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Jeong GJ, Khan F, Tabassum N, Kim YM. Cellular and physiological roles of sigma factors in Vibrio spp.: A comprehensive review. Int J Biol Macromol 2024; 254:127833. [PMID: 37918595 DOI: 10.1016/j.ijbiomac.2023.127833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Vibrio species are motile gram-negative bacteria commonly found in aquatic environments. Vibrio species include pathogenic as well as non-pathogenic strains. Pathogenic Vibrio species have been reported in invertebrates and humans, whereas non-pathogenic strains are involved in symbiotic relationships with their eukaryotic hosts. These bacteria are also able to adapt to fluctuations in temperature, salinity, and pH, in addition to oxidative stress, and osmotic pressure in aquatic ecosystems. Moreover, they have also developed protective mechanisms against the immune systems of their hosts. Vibrio species accomplish adaptation to changing environments outside or inside the host by altering their gene expression profiles. To this end, several sigma factors specifically regulate gene expression, particularly under stressful environmental conditions. Moreover, other sigma factors are associated with biofilm formation and virulence as well. This review discusses different types of sigma and anti-sigma factors of Vibrio species involved in virulence and regulation of gene expression upon changes in environmental conditions. The evolutionary relationships between sigma factors with various physiological roles in Vibrio species are also discussed extensively.
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Affiliation(s)
- Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Fazlurrahman Khan
- Institute of Fisheries Sciences, Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
| | - Nazia Tabassum
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Young-Mog Kim
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
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2
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Sahil M, Singh J, Sahu S, Pal SK, Yadav A, Anand R, Mondal J. Identifying Selectivity Filters in Protein Biosensor for Ligand Screening. JACS AU 2023; 3:2800-2812. [PMID: 37885591 PMCID: PMC10598577 DOI: 10.1021/jacsau.3c00374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/27/2023] [Accepted: 08/31/2023] [Indexed: 10/28/2023]
Abstract
Specialized sensing mechanisms in bacteria enable the identification of cognate ligands with remarkable selectivity in highly xenobiotic-polluted environments where these ligands are utilized as energy sources. Here, via integrating all-atom computer simulation, biochemical assay, and isothermal titration calorimetry measurements, we determine the molecular basis of MopR, a phenol biosensor's complex selection process of ligand entry. Our results reveal a set of strategically placed selectivity filters along the ligand entry pathway of MopR. These filters act as checkpoints, screening diverse aromatic ligands at the protein surface based on their chemical features and sizes. Ligands meeting specific criteria are allowed to enter the sensing site in an orientation-dependent manner. Sequence and structural analyses demonstrate the conservation of this ligand entry mechanism across the sensor class, with individual amino acids along the selectivity filter path playing a critical role in ligand selection. Together, this investigation highlights the importance of interactions with the ligand entry pathway, in addition to interactions within the binding pocket, in achieving ligand selectivity in biological sensing. The findings enhance our understanding of ligand selectivity in bacterial phenol biosensors and provide insights for rational expansion of the biosensor repertoire, particularly for the biotechnologically relevant class of aromatic pollutants.
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Affiliation(s)
- Mohammad Sahil
- Tata
Institute of Fundamental Research, Hyderabad, 500046, India
| | - Jayanti Singh
- Department
of Chemistry, Indian Institute of Technology, Mumbai, 400076, India
| | - Subhankar Sahu
- Department
of Chemistry, Indian Institute of Technology, Mumbai, 400076, India
| | - Sushant Kumar Pal
- Department
of Chemistry, Indian Institute of Technology, Mumbai, 400076, India
| | - Ajit Yadav
- Department
of Chemistry, Indian Institute of Technology, Mumbai, 400076, India
| | - Ruchi Anand
- Department
of Chemistry, Indian Institute of Technology, Mumbai, 400076, India
| | - Jagannath Mondal
- Tata
Institute of Fundamental Research, Hyderabad, 500046, India
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3
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Hwang Y, Na JG, Lee SJ. Transcriptional regulation of soluble methane monooxygenase via enhancer-binding protein derived from Methylosinus sporium 5. Appl Environ Microbiol 2023; 89:e0210422. [PMID: 37668365 PMCID: PMC10537576 DOI: 10.1128/aem.02104-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/07/2023] [Indexed: 09/06/2023] Open
Abstract
Methane is a major greenhouse gas, and methanotrophs regulate the methane level in the carbon cycle. Soluble methane monooxygenase (sMMO) is expressed in various methanotroph genera, including Alphaproteobacteria and Gammaproteobacteria, and catalyzes the hydroxylation of methane to methanol. It has been proposed that MmoR regulates the expression of sMMO as an enhancer-binding protein under copper-limited conditions; however, details on this transcriptional regulation remain limited. Herein, we elucidate the transcriptional pathway of sMMO depending on copper ion concentration, which affects the interaction of MmoR and sigma factor. MmoR and sigma-54 (σ54) from Methylosinus sporium 5 were successfully overexpressed in Escherichia coli and purified to investigate sMMO transcription in methanotrophs. The results indicated that σ54 binds to a promoter positioned -24 (GG) and -12 (TGC) upstream between mmoG and mmoX1. The binding affinity and selectivity are lower (Kd = 184.6 ± 6.2 nM) than those of MmoR. MmoR interacts with the upstream activator sequence (UAS) with a strong binding affinity (Kd = 12.5 ± 0.5 nM). Mutational studies demonstrated that MmoR has high selectivity to its binding partner (ACA-xx-TGT). Titration assays have demonstrated that MmoR does not coordinate with copper ions directly; however, its binding affinity to UAS decreases in a low-copper-containing medium. MmoR strongly interacts with adenosine triphosphate (Kd = 62.8 ± 0.5 nM) to generate RNA polymerase complex. This study demonstrated that the binding events of both MmoR and σ54 that regulate transcription in M. sporium 5 depend on the copper ion concentration. IMPORTANCE This study provides biochemical evidence of transcriptional regulation of soluble methane monooxygenase (sMMO) in methanotrophs that control methane levels in ecological systems. Previous studies have proposed transcriptional regulation of MMOs, including sMMO and pMMO, while we provide further evidence to elucidate its mechanism using a purified enhancer-binding protein (MmoR) and transcription factor (σ54). The characterization studies of σ54 and MmoR identified the promoter binding sites and enhancer-binding sequences essential for sMMO expression. Our findings also demonstrate that MmoR functions as a trigger for sMMO expression due to the high specificity and selectivity for enhancer-binding sequences. The UV-visible spectrum of purified MmoR suggested an iron coordination like other GAF domain, and that ATP is essential for the initiation of enhancer elements. Binding assays indicated that these interactions are blocked by the copper ion. These results provide novel insights into gene regulation of methanotrophs.
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Affiliation(s)
- Yunha Hwang
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
| | - Jeong-Geol Na
- Department of Chemical Engineering, Sogang University , Seoul, South Korea
| | - Seung Jae Lee
- Department of Chemistry, Jeonbuk National University , Jeonju, South Korea
- Institute of Molecular Biology and Genetics, Jeonbuk National University , Jeonju, South Korea
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Shepherd MJ, Reynolds M, Pierce AP, Rice AM, Taylor TB. Transcription factor expression levels and environmental signals constrain transcription factor innovation. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001378. [PMID: 37584667 PMCID: PMC10482368 DOI: 10.1099/mic.0.001378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
Evolutionary innovation of transcription factors frequently drives phenotypic diversification and adaptation to environmental change. Transcription factors can gain or lose connections to target genes, resulting in novel regulatory responses and phenotypes. However the frequency of functional adaptation varies between different regulators, even when they are closely related. To identify factors influencing propensity for innovation, we utilise a Pseudomonas fluorescens SBW25 strain rendered incapable of flagellar mediated motility in soft-agar plates via deletion of the flagellar master regulator (fleQ ). This bacterium can evolve to rescue flagellar motility via gene regulatory network rewiring of an alternative transcription factor to rescue activity of FleQ. Previously, we have identified two members (out of 22) of the RpoN-dependent enhancer binding protein (RpoN-EBP) family of transcription factors (NtrC and PFLU1132) that are capable of innovating in this way. These two transcription factors rescue motility repeatably and reliably in a strict hierarchy – with NtrC the only route in a ∆fleQ background, and PFLU1132 the only route in a ∆fleQ ∆ntrC background. However, why other members in the same transcription factor family have not been observed to rescue flagellar activity is unclear. Previous work shows that protein homology cannot explain this pattern within the protein family (RpoN-EBPs), and mutations in strains that rescued motility suggested high levels of transcription factor expression and activation drive innovation. We predict that mutations that increase expression of the transcription factor are vital to unlock evolutionary potential for innovation. Here, we construct titratable expression mutant lines for 11 of the RpoN-EBPs in P. fluorescens . We show that in five additional RpoN-EBPs (FleR, HbcR, GcsR, DctD, AauR and PFLU2209), high expression levels result in different mutations conferring motility rescue, suggesting alternative rewiring pathways. Our results indicate that expression levels (and not protein homology) of RpoN-EBPs are a key constraining factor in determining evolutionary potential for innovation. This suggests that transcription factors that can achieve high expression through few mutational changes, or transcription factors that are active in the selective environment, are more likely to innovate and contribute to adaptive gene regulatory network evolution.
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Affiliation(s)
- Matthew J. Shepherd
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Mitchell Reynolds
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Aidan P. Pierce
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Alan M. Rice
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Tiffany B. Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
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Warneke R, Garbers TB, Herzberg C, Aschenbrandt G, Ficner R, Stülke J. Ornithine is the central intermediate in the arginine degradative pathway and its regulation in Bacillus subtilis. J Biol Chem 2023; 299:104944. [PMID: 37343703 PMCID: PMC10404663 DOI: 10.1016/j.jbc.2023.104944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023] Open
Abstract
The Gram-positive bacterium Bacillus subtilis can utilize several proteinogenic and non-proteinogenic amino acids as sources of carbon, nitrogen, and energy. The utilization of the amino acids arginine, citrulline, and ornithine is catalyzed by enzymes encoded in the rocABC and rocDEF operons and by the rocG gene. The expression of these genes is controlled by the alternative sigma factor SigL. RNA polymerase associated with this sigma factor depends on ATP-hydrolyzing transcription activators to initiate transcription. The RocR protein acts as a transcription activator for the roc genes. However, the details of amino acid metabolism via this pathway are unknown. Here, we investigated the contributions of all enzymes of the Roc pathway to the degradation of arginine, citrulline, and ornithine. We identified the previously uncharacterized RocB protein as responsible for the conversion of citrulline to ornithine. In vitro assays with the purified enzyme suggest that RocB acts as a manganese-dependent N-carbamoyl-L-ornithine hydrolase that cleaves citrulline to form ornithine and carbamate. Moreover, the molecular effector that triggers transcription activation by RocR has not been unequivocally identified. Using a combination of transcription reporter assays and biochemical experiments, we demonstrate that ornithine is the molecular inducer of RocR activity. Taken together, our work suggests that binding of ATP to RocR triggers its hexamerization, and binding of ornithine then allows ATP hydrolysis and activation of roc gene transcription. Thus, ornithine is the central molecule of the roc degradative pathway as it is the common intermediate of arginine and citrulline degradation and the molecular effector of RocR.
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Affiliation(s)
- Robert Warneke
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Tim Benedict Garbers
- Department of Molecular Structural Biology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Christina Herzberg
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Georg Aschenbrandt
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany.
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Yu G, Li X, Duan Q, Fu J, Zhang Y, Wang H, Luan J. Systematic identification of endogenous strong constitutive promoters from the diazotrophic rhizosphere bacterium Pseudomonas stutzeri DSM4166 to improve its nitrogenase activity. Microb Cell Fact 2023; 22:91. [PMID: 37138314 PMCID: PMC10155442 DOI: 10.1186/s12934-023-02085-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/09/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Biological nitrogen fixation converting atmospheric dinitrogen to ammonia is an important way to provide nitrogen for plants. Pseudomonas stutzeri DSM4166 is a diazotrophic Gram-negative bacterium isolated from the rhizosphere of cereal Sorghum nutans. Endogenous constitutive promoters are important for engineering of the nitrogen fixation pathway, however, they have not been systematically characterized in DSM4166. RESULTS Twenty-six candidate promoters were identified from DSM4166 by RNA-seq analysis. These 26 promoters were cloned and characterized using the firefly luciferase gene. The strengths of nineteen promoters varied from 100 to 959% of the strength of the gentamicin resistance gene promoter. The strongest P12445 promoter was used to overexpress the biological nitrogen fixation pathway-specific positive regulator gene nifA. The transcription level of nitrogen fixation genes in DSM4166 were significantly increased and the nitrogenase activity was enhanced by 4.1 folds determined by the acetylene reduction method. The nifA overexpressed strain produced 359.1 µM of extracellular ammonium which was 25.6 times higher than that produced by the wild-type strain. CONCLUSIONS The endogenous strong constitutive promoters identified in this study will facilitate development of DSM4166 as a microbial cell factory for nitrogen fixation and production of other useful compounds.
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Affiliation(s)
- Guangle Yu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Qiuyue Duan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China
| | - Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Binhai Rd 72, Qingdao, Shandong, 266237, China.
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7
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Martin Del Campo JS, Rigsbee J, Bueno Batista M, Mus F, Rubio LM, Einsle O, Peters JW, Dixon R, Dean DR, Dos Santos PC. Overview of physiological, biochemical, and regulatory aspects of nitrogen fixation in Azotobacter vinelandii. Crit Rev Biochem Mol Biol 2023; 57:492-538. [PMID: 36877487 DOI: 10.1080/10409238.2023.2181309] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Understanding how Nature accomplishes the reduction of inert nitrogen gas to form metabolically tractable ammonia at ambient temperature and pressure has challenged scientists for more than a century. Such an understanding is a key aspect toward accomplishing the transfer of the genetic determinants of biological nitrogen fixation to crop plants as well as for the development of improved synthetic catalysts based on the biological mechanism. Over the past 30 years, the free-living nitrogen-fixing bacterium Azotobacter vinelandii emerged as a preferred model organism for mechanistic, structural, genetic, and physiological studies aimed at understanding biological nitrogen fixation. This review provides a contemporary overview of these studies and places them within the context of their historical development.
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Affiliation(s)
| | - Jack Rigsbee
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | | | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Pozuelo de Alarcón, Spain
| | - Oliver Einsle
- Department of Biochemistry, University of Freiburg, Freiburg, Germany
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Dennis R Dean
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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8
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Deng S. The origin of genetic and metabolic systems: Evolutionary structuralinsights. Heliyon 2023; 9:e14466. [PMID: 36967965 PMCID: PMC10036676 DOI: 10.1016/j.heliyon.2023.e14466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
DNA is derived from reverse transcription and its origin is related to reverse transcriptase, DNA polymerase and integrase. The gene structure originated from the evolution of the first RNA polymerase. Thus, an explanation of the origin of the genetic system must also explain the evolution of these enzymes. This paper proposes a polymer structure model, termed the stable complex evolution model, which explains the evolution of enzymes and functional molecules. Enzymes evolved their functions by forming locally tightly packed complexes with specific substrates. A metabolic reaction can therefore be considered to be the result of adaptive evolution in this way when a certain essential molecule is lacking in a cell. The evolution of the primitive genetic and metabolic systems was thus coordinated and synchronized. According to the stable complex model, almost all functional molecules establish binding affinity and specific recognition through complementary interactions, and functional molecules therefore have the nature of being auto-reactive. This is thermodynamically favorable and leads to functional duplication and self-organization. Therefore, it can be speculated that biological systems have a certain tendency to maintain functional stability or are influenced by an inherent selective power. The evolution of dormant bacteria may support this hypothesis, and inherent selectivity can be unified with natural selection at the molecular level.
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Xiong W, Perna A, Jacob IB, Lundgren BR, Wang G. The Enhancer-Binding Protein MifR, an Essential Regulator of α-Ketoglutarate Transport, Is Required for Full Virulence of Pseudomonas aeruginosa PAO1 in a Mouse Model of Pneumonia. Infect Immun 2022; 90:e0013622. [PMID: 36125307 PMCID: PMC9584295 DOI: 10.1128/iai.00136-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The opportunistic human pathogen Pseudomonas aeruginosa PAO1 has an extensive metabolism, enabling it to utilize a wide range of structurally diverse compounds to meet its nutritional and energy needs. Interestingly, the utilization of some of the more unusual compounds often associated with a eukaryotic-host environment is regulated via enhancer-binding proteins (EBPs) in P. aeruginosa. Whether the utilization of such compounds and the EBPs involved contribute to the pathogenesis of P. aeruginosa remains to be fully understood. To narrow this gap, we investigated the roles of the EBPs EatR (regulator of ethanolamine catabolism), DdaR (regulator of methylarginine catabolism), and MifR (regulator of α-ketoglutarate or α-KG transport) in the virulence of P. aeruginosa PAO1 in a pneumonia-induced septic mouse model. Deletion of genes encoding EatR and DdaR had no significant effect on the mortality of P. aeruginosa PAO1-infected mice compared to wide-type (WT) PAO1-infected mice. In contrast, infected mice with ΔmifR mutant exhibited a significant reduction (~50%) in the mortality rate compared with WT PAO1 (P < 0.05). Infected mice with ΔmifR PAO1 had lower lung injury scores, fewer inflammatory cells, decreased proinflammatory cytokines, and decreased apoptosis and cell death compared to mice infected with WT PAO1 (P < 0.05). Furthermore, molecular analysis revealed decreased NLRP3 inflammasome activation in infected mice with ΔmifR PAO1 compared to WT PAO1 (P < 0.05). These results suggested that the utilization of α-KG was a contributing factor in P. aeruginosa-mediated pneumonia and sepsis and that MifR-associated regulation may be a potential therapeutic target for P. aeruginosa infectious disease.
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Affiliation(s)
- Weichuan Xiong
- Department of Surgery, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People’s Republic of China
| | - Alexander Perna
- Department of Surgery, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA
| | - Ikechukwu B. Jacob
- Department of Surgery, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA
- Department of Microbiology and Immunology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA
| | | | - Guirong Wang
- Department of Surgery, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA
- Department of Microbiology and Immunology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York, USA
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Lin M, Wu K, Zhan Z, Mi D, Xia Y, Niu X, Feng S, Chen Y, He C, Tao J, Li C. The RavA/VemR two-component system plays vital regulatory roles in the motility and virulence of Xanthomonas campestris. MOLECULAR PLANT PATHOLOGY 2022; 23:355-369. [PMID: 34837306 PMCID: PMC8828458 DOI: 10.1111/mpp.13164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 05/08/2023]
Abstract
Xanthomonas campestris pv. campestris (Xcc) can cause black rot in cruciferous plants worldwide. Two-component systems (TCSs) are key for bacterial adaptation to various environments, including hosts. VemR is a TCS response regulator and crucial for Xcc motility and virulence. Here, we report that RavA is the cognate histidine kinase (HK) of VemR and elucidate the signalling pathway by which VemR regulates Xcc motility and virulence. Genetic analysis showed that VemR is epistatic to RavA. Using bacterial two-hybrid experiments and pull-down and phosphorylation assays, we found that RavA can interact with and phosphorylate VemR, suggesting that RavA is the cognate HK of VemR. In addition, we found that RpoN2 and FleQ are epistatic to VemR in regulating bacterial motility and virulence. In vivo and in vitro experiments demonstrated that VemR interacts with FleQ but not with RpoN2. RavA/VemR regulates the expression of the flagellin-encoding gene fliC by activating the transcription of the rpoN2-vemR-fleQ and flhF-fleN-fliA operons. In summary, our data show that the RavA/VemR TCS regulates FleQ activity and thus influences the expression of motility-related genes, thereby affecting Xcc motility and virulence. The identification of this novel signalling pathway will deepen our understanding of Xcc-plant interactions.
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Affiliation(s)
- Maojuan Lin
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouHainanChina
| | - Kejian Wu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouHainanChina
| | - Zhaohong Zhan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouHainanChina
| | - Duo Mi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouHainanChina
| | - Yingying Xia
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouHainanChina
| | - Xiaolei Niu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouHainanChina
| | - Shipeng Feng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouHainanChina
| | - Yinhua Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouHainanChina
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouHainanChina
| | - Jun Tao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouHainanChina
| | - Chunxia Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical CropsHainan UniversityHaikouHainanChina
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11
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Genetic determinants of ammonium excretion in nifL mutants of Azotobacter vinelandii. Appl Environ Microbiol 2022; 88:e0187621. [PMID: 35138932 DOI: 10.1128/aem.01876-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ubiquitous diazotrophic soil bacterium Azotobacter vinelandii has been extensively studied as a model organism for biological nitrogen fixation (BNF). In A. vinelandii, BNF is regulated by the NifL-NifA two-component system, where NifL acts as an anti-activator that tightly controls the activity of the nitrogen fixation specific transcriptional activator, NifA, in response to redox, nitrogen, and carbon status. While several studies reported mutations in A. vinelandii nifL resulted in the deregulation of nitrogenase expression and the release of large quantities of ammonium, knowledge about the specific determinants for this ammonium-excreting phenotype is lacking. In this work, we report that only specific disruptions of nifL lead to large quantities of ammonium accumulated in liquid culture (∼12 mM). The ammonium excretion phenotype is solely associated with deletions of NifL domains combined with the insertion of a promoter sequence in the opposite orientation to nifLA transcription. We further demonstrated that the strength of the inserted promoter could influence the amounts of ammonium excreted by affecting rnf1 gene expression as an additional requirement for ammonium excretion. These ammonium-excreting nifL mutants significantly stimulate the transfer of fixed nitrogen to rice. This work defines discrete determinants that bring about A. vinelandii ammonium excretion and demonstrates that strains can be generated through simple gene editing to provide promising biofertilizers capable of transferring nitrogen to crops. Importance There is a considerable interest in the engineering of ammonium-excreting bacteria for use in agriculture to promote the growth of plants under fixed nitrogen-limiting conditions. This work defines discrete determinants that bring about A. vinelandii ammonium excretion and demonstrates that strains can be generated through simple gene editing to provide promising biofertilizers capable of transferring nitrogen to crops.
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12
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Yu C, Yang F, Xue D, Wang X, Chen H. The Regulatory Functions of σ 54 Factor in Phytopathogenic Bacteria. Int J Mol Sci 2021; 22:ijms222312692. [PMID: 34884502 PMCID: PMC8657755 DOI: 10.3390/ijms222312692] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022] Open
Abstract
σ54 factor (RpoN), a type of transcriptional regulatory factor, is widely found in pathogenic bacteria. It binds to core RNA polymerase (RNAP) and regulates the transcription of many functional genes in an enhancer-binding protein (EBP)-dependent manner. σ54 has two conserved functional domains: the activator-interacting domain located at the N-terminal and the DNA-binding domain located at the C-terminal. RpoN directly binds to the highly conserved sequence, GGN10GC, at the −24/−12 position relative to the transcription start site of target genes. In general, bacteria contain one or two RpoNs but multiple EBPs. A single RpoN can bind to different EBPs in order to regulate various biological functions. Thus, the overlapping and unique regulatory pathways of two RpoNs and multiple EBP-dependent regulatory pathways form a complex regulatory network in bacteria. However, the regulatory role of RpoN and EBPs is still poorly understood in phytopathogenic bacteria, which cause economically important crop diseases and pose a serious threat to world food security. In this review, we summarize the current knowledge on the regulatory function of RpoN, including swimming motility, flagella synthesis, bacterial growth, type IV pilus (T4Ps), twitching motility, type III secretion system (T3SS), and virulence-associated phenotypes in phytopathogenic bacteria. These findings and knowledge prove the key regulatory role of RpoN in bacterial growth and pathogenesis, as well as lay the groundwork for further elucidation of the complex regulatory network of RpoN in bacteria.
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Affiliation(s)
- Chao Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.Y.); (F.Y.)
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.Y.); (F.Y.)
| | - Dingrong Xue
- National Engineering Laboratory of Grain Storage and Logistics, Academy of National Food and Strategic Reserves Administration, No. 11 Baiwanzhuang Street, Xicheng District, Beijing 100037, China;
| | - Xiuna Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.Y.); (F.Y.)
- Correspondence:
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13
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Chakrabortty T, Roy Chowdhury S, Ghosh B, Sen U. Crystal Structure of VpsR Revealed Novel Dimeric Architecture and c-di-GMP Binding Site: Mechanistic Implications in Oligomerization, ATPase Activity and DNA Binding. J Mol Biol 2021; 434:167354. [PMID: 34774564 DOI: 10.1016/j.jmb.2021.167354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 01/09/2023]
Abstract
VpsR, the master regulator of biofilm formation in Vibrio cholerae, is an atypical NtrC1 type bEBP lacking residues essential for σ54-RNAP binding and REC domain phosphorylation. Moreover, transcription from PvpsL, a promoter of biofilm biosynthesis, has been documented in presence of σ70-RNAP/VpsR/c-di-GMP complex. It was proposed that c-di-GMP and VpsR together form an active transcription complex with σ70-RNAP. However, the impact of c-di-GMP imparted on VpsR that leads to transcription activation with σ70-RNAP remained elusive, largely due to the lack of the structure of VpsR and knowledge about c-di-GMP:VpsR interactions. In this direction we have solved the crystal structure of VpsRRA, containing REC and AAA+ domains, in apo, AMPPNP/GMPPNP and c-di-GMP bound states. Structures of VpsRRA unveiled distinctive REC domain orientation that leads to a novel dimeric association and noncanonical ATP/GTP binding. Moreover, we have demonstrated that at physiological pH VpsR remains as monomer having no ATPase activity but c-di-GMP imparted cooperativity to convert it to dimer with potent activity. Crystal structure of c-di-GMP:VpsRRA complex reveals that c-di-GMP binds near the C-terminal end of AAA+ domain. Trp quenching studies on VpsRR, VpsRA, VpsRRA, VpsRAD with c-di-GMP additionally demonstrated that c-di-GMP could potentially bind VpsRD. We propose that c-di-GMP mediated tethering of VpsRD with VpsRA could likely favor generating the specific protein-DNA architecture for transcription activation.
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Affiliation(s)
- Tulika Chakrabortty
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India. https://twitter.com/@TulikaC02382598
| | - Sanghati Roy Chowdhury
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India
| | - Biplab Ghosh
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Udayaditya Sen
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India.
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14
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Zhou T, Huang J, Liu Z, Xu Z, Zhang LH. Molecular Mechanisms Underlying the Regulation of Biofilm Formation and Swimming Motility by FleS/FleR in Pseudomonas aeruginosa. Front Microbiol 2021; 12:707711. [PMID: 34367113 PMCID: PMC8335546 DOI: 10.3389/fmicb.2021.707711] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/28/2021] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa, a major cause of nosocomial infection, can survive under diverse environmental conditions. Its great adaptive ability is dependent on its multiple signaling systems such as the two-component system (TCS). A TCS FleS/FleR has been previously identified to positively regulate a variety of virulence-related traits in P. aeruginosa PAO1 including motility and biofilm formation which are involved in the acute and chronic infections, respectively. However, the molecular mechanisms underlying these regulations are still unclear. In this study, we first analyzed the regulatory roles of each domains in FleS/FleR and characterized key residues in the FleS-HisKA, FleR-REC and FleR-AAA domains that are essential for the signaling. Next, we revealed that FleS/FleR regulates biofilm formation in a c-di-GMP and FleQ dependent manner. Lastly, we demonstrated that FleR can regulate flagellum biosynthesis independently without FleS, which explains the discrepant regulation of swimming motility by FleS and FleR.
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Affiliation(s)
- Tian Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Jiahui Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Zhiqing Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Zeling Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Lian-Hui Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
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15
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Yu C, Nguyen DP, Yang F, Shi J, Wei Y, Tian F, Zhao X, Chen H. Transcriptome Analysis Revealed Overlapping and Special Regulatory Roles of RpoN1 and RpoN2 in Motility, Virulence, and Growth of Xanthomonas oryzae pv. oryzae. Front Microbiol 2021; 12:653354. [PMID: 33746934 PMCID: PMC7970052 DOI: 10.3389/fmicb.2021.653354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/15/2021] [Indexed: 11/13/2022] Open
Abstract
σ54 factor (RpoN) plays a crucial role in bacterial motility, virulence, growth, and other biological functions. In our previous study, two homologous σ54 factors, RpoN1 and RpoN2, were identified in Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial leaf blight in rice. However, their functional roles, i.e., whether they exert combined or independent effects, remain unknown. In the current study, rpoN1 or rpoN2 deletion in Xoo significantly disrupted bacterial swimming motility, flagellar assembly, and virulence. Transcriptome analysis led to the identification of 127 overlapping differentially expressed genes (DEGs) regulated by both RpoN1 and RpoN2. Furthermore, GO and KEGG classification demonstrated that these DEGs were highly enriched in flagellar assembly, chemotaxis, and c-di-GMP pathways. Interestingly, ropN1 deletion decreased ropN2 transcription, while rpoN2 deletion did not affect ropN1 transcription. No interaction between the rpoN2 promoter and RpoN1 was detected, suggesting that RpoN1 indirectly regulates rpoN2 transcription. In addition, RpoN1-regulated DEGs were specially enriched in ribosome, carbon, and nitrogen metabolism pathways. Besides, bacterial growth was remarkably repressed in ΔrpoN1 but not in ΔrpoN2. Taken together, this study demonstrates the overlapping and unique regulatory roles of RpoN1 and RpoN2 in motility, virulence, growth and provides new insights into the regulatory mechanism of σ54 factors in Xoo.
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Affiliation(s)
- Chao Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Doan-Phuong Nguyen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jia Shi
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yiming Wei
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fang Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuxiang Zhao
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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16
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Kim SH, Chelliah R, Ramakrishnan SR, Perumal AS, Bang WS, Rubab M, Daliri EBM, Barathikannan K, Elahi F, Park E, Jo HY, Hwang SB, Oh DH. Review on Stress Tolerance in Campylobacter jejuni. Front Cell Infect Microbiol 2021; 10:596570. [PMID: 33614524 PMCID: PMC7890702 DOI: 10.3389/fcimb.2020.596570] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/03/2020] [Indexed: 01/17/2023] Open
Abstract
Campylobacter spp. are the leading global cause of bacterial colon infections in humans. Enteropathogens are subjected to several stress conditions in the host colon, food complexes, and the environment. Species of the genus Campylobacter, in collective interactions with certain enteropathogens, can manage and survive such stress conditions. The stress-adaptation mechanisms of Campylobacter spp. diverge from other enteropathogenic bacteria, such as Escherichia coli, Salmonella enterica serovar Typhi, S. enterica ser. Paratyphi, S. enterica ser. Typhimurium, and species of the genera Klebsiella and Shigella. This review summarizes the different mechanisms of various stress-adaptive factors on the basis of species diversity in Campylobacter, including their response to various stress conditions that enhance their ability to survive on different types of food and in adverse environmental conditions. Understanding how these stress adaptation mechanisms in Campylobacter, and other enteric bacteria, are used to overcome various challenging environments facilitates the fight against resistance mechanisms in Campylobacter spp., and aids the development of novel therapeutics to control Campylobacter in both veterinary and human populations.
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Affiliation(s)
- Se-Hun Kim
- Food Microbiology Division, Food Safety Evaluation Department, National Institute of Food and Drug Safety Evaluation, Cheongju, South Korea.,College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Ramachandran Chelliah
- College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Sudha Rani Ramakrishnan
- School of Food Science, Department of Food Science and Biotechnology, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | | | - Woo-Suk Bang
- Department of Food and Nutrition, College of Human Ecology and Kinesiology, Yeungnam University, Gyeongsan, South Korea
| | - Momna Rubab
- College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Eric Banan-Mwine Daliri
- College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Kaliyan Barathikannan
- College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Fazle Elahi
- College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Eunji Park
- College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Hyeon Yeong Jo
- College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Su-Bin Hwang
- College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
| | - Deog Hwan Oh
- College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, South Korea
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17
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Jeckelmann JM, Erni B. The mannose phosphotransferase system (Man-PTS) - Mannose transporter and receptor for bacteriocins and bacteriophages. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183412. [PMID: 32710850 DOI: 10.1016/j.bbamem.2020.183412] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023]
Abstract
Mannose transporters constitute a superfamily (Man-PTS) of the Phosphoenolpyruvate Carbohydrate Phosphotransferase System (PTS). The membrane complexes are homotrimers of protomers consisting of two subunits, IIC and IID. The two subunits without recognizable sequence similarity assume the same fold, and in the protomer are structurally related by a two fold pseudosymmetry axis parallel to membrane-plane (Liu et al. (2019) Cell Research 29 680). Two reentrant loops and two transmembrane helices of each subunit together form the N-terminal transport domain. Two three-helix bundles, one of each subunit, form the scaffold domain. The protomer is stabilized by a helix swap between these bundles. The two C-terminal helices of IIC mediate the interprotomer contacts. PTS occur in bacteria and archaea but not in eukaryotes. Man-PTS are abundant in Gram-positive bacteria living on carbohydrate rich mucosal surfaces. A subgroup of IICIID complexes serve as receptors for class IIa bacteriocins and as channel for the penetration of bacteriophage lambda DNA across the inner membrane. Some Man-PTS are associated with host-pathogen and -symbiont processes.
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Affiliation(s)
- Jean-Marc Jeckelmann
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.
| | - Bernhard Erni
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.
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18
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Walsh BJC, Giedroc DP. H 2S and reactive sulfur signaling at the host-bacterial pathogen interface. J Biol Chem 2020; 295:13150-13168. [PMID: 32699012 PMCID: PMC7504917 DOI: 10.1074/jbc.rev120.011304] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial pathogens that cause invasive disease in the vertebrate host must adapt to host efforts to cripple their viability. Major host insults are reactive oxygen and reactive nitrogen species as well as cellular stress induced by antibiotics. Hydrogen sulfide (H2S) is emerging as an important player in cytoprotection against these stressors, which may well be attributed to downstream more oxidized sulfur species termed reactive sulfur species (RSS). In this review, we summarize recent work that suggests that H2S/RSS impacts bacterial survival in infected cells and animals. We discuss the mechanisms of biogenesis and clearance of RSS in the context of a bacterial H2S/RSS homeostasis model and the bacterial transcriptional regulatory proteins that act as "sensors" of cellular RSS that maintain H2S/RSS homeostasis. In addition, we cover fluorescence imaging- and MS-based approaches used to detect and quantify RSS in bacterial cells. Last, we discuss proteome persulfidation (S-sulfuration) as a potential mediator of H2S/RSS signaling in bacteria in the context of the writer-reader-eraser paradigm, and progress toward ascribing regulatory significance to this widespread post-translational modification.
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Affiliation(s)
- Brenna J C Walsh
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, USA.
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19
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Characterization and Comparative Analysis of RWP-RK Proteins from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea. Int J Genomics 2020; 2020:2568640. [PMID: 32908854 PMCID: PMC7474775 DOI: 10.1155/2020/2568640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/30/2020] [Accepted: 08/07/2020] [Indexed: 11/17/2022] Open
Abstract
RWP-RK proteins are important factors involved in nitrate response and gametophyte development in plants, and the functions of RWP-RK proteins have been analyzed in many species. However, the characterization of peanut RWP-RK proteins is limited. In this study, we identified 16, 19, and 32 RWP-RK members from Arachis duranensis, Arachis ipaensis, and Arachis hypogaea, respectively, and investigated their evolution relationships. The RWP-RK proteins were classified into two groups, RWP-RK domain proteins and NODULE-INCEPTION-like proteins. Chromosomal distributions, gene structures, and conserved motifs of RWP-RK genes were compared among wild and cultivated peanuts. In addition, we identified 12 orthologous gene pairs from the two wild peanut species, 13 from A. duranensis and A. hypogaea, and 13 from A. ipaensis and A. hypogaea. One, one, and seventeen duplicated gene pairs were identified within the A. duranensis, A. ipaensis, and A. hypogaea genomes, respectively. Moreover, different numbers of cis-acting elements in the RWP-RK promoters were found in wild and cultivated species (87 in A. duranensis, 89 in A. ipaensis, and 92 in A. hypogaea), and as a result, many RWP-RK genes showed distinct expression patterns in different tissues. Our study will provide useful information for further functional and evolutionary analysis of the RWP-RK genes.
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20
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Li K, Wu G, Liao Y, Zeng Q, Wang H, Liu F. RpoN1 and RpoN2 play different regulatory roles in virulence traits, flagellar biosynthesis, and basal metabolism in Xanthomonas campestris. MOLECULAR PLANT PATHOLOGY 2020; 21:907-922. [PMID: 32281725 PMCID: PMC7280030 DOI: 10.1111/mpp.12938] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 05/08/2023]
Abstract
Homologous regulatory factors are widely present in bacteria, but whether homologous regulators synergistically or differentially regulate different biological functions remains mostly unknown. Here, we report that the homologous regulators RpoN1 and RpoN2 of the plant pathogen Xanthomonas campestris pv. campestris (Xcc) play different regulatory roles with respect to virulence traits, flagellar biosynthesis, and basal metabolism. RpoN2 directly regulated Xcc fliC and fliQ to modulate flagellar synthesis in X. campestris, thus affecting the swimming motility of X. campestris. Mutation of rpoN2 resulted in reduced production of biofilms and extracellular polysaccharides in Xcc. These defects may together cause reduced virulence of the rpoN2 mutant against the host plant. Moreover, we demonstrated that RpoN1 could regulate branched-chain fatty acid production and modulate the synthesis of diffusible signal factor family quorum sensing signals. Although RpoN1 and RpoN2 are homologues, the regulatory roles and biological functions of these proteins were not interchangeable. Overall, our report provides new insights into the two different molecular roles that form the basis for the transcriptional specialization of RpoN homologues.
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Affiliation(s)
- Kaihuai Li
- College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
| | - Guichun Wu
- Institute of Plant ProtectionJiangsu Academy of Agricultural SciencesNanjingChina
| | - Yuling Liao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural OrganismsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Quan Zeng
- Department of Plant Pathology and EcologyThe Connecticut Agricultural Experiment StationNew HavenCTUSA
| | - Haihong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural OrganismsCollege of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Fengquan Liu
- College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Institute of Plant ProtectionJiangsu Academy of Agricultural SciencesNanjingChina
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21
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Quorum sensing regulation confronts the development of a viable but
non‐culturable
state in
Vibrio cholerae. Environ Microbiol 2020; 22:4314-4322. [DOI: 10.1111/1462-2920.15026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 12/01/2022]
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22
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Yu C, Nguyen DP, Ren Z, Liu J, Yang F, Tian F, Fan S, Chen H. The RpoN2-PilRX regulatory system governs type IV pilus gene transcription and is required for bacterial motility and virulence in Xanthomonas oryzae pv. oryzae. MOLECULAR PLANT PATHOLOGY 2020; 21:652-666. [PMID: 32112711 PMCID: PMC7170775 DOI: 10.1111/mpp.12920] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
The type IV pilus (T4P), a special class of bacterial surface filament, plays crucial roles in surface adhesion, motility, biofilm formation, and virulence in pathogenic bacteria. However, the regulatory mechanism of T4P and its relationship to bacterial virulence are still little understood in Xanthomonas oryzae pv. oryzae (Xoo), the causal pathogen of bacterial blight of rice. Our previous studies showed that the σ54 factor RpoN2 regulated bacterial virulence on rice in a flagellum-independent manner in Xoo. In this study, both yeast two-hybrid and pull-down assays revealed that RpoN2 directly and specifically interacted with PilRX, a homolog of the response regulator PilR of the two-component system PilS-PilR in the pilus gene cluster. Genomic sequence and reverse transcription PCR (RT-PCR) analysis showed 13 regulons containing 25 genes encoding T4P structural components and putative regulators. A consensus RpoN2-binding sequence GGN10 GC was identified in the promoter sequences of most T4P gene transcriptional units. Electrophoretic mobility shift assays confirmed the direct binding of RpoN2 to the promoter of the major pilin gene pilAX, the inner membrane platform protein gene pilCX, and pilRX. Promoter activity and quantitative RT-PCR assays demonstrated direct and indirect transcriptional regulation by RpoN2 of the T4P genes. In addition, individual deletions of pilAX, pilCX, and pilRX resulted in significantly reduced twitching and swimming motility, biofilm formation, and virulence in rice. Taken together, the findings from the current study suggest that the RpoN2-PilRX regulatory system controls bacterial motility and virulence by regulating T4P gene transcription in Xoo.
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Affiliation(s)
- Chao Yu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Doan-Phuong Nguyen
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Zhaoyu Ren
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Jianan Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Fang Tian
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Susu Fan
- Shandong Provincial Key Laboratory of Applied MicrobiologyEcology InstituteQilu University of Technology (Shandong Academy of Sciences)Ji’nanChina
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
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23
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Acclimation of bacterial cell state for high-throughput enzyme engineering using a DmpR-dependent transcriptional activation system. Sci Rep 2020; 10:6091. [PMID: 32269250 PMCID: PMC7142073 DOI: 10.1038/s41598-020-62892-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/26/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic circuit-based biosensors have emerged as an effective analytical tool in synthetic biology; these biosensors can be applied to high-throughput screening of new biocatalysts and metabolic pathways. Sigma 54 (σ54)-dependent transcription factor (TF) can be a valuable component of these biosensors owing to its intrinsic silent property compared to most of the housekeeping sigma 70 (σ70) TFs. Here, we show that these unique characteristics of σ54-dependent TFs can be used to control the host cell state to be more appropriate for high-throughput screening. The acclimation of cell state was achieved by using guanosine (penta)tetraphosphate ((p)ppGpp)-related genes (relA, spoT) and nutrient conditions, to link the σ54 TF-based reporter expression with the target enzyme activity. By controlling stringent programmed responses and optimizing assay conditions, catalytically improved tyrosine phenol lyase (TPL) enzymes were successfully obtained using a σ54-dependent DmpR as the TF component, demonstrating the practical feasibility of this biosensor. This combinatorial strategy of biosensors using σ factor-dependent TFs will allow for more effective high-throughput enzyme engineering with broad applicability.
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Ferrous-Iron-Activated Transcriptional Factor AdhR Regulates Redox Homeostasis in Clostridium beijerinckii. Appl Environ Microbiol 2020; 86:AEM.02782-19. [PMID: 32005735 DOI: 10.1128/aem.02782-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 01/27/2020] [Indexed: 11/20/2022] Open
Abstract
The AdhR regulatory protein is an activator of σ54-dependent transcription of adhA1 and adhA2 genes, which are required for alcohol synthesis in Clostridium beijerinckii Here, we identified the signal perceived by AdhR and determined the regulatory mechanism of AdhR activity. By assaying the activity of AdhR in N-terminally truncated forms, a negative control mechanism of AdhR activity was identified in which the central AAA+ domain is subject to repression by the N-terminal GAF and PAS domains. Binding of Fe2+ to the GAF domain was found to relieve intramolecular repression and stimulate the ATPase activity of AdhR, allowing the AdhR to activate transcription. This control mechanism enables AdhR to regulate transcription of adhA1 and adhA2 in response to cellular redox status. The mutants deficient in AdhR or σ54 showed large shifts in intracellular redox state indicated by the NADH/NAD+ ratio under conditions of increased electron availability or oxidative stress. We demonstrated that the Fe2+-activated transcriptional regulator AdhR and σ54 control alcohol synthesis to maintain redox homeostasis in clostridial cells. Expression of N-terminally truncated forms of AdhR resulted in improved solvent production by C. beijerinckii IMPORTANCE Solventogenic clostridia are anaerobic bacteria that can produce butanol, ethanol, and acetone, which can be used as biofuels or building block chemicals. Here, we show that AdhR, a σ54-dependent transcriptional activator, senses the intracellular redox status and controls alcohol synthesis in Clostridium beijerinckii AdhR provides a new example of a GAF domain coordinating a mononuclear non-heme iron to sense and transduce the redox signal. Our study reveals a previously unrecognized functional role of σ54 in control of cellular redox balance and provides new insights into redox signaling and regulation in clostridia. Our results reveal AdhR as a novel engineering target for improving solvent production by C. beijerinckii and other solventogenic clostridia.
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Contribution of σ 70 and σ N Factors to Expression of Class II pilE in Neisseria meningitidis. J Bacteriol 2019; 201:JB.00170-19. [PMID: 31331980 PMCID: PMC6755734 DOI: 10.1128/jb.00170-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 07/16/2019] [Indexed: 02/06/2023] Open
Abstract
Neisseria meningitidis expresses multicomponent organelles called type four pili (Tfp), which are key virulence factors required for attachment to human cells during carriage and disease. Pilin (PilE) is the main component of Tfp, and N. meningitidis isolates either have a class I pilE locus and express pilins that undergo antigenic variation or have a class II pilE locus and express invariant pilins. The transcriptional regulation of class I pilE has been studied in both N. meningitidis and Neisseria gonorrhoeae, while the control of expression of class II pilE has been elucidated in the nonpathogenic species Neisseria elongata However, the factors that govern the regulation of the class II pilE gene in N. meningitidis are not known. In this work, we have bioinformatically and experimentally identified the class II pilE promoter. We confirmed the presence of conserved σ70 and σN-dependent promoters upstream of pilE in a collection of meningococcal genomes and demonstrated that class II pilE expression initiates from the σ70 family-dependent promoter. By deletion or overexpression of sigma factors, we showed that σN, σH, and σE do not affect class II pilin expression. These findings are consistent with a role of the housekeeping σD in expression of this important component of Tfp. Taken together, our data indicate that the σ-dependent network responsible for the expression of class II pilE has been selected to maintain pilE expression, consistent with the essential roles of Tfp in colonization and pathogenesis.IMPORTANCE The type four pilus (Tfp) of Neisseria meningitidis contributes to fundamental processes such as adhesion, transformation, and disease pathology. Meningococci express one of two distinct classes of Tfp (class I or class II), which can be distinguished antigenically or by the major subunit (pilE) locus and its genetic context. The factors that govern transcription of the class II pilE gene are not known, even though it is present in isolates that cause epidemic disease. Here we show that the transcription of class II pilE is maintained throughout growth and under different stress conditions and is driven by a σ70-dependent promoter. This is distinct from Tfp regulation in nonpathogenic Neisseria spp. and may confer an advantage during host-cell interaction and infection.
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Abstract
Rhizobia are α- and β-proteobacteria that form a symbiotic partnership with legumes, fixing atmospheric dinitrogen to ammonia and providing it to the plant. Oxygen regulation is key in this symbiosis. Fixation is performed by an oxygen-intolerant nitrogenase enzyme but requires respiration to meet its high energy demands. To satisfy these opposing constraints the symbiotic partners cooperate intimately, employing a variety of mechanisms to regulate and respond to oxygen concentration. During symbiosis rhizobia undergo significant changes in gene expression to differentiate into nitrogen-fixing bacteroids. Legumes host these bacteroids in specialized root organs called nodules. These generate a near-anoxic environment using an oxygen diffusion barrier, oxygen-binding leghemoglobin and control of mitochondria localization. Rhizobia sense oxygen using multiple interconnected systems which enable a finely-tuned response to the wide range of oxygen concentrations they experience when transitioning from soil to nodules. The oxygen-sensing FixL-FixJ and hybrid FixL-FxkR two-component systems activate at relatively high oxygen concentration and regulate fixK transcription. FixK activates the fixNOQP and fixGHIS operons producing a high-affinity terminal oxidase required for bacterial respiration in the microaerobic nodule. Additionally or alternatively, some rhizobia regulate expression of these operons by FnrN, an FNR-like oxygen-sensing protein. The final stage of symbiotic establishment is activated by the NifA protein, regulated by oxygen at both the transcriptional and protein level. A cross-species comparison of these systems highlights differences in their roles and interconnections but reveals common regulatory patterns and themes. Future work is needed to establish the complete regulon of these systems and identify other regulatory signals.
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Affiliation(s)
- Paul J Rutten
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Liu Y, Wan X, Wang B. Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria. Nat Commun 2019; 10:3693. [PMID: 31451697 PMCID: PMC6710252 DOI: 10.1038/s41467-019-11479-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/16/2019] [Indexed: 11/21/2022] Open
Abstract
Transcriptional regulation by nuclease-deficient CRISPR/Cas is a popular and valuable tool for routine control of gene expression. CRISPR interference in bacteria can be reliably achieved with high efficiencies. Yet, options for CRISPR activation (CRISPRa) remained limited in flexibility and activity because they relied on σ70 promoters. Here we report a eukaryote-like bacterial CRISPRa system based on σ54-dependent promoters, which supports long distance, and hence multi-input regulation with high dynamic ranges. Our CRISPRa device can activate σ54-dependent promoters with biotechnology relevance in non-model bacteria. It also supports orthogonal gene regulation on multiple levels. Combining our CRISPRa with dxCas9 further expands flexibility in DNA targeting, and boosts dynamic ranges into regimes that enable construction of cascaded CRISPRa circuits. Application-wise, we construct a reusable scanning platform for readily optimizing metabolic pathways without library reconstructions. This eukaryote-like CRISPRa system is therefore a powerful and versatile synthetic biology tool for diverse research and industrial applications.
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Affiliation(s)
- Yang Liu
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Xinyi Wan
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK.
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Yu H, Chen Z, Wang N, Yu S, Yan Y, Huo YX. Engineering transcription factor BmoR for screening butanol overproducers. Metab Eng 2019; 56:28-38. [PMID: 31449878 DOI: 10.1016/j.ymben.2019.08.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/09/2019] [Accepted: 08/22/2019] [Indexed: 01/15/2023]
Abstract
The wild-type transcription factors are sensitive to their corresponding signal molecules. Using wild-type transcription factors as biosensors to screen industrial overproducers are generally impractical because of their narrow detection ranges. This study took transcription factor BmoR as an example and aimed to expand the detection range of BmoR for screening alcohols overproducers. Firstly, a BmoR mutation library was established, and the mutations distributed randomly in all predicted functional domains of BmoR. Structure of BmoR-isobutanol complex were modelled, and isobutanol binding sites were confirmed by site-directed mutagenesis. Subsequently, the effects of the mutations on the detection range or output were confirmed in the BmoR mutants. Four combinatorial mutants containing one increased-detection-range mutation and one enhanced-output mutation were constructed. Compared with wild-type BmoR, F276A/E627N BmoR and D333N/E627N BmoR have wider detection ranges (0-100 mM) and relatively high outputs to the isobutanol added quantitatively or produced intracellularly, demonstrating they have potential for screening isobutanol overproduction strains. This work presented an example of engineering the wild-type transcription factors with physiological significance for industrial utilization.
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Affiliation(s)
- Huan Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China; UCLA Institute for Technology Advancement (Suzhou), 10 Yueliangwan Road, Suzhou Industrial Park, 215123, Suzhou, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, 30602, GA, USA
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China; UCLA Institute for Technology Advancement (Suzhou), 10 Yueliangwan Road, Suzhou Industrial Park, 215123, Suzhou, China.
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Nie X, Dong W, Yang C. Genomic reconstruction of σ 54 regulons in Clostridiales. BMC Genomics 2019; 20:565. [PMID: 31288763 PMCID: PMC6615313 DOI: 10.1186/s12864-019-5918-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 06/20/2019] [Indexed: 12/21/2022] Open
Abstract
Background The σ54 factor controls unique promoters and interacts with a specialized activator (enhancer binding proteins [EBP]) for transcription initiation. Although σ54 is present in many Clostridiales species that have great importance in human health and biotechnological applications, the cellular processes controlled by σ54 remain unknown. Results For systematic analysis of the regulatory functions of σ54, we performed comparative genomic reconstruction of transcriptional regulons of σ54 in 57 species from the Clostridiales order. The EBP-binding DNA motifs and regulated genes were identified for 263 EBPs that constitute 39 distinct groups. The reconstructed σ54 regulons contain the genes involved in fermentation and amino acid catabolism. The predicted σ54 binding sites in the genomes of Clostridiales spp. were verified by in vitro binding assays. To our knowledge, this is the first report about direct regulation of the Stickland reactions and butyrate and alcohols synthesis by σ54 and the respective EBPs. Considerable variations were demonstrated in the sizes and gene contents of reconstructed σ54 regulons between different Clostridiales species. It is proposed that σ54 controls butyrate and alcohols synthesis in solvent-producing species, regulates autotrophic metabolism in acetogenic species, and affects the toxin production in pathogenic species. Conclusions This study reveals previously unrecognized functions of σ54 and provides novel insights into the regulation of fermentation and amino acid metabolism in Clostridiales species, which could have potential applications in guiding the treatment and efficient utilization of these species. Electronic supplementary material The online version of this article (10.1186/s12864-019-5918-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoqun Nie
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wenyue Dong
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chen Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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Hsieh ML, Hinton DM, Waters CM. VpsR and cyclic di-GMP together drive transcription initiation to activate biofilm formation in Vibrio cholerae. Nucleic Acids Res 2019; 46:8876-8887. [PMID: 30007313 PMCID: PMC6158489 DOI: 10.1093/nar/gky606] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/09/2018] [Indexed: 11/14/2022] Open
Abstract
The small molecule cyclic di-GMP (c-di-GMP) is known to affect bacterial gene expression in myriad ways. In Vibrio cholerae in vivo, the presence of c-di-GMP together with the response regulator VpsR results in transcription from PvpsL, a promoter of biofilm biosynthesis genes. VpsR shares homology with enhancer binding proteins that activate σ54-RNA polymerase (RNAP), but it lacks conserved residues needed to bind to σ54-RNAP and to hydrolyze adenosine triphosphate, and PvpsL transcription does not require σ54 in vivo. Consequently, the mechanism of this activation has not been clear. Using an in vitro transcription system, we demonstrate activation of PvspL in the presence of VpsR, c-di-GMP and σ70-RNAP. c-di-GMP does not significantly change the affinity of VpsR for PvpsL DNA or the DNase I footprint of VpsR on the DNA, and it is not required for VpsR to dimerize. However, DNase I and KMnO4 footprints reveal that the σ70-RNAP/VpsR/c-di-GMP complex on PvpsL adopts a different conformation from that formed by σ70-RNAP alone, with c-di-GMP or with VpsR. Our results suggest that c-di-GMP is required for VpsR to generate the specific protein–DNA architecture needed for activated transcription, a previously unrecognized role for c-di-GMP in gene expression.
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Affiliation(s)
- Meng-Lun Hsieh
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.,Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Deborah M Hinton
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher M Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
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Wu W, Zhao Z, Luo X, Fan X, Zhuo T, Hu X, Liu J, Zou H. Response regulator VemR regulates the transcription of flagellar rod gene flgG by interacting with σ 54 factor RpoN2 in Xanthomonas citri ssp. citri. MOLECULAR PLANT PATHOLOGY 2019; 20:372-381. [PMID: 30353625 PMCID: PMC6637908 DOI: 10.1111/mpp.12762] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Xanthomonas citri ssp. citri, a polar flagellated bacterium, causes citrus canker disease worldwide. In this study, we found that the X. citri ssp. citri response regulator VemR plays a regulatory role in flagellum-derived cell motility. Deletion of the vemR gene resulted in a reduction in cell motility, as well as reductions in virulence and exopolysaccharide production. Reverse transcription-polymerase chain reaction (RT-PCR) demonstrated that vemR is transcribed in an operon together with rpoN2 and fleQ. In the vemR mutant, the flagellar distal rod gene flgG was significantly down-regulated. Because flgG is also rpoN2 dependent, we speculated that VemR and RpoN2 physically interact, which was confirmed by yeast two-hybrid and maltose-binding protein (MBP) pull-down assays. This suggested that the transcription of flgG is synergistically controlled by VemR and RpoN2. To confirm this, we constructed a vemR and rpoN2 double mutant. In this mutant, the reductions in cell motility and flgG transcription were unable to be restored by the expression of either vemR or rpoN2 alone. In contrast, the expression of both vemR and rpoN2 together in the double mutant restored the wild-type phenotype. Together, our data demonstrate that the response regulator VemR functions as an RpoN2 cognate activator to positively regulate the transcription of the rod gene flgG in X. citri ssp. citri.
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Affiliation(s)
- Wei Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian University Key Laboratory for Plant–Microbe Interaction, College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Zhiwen Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian University Key Laboratory for Plant–Microbe Interaction, College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Xuming Luo
- State Key Laboratory of Plant Genomics, Institute of MicrobiologyChinese Academy of SciencesBeijing100101China
| | - Xiaojing Fan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian University Key Laboratory for Plant–Microbe Interaction, College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Tao Zhuo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian University Key Laboratory for Plant–Microbe Interaction, College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Xun Hu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian University Key Laboratory for Plant–Microbe Interaction, College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Jun Liu
- State Key Laboratory of Plant Genomics, Institute of MicrobiologyChinese Academy of SciencesBeijing100101China
| | - Huasong Zou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian University Key Laboratory for Plant–Microbe Interaction, College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhou350002China
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SfnR2 Regulates Dimethyl Sulfide-Related Utilization in Pseudomonas aeruginosa PAO1. J Bacteriol 2019; 201:JB.00606-18. [PMID: 30478084 DOI: 10.1128/jb.00606-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/20/2018] [Indexed: 12/14/2022] Open
Abstract
Dimethyl sulfide (DMS) is a volatile sulfur compound produced mainly from the degradation of dimethylsulfoniopropionate (DMSP) in marine environments. DMS undergoes oxidation to form dimethyl sulfoxide (DMSO), dimethyl sulfone (DMSO2), and methanesulfonate (MSA), all of which occur in terrestrial environments and are accessible for consumption by various microorganisms. The purpose of the present study was to determine how the enhancer-binding proteins SfnR1 and SfnR2 contribute to the utilization of DMS and its derivatives in Pseudomonas aeruginosa PAO1. First, results from cell growth experiments showed that deletion of either sfnR2 or sfnG, a gene encoding a DMSO2-monooxygenase, significantly inhibits the ability of P. aeruginosa PAO1 to use DMSP, DMS, DMSO, and DMSO2 as sulfur sources. Deletion of the sfnR1 or msuEDC genes, which encode a MSA desulfurization pathway, did not abolish the growth of P. aeruginosa PAO1 on any sulfur compound tested. Second, data collected from β-galactosidase assays revealed that the msuEDC-sfnR1 operon and the sfnG gene are induced in response to sulfur limitation or nonpreferred sulfur sources, such as DMSP, DMS, and DMSO, etc. Importantly, SfnR2 (and not SfnR1) is essential for this induction. Expression of sfnR2 is induced under sulfur limitation but independently of SfnR1 or SfnR2. Finally, the results of this study suggest that the main function of SfnR2 is to direct the initial activation of the msuEDC-sfnR1 operon in response to sulfur limitation or nonpreferred sulfur sources. Once expressed, SfnR1 contributes to the expression of msuEDC-sfnR1, sfnG, and other target genes involved in DMS-related metabolism in P. aeruginosa PAO1.IMPORTANCE Dimethyl sulfide (DMS) is an important environmental source of sulfur, carbon, and/or energy for microorganisms. For various bacteria, including Pseudomonas, Xanthomonas, and Azotobacter, DMS utilization is thought to be controlled by the transcriptional regulator SfnR. Adding more complexity, some bacteria, such as Acinetobacter baumannii, Enterobacter cloacae, and Pseudomonas aeruginosa, possess two, nonidentical SfnR proteins. In this study, we demonstrate that SfnR2 and not SfnR1 is the principal regulator of DMS metabolism in P. aeruginosa PAO1. Results suggest that SfnR1 has a supportive but nonessential role in the positive regulation of genes required for DMS utilization. This study not only enhances our understanding of SfnR regulation but, importantly, also provides a framework for addressing gene regulation through dual SfnR proteins in other bacteria.
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Barroso R, García-Mauriño SM, Tomás-Gallardo L, Andújar E, Pérez-Alegre M, Santero E, Canosa I. The CbrB Regulon: Promoter dissection reveals novel insights into the CbrAB expression network in Pseudomonas putida. PLoS One 2018; 13:e0209191. [PMID: 30557364 PMCID: PMC6296734 DOI: 10.1371/journal.pone.0209191] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/30/2018] [Indexed: 11/18/2022] Open
Abstract
CbrAB is a high ranked global regulatory system exclusive of the Pseudomonads that responds to carbon limiting conditions. It has become necessary to define the particular regulon of CbrB and discriminate it from the downstream cascades through other regulatory components. We have performed in vivo binding analysis of CbrB in P. putida and determined that it directly controls the expression of at least 61 genes; 20% involved in regulatory functions, including the previously identified CrcZ and CrcY small regulatory RNAs. The remaining are porines or transporters (20%), metabolic enzymes (16%), activities related to protein translation (5%) and orfs of uncharacterised function (38%). Amongst the later, we have selected the operon PP2810-13 to make an exhaustive analysis of the CbrB binding sequences, together with those of crcZ and crcY. We describe the implication of three independent non-palindromic subsites with a variable spacing in three different targets; CrcZ, CrcY and operon PP2810-13 in the CbrAB activation. CbrB is a quite peculiar σN-dependent activator since it is barely dependent on phosphorylation for transcriptional activation. With the depiction of the precise contacts of CbrB with the DNA, the analysis of the multimerisation status and its dependence on other factors such as RpoN o IHF, we propose a model of transcriptional activation.
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Affiliation(s)
- Rocío Barroso
- Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo/ Consejo Superior de Investigaciones Científicas/ Junta de Andalucía, Seville, Spain
| | - Sofía M. García-Mauriño
- Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo/ Consejo Superior de Investigaciones Científicas/ Junta de Andalucía, Seville, Spain
| | | | - Eloísa Andújar
- Genomics unit, CABIMER/ CSIC/ Universidad de Sevilla/ Universidad Pablo de Olavide/ Junta de Andalucía, Seville, Spain
| | - Mónica Pérez-Alegre
- Genomics unit, CABIMER/ CSIC/ Universidad de Sevilla/ Universidad Pablo de Olavide/ Junta de Andalucía, Seville, Spain
| | - Eduardo Santero
- Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo/ Consejo Superior de Investigaciones Científicas/ Junta de Andalucía, Seville, Spain
| | - Inés Canosa
- Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo/ Consejo Superior de Investigaciones Científicas/ Junta de Andalucía, Seville, Spain
- * E-mail:
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Bae N, Park HJ, Park H, Kim M, Do E, Han SW. Elucidating Functions of FleQ in Xanthomonas oryzae pv . oryzae by Comparative Proteomic and Phenotypic Analyses. Int J Mol Sci 2018; 19:ijms19103038. [PMID: 30301162 PMCID: PMC6213323 DOI: 10.3390/ijms19103038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 01/03/2023] Open
Abstract
To acclimate to different environments, gene expression has to be controlled using diverse transcriptional activators. FleQ activates σ54-dependent transcription initiation and regulates flagellar biosynthesis and other mechanisms in several bacteria. Xanthomonas oryzae pv. oryzae (Xoo), which is a causal agent of bacterial leaf blight on rice, lacking FleQ loses swimming motility and virulence is not altered. However, other biological mechanisms related with FleQ in Xoo are unknown. In this study, we generated the FleQ-overexpressing strain, Xoo(FleQ), and knockout mutant, XooΔfleQ. To predict the mechanisms affected by FleQ, label-free shotgun comparative proteomics was carried out. Based on proteomic results, we performed diverse phenotypic assays. Xoo(FleQ) had reduced ability to elicit disease symptoms and exopolysaccharide production. Additionally, the ability of XooΔfleQ(EV) (empty vector) and Xoo(FleQ) to form biofilm was decreased. Swarming motility of XooΔfleQ(EV) was abolished, but was only reduced for Xoo(FleQ). Additionally, abnormal twitching motility was observed in both strains. Siderophore production of Xoo(FleQ) was enhanced in iron-rich conditions. The proteomic and phenotypic analyses revealed that FleQ is involved in flagellar-dependent motility and other mechanisms, including symptom development, twitching motility, exopolysaccharide production, biofilm formation, and siderophore production. Thus, this study provides fundamental information about a σ54-dependent transcription activator in Xoo.
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Affiliation(s)
- Nahee Bae
- Department of Integrative Plant Science, Chung-Ang University, Anseong 17456, Korea.
| | - Hye-Jee Park
- Department of Integrative Plant Science, Chung-Ang University, Anseong 17456, Korea.
| | - Hanbi Park
- Department of Integrative Plant Science, Chung-Ang University, Anseong 17456, Korea.
| | - Minyoung Kim
- Department of Integrative Plant Science, Chung-Ang University, Anseong 17456, Korea.
| | - Eunsoo Do
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17456, Korea.
| | - Sang-Wook Han
- Department of Integrative Plant Science, Chung-Ang University, Anseong 17456, Korea.
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Ray S, Panjikar S, Anand R. Design of Protein-Based Biosensors for Selective Detection of Benzene Groups of Pollutants. ACS Sens 2018; 3:1632-1638. [PMID: 30084640 DOI: 10.1021/acssensors.8b00190] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Benzene and its derivatives form a class of priority pollutants whose exposure poses grave risk to human health. Since benzene lacks active functional groups, devising specific sensors for its direct detection from a milieu of aromatics has remained a daunting task. Here, we report three engineered protein-based biosensors that exclusively and specifically detect benzene and its derivatives up to a detection limit of 0.3 ppm. Further, the biosensor design has been engineered to create templates that possess the ability to specifically discriminate between alkyl substituted benzene derivatives; such as toluene, m-xylene, and mesitylene. Interference tests with simulated wastewater samples reveal that the engineered biosensors can selectively detect a specific benzene compound in water samples containing a milieu of high concentrations of commonly occurring pollutants. This work demonstrates the potential of structure guided protein engineering as a competent strategy toward design of selective biosensors for direct detection of benzene group of pollutants from real time environmental samples.
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Affiliation(s)
- Shamayeeta Ray
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra India
| | - Santosh Panjikar
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
- Australian Synchrotron, Victoria 3168, Australia
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra India
- Wadhwani Research Center for Bioengineering, IIT Bombay, Mumbai 400076, India
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Liu M, Chang W, Fan Y, Sun W, Qu C, Zhang K, Liu L, Xu X, Tang Z, Li J, Lu K. Genome-Wide Identification and Characterization of NODULE-INCEPTION-Like Protein (NLP) Family Genes in Brassica napus. Int J Mol Sci 2018; 19:E2270. [PMID: 30072649 PMCID: PMC6121332 DOI: 10.3390/ijms19082270] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 07/30/2018] [Indexed: 12/30/2022] Open
Abstract
NODULE-INCEPTION-like proteins (NLPs) are conserved, plant-specific transcription factors that play crucial roles in responses to nitrogen deficiency. However, the evolutionary relationships and characteristics of NLP family genes in Brassica napus are unclear. In this study, we identified 31 NLP genes in B. napus, including 16 genes located in the A subgenome and 15 in the C subgenome. Subcellular localization predictions indicated that most BnaNLP proteins are localized to the nucleus. Phylogenetic analysis suggested that the NLP gene family could be divided into three groups and that at least three ancient copies of NLP genes existed in the ancestor of both monocots and dicots prior to their divergence. The ancestor of group III NLP genes may have experienced duplication more than once in the Brassicaceae species. Three-dimensional structural analysis suggested that 14 amino acids in BnaNLP7-1 protein are involved in DNA binding, whereas no binding sites were identified in the two RWP-RK and PB1 domains conserved in BnaNLP proteins. Expression profile analysis indicated that BnaNLP genes are expressed in most organs but tend to be highly expressed in a single organ. For example, BnaNLP6 subfamily members are primarily expressed in roots, while the four BnaNLP7 subfamily members are highly expressed in leaves. BnaNLP genes also showed different expression patterns in response to nitrogen-deficient conditions. Under nitrogen deficiency, all members of the BnaNLP1/4/5/9 subfamilies were upregulated, all BnaNLP2/6 subfamily members were downregulated, and BnaNLP7/8 subfamily members showed various expression patterns in different organs. These results provide a comprehensive evolutionary history of NLP genes in B. napus, and insight into the biological functions of BnaNLP genes in response to nitrogen deficiency.
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Affiliation(s)
- Miao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Wei Chang
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Shennong Class, Southwest University, Beibei, Chongqing 400715, China.
| | - Yonghai Fan
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Wei Sun
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Xingfu Xu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Zhanglin Tang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
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Tanner AW, Carabetta VJ, Dubnau D. ClpC and MecA, components of a proteolytic machine, prevent Spo0A-P-dependent transcription without degradation. Mol Microbiol 2018; 108:178-186. [PMID: 29446505 PMCID: PMC5897911 DOI: 10.1111/mmi.13928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2018] [Indexed: 01/23/2023]
Abstract
In Bacillus subtilis, a proteolytic machine composed of MecA, ClpC and ClpP degrades the transcription factor ComK, controlling its accumulation during growth. MecA also inhibits sporulation and biofilm formation by down-regulating spoIIG and sinI, genes that are dependent for their transcription on the phosphorylated protein Spo0A-P. Additionally, MecA has been shown to interact in vitro with Spo0A. Although the inhibitory effect on transcription requires MecA's binding partner ClpC, inhibition is not accompanied by the degradation of Spo0A, pointing to a previously unsuspected regulatory mechanism involving these proteins. Here, we further investigate the MecA and ClpC effects on Spo0A-P-dependent transcription. We show that MecA inhibits the transcription of several Spo0A-P activated genes, but fails to de-repress several Spo0A-P repressed promoters. This demonstrates that MecA and ClpC do not act by preventing the binding of Spo0A-P to its target promoters. Consistent with this, MecA by itself has no effect in vitro on the transcription from PspoIIG while the addition of both MecA and ClpC has a strong inhibitory effect. A complex of MecA and ClpC likely binds to Spo0A-P on its target promoters, preventing the activation of transcription. Thus, components of a degradative machine have been harnessed to directly repress transcription.
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Affiliation(s)
- Andrew W. Tanner
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Valerie J. Carabetta
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - David Dubnau
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
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Wang Z, Zhang L, Sun C, Gu R, Mi G, Yuan L. Phylogenetic, expression and functional characterizations of the maize NLP transcription factor family reveal a role in nitrate assimilation and signaling. PHYSIOLOGIA PLANTARUM 2018; 163:269-281. [PMID: 29364528 DOI: 10.1111/ppl.12696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/07/2018] [Accepted: 01/17/2018] [Indexed: 05/09/2023]
Abstract
Although nitrate represents an important nitrogen (N) source for maize, a major crop of dryland areas, the molecular mechanisms of nitrate uptake and assimilation remain poorly understood. Here, we identified nine maize NIN-like protein (ZmNLP) genes and analyzed the function of one member, ZmNLP3.1, in nitrate nutrition and signaling. The NLP family genes were clustered into three clades in a phylogenic tree. Comparative genomic analysis showed that most ZmNLP genes had collinear relationships to the corresponding NLPs in rice, and that the expansion of the ZmNLP family resulted from segmental duplications in the maize genome. Quantitative PCR analysis revealed the expression of ZmNLP2.1, ZmNLP2.2, ZmNLP3.1, ZmNLP3.2, ZmNLP3.3, and ZmNLP3.4 was induced by nitrate in maize roots. The function of ZmNLP3.1 was investigated by overexpressing it in the Arabidopsis nlp7-1 mutant, which is defective in the AtNLP7 gene for nitrate signaling and assimilation. Ectopic expression of ZmNLP3.1 restored the N-deficient phenotypes of nlp7-1 under nitrate-replete conditions in terms of shoot biomass, root morphology and nitrate assimilation. Furthermore, the nitrate induction of NRT2.1, NIA1, and NiR1 gene expression was recovered in the 35S::ZmNLP3.1/nlp7-1 transgenic lines, indicating that ZmNLP3.1 plays essential roles in nitrate signaling. Taken together, these results suggest that ZmNLP3.1 plays an essential role in regulating nitrate signaling and assimilation processes, and represents a valuable candidate for developing transgenic maize cultivars with high N-use efficiency.
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Affiliation(s)
- Zhangkui Wang
- Key Laboratory of Plant-Soil Interactions, MOE, Center for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Lei Zhang
- Key Laboratory of Plant-Soil Interactions, MOE, Center for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Beijing Soil Fertilizer Extension Service Station, Beijing, 100029, China
| | - Ci Sun
- Key Laboratory of Plant-Soil Interactions, MOE, Center for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Riliang Gu
- Key Laboratory of Plant-Soil Interactions, MOE, Center for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Guohua Mi
- Key Laboratory of Plant-Soil Interactions, MOE, Center for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Lixing Yuan
- Key Laboratory of Plant-Soil Interactions, MOE, Center for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
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Deng C, Li J, Shin HD, Du G, Chen J, Liu L. Efficient expression of cyclodextrin glycosyltransferase from Geobacillus stearothermophilus in Escherichia coli by promoter engineering and downstream box evolution. J Biotechnol 2017; 266:77-83. [PMID: 29247671 DOI: 10.1016/j.jbiotec.2017.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/14/2017] [Accepted: 12/09/2017] [Indexed: 11/28/2022]
Abstract
Cyclodextrin glycosyltransferase (CGTase) catalyzes hydrolysis, cyclization, coupling, and disproportionation reactions and is widely used in the starch processing industry. In this work, the expression of CGTase from Geobacillus stearothermophilus in Escherichia coli BL21 (DE3) was significantly improved by promoter engineering and downstream box evolution. Firstly, the effects of the promoter type (PT7, Ptrp, PlacUV5, and the hybrid promoters PtacI and PtacII) and spacer sequence on the expression of CGTase were examined. PtacI demonstrated the highest rate of transcriptional activity, which was 4.4-, 7.1-, 3.3-, and 1.5-fold greater than that of PT7, Ptrp, PlacUV5, and PtacII, respectively. The spacer sequence of the promoter was optimized using a degenerate base library, and the GC content of the spacer was found to be inversely proportional to CGTase expression. In addition, CGTase expression was higher when TG:CA and TA:TA dimers were present in the spacer sequence. Under the control of the PtacI promoter with an optimized spacer sequence, extracellular CGTase activity reached 170.6 U/mL, which was seven times higher than that of the original strain (25.2 U/mL). Directed evolution of the downstream box sequence was then performed by randomization of the sequence using degenerate codons, similarly as for the optimization of the spacer sequence. After optimizing the downstream box sequence, CGTase activity increased from 170.6 to 214 U/mL. The results obtained here indicate that in addition to promoter type, the spacer sequence of the promoter and the downstream box are important target elements for improved gene expression.
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Affiliation(s)
- Chen Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Hyun-Dong Shin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, 30332, USA
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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Liu J, Lopez N, Ahn Y, Goldberg T, Bromberg Y, Kerkhof LJ, Häggblom MM. Novel reductive dehalogenases from the marine sponge associated bacterium Desulfoluna spongiiphila. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:537-549. [PMID: 28618195 DOI: 10.1111/1758-2229.12556] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 05/08/2017] [Accepted: 06/03/2017] [Indexed: 06/07/2023]
Abstract
Desulfoluna spongiiphila strain AA1 is an organohalide respiring bacterium, isolated from the marine sponge Aplysina aerophoba, that can use brominated and iodinated phenols, in addition to sulfate and thiosulfate as terminal electron acceptors. The genome of Desulfoluna spongiiphila strain AA1 is approximately 6.5 Mb. Three putative reductive dehalogenase (rdhA) genes involved in respiratory metabolism of organohalides were identified within the sequence. Conserved motifs found in respiratory reductive dehalogenases (a twin arginine translocation signal sequence and two iron-sulfur clusters) were present in all three putative AA1 rdhA genes. Transcription of one of the three rdhA genes was significantly upregulated during respiration of 2,6-dibromophenol and sponge extracts. Strain AA1 appears to have the ability to synthesize cobalamin, the key cofactor of most characterized reductive dehalogenase enzymes. The genome contains genes involved in cobalamin synthesis and uptake and can grow without cobalamin supplementation. Identification of this target gene associated with debromination lays the foundation for understanding how dehalogenating bacteria control the fate of organohalide compounds in sponges and their role in a symbiotic organobromine cycle. In the sponge environment, D. spongiiphila strain AA1 may thus take advantage of both brominated compounds and sulfate as electron acceptors for respiration.
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Affiliation(s)
- Jie Liu
- Departments of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Nora Lopez
- Departments of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Youngbeom Ahn
- Departments of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Tatyana Goldberg
- Department for Bioinformatics and Computational Biology, Technical University Munich, Garching, 85748, Germany
| | - Yana Bromberg
- Departments of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Lee J Kerkhof
- Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Max M Häggblom
- Departments of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
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Liu Y, Lardi M, Pedrioli A, Eberl L, Pessi G. NtrC-dependent control of exopolysaccharide synthesis and motility in Burkholderia cenocepacia H111. PLoS One 2017; 12:e0180362. [PMID: 28662146 PMCID: PMC5491218 DOI: 10.1371/journal.pone.0180362] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/14/2017] [Indexed: 11/18/2022] Open
Abstract
Burkholderia cenocepacia is a versatile opportunistic pathogen that survives in a wide variety of environments, which can be limited in nutrients such as nitrogen. We have previously shown that the sigma factor σ54 is involved in the control of nitrogen assimilation and virulence in B. cenocepacia H111. In this work, we investigated the role of the σ54 enhancer binding protein NtrC in response to nitrogen limitation and in the pathogenicity of H111. Of 95 alternative nitrogen sources tested the ntrC showed defects in the utilisation of nitrate, urea, L-citrulline, acetamide, DL-lactamide, allantoin and parabanic acid. RNA-Seq and phenotypic analyses of an ntrC mutant strain showed that NtrC positively regulates two important phenotypic traits: exopolysaccharide (EPS) production and motility. However, the ntrC mutant was not attenuated in C. elegans virulence.
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Affiliation(s)
- Yilei Liu
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Martina Lardi
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Alessandro Pedrioli
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- * E-mail: (LE); (GP)
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- * E-mail: (LE); (GP)
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Regulation of a Glycerol-Induced Quinoprotein Alcohol Dehydrogenase by σ 54 and a LuxR-Type Regulator in Azospirillum brasilense Sp7. J Bacteriol 2017; 199:JB.00035-17. [PMID: 28439037 DOI: 10.1128/jb.00035-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/08/2017] [Indexed: 02/02/2023] Open
Abstract
Azospirillum brasilense Sp7 uses glycerol as a carbon source for growth and nitrogen fixation. When grown in medium containing glycerol as a source of carbon, it upregulates the expression of a protein which was identified as quinoprotein alcohol dehydrogenase (ExaA). Inactivation of exaA adversely affects the growth of A. brasilense on glycerol. A determination of the transcription start site of exaA revealed an RpoN-dependent -12/-24 promoter consensus. The expression of an exaA::lacZ fusion was induced maximally by glycerol and was dependent on σ54 Bioinformatic analysis of the sequence flanking the -12/-24 promoter revealed a 17-bp sequence motif with a dyad symmetry of 6 nucleotides upstream of the promoter, the disruption of which caused a drastic reduction in promoter activity. The electrophoretic mobility of a DNA fragment containing the 17-bp sequence motif was retarded by purified EraR, a LuxR-type transcription regulator that is transcribed divergently from exaA EraR also showed a positive interaction with RpoN in two-hybrid and pulldown assays.IMPORTANCE Quinoprotein alcohol dehydrogenase (ExaA) plays an important role in the catabolism of alcohols in bacteria. Although exaA expression is thought to be regulated by a two-component system consisting of EraS and EraR, the mechanism of regulation was not known. This study shows the details of the regulation of expression of the exaA gene in A. brasilense We have shown here that exaA of A. brasilense is maximally induced by glycerol and harbors a σ54-dependent promoter. The response regulator EraR binds to an inverted repeat located upstream of the exaA promoter. This study shows that a LuxR-type response regulator (EraR) binds upstream of the exaA gene and physically interacts with σ54 The unique feature of this regulation is that EraR is a LuxR-type transcription regulator that lacks the GAFTGA motif, a characteristic feature of the enhancer binding proteins that are known to interact with σ54 in other bacteria.
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DdaR (PA1196) Regulates Expression of Dimethylarginine Dimethylaminohydrolase for the Metabolism of Methylarginines in Pseudomonas aeruginosa PAO1. J Bacteriol 2017; 199:JB.00001-17. [PMID: 28167521 DOI: 10.1128/jb.00001-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/31/2017] [Indexed: 11/20/2022] Open
Abstract
Dimethylarginine dimethylaminohydrolases (DDAHs) catalyze the hydrolysis of methylarginines to yield l-citrulline and methylamines as products. DDAHs and their central roles in methylarginine metabolism have been characterized for eukaryotic cells. While DDAHs are known to exist in some bacteria, including Streptomyces coelicolor and Pseudomonas aeruginosa, the physiological importance and genetic regulation of bacterial DDAHs remain poorly understood. To provide some insight into bacterial methylarginine metabolism, this study focused on identifying the key elements or factors regulating DDAH expression in P. aeruginosa PAO1. First, results revealed that P. aeruginosa can utilize NG ,NG -dimethyl-l-arginine (ADMA) as a sole source of nitrogen but not carbon. Second, expression of the ddaH gene was observed to be induced in the presence of methylarginines, including NG -monomethyl-l-arginine (l-NMMA) and ADMA. Third, induction of the ddaH gene was shown to be achieved through a mechanism consisting of the putative enhancer-binding protein PA1196 and the alternative sigma factor RpoN. Both PA1196 and RpoN were essential for the expression of the ddaH gene in response to methylarginines. On the basis of the results of this study, PA1196 was given the name DdaR, for dimethylarginine dimethylaminohydrolase regulator. Interestingly, DdaR and its target ddaH gene are conserved only among P. aeruginosa strains, suggesting that this particular Pseudomonas species has evolved to utilize methylarginines from its environment.IMPORTANCE Methylated arginine residues are common constituents of eukaryotic proteins. During proteolysis, methylarginines are released in their free forms and become accessible nutrients for bacteria to utilize as growth substrates. In order to have a clearer and better understanding of this process, we explored methylarginine utilization in the metabolically versatile bacterium Pseudomonas aeruginosa PAO1. Our results show that the transcriptional regulator DdaR (PA1196) and the sigma factor RpoN positively regulate expression of dimethylarginine dimethylaminohydrolases (DDAHs) in response to exogenous methylarginines. DDAH is the central enzyme of methylarginine degradation, and its transcriptional regulation by DdaR-RpoN is expected to be conserved among P. aeruginosa strains.
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Wong KS, Bhandari V, Janga SC, Houry WA. The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex. J Mol Biol 2017; 429:324-344. [DOI: 10.1016/j.jmb.2016.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/05/2016] [Accepted: 12/05/2016] [Indexed: 01/02/2023]
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Li LF, Fu LJ, Lin JQ, Pang X, Liu XM, Wang R, Wang ZB, Lin JQ, Chen LX. The σ54-dependent two-component system regulating sulfur oxidization (Sox) system in Acidithiobacillus caldus and some chemolithotrophic bacteria. Appl Microbiol Biotechnol 2016; 101:2079-2092. [DOI: 10.1007/s00253-016-8026-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/20/2016] [Accepted: 11/23/2016] [Indexed: 11/30/2022]
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Spontaneous Reversions of an Evolutionary Trait Loss Reveal Regulators of a Small RNA That Controls Multicellular Development in Myxobacteria. J Bacteriol 2016; 198:3142-3151. [PMID: 27621281 PMCID: PMC5105895 DOI: 10.1128/jb.00389-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/26/2016] [Indexed: 11/20/2022] Open
Abstract
Lost traits can reevolve, but the probability of trait reversion depends partly on a trait's genetic complexity. Myxobacterial fruiting body development is a complex trait controlled by the small RNA (sRNA) Pxr, which blocks development under conditions of nutrient abundance. In developmentally proficient strains of Myxococcus xanthus, starvation relaxes the inhibition by Pxr, thereby allowing development to proceed. In contrast, the lab-evolved strain OC does not develop because it fails to relay an early starvation signal that alleviates inhibition by Pxr. A descendant of OC, strain PX, previously reevolved developmental proficiency via a mutation in pxr that inactivates its function. A single-colony screen was used to test whether reversion of OC to developmental proficiency occurs only by mutation of pxr or might also occur through alternative regulatory loci. Five spontaneous mutants of OC that exhibited restored development were isolated, and all five showed defects in Pxr synthesis, structure, or processing, including one that incurred an eight-nucleotide deletion in pxr Two mutations occurred in the σ54 response regulator (RR) gene MXAN_1078 (named pxrR here), immediately upstream of pxr PxrR was found to positively regulate pxr transcription, presumably via the σ54 promoter of pxr Two other mutations were identified in a histidine kinase (HK) gene (MXAN_1077; named pxrK here) immediately upstream of pxrR Evolutionarily, the rate of trait restoration documented in this study suggests that reversion of social defects in natural microbial populations may be common. Molecularly, these results suggest a mechanism by which the regulatory functions of an HK-RR two-component signaling system and an sRNA are integrated to control initiation of myxobacterial development. IMPORTANCE Many myxobacteria initiate a process of multicellular fruiting body development upon starvation, but key features of the regulatory network controlling the transition from growth to development remain obscure. Previous work with Myxococcus xanthus identified the first small RNA (sRNA) regulator (Pxr) known to serve as a gatekeeper in this life history transition, as it blocks development when nutrients are abundant. In the present study, a screen for spontaneous mutants of M. xanthus was developed that revealed a two-component system operon (encoding a histidine kinase and a σ54 response regulator) associated with the production and processing of Pxr sRNA. This discovery broadens our knowledge of early developmental gene regulation and also represents an evolutionary integration of two-component signaling and sRNA gene regulation to control a bacterial social trait.
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Tu N, Carroll RK, Weiss A, Shaw LN, Nicolas G, Thomas S, Lima A, Okaro U, Anderson B. A family of genus-specific RNAs in tandem with DNA-binding proteins control expression of the badA major virulence factor gene in Bartonella henselae. Microbiologyopen 2016; 6. [PMID: 27790856 PMCID: PMC5387305 DOI: 10.1002/mbo3.420] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/21/2016] [Accepted: 09/28/2016] [Indexed: 12/28/2022] Open
Abstract
Bartonella henselae is a gram‐negative zoonotic bacterium that causes infections in humans including endocarditis and bacillary angiomatosis. B. henselae has been shown to grow as large aggregates and form biofilms in vitro. The aggregative growth and the angiogenic host response requires the trimeric autotransporter adhesin BadA. We examined the transcriptome of the Houston‐1 strain of B. henselae using RNA‐seq revealing nine novel, highly‐expressed intergenic transcripts (Bartonella regulatory transcript, Brt1‐9). The Brt family of RNAs is unique to the genus Bartonella and ranges from 194 to 203 nucleotides with high homology and stable predicted secondary structures. Immediately downstream of each of the nine RNA genes is a helix‐turn‐helix DNA‐binding protein (transcriptional regulatory protein, Trp1‐9) that is poorly transcribed under the growth conditions used for RNA‐seq. Using knockdown or overexpressing strains, we show a role of both the Brt1 and Trp1 in the regulation of badA and also in biofilm formation. Based on these data, we hypothesize that Brt1 is a trans‐acting sRNA that also serves as a cis‐acting riboswitch to control the expression of badA. This family of RNAs together with the downstream Trp DNA‐binding proteins represents a novel coordinated regulatory circuit controlling expression of virulence‐associated genes in the bartonellae.
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Affiliation(s)
- Nhan Tu
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Ronan K Carroll
- Department of Biological Sciences, Ohio University, Athens, OH, USA
| | - Andy Weiss
- Department of Cellular, Molecular and Microbiology, College of Arts and Sciences, University of South Florida, Tampa, FL, USA
| | - Lindsey N Shaw
- Department of Cellular, Molecular and Microbiology, College of Arts and Sciences, University of South Florida, Tampa, FL, USA
| | - Gael Nicolas
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Sarah Thomas
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Amorce Lima
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Udoka Okaro
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Burt Anderson
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
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Ouyang Z, Zhou J. The putative Walker A and Walker B motifs of Rrp2 are required for the growth of Borrelia burgdorferi. Mol Microbiol 2016; 103:86-98. [PMID: 27696536 DOI: 10.1111/mmi.13545] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2016] [Indexed: 01/09/2023]
Abstract
Rrp2 encodes a putative bacterial enhancer binding protein (bEBP) in Borrelia burgdorferi. Point mutation (G239C) of Rrp2 abolishes the transcriptional activation of σ54 -dependent rpoS. In contrast to canonical bEBPs that are dispensable for bacterial growth, Rrp2 is essential for borrelial growth in BSK medium. It has been believed that Rrp2's ATPase activity is not required for cell growth, but experimental evidence supporting this notion has been lacking. In particular, it has remained unclear whether the residue G239 is involved in Rrp2's presumptive ATPase activity. To address these information gaps, we examined the roles of Rrp2's potential strategic signatures including the G239 residue and the putative Walker A and Walker B motifs. Herein it was showed that Rrp2 has ATP binding and hydrolysis activities engendered by the Walker A and B motifs respectively. However, these activities were not significantly impaired by a G239C mutation. Further mutagenesis analyses indicated that Rrp2's Walker A and B motifs are required for borrelial growth; mutations of key residues in these two motifs were lethal to B. burgdorferi. The combined data suggest that the Walker A and Walker B motifs of Rrp2 are involved in the control of another unknown RpoS-independent gene product(s) associated with borrelial replication.
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Affiliation(s)
- Zhiming Ouyang
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jianli Zhou
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
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Siegel AR, Wemmer DE. Role of the σ 54 Activator Interacting Domain in Bacterial Transcription Initiation. J Mol Biol 2016; 428:4669-4685. [PMID: 27732872 DOI: 10.1016/j.jmb.2016.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/03/2016] [Accepted: 10/04/2016] [Indexed: 01/05/2023]
Abstract
Bacterial sigma factors are subunits of RNA polymerase that direct the holoenzyme to specific sets of promoters in the genome and are a central element of regulating transcription. Most polymerase holoenzymes open the promoter and initiate transcription rapidly after binding. However, polymerase containing the members of the σ54 family must be acted on by a transcriptional activator before DNA opening and initiation occur. A key domain in these transcriptional activators forms a hexameric AAA+ ATPase that acts through conformational changes brought on by ATP hydrolysis. Contacts between the transcriptional activator and σ54 are primarily made through an N-terminal σ54 activator interacting domain (AID). To better understand this mechanism of bacterial transcription initiation, we characterized the σ54 AID by NMR spectroscopy and other biophysical methods and show that it is an intrinsically disordered domain in σ54 alone. We identified a minimal construct of the Aquifex aeolicus σ54 AID that consists of two predicted helices and retains native-like binding affinity for the transcriptional activator NtrC1. Using the NtrC1 ATPase domain, bound with the non-hydrolyzable ATP analog ADP-beryllium fluoride, we studied the NtrC1-σ54 AID complex using NMR spectroscopy. We show that the σ54 AID becomes structured after associating with the core loops of the transcriptional activators in their ATP state and that the primary site of the interaction is the first predicted helix. Understanding this complex, formed as the first step toward initiation, will help unravel the mechanism of σ54 bacterial transcription initiation.
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Affiliation(s)
- Alexander R Siegel
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
| | - David E Wemmer
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, CA 94720, USA.
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Bonato P, Alves LR, Osaki JH, Rigo LU, Pedrosa FO, Souza EM, Zhang N, Schumacher J, Buck M, Wassem R, Chubatsu LS. The NtrY-NtrX two-component system is involved in controlling nitrate assimilation in Herbaspirillum seropedicae strain SmR1. FEBS J 2016; 283:3919-3930. [PMID: 27634462 DOI: 10.1111/febs.13897] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/15/2016] [Accepted: 09/13/2016] [Indexed: 10/21/2022]
Abstract
Herbaspirillum seropedicae is a diazotrophic β-Proteobacterium found endophytically associated with gramineae (Poaceae or graminaceous plants) such as rice, sorghum and sugar cane. In this work we show that nitrate-dependent growth in this organism is regulated by the master nitrogen regulatory two-component system NtrB-NtrC, and by NtrY-NtrX, which functions to specifically regulate nitrate metabolism. NtrY is a histidine kinase sensor protein predicted to be associated with the membrane and NtrX is the response regulator partner. The ntrYntrX genes are widely distributed in Proteobacteria. In α-Proteobacteria they are frequently located downstream from ntrBC, whereas in β-Proteobacteria these genes are located downstream from genes encoding an RNA methyltransferase and a proline-rich protein with unknown function. The NtrX protein of α-Proteobacteria has an AAA+ domain, absent in those from β-Proteobacteria. An ntrY mutant of H. seropedicae showed the wild-type nitrogen fixation phenotype, but the nitrate-dependent growth was abolished. Gene fusion assays indicated that NtrY is involved in the expression of genes coding for the assimilatory nitrate reductase as well as the nitrate-responsive two-component system NarX-NarL (narK and narX promoters, respectively). The purified NtrX protein was capable of binding the narK and narX promoters, and the binding site at the narX promoter for the NtrX protein was determined by DNA footprinting. In silico analyses revealed similar sequences in other promoter regions of H. seropedicae that are related to nitrate assimilation, supporting the role of the NtrY-NtrX system in regulating nitrate metabolism in H. seropedicae.
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Affiliation(s)
- Paloma Bonato
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Lysangela R Alves
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Juliana H Osaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Liu U Rigo
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Fabio O Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Emanuel M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Nan Zhang
- Department of Life Sciences, Imperial College London, UK
| | | | - Martin Buck
- Department of Life Sciences, Imperial College London, UK
| | - Roseli Wassem
- Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil
| | - Leda S Chubatsu
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
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