agriculture, Lincoln Research Centre, Lincoln, New Zealand
| | - Maureen O'Callaghan
- AgResearch, Resilient Agriculture, Lincoln Research Centre, Lincoln, New Zealand
| | - Charles Hefer
- AgResearch, Resilient Agriculture, Lincoln Research Centre, Lincoln, New Zealand
| | - Travis R Glare
- Wine and Molecular Biosciences Dept, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Amber R Paulson
- British Columbia Ministry of Environment and Climate Change Strategy, Victoria, British Columbia, Canada
| | - Mark R H Hurst
- AgResearch, Resilient Agriculture, Lincoln Research Centre, Lincoln, New Zealand
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14
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Escobar-Salom M, Barceló IM, Jordana-Lluch E, Torrens G, Oliver A, Juan C. Bacterial virulence regulation through soluble peptidoglycan fragments sensing and response: knowledge gaps and therapeutic potential. FEMS Microbiol Rev 2023; 47:fuad010. [PMID: 36893807 PMCID: PMC10039701 DOI: 10.1093/femsre/fuad010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 02/10/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
Given the growing clinical-epidemiological threat posed by the phenomenon of antibiotic resistance, new therapeutic options are urgently needed, especially against top nosocomial pathogens such as those within the ESKAPE group. In this scenario, research is pushed to explore therapeutic alternatives and, among these, those oriented toward reducing bacterial pathogenic power could pose encouraging options. However, the first step in developing these antivirulence weapons is to find weak points in the bacterial biology to be attacked with the goal of dampening pathogenesis. In this regard, during the last decades some studies have directly/indirectly suggested that certain soluble peptidoglycan-derived fragments display virulence-regulatory capacities, likely through similar mechanisms to those followed to regulate the production of several β-lactamases: binding to specific transcriptional regulators and/or sensing/activation of two-component systems. These data suggest the existence of intra- and also intercellular peptidoglycan-derived signaling capable of impacting bacterial behavior, and hence likely exploitable from the therapeutic perspective. Using the well-known phenomenon of peptidoglycan metabolism-linked β-lactamase regulation as a starting point, we gather and integrate the studies connecting soluble peptidoglycan sensing with fitness/virulence regulation in Gram-negatives, dissecting the gaps in current knowledge that need filling to enable potential therapeutic strategy development, a topic which is also finally discussed.
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Affiliation(s)
- María Escobar-Salom
- Research Unit and Microbiology Department, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Crtra. Valldemossa 79, 07010 Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC). Av. Monforte de Lemos 3-5, 28029, Madrid, Spain
| | - Isabel María Barceló
- Research Unit and Microbiology Department, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Crtra. Valldemossa 79, 07010 Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC). Av. Monforte de Lemos 3-5, 28029, Madrid, Spain
| | - Elena Jordana-Lluch
- Research Unit and Microbiology Department, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Crtra. Valldemossa 79, 07010 Palma, Spain
| | - Gabriel Torrens
- Research Unit and Microbiology Department, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Crtra. Valldemossa 79, 07010 Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC). Av. Monforte de Lemos 3-5, 28029, Madrid, Spain
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University. Försörjningsvägen 2A, SE-901 87 Umeå, Sweden
| | - Antonio Oliver
- Research Unit and Microbiology Department, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Crtra. Valldemossa 79, 07010 Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC). Av. Monforte de Lemos 3-5, 28029, Madrid, Spain
| | - Carlos Juan
- Research Unit and Microbiology Department, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Crtra. Valldemossa 79, 07010 Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC). Av. Monforte de Lemos 3-5, 28029, Madrid, Spain
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15
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Pushparajan AR, Edison LK, Ajay Kumar R. Mycobacterium tuberculosis transcriptional regulator Rv1019 is upregulated in hypoxia, and negatively regulates Rv3230c-Rv3229c operon encoding enzymes in the oleic acid biosynthetic pathway. FEBS J 2023; 290:1583-1595. [PMID: 36209365 DOI: 10.1111/febs.16647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/19/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022]
Abstract
The main obstacle in eradicating tuberculosis is the ability of Mycobacterium tuberculosis to remain dormant in the host, and then to get reactivated even years later under immunocompromised conditions. Transcriptional regulation in intracellular pathogens plays an important role in their adapting to the challenging environment inside the host cells. Previously, we demonstrated that Rv1019, a putative transcriptional regulator of M. tuberculosis H37Rv, is an autorepressor. We showed that Rv1019 is cotranscribed with Rv1020 (mfd) and Rv1021 (mazG) which encode DNA repair proteins and negatively regulates the expression of these genes. In the present study, we show that Rv1019 regulates the expression of the genes Rv3230c and Rv3229c (desA3) also which form a two-gene operon in M. tuberculosis. Overexpression of Rv1019 in M. tuberculosis significantly downregulated the expression of these genes. Employing Wayne's hypoxia-induced dormancy model of M. tuberculosis, we show that Rv1019 is upregulated three-fold under hypoxia. Finally, by reporter assay, using Mycobacterium smegmatis as a model, we validate that Rv1019 is recruited to the promoter of Rv3230c-Rv3229c during hypoxia, and negatively regulates this operon which is involved in the biosynthesis of oleic acid.
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Affiliation(s)
- Akhil Raj Pushparajan
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India.,Department of Biotechnology, Faculty of Applied Sciences and Technology, University of Kerala, Thiruvananthapuram, India
| | - Lekshmi K Edison
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Ramakrishnan Ajay Kumar
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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Gavira JA, Rico-Jiménez M, Ortega Á, Petukhova NV, Bug DS, Castellví A, Porozov YB, Zhulin IB, Krell T, Matilla MA. Emergence of an Auxin Sensing Domain in Plant-Associated Bacteria. mBio 2023; 14:e0336322. [PMID: 36602305 DOI: 10.1128/mbio.03363-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Bacteria have evolved a sophisticated array of signal transduction systems that allow them to adapt their physiology and metabolism to changing environmental conditions. Typically, these systems recognize signals through dedicated ligand binding domains (LBDs) to ultimately trigger a diversity of physiological responses. Nonetheless, an increasing number of reports reveal that signal transduction receptors also bind antagonists to inhibit responses mediated by agonists. The mechanisms by which antagonists block the downstream signaling cascade remain largely unknown. To advance our knowledge in this field, we used the LysR-type transcriptional regulator AdmX as a model. AdmX activates the expression of an antibiotic biosynthetic cluster in the rhizobacterium Serratia plymuthica. AdmX specifically recognizes the auxin phytohormone indole-3-acetic acid (IAA) and its biosynthetic intermediate indole-3-pyruvic acid (IPA) as signals. However, only IAA, but not IPA, was shown to regulate antibiotic production in S. plymuthica. Here, we report the high-resolution structures of the LBD of AdmX in complex with IAA and IPA. We found that IAA and IPA compete for binding to AdmX. Although IAA and IPA binding does not alter the oligomeric state of AdmX, IPA binding causes a higher degree of compactness in the protein structure. Molecular dynamics simulations revealed significant differences in the binding modes of IAA and IPA by AdmX, and the inspection of the three-dimensional structures evidenced differential agonist- and antagonist-mediated structural changes. Key residues for auxin binding were identified and an auxin recognition motif defined. Phylogenetic clustering supports the recent evolutionary emergence of this motif specifically in plant-associated enterobacteria. IMPORTANCE Although antagonists were found to bind different bacterial signal transduction receptors, we are still at the early stages of understanding the molecular details by which these molecules exert their inhibitory effects. Here, we provide insight into the structural changes resulting from the binding of an agonist and an antagonist to a sensor protein. Our data indicate that agonist and antagonist recognition is characterized by small conformational differences in the LBDs that can be efficiently transmitted to the output domain to modulate the final response. LBDs are subject to strong selective pressures and are rapidly evolving domains. An increasing number of reports support the idea that environmental factors drive the evolution of sensor domains. Given the recent evolutionary history of AdmX homologs, as well as their narrow phyletic distribution within plant-associated bacteria, our results are in accordance with a plant-mediated evolutionary process that resulted in the emergence of receptor proteins that specifically sense auxin phytohormones.
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Cerutti C, Shi JR, Vanacker JM. Multifaceted Transcriptional Network of Estrogen-Related Receptor Alpha in Health and Disease. Int J Mol Sci 2023; 24:ijms24054265. [PMID: 36901694 PMCID: PMC10002233 DOI: 10.3390/ijms24054265] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/15/2023] [Accepted: 02/18/2023] [Indexed: 02/23/2023] Open
Abstract
Estrogen-related receptors (ERRα, β and γ in mammals) are orphan members of the nuclear receptor superfamily acting as transcription factors. ERRs are expressed in several cell types and they display various functions in normal and pathological contexts. Amongst others, they are notably involved in bone homeostasis, energy metabolism and cancer progression. In contrast to other nuclear receptors, the activities of the ERRs are apparently not controlled by a natural ligand but they rely on other means such as the availability of transcriptional co-regulators. Here we focus on ERRα and review the variety of co-regulators that have been identified by various means for this receptor and their reported target genes. ERRα cooperates with distinct co-regulators to control the expression of distinct sets of target genes. This exemplifies the combinatorial specificity of transcriptional regulation that induces discrete cellular phenotypes depending on the selected coregulator. We finally propose an integrated view of the ERRα transcriptional network.
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18
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Liu D, Song H, Li Y, Huang R, Liu H, Tang K, Jiao N, Liu J. The Transcriptional Repressor PerR Senses Sulfane Sulfur by Cysteine Persulfidation at the Structural Zn(2+) Site in Synechococcus sp. PCC7002. Antioxidants (Basel) 2023; 12. [PMID: 36829981 DOI: 10.3390/antiox12020423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Cyanobacteria can perform both anoxygenic and oxygenic photosynthesis, a characteristic which ensured that these organisms were crucial in the evolution of the early Earth and the biosphere. Reactive oxygen species (ROS) produced in oxygenic photosynthesis and reactive sulfur species (RSS) produced in anoxygenic photosynthesis are closely related to intracellular redox equilibrium. ROS comprise superoxide anion (O2●-), hydrogen peroxide (H2O2), and hydroxyl radicals (●OH). RSS comprise H2S and sulfane sulfur (persulfide, polysulfide, and S8). Although the sensing mechanism for ROS in cyanobacteria has been explored, that of RSS has not been elucidated. Here, we studied the function of the transcriptional repressor PerR in RSS sensing in Synechococcus sp. PCC7002 (PCC7002). PerR was previously reported to sense ROS; however, our results revealed that it also participated in RSS sensing. PerR repressed the expression of prxI and downregulated the tolerance of PCC7002 to polysulfide (H2Sn). The reporter system indicated that PerR sensed H2Sn. Cys121 of the Cys4:Zn2+ site, which contains four cysteines (Cys121, Cys124, Cys160, and Cys163) bound to one zinc atom, could be modified by H2Sn to Cys121-SSH, as a result of which the zinc atom was released from the site. Moreover, Cys19 could also be modified by polysulfide to Cys19-SSH. Thus, our results reveal that PerR, a representative of the Cys4 zinc finger proteins, senses H2Sn. Our findings provide a new perspective to explore the adaptation strategy of cyanobacteria in Proterozoic and contemporary sulfurization oceans.
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Park J, Park S, Lee JS. Role of the Paf1 complex in the maintenance of stem cell pluripotency and development. FEBS J 2023; 290:951-961. [PMID: 35869661 DOI: 10.1111/febs.16582] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/26/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
Cell identity is determined by the transcriptional regulation of a cell-type-specific gene group. The Paf1 complex (Paf1C), an RNA polymerase II-associating factor, is an important transcriptional regulator that not only participates in transcription elongation and termination but also affects transcription-coupled histone modifications and chromatin organisation. Recent studies have shown that Paf1C is involved in the expression of genes required for self-renewal and pluripotency in stem cells and tumorigenesis. In this review, we focused on the role of Paf1C as a critical transcriptional regulator in cell fate decisions. Paf1C affects the pluripotency of stem cells by regulating the expression of core transcription factors such as Oct4 and Nanog. In addition, Paf1C directly binds to the promoters or distant elements of target genes, thereby maintaining the pluripotency in embryonic stem cells derived from an early stage of the mammalian embryo. Paf1C is upregulated in cancer stem cells, as compared with that in cancer cells, suggesting that Paf1C may be a target for cancer therapy. Interestingly, Paf1C is involved in multiple developmental stages in Drosophila, zebrafish, mice and even humans, thereby displaying a trend for the correlation between Paf1C and cell fate. Thus, we propose that Paf1C is a critical contributor to cell differentiation, cell specification and its characteristics and could be employed as a therapeutic target in developmental diseases.
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Affiliation(s)
- Jiyeon Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon-si, Korea
| | - Shinae Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon-si, Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon-si, Korea
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Yang R, Wang Z, Xia Y, Zheng F, Kang F, Meng X, Zhang W, Liu W. Role of the Nitrogen Metabolism Regulator TAM1 in Regulation of Cellulase Gene Expression in Trichoderma reesei. Appl Environ Microbiol 2023; 89:e0142122. [PMID: 36602369 DOI: 10.1128/aem.01421-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The filamentous fungus Trichoderma reesei is one of the most prolific cellulase producers and has been established as a model microorganism for investigating mechanisms modulating eukaryotic gene expression. Identification and functional characterization of transcriptional regulators involved in complex and stringent regulation of cellulase genes are, however, not yet complete. Here, a Zn(II)2Cys6-type transcriptional factor TAM1 that is homologous to Aspergillus nidulans TamA involved in nitrogen metabolism, was found not only to regulate ammonium utilization but also to control cellulase gene expression in T. reesei. Whereas Δtam1 cultivated with peptone as a nitrogen source did not exhibit a growth defect that was observed on ammonium, it was still significantly compromised in cellulase biosynthesis. The absence of TAM1 almost fully abrogated the rapid cellulase gene induction in a resting-cell-inducing system. Overexpression of gdh1 encoding the key ammonium assimilatory enzyme in Δtam1 rescued the growth defect on ammonium but not the defect in cellulase gene expression. Of note, mutation of the Zn(II)2Cys6 DNA-binding motif of TAM1 hardly affected cellulase gene expression, while a truncated ARE1 mutant lacking the C-terminal 12 amino acids that are required for the interaction with TAM1 interfered with cellulase biosynthesis. The defect in cellulase induction of Δtam1 was rescued by overexpression of the key transactivator for cellulase gene, XYR1. Our results thus identify a nitrogen metabolism regulator as a new modulator participating in the regulation of induced cellulase gene expression. IMPORTANCE Transcriptional regulators are able to integrate extracellular nutrient signals and exert a combinatorial control over various metabolic genes. A plethora of such factors therefore constitute a complex regulatory network ensuring rapid and accurate cellular response to acquire and utilize nutrients. Despite the in-depth mechanistic studies of functions of the Zn(II)2Cys6-type transcriptional regulator TamA and its orthologues in nitrogen utilization, their involvement in additional physiological processes remains unknown. In this study, we demonstrated that TAM1 exerts a dual regulatory role in mediating ammonium utilization and induced cellulase production in the well known cellulolytic fungus Trichoderma reesei, suggesting a potentially converged regulatory node between nitrogen utilization and cellulase biosynthesis. This study not only contributes to unveiling the intricate regulatory network underlying cellulase gene expression in cellulolytic fungus but also helps expand our knowledge of fungal strategies to achieve efficient and coordinated nutrient acquisition for rapid propagation.
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Shao Y, Tang G, Huang Y, Ke W, Wang S, Zheng D, Ruan L. Transcriptional regulator Sar regulates the multiple secretion systems in Xanthomonas oryzae. Mol Plant Pathol 2023; 24:16-27. [PMID: 36177860 PMCID: PMC9742495 DOI: 10.1111/mpp.13272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a notorious plant pathogen that causes leaf blight of rice cultivars. The pathogenic bacteria possess numerous transcriptional regulators to regulate various biological processes, such as pathogenicity in the host plant. Our previous study identified a new master regulator PXO_RS20790 that is involved in pathogenicity for Xoo against the host rice. However, the molecular functions of PXO_RS20790 are still unclear. Here, we demonstrate that transcriptional regulator Sar (PXO_RS20790) regulates multiple secretion systems. The RNA-sequencing analysis, bacterial one-hybrid assay, and electrophoretic mobility shift assay revealed that Sar enables binding of the promoters of the T1SS-related genes, the avirulence gene, raxX, and positively regulates these genes' expression. Meanwhile, we found that Sar positively regulated the T6SS-1 clusters but did not regulate the T6SS-2 clusters. Furthermore, we revealed that only T6SS-2 is involved in interbacterial competition. We also indicated that Sar could bind the promoters of the T3SS regulators, hrpG and hrpX, to activate these two genes' transcription. Our findings revealed that Sar is a crucial regulator of multiple secretion systems and virulence.
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Affiliation(s)
- Yanan Shao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Guiyu Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yuanyuan Huang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Wenli Ke
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Shasha Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Dehong Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- National Demonstration Center for Experimental Plant Science Education, College of AgricultureGuangxi UniversityNanningChina
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- College of Resources and EnvironmentTibet Agriculture & Animal Husbandry UniversityLinzhiChina
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22
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Choi WW, Jeong H, Kim Y, Lee HS. Gene nceA encodes a Ni/Co-sensing transcription factor to regulate metal efflux in Corynebacterium glutamicum. Metallomics 2022; 14:6865361. [PMID: 36460048 DOI: 10.1093/mtomcs/mfac094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/23/2022] [Indexed: 12/04/2022]
Abstract
The function of Corynebacterium glutamicum open reading frame (ORF) NCgl2684 (named nceA in this study), which was annotated to encode a metalloregulator, was assessed using physiological, genetic, and biochemical approaches. Cells with deleted-nceA (ΔnceA) showed a resistant phenotype to NiSO4 and CoSO4 and showed faster growth in minimal medium containing 20 μM NiSO4 or 10 μM CoSO4 than both the wild-type and nceA-overexpressing (P180-nceA) cells. In the ΔnceA strain, the transcription of the downstream-located ORF NCgl2685 (nceB), annotated to encode efflux protein, was increased approximately 4-fold, whereas gene transcription decreased down to 30% level in the P180-nceA strain. The transcriptions of the nceA and nceB genes were stimulated, even when as little as 5 nM NiSO4 was added to the growth medium. Protein NceA was able to bind DNA comprising the promoter region (from -14 to + 18) of the nceA--nceB operon. The protein-DNA interaction was abolished in the presence of 20 μM NiSO4, 50 μM CoSO4, or 50 μM CdSO4. Although manganese induced the transcription of the nceA and nceB genes, it failed to interrupt protein-DNA interaction. Simultaneously, the P180-nceA cells showed increased sensitivity to oxidants such as menadione, hydrogen peroxide, and cumene hydroperoxide, but not diamide. Collectively, our data show that NceA is a nickel- and cobalt-sensing transcriptional regulator that controls the transcription of the probable efflux protein-encoding nceB. The genes are able to suppress intracellular levels of nickel to prevent reactions, which can cause oxidative damage to cellular components.
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Affiliation(s)
- Won-Woo Choi
- 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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Burkart RC, Eljebbawi A, Stahl Y. Come together now: Dynamic body-formation of key regulators integrates environmental cues in plant development. Front Plant Sci 2022; 13:1052107. [PMID: 36452084 PMCID: PMC9702078 DOI: 10.3389/fpls.2022.1052107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Plants as sessile organisms are constantly exposed to changing environmental conditions, challenging their growth and development. Indeed, not only above-ground organs but also the underground root system must adapt accordingly. Consequently, plants respond to these constraints at a gene-regulatory level to ensure their survival and well-being through key transcriptional regulators involved in different developmental processes. Recently, intrinsically disordered domains within these regulators are emerging as central nodes necessary not only for interactions with other factors but also for their partitioning into biomolecular condensates, so-called bodies, possibly driven by phase separation. Here, we summarize the current knowledge about body-forming transcriptional regulators important for plant development and highlight their functions in a possible environmental context. In this perspective article, we discuss potential mechanisms for the formation of membrane-less bodies as an efficient and dynamic program needed for the adaptation to external cues with a particular focus on the Arabidopsis root. Hereby, we aim to provide a perspective for future research on transcriptional regulators to investigate body formation as an expeditious mechanism of plant-environment interactions.
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Affiliation(s)
- Rebecca C. Burkart
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Ali Eljebbawi
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University, Düsseldorf, Germany
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24
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Kim S, Jang YJ, Gong G, Lee SM, Um Y, Kim KH, Ko JK. Engineering Cupriavidus necator H16 for enhanced lithoautotrophic poly(3-hydroxybutyrate) production from CO 2. Microb Cell Fact 2022; 21:231. [PMCID: PMC9636797 DOI: 10.1186/s12934-022-01962-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Background A representative hydrogen-oxidizing bacterium Cupriavidus necator H16 has attracted much attention as hosts to recycle carbon dioxide (CO2) into a biodegradable polymer, poly(R)-3-hydroxybutyrate (PHB). Although C. necator H16 has been used as a model PHB producer, the PHB production rate from CO2 is still too low for commercialization. Results Here, we engineer the carbon fixation metabolism to improve CO2 utilization and increase PHB production. We explore the possibilities to enhance the lithoautotrophic cell growth and PHB production by introducing additional copies of transcriptional regulators involved in Calvin Benson Bassham (CBB) cycle. Both cbbR and regA-overexpressing strains showed the positive phenotypes for 11% increased biomass accumulation and 28% increased PHB production. The transcriptional changes of key genes involved in CO2—fixing metabolism and PHB production were investigated. Conclusions The global transcriptional regulator RegA plays an important role in the regulation of carbon fixation and shows the possibility to improve autotrophic cell growth and PHB accumulation by increasing its expression level. This work represents another step forward in better understanding and improving the lithoautotrophic PHB production by C. necator H16. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01962-7.
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Affiliation(s)
- Soyoung Kim
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Yong Jae Jang
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Gyeongtaek Gong
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
| | - Sun-Mi Lee
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
| | - Youngsoon Um
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
| | - Kyoung Heon Kim
- grid.222754.40000 0001 0840 2678Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 Republic of Korea
| | - Ja Kyong Ko
- grid.35541.360000000121053345Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea ,grid.412786.e0000 0004 1791 8264Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792 Republic of Korea
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Mauran S, Perera NT, Perera IC. [MxyR of Mycobacterium tuberculosis Responds to Xylan; an Unusual Ligand for a MarR Family Transcriptional Regulator]. Mol Biol (Mosk) 2022; 56:103-117. [PMID: 35082266 DOI: 10.31857/s0026898422010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/28/2021] [Indexed: 06/14/2023]
Abstract
Among the repertoire of MarR family transcriptional regulators in Mycobacterium tuberculosis, gene rv3095 (mxyR) encodes Mycobacterial Xylan Regulator, MxyR. Gene mxyR is divergently oriented from a hydrolase (rv3094c), oxidoreductase (rv3093c) and an ABC transporter (rv3092c) and convergently oriented with xylanase (rv3096). Xylanase is commonly used by plant pathogenic microbes where they degrade xylan, the major component of hemicellulose. We have purified the transcriptional regulatory protein encoded by rv3095 and its molecular interactions were studied in detail using electrophoretic mobility shift assay. MxyR interacts with its upstream intergenic region mxyO with high specificity and at a dissociation constant of 5.01 ± 0.017 nM. Notably, this binding is attenuated by specific carbohydrate ligands such as xylan, L-Arabinose and D-Galactose with an IC50 values of 22.7 ± 1.02 ng/μL, 360.8 ± 24.25 ng/μL and 2320.0 ± 96.97 μg/μL, respectively. Consequently, it is evident that this association changes the conformation of the DNA binding helix α4 making the transcriptional regulator incompatible with binding to its cognate DNA, allowing xylanase and other genes to be transcribed. This study establishes the natural ligands of MxyR of M. tuberculosis providing insight on metabolic regulation of the carbohydrate, xylan.
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Affiliation(s)
- S Mauran
- Synthetic Biology Laboratory, Department of Zoology and Environment Sciences, Faculty of Science, University of Colombo, Colombo 03, Sri Lanka
| | - N T Perera
- Department of Chemistry, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - I C Perera
- Synthetic Biology Laboratory, Department of Zoology and Environment Sciences, Faculty of Science, University of Colombo, Colombo 03, Sri Lanka
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Wang H, Zhou W, Gao J, Ren C, Xu Y. Revealing the Characteristics of Glucose- and Lactate-Based Chain Elongation for Caproate Production by Caproicibacterium lactatifermentans through Transcriptomic, Bioenergetic, and Regulatory Analyses. mSystems 2022; 7:e0053422. [PMID: 36073803 DOI: 10.1128/msystems.00534-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Caproate, an important medium-chain fatty acid, can only be synthesized by limited bacterial species by using ethanol, lactate, or certain saccharides. Caproicibacterium lactatifermentans is a promising caproate producer due to its glucose and lactate utilization capabilities. However, the global cellular responses of this bacterium to different carbon sources were not well understood. Here, C. lactatifermentans showed robust growth on glucose but more active caproate synthesis on lactate. Comparative transcriptome revealed that the genes involved in reverse β-oxidation for caproate synthesis and V-type ATPase-dependent ATP generation were upregulated under lactate condition, while several genes responsible for biomass synthesis were upregulated under glucose condition. Based on metabolic pathway reconstructions and bioenergetics analysis, the biomass accumulation on glucose condition may be supported by sufficient supplies of ATP and metabolite intermediates via glycolysis. In contrast, the ATP yield per glucose equivalent from lactate conversion into caproate was only 20% of that from glucose. Thus, the upregulation of the reverse β-oxidation genes may be essential for cell survival under lactate conditions. Furthermore, the remarkably decreased lactate utilization was observed after glucose acclimatization, indicating the negative modulation of lactate utilization by glucose metabolism. Based on the cotranscription of the lactate utilization repressor gene lldR with sugar-specific PTS genes and the opposite expression patterns of lldR and lactate utilization genes, a novel regulatory mechanism of glucose-repressed lactate utilization mediated via lldR was proposed. The results of this study suggested the molecular mechanism underlying differential physiologic and metabolic characteristics of C. lactatifermentans grown on glucose and lactate. IMPORTANCE Caproicibacterium lactatifermentans is a unique and robust caproate-producing bacterium in the family Oscillospiraceae due to its lactate utilization capability, whereas its close relatives such as Caproicibacterium amylolyticum, Caproiciproducens galactitolivorans, and Caproicibacter fermentans cannot utilize lactate but produce lactate as the main fermentation end product. Moreover, C. lactatifermentans can also utilize several saccharides such as glucose and maltose. Although the metabolic versatility of the bacterium makes it to be a promising industrial caproate producer, the cellular responses of C. lactatifermentans to different carbon sources were unknown. Here, the molecular mechanisms of biomass synthesis supported by glucose utilization and the cell survival supported by lactate utilization were revealed. A novel insight into the regulatory machinery in which glucose negatively regulates lactate utilization was proposed. This study provides a valuable basis to control and optimize caproate production, which will contribute to achieving a circular economy and environmental sustainability.
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Chen S, Hu M, Hu A, Xue Y, Wang S, Liu F, Li C, Zhou X, Zhou J. The integration host factor regulates multiple virulence pathways in bacterial pathogen Dickeya zeae MS2. Mol Plant Pathol 2022; 23:1487-1507. [PMID: 35819797 PMCID: PMC9452768 DOI: 10.1111/mpp.13244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Dickeya zeae is an aggressive bacterial phytopathogen that infects a wide range of host plants. It has been reported that integration host factor (IHF), a nucleoid-associated protein consisting of IHFα and IHFβ subunits, regulates gene expression by influencing nucleoid structure and DNA bending. To define the role of IHF in the pathogenesis of D. zeae MS2, we deleted either and both of the IHF subunit encoding genes ihfA and ihfB, which significantly reduced the production of cell wall-degrading enzymes (CWDEs), an unknown novel phytotoxin and the virulence factor-modulating (VFM) quorum-sensing (QS) signal, cell motility, biofilm formation, and thereafter the infection ability towards both potato slices and banana seedlings. To characterize the regulatory pathways of IHF protein associated with virulence, IHF binding sites (consensus sequence 5'-WATCAANNNNTTR-3') were predicted and 272 binding sites were found throughout the genome. The expression of 110 tested genes was affected by IHF. Electrophoretic mobility shift assay (EMSA) showed direct interaction of IhfA protein with the promoters of vfmE, speA, pipR, fis, slyA, prtD, hrpL, hecB, hcp, indA, hdaA, flhD, pilT, gcpJ, arcA, arcB, and lysR. This study clarified the contribution of IHF in the pathogenic process of D. zeae by controlling the production of VFM and putrescine QS signals, phytotoxin, and indigoidine, the luxR-solo system, Fis, SlyA, and FlhD transcriptional regulators, and secretion systems from type I to type VI. Characterization of the regulatory networks of IHF in D. zeae provides a target for prevention and control of plant soft rot disease.
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Affiliation(s)
- Shanshan Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Ming Hu
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Anqun Hu
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Yang Xue
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Si Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Fan Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Chuhao Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
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King S, Quick A, King K, Walker AR, Shields RC. Activation of TnSmu1, an integrative and conjugative element, by an ImmR-like transcriptional regulator in Streptococcus mutans. Microbiology (Reading) 2022; 168. [PMID: 36201342 DOI: 10.1099/mic.0.001254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Integrative and conjugative elements (ICEs) are chromosomally encoded mobile genetic elements that can transfer DNA between bacterial strains. Recently, as part of efforts to determine hypothetical gene functions, we have discovered an important regulatory module encoded on an ICE known as TnSmu1 on the Streptococcus mutans chromosome. The regulatory module consists of a cI-like repressor with a helix-turn-helix DNA binding domain immR Smu (immunity repressor) and a metalloprotease immA Smu (anti-repressor). It is not possible to create an in-frame deletion mutant of immR Smu and repression of immR Smu with CRISPRi (CRISPR interference) causes substantial cell defects. We used a bypass of essentiality (BoE) screen to discover genes that allow deletion of the regulatory module. This revealed that conjugation genes, located within TnSmu1, can restore the viability of an immR Smu mutant. Deletion of immR Smu also leads to production of a circular intermediate form of TnSmu1, which is also inducible by the genotoxic agent mitomycin C. To gain further insights into potential regulation of TnSmu1 by ImmRSmu and broader effects on S. mutans UA159 physiology, we used CRISPRi and RNA-seq. Strongly induced genes included all the TnSmu1 mobile element, genes involved in amino acid metabolism, transport systems and a type I-C CRISPR-Cas system. Lastly, bioinformatic analysis shows that the TnSmu1 mobile element and its associated genes are well distributed across S. mutans isolates. Taken together, our results show that activation of TnSmu1 is controlled by the immRA Smu module, and that activation is deleterious to S. mutans, highlighting the complex interplay between mobile elements and their host.
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Affiliation(s)
- Shawn King
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Allison Quick
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Kalee King
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | | | - Robert C Shields
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
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Hartline CJ, Zhang F. The Growth Dependent Design Constraints of Transcription-Factor-Based Metabolite Biosensors. ACS Synth Biol 2022; 11:2247-2258. [PMID: 35700119 PMCID: PMC9994378 DOI: 10.1021/acssynbio.2c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metabolite biosensors based on metabolite-responsive transcription factors are key synthetic biology components for sensing and precisely controlling cellular metabolism. Biosensors are often designed under laboratory conditions but are deployed in applications where cellular growth rate differs drastically from its initial characterization. Here we asked how growth rate impacts the minimum and maximum biosensor outputs and the dynamic range, which are key metrics of biosensor performance. Using LacI, TetR, and FadR-based biosensors in Escherichia coli as models, we find that the dynamic range of different biosensors have different growth rate dependencies. We developed a kinetic model to explore how tuning biosensor parameters impact the dynamic range growth rate dependence. Our modeling and experimental results revealed that the effects to dynamic range and its growth rate dependence are often coupled, and the metabolite transport mechanisms shape the dynamic range-growth rate response. This work provides a systematic understanding of biosensor performance under different growth rates, which will be useful for predicting biosensor behavior in broad synthetic biology and metabolic engineering applications.
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Affiliation(s)
- Christopher J Hartline
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States.,Division of Biology & Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missouri 63130, United States.,Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
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30
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Ye Y, Jin Q, Gong Q, Li A, Sun M, Jiang S, Jin Y, Zhang Z, He J, Zhuang L. Bioinformatics and Experimental Analyses Reveal NFIC as an Upstream Transcriptional Regulator for Ischemic Cardiomyopathy. Genes (Basel) 2022; 13:1051. [PMID: 35741813 DOI: 10.3390/genes13061051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 02/06/2023] Open
Abstract
Ischemic cardiomyopathy (ICM) caused by coronary artery disease always leads to myocardial infarction and heart failure. Identification of novel transcriptional regulators in ICM is an effective method to establish new diagnostic and therapeutic strategies. In this study, we used two RNA-seq datasets and one microarray dataset from different studies, including 25 ICM and 21 non-failing control (NF) samples of human left ventricle tissues for further analysis. In total, 208 differentially expressed genes (DEGs) were found by combining two RNA-seq datasets with batch effects removed. GO and KEGG analyses of DEGs indicated that the response to wounding, positive regulation of smooth muscle contraction, chromatin, PI3K-Akt signaling pathway, and transporters pathways are involved in ICM. Simple Enrichment Analysis found that NFIC-binding motifs are enriched in promoter regions of downregulated genes. The Gene Importance Calculator further proved that NFIC is vital. NFIC and its downstream genes were verified in the validating microarray dataset. Meanwhile, in rat cardiomyocyte cell line H9C2 cells, two genes (Tspan1 and Hopx) were confirmed, which decreased significantly along with knocking down Nfic expression. In conclusion, NFIC participates in the ICM process by regulating TSPAN1 and HOPX. NFIC and its downstream genes may be marker genes and potential diagnostic and therapeutic targets for ICM.
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31
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Zhang X, Liu W, Edaki K, Nakazawa Y, Takahashi S, Sunakawa H, Mizoi K, Ogihara T. Slug Mediates MRP2 Expression in Non-Small Cell Lung Cancer Cells. Biomolecules 2022; 12:biom12060806. [PMID: 35740931 PMCID: PMC9220960 DOI: 10.3390/biom12060806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 02/01/2023] Open
Abstract
Transcriptional factors, such as Snail, Slug, and Smuc, that cause epithelial-mesenchymal transition are thought to regulate the expression of Ezrin, Radixin, and Moesin (ERM proteins), which serve as anchors for efflux transporters on the plasma membrane surface. Our previous results using lung cancer clinical samples indicated a correlation between Slug and efflux transporter MRP2. In the current study, we aimed to evaluate the relationships between MRP2, ERM proteins, and Slug in lung cancer cells. HCC827 cells were transfected by Mock and Slug plasmid. Both mRNA expression levels and protein expression levels were measured. Then, the activity of MRP2 was evaluated using CDCF and SN-38 (MRP2 substrates). HCC827 cells transfected with the Slug plasmid showed significantly higher mRNA expression levels of MRP2 than the Mock-transfected cells. However, the mRNA expression levels of ERM proteins did not show a significant difference between Slug-transfected cells and Mock-transfected cells. Protein expression of MRP2 was increased in Slug-transfected cells. The uptake of both CDCF and SN-38 was significantly decreased after transfection with Slug. This change was abrogated by treatment with MK571, an MRP2 inhibitor. The viability of Slug-transfected cells, compared to Mock cells, significantly increased after incubation with SN-38. Thus, Slug may increase the mRNA and protein expression of MRP2 without regulation by ERM proteins in HCC827 cells, thereby enhancing MRP2 activity. Inhibition of Slug may reduce the efficacy of multidrug resistance in lung cancer.
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Affiliation(s)
- Xieyi Zhang
- Laboratory of Biopharmaceutics, Department of Pharmacology, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-chou, Takasaki-shi 370-0033, Gunma, Japan; (K.E.); (Y.N.); (S.T.); (K.M.); (T.O.)
- Correspondence: ; Tel.: +81-273521180; Fax: +81-273521118
| | - Wangyang Liu
- Laboratory of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi 370-0033, Gunma, Japan; (W.L.); (H.S.)
| | - Kazue Edaki
- Laboratory of Biopharmaceutics, Department of Pharmacology, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-chou, Takasaki-shi 370-0033, Gunma, Japan; (K.E.); (Y.N.); (S.T.); (K.M.); (T.O.)
| | - Yuta Nakazawa
- Laboratory of Biopharmaceutics, Department of Pharmacology, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-chou, Takasaki-shi 370-0033, Gunma, Japan; (K.E.); (Y.N.); (S.T.); (K.M.); (T.O.)
| | - Saori Takahashi
- Laboratory of Biopharmaceutics, Department of Pharmacology, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-chou, Takasaki-shi 370-0033, Gunma, Japan; (K.E.); (Y.N.); (S.T.); (K.M.); (T.O.)
| | - Hiroki Sunakawa
- Laboratory of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi 370-0033, Gunma, Japan; (W.L.); (H.S.)
| | - Kenta Mizoi
- Laboratory of Biopharmaceutics, Department of Pharmacology, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-chou, Takasaki-shi 370-0033, Gunma, Japan; (K.E.); (Y.N.); (S.T.); (K.M.); (T.O.)
| | - Takuo Ogihara
- Laboratory of Biopharmaceutics, Department of Pharmacology, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-chou, Takasaki-shi 370-0033, Gunma, Japan; (K.E.); (Y.N.); (S.T.); (K.M.); (T.O.)
- Laboratory of Clinical Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi 370-0033, Gunma, Japan; (W.L.); (H.S.)
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32
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Yue X, Liang Y, Wei Z, Lv J, Cai Y, Fan X, Zhang W, Chen J. Genome-wide in vitro and in vivo RNAi screens reveal Fer3 to be an important regulator of kkv transcription in Drosophila. Insect Sci 2022; 29:614-630. [PMID: 34351065 DOI: 10.1111/1744-7917.12954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/24/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Krotzkopf verkehrt (kkv) is a key enzyme that catalyzes the synthesis of chitin, an important component of the Drosophila epidermis, trachea, and other tissues. Here, we report the use of comprehensive RNA interference (RNAi) analyses to search for kkv transcriptional regulators. A cell-based RNAi screen identified 537 candidate kkv regulators on a genome-wide scale. Subsequent use of transgenic Drosophila lines expressing RNAi constructs enabled in vivo validation, and we identified six genes as potential kkv transcriptional regulators. Weakening of the kkvDsRed signal, an in vivo reporter indicating kkv promoter activity, was observed when the expression of Akirin, NFAT, 48 related 3 (Fer3), or Autophagy-related 101(Atg101) was knocked down in Drosophila at the 3rd-instar larval stage; whereas we observed disoriented taenidial folds on larval tracheae when Lines (lin) or Autophagy-related 3 (Atg3) was knocked down in the tracheae. Fer3, in particular, has been shown to be an important factor in the activation of kkv transcription via specific binding with the kkv promoter. The genes involved in the chitin synthesis pathway were widely affected by the downregulation of Fer3. Furthermore, Atg101, Atg3, Akirin, Lin, NFAT, Pnr, and Abd-A showed that the potential complex mechanism of kkv transcription is regulated by an interaction network with bithorax complex components. Our study revealed the hitherto unappreciated diversity of modulators impinging on kkv transcription and opens new avenues in the study of kkv regulation and chitin biosynthesis.
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Affiliation(s)
- Xiangzhao Yue
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- College of Life Sciences, Shangrao Normal University, Shangrao, Jiangxi Province, China
| | - Yongkang Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhishuang Wei
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jun Lv
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yongjin Cai
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaobin Fan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jie Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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33
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Zeng L, Chen H, Wang Y, Hicks D, Ke H, Pruneda-Paz J, Dehesh K. ORA47 is a transcriptional regulator of a general stress response hub. Plant J 2022; 110:562-571. [PMID: 35092704 DOI: 10.1111/tpj.15688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/14/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Transcriptional regulators of the general stress response (GSR) reprogram the expression of selected genes to transduce informational signals into cellular events, ultimately manifested in a plant's ability to cope with environmental challenges. Identification of the core GSR regulatory proteins will uncover the principal modules and their mode of action in the establishment of adaptive responses. To define the GSR regulatory components, we employed a yeast-one-hybrid assay to identify the protein(s) binding to the previously established functional GSR motif, termed the rapid stress response element (RSRE). This led to the isolation of octadecanoid-responsive AP2/ERF-domain transcription factor 47 (ORA47), a methyl jasmonate inducible protein. Subsequently, ORA47 transcriptional activity was confirmed using the RSRE-driven luciferase (LUC) activity assay performed in the ORA47 loss- and gain-of-function lines introgressed into the 4xRSRE::Luc background. In addition, the prime contribution of CALMODULIN-BINDING TRANSCRIPTIONAL ACTIVATOR3 (CAMTA3) protein in the induction of RSRE was reaffirmed by genetic studies. Moreover, exogenous application of methyl jasmonate led to enhanced levels of ORA47 and CAMTA3 transcripts, as well as the induction of RSRE::LUC activity. Metabolic analyses illustrated the reciprocal functional inputs of ORA47 and CAMTA3 in increasing JA levels. Lastly, transient assays identified JASMONATE ZIM-domain1 (JAZ1) as a repressor of RSRE::LUC activity. Collectively, the present study provides fresh insight into the initial features of the mechanism that transduces informational signals into adaptive responses. This mechanism involves the functional interplay between the JA biosynthesis/signaling cascade and the transcriptional reprogramming that potentiates GSR. Furthermore, these findings offer a window into the role of intraorganellar communication in the establishment of adaptive responses.
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Affiliation(s)
- Liping Zeng
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
| | - Hao Chen
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yaqi Wang
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
| | - Derrick Hicks
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Haiyan Ke
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
| | - Jose Pruneda-Paz
- Section of Cell and Developmental Biology, University of California, La Jolla, CA, 92093, USA
| | - Katayoon Dehesh
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
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34
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Shen L, Zhang J, Xue J, Du L, Yuan L, Nie H, Dai S, Yu Q, Li Y. Regulation of ECP fimbriae-related genes by the transcriptional regulator RcsAB in Klebsiella pneumoniae NTUH-K2044. J Basic Microbiol 2022; 62:593-603. [PMID: 35132658 DOI: 10.1002/jobm.202100595] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/06/2022] [Accepted: 01/15/2022] [Indexed: 11/11/2022]
Abstract
Klebsiella pneumoniae is one of the major pathogens causing nosocomial infections. The regulator of capsule synthesis (Rcs) system is a complex signal transduction pathway that is involved in the regulation of virulence factors of K. pneumoniae as an important transcriptional regulator. The RcsAB box-like sequence was found to be present in the promoter-proximal regions of ykgK, one of the ECP fimbriae-related genes, which suggested the expression of ECP fimbriae may be regulated by RcsAB. The ykgK gene in K. pneumoniae has 86% similarity to the ecpR gene in Escherichia coli. Nucleotide sequence alignment revealed a similar ECP fimbriae gene cluster including six genes in K. pneumoniae, which was proved to be on the same operon in this study. The electrophoretic mobility shift assay and DNase I assay, relative fluorescence expression, β-galactosidase activity, and relative gene expression of ykgK in the wild-type and mutant strains were performed to determine the transcriptional regulation mechanism of RcsAB on ECP fimbriae. The mutant ΔykgK and complementary strain ΔykgK/cΔykgK were constructed to complete the Galleria mellonella larvae infection experiment and biofilm formation assay. This study showed that RcsAB binds directly to the promoter region of the ykgK gene to positively regulate ECP fimbriae-related gene clusters, and then positively affect the biofilm formation.
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Affiliation(s)
- Lifei Shen
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Jiaxue Zhang
- Chongqing Jiangbei District Center for Disease Control and Prevention, Chongqing, China
| | - Jian Xue
- Zunyi Medical and Pharmaceutical College, Zunyi, China
| | - Ling Du
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Lingyue Yuan
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Hao Nie
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Sue Dai
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Qian Yu
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Yingli Li
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
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35
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Sun L, Wang D, Yin Z, Zhang C, Bible A, Xie Z. The FtcR-Like Protein ActR in Azorhizobium caulinodans ORS571 Is Involved in Bacterial Motility and Symbiosis With the Host Plant. Front Microbiol 2021; 12:744268. [PMID: 34867860 PMCID: PMC8639532 DOI: 10.3389/fmicb.2021.744268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/20/2021] [Indexed: 12/22/2022] Open
Abstract
Bacterial signal transduction pathways are important for a variety of adaptive responses to environment, such as two-component systems (TCSs). In this paper, we reported the characterization of a transcriptional regulator in Azorhizobium caulinodans ORS571, ActR, with an N-terminal receiver domain and one C-terminal OmpR/PhoB-type DNA binding domain. Sequence analysis showed that ActR shared a high similarity with FtcR regulator of Brucella melitensis 16M known to be involved in flagellar regulation. The structural gene of this regulator was largely distributed in Alphaproteobacteria, in particular in Rhizobiales and Rhodobacterales, and was located within clusters of genes related to motility functions. Furthermore, we studied the biological function of ActR in A. caulinodans grown at the free-living state or in association with Sesbania rostrata by constructing actR gene deletion mutant. In the free-living state, the bacterial flagellum and motility ability were entirely deleted, the expression of flagellar genes was downregulated; and the exopolysaccharide production, biofilm formation, and cell flocculation decreased significantly compared with those of the wild-type strain. In the symbiotic state, ΔactR mutant strain showed weakly competitive colonization and nodulation on the host plant. These results illustrated that FtcR-like regulator in A. caulinodans is involved in flagellar biosynthesis and provide bacteria with an effective competitive nodulation for symbiosis. These findings improved our knowledge of FtcR-like transcriptional regulator in A. caulinodans.
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Affiliation(s)
- Li Sun
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Dandan Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Zhiqiu Yin
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Chengsheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Amber Bible
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, United States
| | - Zhihong Xie
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China.,Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
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36
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Yan XF, Yang C, Wang M, Yong Y, Deng Y, Gao YG. Structural analyses of the AAA+ ATPase domain of the transcriptional regulator GtrR in the BDSF quorum-sensing system in Burkholderia cenocepacia. FEBS Lett 2021; 596:71-80. [PMID: 34837384 DOI: 10.1002/1873-3468.14244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/08/2021] [Accepted: 11/23/2021] [Indexed: 11/11/2022]
Abstract
Global transcriptional regulator downstream RpfR (GtrR) is a key downstream regulator for quorum-sensing signaling molecule cis-2-dodecenoic acid (BDSF). As a bacterial enhancer-binding protein (bEBP), GtrR is composed of an N-terminal receiver domain, a central ATPases associated with diverse cellular activities (AAA+) ATPase σ54 -interaction domain, and a C-terminal helix-turn-helix DNA-binding domain. In this work, we solved its AAA+ ATPase domain in both apo and GTP-bound forms. The structure revealed how GtrR specifically recognizes GTP. In addition, we also revealed that GtrR has moderate GTPase activity in vitro in the absence of its activation signal. Finally, we found the residues K170, D236, R311, and R357 in GtrR that are crucial to its biological function, any single mutation leading to completely abolishing GtrR activity.
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Affiliation(s)
- Xin-Fu Yan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chunxi Yang
- Jiangxi provincial People's Hospital Affiliated to Nanchang University, Nanchang, China
| | - Mingfang Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yonlada Yong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yinyue Deng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
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37
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Cai C, Bi D, Bick G, Wei Q, Liu H, Lu L, Zhang X, Qin H. Hepatocyte nuclear factor HNF1A is a potential regulator in shaping the super-enhancer landscape in colorectal cancer liver metastasis. FEBS Lett 2021; 595:3056-3071. [PMID: 34719039 DOI: 10.1002/1873-3468.14219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/10/2021] [Accepted: 10/17/2021] [Indexed: 01/15/2023]
Abstract
Super-enhancers (SEs) play essential roles in colorectal cancer (CRC) progression. However, how the SE landscape is orchestrated by transcriptional regulators and evolves is not clear. Using de novo motif analysis, we show that the hepatocyte nuclear factor 1 (HNF1)-binding motif is enriched in SEs in cell lines derived from liver metastases, but not in those from primary tumors. This finding was further validated by extending the method to pancreatic cancer and a pair of isogenic CRC lines. Next, we revealed HNF1-alpha (HNF1A) was majorly expressed and upregulated in CRC liver metastatic cell lines. Clinically, HNF1A was remarkably upregulated in synchronous liver metastases as compared to localized tumors. Collectively, our study implicates HNF1A as a key regulator in shaping the SE landscape in CRC liver metastasis.
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Affiliation(s)
- Chunmiao Cai
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Dexi Bi
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Gregory Bick
- Department of Cancer Biology, University of Cincinnati College of Medicine, OH, USA
| | - Qing Wei
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hu Liu
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ling Lu
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoting Zhang
- Department of Cancer Biology, University of Cincinnati College of Medicine, OH, USA
| | - Huanlong Qin
- Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
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38
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Lin YS, Kuo TT, Lo CC, Cheng WC, Chang WC, Tseng GC, Bai ST, Huang YK, Hsieh CY, Hsu HS, Jiang YF, Lin CY, Lai LC, Li XG, Sher YP. ADAM9 functions as a transcriptional regulator to drive angiogenesis in esophageal squamous cell carcinoma. Int J Biol Sci 2021; 17:3898-3910. [PMID: 34671207 PMCID: PMC8495400 DOI: 10.7150/ijbs.65488] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/29/2021] [Indexed: 11/25/2022] Open
Abstract
Hypoxia and angiogenesis play key roles in the pathogenesis of esophageal squamous cell carcinoma (ESCC), but regulators linking these two pathways to drive tumor progression remain elusive. Here we provide evidence of ADAM9's novel function in ESCC progression. Increasing expression of ADAM9 was correlated with poor clinical outcomes in ESCC patients. Suppression of ADAM9 function diminished ESCC cell migration and in vivo metastasis in ESCC xenograft mouse models. Using cellular fractionation and imaging, we found a fraction of ADAM9 was present in the nucleus and was uniquely associated with gene loci known to be linked to the angiogenesis pathway demonstrated by genome-wide ChIP-seq. Mechanistically, nuclear ADAM9, triggered by hypoxia-induced translocation, functions as a transcriptional repressor by binding to promoters of genes involved in the negative regulation of angiogenesis, and thereby promotes tumor angiogenesis in plasminogen/plasmin pathway. Moreover, ADAM9 suppresses plasminogen activator inhibitor-1 gene transcription by interacting with its transcription factors at the promoter. Our findings uncover a novel regulatory mechanism of ADAM9 as a transcriptional regulator in angiogenesis and highlight ADAM9 as a promising therapeutic target for ESCC treatment.
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Affiliation(s)
- Yu-Sen Lin
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung 404, Taiwan.,Division of Thoracic Surgery, China Medical University Hospital, Taichung 404, Taiwan
| | - Ting-Ting Kuo
- Center for Molecular Medicine, China Medical University Hospital, Taichung 404, Taiwan
| | - Chia-Chien Lo
- Center for Molecular Medicine, China Medical University Hospital, Taichung 404, Taiwan
| | - Wei-Chung Cheng
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan
| | - Wei-Chao Chang
- Center for Molecular Medicine, China Medical University Hospital, Taichung 404, Taiwan
| | - Guan-Chin Tseng
- Department of Anatomic Pathology, Nantou Hospital of the Ministry of Health and Welfare, Nantou 540, Taiwan
| | - Shih-Ting Bai
- Center for Molecular Medicine, China Medical University Hospital, Taichung 404, Taiwan
| | - Yu-Kai Huang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan
| | - Chih-Ying Hsieh
- Center for Molecular Medicine, China Medical University Hospital, Taichung 404, Taiwan
| | - Han-Shui Hsu
- Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 112, Taiwan.,Institute of Emergency and Care Medicine, School of Medicine, National Yang-Ming University, Taipei 112, Taiwan
| | - Yi-Fan Jiang
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei 106, Taiwan
| | - Chen-Yuan Lin
- School of Pharmacy, China Medical University, Taichung 404, Taiwan.,Division of Hematology and Oncology, China Medical University Hospital, Taichung 404, Taiwan
| | - Liang-Chuan Lai
- Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Xing-Guo Li
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan
| | - Yuh-Pyng Sher
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung 404, Taiwan.,Center for Molecular Medicine, China Medical University Hospital, Taichung 404, Taiwan.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan.,Chinese Medicine Research Center, China Medical University, Taichung 404, Taiwan
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Luo G, Shen L, Zhao S, Li R, Song Y, Song S, Yu K, Yang W, Li X, Sun J, Wang Y, Gao C, Liu D, Zhang A. Genome-wide identification of seed storage protein gene regulators in wheat through coexpression analysis. Plant J 2021; 108:1704-1720. [PMID: 34634158 DOI: 10.1111/tpj.15538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 09/27/2021] [Indexed: 12/31/2022]
Abstract
Only a few transcriptional regulators of seed storage protein (SSP) genes have been identified in common wheat (Triticum aestivum L.). Coexpression analysis could be an efficient approach to characterize novel transcriptional regulators at the genome-scale considering the correlated expression between transcriptional regulators and target genes. As the A genome donor of common wheat, Triticum urartu is more suitable for coexpression analysis than common wheat considering the diploid genome and single gene copy. In this work, the transcriptome dynamics in endosperm of T. urartu throughout grain filling were revealed by RNA-Seq analysis. In the coexpression analysis, a total of 71 transcription factors (TFs) from 23 families were found to be coexpressed with SSP genes. Among these TFs, TuNAC77 enhanced the transcription of SSP genes by binding to cis-elements distributed in promoters. The homolog of TuNAC77 in common wheat, TaNAC77, shared an identical function, and the total SSPs were reduced by about 24% in common wheat when TaNAC77 was knocked down. This is the first genome-wide identification of transcriptional regulators of SSP genes in wheat, and the newly characterized transcriptional regulators will undoubtedly expand our knowledge of the transcriptional regulation of SSP synthesis.
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Affiliation(s)
- Guangbin Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Lisha Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Ruidong Li
- Graduate Program in Genetics, Genomics and Bioinformatics, University of California, Riverside, CA, USA
| | - Yanhong Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Shuyi Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Kang Yu
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Wenlong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Dongcheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071000, China
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40
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Wang J, Luo Y, Gu Y, Wei HL. Characterization of the SPI-1 Type III Secretion System in Pseudomonas fluorescens 2P24. Front Microbiol 2021; 12:749037. [PMID: 34621260 PMCID: PMC8490769 DOI: 10.3389/fmicb.2021.749037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/31/2021] [Indexed: 12/04/2022] Open
Abstract
Pseudomonas fluorescens 2P24 is a plant growth-promoting rhizobacterium (PGPR) isolated from wheat take-all decline soil. Genomic analysis of strain 2P24 revealed the presence of a complete SPI-1 type III secretion system (T3SS) gene cluster on the chromosome with an organization and orientation similar to the SPI-1 T3SS gene clusters of Salmonella enterica and P. kilonensis F113. Phylogenetic analysis revealed that the SPI-1 T3SS gene cluster of strain 2P24 might be obtained from Salmonella and Shigella by horizontal gene transfer. Two transcriptional regulator homologs of HilA and InvF were found from the SPI-1 T3SS gene cluster of strain 2P24. HilA regulated the expression of the structural genes positively, such as invG, sipB, sipD, prgI, and prgK. Prediction of transcriptional binding sites and RNA-seq analysis revealed 14 genes were up-regulated by InvF in strain 2P24. Exploring potential roles of SPI-1 T3SS revealed that it was not associated with motility. However, 2P24ΔinvF reduced resistance against Fusarium graminearum significantly. 2P24ΔhilA enhanced formation of biofilm significantly at 48 h. All three mutants 2P24ΔhilA, 2P24ΔinvF, and 2P24ΔinvE-C reduced the chemotactic responses to glucose significantly. Finally, the determination of SPI-1 mutants to trigger innate immunity in Nicotiana benthamiana showed that 2P24ΔinvE-C reduced the ability to induce the production of reactive oxygen species compared with the wild type strain 2P24.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yuan Luo
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yilin Gu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Hai-Lei Wei
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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Eugénie N, Zivanovic Y, Lelandais G, Coste G, Bouthier de la Tour C, Bentchikou E, Servant P, Confalonieri F. Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses. Cells 2021; 10:cells10102536. [PMID: 34685516 PMCID: PMC8533742 DOI: 10.3390/cells10102536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 12/02/2022] Open
Abstract
Numerous genes are overexpressed in the radioresistant bacterium Deinococcus radiodurans after exposure to radiation or prolonged desiccation. It was shown that the DdrO and IrrE proteins play a major role in regulating the expression of approximately twenty genes. The transcriptional repressor DdrO blocks the expression of these genes under normal growth conditions. After exposure to genotoxic agents, the IrrE metalloprotease cleaves DdrO and relieves gene repression. At present, many questions remain, such as the number of genes regulated by DdrO. Here, we present the first ChIP-seq analysis performed at the genome level in Deinococcus species coupled with RNA-seq, which was achieved in the presence or not of DdrO. We also resequenced our laboratory stock strain of D. radiodurans R1 ATCC 13939 to obtain an accurate reference for read alignments and gene expression quantifications. We highlighted genes that are directly under the control of this transcriptional repressor and showed that the DdrO regulon in D. radiodurans includes numerous other genes than those previously described, including DNA and RNA metabolism proteins. These results thus pave the way to better understand the radioresistance pathways encoded by this bacterium and to compare the stress-induced responses mediated by this pair of proteins in diverse bacteria.
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Gahlot DK, Ifill G, MacIntyre S. Optimised Heterologous Expression and Functional Analysis of the Yersinia pestis F1-Capsular Antigen Regulator Caf1R. Int J Mol Sci 2021; 22:9805. [PMID: 34575967 DOI: 10.3390/ijms22189805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 12/14/2022] Open
Abstract
The bacterial pathogen, Yersinia pestis, has caused three historic pandemics and continues to cause small outbreaks worldwide. During infection, Y. pestis assembles a capsule-like protective coat of thin fibres of Caf1 subunits. This F1 capsular antigen has attracted much attention due to its clinical value in plague diagnostics and anti-plague vaccine development. Expression of F1 is tightly regulated by a transcriptional activator, Caf1R, of the AraC/XylS family, proteins notoriously prone to aggregation. Here, we have optimised the recombinant expression of soluble Caf1R. Expression from the native and synthetic codon-optimised caf1R cloned in three different expression plasmids was examined in a library of E. coli host strains. The functionality of His-tagged Caf1R was demonstrated in vivo, but insolubility was a problem with overproduction. High levels of soluble MBP-Caf1R were produced from codon optimised caf1R. Transcriptional-lacZ reporter fusions defined the PM promoter and Caf1R binding site responsible for transcription of the cafMA1 operon. Use of the identified Caf1R binding caf DNA sequence in an electrophoretic mobility shift assay (EMSA) confirmed correct folding and functionality of the Caf1R DNA-binding domain in recombinant MBP-Caf1R. Availability of functional recombinant Caf1R will be a valuable tool to elucidate control of expression of F1 and Caf1R-regulated pathophysiology of Y. pestis.
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Luo G, Shen L, Song Y, Yu K, Ji J, Zhang C, Yang W, Li X, Sun J, Zhan K, Cui D, Wang Y, Gao C, Liu D, Zhang A. The MYB family transcription factor TuODORANT1 from Triticum urartu and the homolog TaODORANT1 from Triticum aestivum inhibit seed storage protein synthesis in wheat. Plant Biotechnol J 2021; 19:1863-1877. [PMID: 33949074 PMCID: PMC8428827 DOI: 10.1111/pbi.13604] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/11/2021] [Indexed: 05/08/2023]
Abstract
Seed storage proteins (SSPs) are determinants of wheat end-product quality. SSP synthesis is mainly regulated at the transcriptional level. Few transcriptional regulators of SSP synthesis have been identified in wheat and this study aims to identify novel SSP gene regulators. Here, the R2R3 MYB transcription factor TuODORANT1 from Triticum urartu was found to be preferentially expressed in the developing endosperm during grain filling. In common wheat (Triticum aestivum) overexpressing TuODORANT1, the transcription levels of all the SSP genes tested by RNA-Seq analysis were reduced by 49.71% throughout grain filling, which contributed to 13.38%-35.60% declines in the total SSP levels of mature grains. In in vitro assays, TuODORANT1 inhibited both the promoter activities and the transcription of SSP genes by 1- to 13-fold. The electrophoretic mobility shift assay (EMSA) and ChIP-qPCR analysis demonstrated that TuODORANT1 bound to the cis-elements 5'-T/CAACCA-3' and 5'-T/CAACT/AG-3' in SSP gene promoters both in vitro and in vivo. Similarly, the homolog TaODORANT1 in common wheat hindered both the promoter activities and the transcription of SSP genes by 1- to 112-fold in vitro. Knockdown of TaODORANT1 in common wheat led to 14.73%-232.78% increases in the transcription of the tested SSP genes, which contributed to 11.43%-19.35% elevation in the total SSP levels. Our data show that both TuODORANT1 and TaODORANT1 are repressors of SSP synthesis.
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Affiliation(s)
- Guangbin Luo
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Lisha Shen
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yanhong Song
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- BGI GenomicsBGI‐ShenzhenShenzhenChina
| | - Kang Yu
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Jingjing Ji
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Chi Zhang
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Wenlong Yang
- State Key Laboratory of North China Crop Improvement and RegulationCollege of AgronomyHebei Agricultural UniversityBaodingHebeiChina
| | - Xin Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | | | | | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Dongcheng Liu
- College of Agronomy/Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringNational Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
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Fujita D, Tobe R, Tajima H, Anma Y, Nishida R, Mihara H. Genetic analysis of tellurate reduction reveals the selenate/tellurate reductase genes ynfEF and the transcriptional regulation of moeA by NsrR in Escherichia coli. J Biochem 2021; 169:477-484. [PMID: 33136147 DOI: 10.1093/jb/mvaa120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/20/2020] [Indexed: 01/25/2023] Open
Abstract
Several bacteria can reduce tellurate into the less toxic elemental tellurium, but the genes responsible for this process have not yet been identified. In this study, we screened the Keio collection of single-gene knockouts of Escherichia coli responsible for decreased tellurate reduction and found that deletions of 29 genes, including those for molybdenum cofactor (Moco) biosynthesis, iron-sulphur biosynthesis, and the twin-arginine translocation pathway resulted in decreased tellurate reduction. Among the gene knockouts, deletions of nsrR, moeA, yjbB, ynbA, ydaS and yidH affected tellurate reduction more severely than those of other genes. Based on our findings, we determined that the ynfEF genes, which code for the components of the selenate reductase YnfEFGH, are responsible for tellurate reduction. Assays of several molybdoenzymes in the knockouts suggested that nsrR, yjbB, ynbA, ydaS and yidH are essential for the activities of molybdoenzymes in E. coli. Furthermore, we found that the nitric oxide sensor NsrR positively regulated the transcription of the Moco biosynthesis gene moeA. These findings provided new insights into the complexity and regulation of Moco biosynthesis in E. coli.
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Affiliation(s)
- Daiki Fujita
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Ryuta Tobe
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Hirotaka Tajima
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Yukari Anma
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Ryo Nishida
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Hisaaki Mihara
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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Zannoni A, Pelliciari S, Musiani F, Chiappori F, Roncarati D, Scarlato V. Definition of the Binding Architecture to a Target Promoter of HP1043, the Essential Master Regulator of Helicobacter pylori. Int J Mol Sci 2021; 22:ijms22157848. [PMID: 34360614 PMCID: PMC8345958 DOI: 10.3390/ijms22157848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/30/2022] Open
Abstract
HP1043 is an essential orphan response regulator of Helicobacter pylori orchestrating multiple crucial cellular processes. Classified as a member of the OmpR/PhoB family of two-component systems, HP1043 exhibits a highly degenerate receiver domain and evolved to function independently of phosphorylation. Here, we investigated the HP1043 binding mode to a target sequence in the hp1227 promoter (Php1227). Scanning mutagenesis of HP1043 DNA-binding domain and consensus sequence led to the identification of residues relevant for the interaction of the protein with a target DNA. These determinants were used as restraints to guide a data-driven protein-DNA docking. Results suggested that, differently from most other response regulators of the same family, HP1043 binds in a head-to-head conformation to the Php1227 target promoter. HP1043 interacts with DNA largely through charged residues and contacts with both major and minor grooves of the DNA are required for a stable binding. Computational alanine scanning on molecular dynamics trajectory was performed to corroborate our findings. Additionally, in vitro transcription assays confirmed that HP1043 positively stimulates the activity of RNA polymerase.
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Affiliation(s)
- Annamaria Zannoni
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
| | - Simone Pelliciari
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
| | - Federica Chiappori
- Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche (ITB-CNR), 20054 Segrate, Italy;
| | - Davide Roncarati
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
- Correspondence: (D.R.); (V.S.)
| | - Vincenzo Scarlato
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
- Correspondence: (D.R.); (V.S.)
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Geng H, Wang M, Gong J, Xu Y, Ma S. An Arabidopsis expression predictor enables inference of transcriptional regulators for gene modules. Plant J 2021; 107:597-612. [PMID: 33974299 DOI: 10.1111/tpj.15315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/08/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
The regulation of gene expression by transcription factors (TFs) has been studied for a long time, but no model that can accurately predict transcriptome profiles based on TF activities currently exists. Here, we developed a computational approach, named EXPLICIT (Expression Prediction via Log-linear Combination of Transcription Factors), to construct a universal predictor for Arabidopsis to predict the expression of 29 182 non-TF genes using 1678 TFs. When applied to RNA-Seq samples from diverse tissues, EXPLICIT generated accurate predicted transcriptomes correlating well with actual expression, with an average correlation coefficient of 0.986. After recapitulating the quantitative relationships between TFs and their target genes, EXPLICIT enabled downstream inference of TF regulators for genes and gene modules functioning in diverse plant pathways, including those involved in suberin, flavonoid, glucosinolate metabolism, lateral root, xylem, secondary cell wall development or endoplasmic reticulum stress response. Our approach showed a better ability to recover the correct TF regulators when compared with existing plant tools, and provides an innovative way to study transcriptional regulation.
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Affiliation(s)
- Haiying Geng
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Meng Wang
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Jiazhen Gong
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Yupu Xu
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
| | - Shisong Ma
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Innovation Academy for Seed Design, Chinese Academy of Sciences, Hefei, China
- School of Data Science, University of Science and Technology of China, Hefei, China
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Chen Y, Lei X, Jiang Z, Fitzgerald KA. Cellular nucleic acid-binding protein is essential for type I interferon-mediated immunity to RNA virus infection. Proc Natl Acad Sci U S A 2021; 118:e2100383118. [PMID: 34168080 PMCID: PMC8255963 DOI: 10.1073/pnas.2100383118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Type I interferons (IFNs) are innate immune cytokines required to establish cellular host defense. Precise control of IFN gene expression is crucial to maintaining immune homeostasis. Here, we demonstrated that cellular nucleic acid-binding protein (CNBP) was required for the production of type I IFNs in response to RNA virus infection. CNBP deficiency markedly impaired IFN production in macrophages and dendritic cells that were infected with a panel of RNA viruses or stimulated with synthetic double-stranded RNA. Furthermore, CNBP-deficient mice were more susceptible to influenza virus infection than were wild-type mice. Mechanistically, CNBP was phosphorylated and translocated to the nucleus, where it directly binds to the promoter of IFNb in response to RNA virus infection. Furthermore, CNBP controlled the recruitment of IFN regulatory factor (IRF) 3 and IRF7 to IFN promoters for the maximal induction of IFNb gene expression. These studies reveal a previously unrecognized role for CNBP as a transcriptional regulator of type I IFN genes engaged downstream of RNA virus-mediated innate immune signaling, which provides an additional layer of control for IRF3- and IRF7-dependent type I IFN gene expression and the antiviral innate immune response.
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Affiliation(s)
- Yongzhi Chen
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Xuqiu Lei
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Zhaozhao Jiang
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01605
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Hwang SH, Im H, Choi SH. A Master Regulator BrpR Coordinates the Expression of Multiple Loci for Robust Biofilm and Rugose Colony Development in Vibrio vulnificus. Front Microbiol 2021; 12:679854. [PMID: 34248894 PMCID: PMC8268162 DOI: 10.3389/fmicb.2021.679854] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/31/2021] [Indexed: 01/22/2023] Open
Abstract
Vibrio vulnificus, a fulminating human pathogen, forms biofilms to enhance its survival in nature and pathogenicity during host infection. BrpR is the transcriptional regulator governing robust biofilm and rugose colony formation in V. vulnificus, but little is known about both the direct regulon of BrpR and the role of BrpR in regulation of downstream genes. In this study, transcript analyses revealed that BrpR is highly expressed and thus strongly regulates the downstream gene in the stationary and elevated cyclic di-GMP conditions. Transcriptome analyses discovered the genes, whose expression is affected by BrpR but not by the downstream regulator BrpT. Two unnamed adjacent genes (VV2_1626-1627) were newly identified among the BrpR regulon and designated as brpL and brpG in this study. Genetic analyses showed that the deletion of brpL and brpG impairs the biofilm and rugose colony formation, indicating that brpLG plays a crucial role in the development of BrpR-regulated biofilm phenotypes. Comparison of the colony morphology and exopolysaccharide (EPS) production suggested that although the genetic location and regulation of brpLG are distinct from the brp locus, brpABCDFHIJK (VV2_1574-1582), brpLG is also responsible for the robust EPS production together with the brp locus genes. Electrophoretic mobility shift assays and DNase I protection assays demonstrated that BrpR regulates the expression of downstream genes in distinct loci by directly binding to their upstream regions, revealing a palindromic binding sequence. Altogether, this study suggests that BrpR is a master regulator coordinating the expression of multiple loci responsible for EPS production and thus, contributing to the robust biofilm and rugose colony formation of V. vulnificus.
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Affiliation(s)
- Seung-Ho Hwang
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
| | - Hanhyeok Im
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
| | - Sang Ho Choi
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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Yang M, Jia SH, Tao HL, Zhu C, Jia WZ, Hu LH, Gao CH. Cd(II)-binding transcriptional regulator interacts with isoniazid and regulates drug susceptibility in mycobacteria. J Biochem 2021; 169:43-53. [PMID: 32706888 DOI: 10.1093/jb/mvaa086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/16/2020] [Indexed: 02/03/2023] Open
Abstract
It is urgent to understand the regulatory mechanism of drug resistance in widespread bacterial pathogens. In Mycobacterium tuberculosis, several transcriptional regulators have been found to play essential roles in regulating its drug resistance. In this study, we found that an ArsR family transcription regulator encoded by Rv2642 (CdiR) responds to isoniazid (INH), a widely used anti-tuberculosis (TB) drug. CdiR negatively regulates self and adjacent genes, including arsC (arsenic-transport integral membrane protein ArsC). CdiR directly interacts with INH and Cd(II). The binding of INH and Cd(II) both reduce its DNA-binding activity. Disrupting cdiR increased the drug susceptibility to INH, whereas overexpressing cdiR decreased the susceptibility. Strikingly, overexpressing arsC increased the drug susceptibility as well as cdiR. Additionally, both changes in cdiR and arsC expression caused sensitivity to other drugs such as rifamycin and ethambutol, where the minimal inhibitory concentrations in the cdiR deletion strain were equal to those of the arsC-overexpressing strain, suggesting that the function of CdiR in regulating drug resistance primarily depends on arsC. Furthermore, we found that Cd(II) enhances bacterial resistance to INH in a CdiR-dependent manner. As a conclusion, CdiR has a critical role in directing the interplay between Cd(II) metal ions and drug susceptibility in mycobacteria.
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Affiliation(s)
- Min Yang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shi-Hua Jia
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hui-Ling Tao
- International Agricultural Institute, Yunnan Academy of Agricultural Sciences, Kunming 650224, China
| | - Chen Zhu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wan-Zhong Jia
- The State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Li-Hua Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chun-Hui Gao
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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50
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Choi G, Kim D, Im H, Choi SH. A Nitric Oxide-Responsive Transcriptional Regulator NsrR Cooperates With Lrp and CRP to Tightly Control the hmpA Gene in Vibrio vulnificus. Front Microbiol 2021; 12:681196. [PMID: 34093504 PMCID: PMC8175989 DOI: 10.3389/fmicb.2021.681196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
Nitric oxide (NO) is an important antimicrobial effector produced by the host innate immune system to counteract invading pathogens. To survive and establish a successful infection, a fulminating human pathogen Vibrio vulnificus expresses the hmpA gene encoding an NO dioxygenase in an NO-responsive manner. In this study, we identified an Rrf2-family transcriptional regulator NsrR that is predicted to contain the Fe-S cluster coordinated by three cysteine residues. Transcriptome analysis showed that NsrR controls the expression of multiple genes potentially involved in nitrosative stress responses. Particularly, NsrR acts as a strong repressor of hmpA transcription and relieves the repression of hmpA upon exposure to NO. Notably, nsrR and hmpA are transcribed divergently, and their promoter regions overlap with each other. Molecular biological analyses revealed that NsrR directly binds to this overlapping promoter region, which is alleviated by loss of the Fe-S cluster, leading to the subsequent derepression of hmpA under nitrosative stress. We further found that a leucine-responsive regulatory protein (Lrp) negatively regulates hmpA in an NsrR-dependent manner by directly binding to the promoter region, presumably resulting in a DNA conformation change to support the repression by NsrR. Meanwhile, a cyclic AMP receptor protein (CRP) positively regulates hmpA probably through repression of nsrR and lrp by directly binding to each promoter region in a sequential cascade. Altogether, this collaborative regulation of NsrR along with Lrp and CRP enables an elaborate control of hmpA transcription, contributing to survival under host-derived nitrosative stress and thereby the pathogenesis of V. vulnificus.
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Affiliation(s)
- Garam Choi
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
| | - Dukyun Kim
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Hanhyeok Im
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
| | - Sang Ho Choi
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
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