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You D, Zhao LC, Fu Y, Peng ZY, Chen ZQ, Ye BC. Allosteric regulation by c-di-AMP modulates a complete N-acetylglucosamine signaling cascade in Saccharopolyspora erythraea. Nat Commun 2024; 15:3825. [PMID: 38714645 PMCID: PMC11076491 DOI: 10.1038/s41467-024-48063-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 04/18/2024] [Indexed: 05/10/2024] Open
Abstract
c-di-AMP is an essential and widespread nucleotide second messenger in bacterial signaling. For most c-di-AMP synthesizing organisms, c-di-AMP homeostasis and the molecular mechanisms pertaining to its signal transduction are of great concern. Here we show that c-di-AMP binds the N-acetylglucosamine (GlcNAc)-sensing regulator DasR, indicating a direct link between c-di-AMP and GlcNAc signaling. Beyond its foundational role in cell-surface structure, GlcNAc is attractive as a major nutrient and messenger molecule regulating multiple cellular processes from bacteria to humans. We show that increased c-di-AMP levels allosterically activate DasR as a master repressor of GlcNAc utilization, causing the shutdown of the DasR-mediated GlcNAc signaling cascade and leading to a consistent enhancement in the developmental transition and antibiotic production in Saccharopolyspora erythraea. The expression of disA, encoding diadenylate cyclase, is directly repressed by the regulator DasR in response to GlcNAc signaling, thus forming a self-sustaining transcriptional feedback loop for c-di-AMP synthesis. These findings shed light on the allosteric regulation by c-di-AMP, which appears to play a prominent role in global signal integration and c-di-AMP homeostasis in bacteria and is likely widespread in streptomycetes that produce c-di-AMP.
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Affiliation(s)
- Di You
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Liu-Chang Zhao
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yu Fu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhi-Yao Peng
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Zong-Qin Chen
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China.
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2
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Vockenhuber MP, Hoetzel J, Maurer LM, Fröhlich P, Weiler S, Muller YA, Koeppl H, Suess B. A Novel RNA Aptamer as Synthetic Inducer of DasR Controlled Transcription. ACS Synth Biol 2024; 13:319-327. [PMID: 38127784 DOI: 10.1021/acssynbio.3c00553] [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] [Indexed: 12/23/2023]
Abstract
Progress in the synthetic biology field is driven by the development of new tools for synthetic circuit engineering. Traditionally, the focus has relied on protein-based designs. In recent years, the use of RNA-based tools has tremendously increased, due to their versatile functionality and applicability. A promising class of molecules is RNA aptamers, small, single-stranded RNA molecules that bind to a target molecule with high affinity and specificity. When targeting bacterial repressors, RNA aptamers allow one to add a new layer to an established protein-based regulation. In the present study, we selected an RNA aptamer binding the bacterial repressor DasR, preventing its binding to its operator sequence and activating DasR-controlled transcription in vivo. This was made possible only by the combination of an in vitro selection and subsequent in vivo screening. Next-generation sequencing of the selection process proved the importance of the in vivo screening for the discovery of aptamers functioning in the cell. Mutational and biochemical studies led to the identification of the minimal necessary binding motif. Taken together, the resulting combination of bacterial repressor and RNA aptamer enlarges the synthetic biology toolbox by adding a new level of regulation.
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Affiliation(s)
- Michael-Paul Vockenhuber
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Strasse 14, 35043 Marburg, Germany
| | - Janis Hoetzel
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Lisa-Marie Maurer
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Philipp Fröhlich
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sigrid Weiler
- Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Henkestr. 91, 91052 Erlangen, Germany
| | - Yves A Muller
- Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Henkestr. 91, 91052 Erlangen, Germany
| | - Heinz Koeppl
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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3
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Chauhan NK, Anand A, Sharma A, Dhiman K, Gosain TP, Singh P, Singh P, Khan E, Chattopadhyay G, Kumar A, Sharma D, Ashish, Sharma TK, Singh R. Structural and Functional Characterization of Rv0792c from Mycobacterium tuberculosis: Identifying Small Molecule Inhibitor against HutC Protein. Microbiol Spectr 2023; 11:e0197322. [PMID: 36507689 PMCID: PMC9927256 DOI: 10.1128/spectrum.01973-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In order to adapt in host tissues, microbial pathogens regulate their gene expression through a variety of transcription factors. Here, we have functionally characterized Rv0792c, a HutC homolog from Mycobacterium tuberculosis. In comparison to the parental strain, a strain of M. tuberculosis with a Rv0792c mutant was compromised for survival upon exposure to oxidative stress and infection in guinea pigs. RNA sequencing analysis revealed that Rv0792c regulates the expression of genes involved in stress adaptation and virulence of M. tuberculosis. Solution small-angle X-ray scattering (SAXS) data-steered model building confirmed that the C-terminal region plays a pivotal role in dimer formation. Systematic evolution of ligands by exponential enrichment (SELEX) resulted in the identification of single-strand DNA (ssDNA) aptamers that can be used as a tool to identify small-molecule inhibitors targeting Rv0792c. Using SELEX and SAXS data-based modeling, we identified residues essential for Rv0792c's aptamer binding activity. In this study, we also identified I-OMe-Tyrphostin as an inhibitor of Rv0792c's aptamer and DNA binding activity. The identified small molecule reduced the growth of intracellular M. tuberculosis in macrophages. The present study thus provides a detailed shape-function characterization of a HutC family of transcription factor from M. tuberculosis. IMPORTANCE Prokaryotes encode a large number of GntR family transcription factors that are involved in various fundamental biological processes, including stress adaptation and pathogenesis. Here, we investigated the structural and functional role of Rv0792c, a HutC homolog from M. tuberculosis. We demonstrated that Rv0792c is essential for M. tuberculosis to adapt to oxidative stress and establish disease in guinea pigs. Using a systematic evolution of ligands by exponential enrichment (SELEX) approach, we identified ssDNA aptamers from a random ssDNA library that bound to Rv0792c protein. These aptamers were thoroughly characterized using biochemical and biophysical assays. Using SAXS, we determined the structural model of Rv0792c in both the presence and absence of the aptamers. Further, using a combination of SELEX and SAXS methodologies, we identified I-OMe-Tyrphostin as a potential inhibitor of Rv0792c. Here we provide a detailed functional characterization of a transcription factor belonging to the HutC family from M. tuberculosis.
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Affiliation(s)
- Neeraj Kumar Chauhan
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Anjali Anand
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Arun Sharma
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Kanika Dhiman
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Tannu Priya Gosain
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Prashant Singh
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Padam Singh
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Eshan Khan
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indoregrid.450280.b, Indore, India
| | | | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indoregrid.450280.b, Indore, India
| | - Deepak Sharma
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Ashish
- Institute of Microbial Technologygrid.417641.1, Council of Scientific and Industrial Research, Chandigarh, India
| | - Tarun Kumar Sharma
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
| | - Ramandeep Singh
- Translational Health Science and Technology Institutegrid.464764.3, Faridabad, Haryana, India
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Alonso-Fernández S, Arribas-Díez I, Fernández-García G, González-Quiñónez N, Jensen ON, Manteca A. Quantitative phosphoproteome analysis of Streptomyces coelicolor by immobilized zirconium (IV) affinity chromatography and mass spectrometry reveals novel regulated protein phosphorylation sites and sequence motifs. J Proteomics 2022; 269:104719. [PMID: 36089190 DOI: 10.1016/j.jprot.2022.104719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/25/2022] [Accepted: 09/03/2022] [Indexed: 11/12/2022]
Abstract
Streptomycetes are multicellular gram-positive bacteria that produce many bioactive compounds, including antibiotics, antitumorals and immunosuppressors. The Streptomyces phosphoproteome remains largely uncharted even though protein phosphorylation at Ser/Thr/Tyr is known to modulate morphological differentiation and specialized metabolic processes. We here expand the S. coelicolor phosphoproteome by optimised immobilized zirconium (IV) affinity chromatography and mass spectrometry to identify phosphoproteins at the vegetative and sporulating stages. We mapped 361 phosphorylation sites (41% pSer, 56.2% pThr, 2.8% pTyr) and discovered four novel Thr phosphorylation motifs ("Kxxxx(pT)xxxxK", "DxE(pT)", "D(pT)" and "Exxxxx(pT)") in 351 phosphopeptides derived from 187 phosphoproteins. We identified 154 novel phosphoproteins, thereby almost doubling the number of experimentally verified Streptomyces phosphoproteins. Novel phosphoproteins included cell division proteins (FtsK, CrgA) and specialized metabolism regulators (ArgR, AfsR, CutR and HrcA) that were differentially phosphorylated in the vegetative and in the antibiotic producing sporulating stages. Phosphoproteins involved in primary metabolism included 27 novel ribosomal proteins that were phosphorylated during the vegetative stage. Phosphorylation of these proteins likely participate in the intricate and incompletely understood regulation of Streptomyces development and secondary metabolism. We conclude that Zr(IV)-IMAC is an efficient and sensitive method to study protein phosphorylation and regulation in bacteria and enhance our understanding of bacterial signalling. SIGNIFICANCE: Two thirds of the secondary metabolites used in clinic, especially antibiotics, were discovered in Streptomyces strains. Antibiotic resistance became one of the major challenges in clinic, and new antibiotics are urgently required in clinic. Next-generation sequencing analyses revealed that streptomycetes harbour many cryptic secondary metabolite pathways, i.e. pathways not expressed in the laboratory. Secondary metabolism is tightly connected with hypha differentiation and sporulation, and understanding Streptomyces differentiation is one of the main challenges in industrial microbiology, in order to activate the expression of cryptic pathways in the laboratory. Protein phosphorylation at Ser/Thr/Tyr modulates development and secondary metabolism, but the Streptomyces phosphoproteome is still largely uncharted. Previous S. coelicolor phosphoproteomic studies used TiO2 affinity enrichment and LC-MS/MS identifying a total of 184 Streptomyces phosphoproteins. Here, we used by first time zirconium (IV) affinity chromatography and mass spectrometry, identifying 186 S. coelicolor phosphoproteins. Most of these phosphoproteins (154) were not identified in previous phosphoproteomic studies using TiO2 affinity enrichment. Thereby we almost doubling the number of experimentally verified Streptomyces phosphoproteins. Zr(IV)-IMAC affinity chromatography also worked in E. coli, allowing the identification of phosphoproteins that were not identified by TiO2 affinity chromatography. We conclude that Zr(IV)-IMAC is an efficient and sensitive method for studies of protein phosphorylation and regulation in bacteria to enhance our understanding of bacterial signalling networks. Moreover, the new Streptomyces phosphoproteins identified will contribute to design further works to understand and modulate Streptomyces secondary metabolism activation.
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Affiliation(s)
- Sergio Alonso-Fernández
- Área de Microbiología, Departamento de Biología Funcional, IUOPA, ISPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ignacio Arribas-Díez
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Gemma Fernández-García
- Área de Microbiología, Departamento de Biología Funcional, IUOPA, ISPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Nathaly González-Quiñónez
- Área de Microbiología, Departamento de Biología Funcional, IUOPA, ISPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
| | - Angel Manteca
- Área de Microbiología, Departamento de Biología Funcional, IUOPA, ISPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain.
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5
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Abeywickrama TD, Perera IC. In Silico Characterization and Virtual Screening of GntR/HutC Family Transcriptional Regulator MoyR: A Potential Monooxygenase Regulator in Mycobacterium tuberculosis. BIOLOGY 2021; 10:biology10121241. [PMID: 34943156 PMCID: PMC8698889 DOI: 10.3390/biology10121241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/31/2022]
Abstract
Simple Summary In an era where the world faces new diseases and pathogens, another emerging challenge is neglected pathogens becoming more notorious. Transcriptional regulators play a vital role in the pathogenesis and survival of these pathogens. Hence, characterizing transcriptional regulators, either in vitro or in silico, is of great importance. Here, we present the first structural characterization of a GntR/HutC regulator in Mycobacterium tuberculosis via in silico methods. We have suggested its possible role and potential as a drug target as well as identified possible drug leads that can be used for further improvements. Abstract Mycobacterium tuberculosis is a well-known pathogen due to the emergence of drug resistance associated with it, where transcriptional regulators play a key role in infection, colonization and persistence. The genome of M. tuberculosis encodes many transcriptional regulators, and here we report an in-depth in silico characterization of a GntR regulator: MoyR, a possible monooxygenase regulator. Homology modelling provided a reliable structure for MoyR, showing homology with a HutC regulator DasR from Streptomyces coelicolor. In silico physicochemical analysis revealed that MoyR is a cytoplasmic protein with higher thermal stability and higher pI. Four highly probable binding pockets were determined in MoyR and the druggability was higher in the orthosteric binding site consisting of three conserved critical residues: TYR179, ARG223 and GLU234. Two highly conserved leucine residues were identified in the effector-binding region of MoyR and other HutC homologues, suggesting that these two residues can be crucial for structure stability and oligomerization. Virtual screening of drug leads resulted in four drug-like compounds with greater affinity to MoyR with potential inhibitory effects for MoyR. Our findings support that this regulator protein can be valuable as a therapeutic target that can be used for developing drug leads.
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6
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Tishchenko SV, Mikhailina AO, Lekontseva NV, Stolboushkina EA, Nikonova EY, Nikonov OS, Nikulin AD. Structural Investigations of RNA–Protein Complexes in Post-Ribosomal Era. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Structural studies of RNA–protein complexes are important for understanding many molecular mechanisms occurring in cells (e.g., regulation of protein synthesis and RNA-chaperone activity of proteins). Various objects investigated at the Institute of Protein Research of the Russian Academy of Sciences are considered. Based on the analysis of the structures of the complexes of the ribosomal protein L1 with specific regions on both mRNA and rRNA, the principles of regulation of the translation of the mRNA of its own operon are presented. The studies of the heterotrimeric translation initiation factor IF2 of archaea and eukaryotes are described, and the data on the interaction of glycyl-tRNA-synthetase with viral IRES are reported. The results of studying the interaction of RNA molecules with one of functionally important sites of the Hfq protein are presented, and the differences in the RNA-binding properties of the Hfq and archaeal Lsm proteins are revealed.
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7
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Lin Z, Sun Y, Liu Y, Tong S, Shang Z, Cai Y, Lin W. Structural and Functional Analyses of the Transcription Repressor DgoR From Escherichia coli Reveal a Divalent Metal-Containing D-Galactonate Binding Pocket. Front Microbiol 2020; 11:590330. [PMID: 33224125 PMCID: PMC7674646 DOI: 10.3389/fmicb.2020.590330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/20/2020] [Indexed: 11/21/2022] Open
Abstract
The transcription repressor of D-galactonate metabolism, DgoR, from Escherichia coli belongs to the FadR family of the GntR superfamily. In the presence of D-galactonate, DgoR binds to two inverted repeats overlapping the dgo cis-acting promoter repressing the expression of genes involved in D-galactonate metabolism. To further understand the structural and molecular details of ligand and effector interactions between D-galactonate and this FadR family member, herein we solved the crystal structure of C-terminal domain of DgoR (DgoR_C), which revealed a unique divalent metal-containing substrate binding pocket. The metal ion is required for D-galactonate binding, as evidenced by the dramatically decreased affinity between D-galactonate and DgoR in the presence of EDTA, which can be reverted by the addition of Zn2+, Mg2+, and Ca2+. The key amino acid residues involved in the interactions between D-galactonate and DgoR were revealed by molecular docking studies and further validated with biochemical studies by site-directed mutagenesis. It was found that changes to alanine in residues R102, W181, T191, and R224 resulted in significantly decreased binding affinities for D-galactonate, as determined by EMSA and MST assays. These results suggest that the molecular modifications induced by a D-galactonate and a metal binding in the DgoR are required for DNA binding activity and consequently, transcriptional inhibition.
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Affiliation(s)
- Zhaozhu Lin
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yi Sun
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yu Liu
- Department of Chemistry, Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States
| | - Shujuan Tong
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhuo Shang
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuanheng Cai
- Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, NY, United States
| | - Wei Lin
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
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8
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Graf von Armansperg B, Koller F, Gericke N, Hellwig M, Jagtap PKA, Heermann R, Hennig J, Henle T, Lassak J. Transcriptional regulation of the N ε -fructoselysine metabolism in Escherichia coli by global and substrate-specific cues. Mol Microbiol 2020; 115:175-190. [PMID: 32979851 DOI: 10.1111/mmi.14608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/19/2022]
Abstract
Thermally processed food is an important part of the human diet. Heat-treatment, however, promotes the formation of so-called Amadori rearrangement products, such as fructoselysine. The gut microbiota including Escherichia coli can utilize these compounds as a nutrient source. While the degradation route for fructoselysine is well described, regulation of the corresponding pathway genes frlABCD remained poorly understood. Here, we used bioinformatics combined with molecular and biochemical analyses and show that fructoselysine metabolism in E. coli is tightly controlled at the transcriptional level. The global regulator CRP (CAP) as well as the alternative sigma factor σ32 (RpoH) contribute to promoter activation at high cAMP-levels and inside warm-blooded hosts, respectively. In addition, we identified and characterized a transcriptional regulator FrlR, encoded adjacent to frlABCD, as fructoselysine-6-phosphate specific repressor. Our study provides profound evidence that the interplay of global and substrate-specific regulation is a perfect adaptation strategy to efficiently utilize unusual substrates within the human gut environment.
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Affiliation(s)
| | - Franziska Koller
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Gericke
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Hellwig
- Chair of Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | | | - Ralf Heermann
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Thomas Henle
- Chair of Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
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9
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Global Regulatory Roles of the Histidine-Responsive Transcriptional Repressor HutC in Pseudomonas fluorescens SBW25. J Bacteriol 2020; 202:JB.00792-19. [PMID: 32291279 DOI: 10.1128/jb.00792-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/04/2020] [Indexed: 12/19/2022] Open
Abstract
HutC is known as a transcriptional repressor specific for histidine utilization (hut) genes in Gram-negative bacteria, including Pseudomonas fluorescens SBW25. However, its precise mode of protein-DNA interactions hasn't been examined with purified HutC proteins. Here, we performed electrophoretic mobility shift assay (EMSA) and DNase I footprinting using His6-tagged HutC and biotin-labeled probe of the hut promoter (PhutU). Results revealed a complex pattern of HutC oligomerization, and the specific protein-DNA interaction is disrupted by urocanate, a histidine derivative, in a concentration-dependent manner. Next, we searched for putative HutC-binding sites in the SBW25 genome. This led to the identification of 143 candidate targets with a P value less than 10-4 HutC interaction with eight selected candidate sites was subsequently confirmed by EMSA analysis, including the type IV pilus assembly protein PilZ, phospholipase C (PlcC) for phosphatidylcholine hydrolyzation, and key regulators of cellular nitrogen metabolism (NtrBC and GlnE). Finally, an isogenic hutC deletion mutant was subjected to transcriptome sequencing (RNA-seq) analysis and phenotypic characterization. When bacteria were grown on succinate and histidine, hutC deletion caused upregulation of 794 genes and downregulation of 525 genes at a P value of <0.05 with a fold change cutoff of 2.0. The hutC mutant displayed an enhanced spreading motility and pyoverdine production in laboratory media, in addition to the previously reported growth defect on the surfaces of plants. Together, our data indicate that HutC plays global regulatory roles beyond histidine catabolism through low-affinity binding with operator sites located outside the hut locus.IMPORTANCE HutC in Pseudomonas is a representative member of the GntR/HutC family of transcriptional regulators, which possess a N-terminal winged helix-turn-helix (wHTH) DNA-binding domain and a C-terminal substrate-binding domain. HutC is generally known to repress expression of histidine utilization (hut) genes through binding to the PhutU promoter with urocanate (the first intermediate of the histidine degradation pathway) as the direct inducer. Here, we first describe the detailed molecular interactions between HutC and its PhutU target site in a plant growth-promoting bacterium, P. fluorescens SBW25, and further show that HutC possesses specific DNA-binding activities with many targets in the SBW25 genome. Subsequent RNA-seq analysis and phenotypic assays revealed an unexpected global regulatory role of HutC for successful bacterial colonization in planta.
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10
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Xia H, Li X, Li Z, Zhan X, Mao X, Li Y. The Application of Regulatory Cascades in Streptomyces: Yield Enhancement and Metabolite Mining. Front Microbiol 2020; 11:406. [PMID: 32265866 PMCID: PMC7105598 DOI: 10.3389/fmicb.2020.00406] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Streptomyces is taken as an important resource for producing the most abundant antibiotics and other bio-active natural products, which have been widely used in pharmaceutical and agricultural areas. Usually they are biosynthesized through secondary metabolic pathways encoded by cluster situated genes. And these gene clusters are stringently regulated by interweaved transcriptional regulatory cascades. In the past decades, great advances have been made to elucidate the regulatory mechanisms involved in antibiotic production in Streptomyces. In this review, we summarized the recent advances on the regulatory cascades of antibiotic production in Streptomyces from the following four levels: the signals triggering the biosynthesis, the global regulators, the pathway-specific regulators and the feedback regulation. The production of antibiotic can be largely enhanced by rewiring the regulatory networks, such as overexpression of positive regulators, inactivation of repressors, fine-tuning of the feedback and ribosomal engineering in Streptomyces. The enormous amount of genomic sequencing data implies that the Streptomyces has potential to produce much more antibiotics for the great diversities and wide distributions of biosynthetic gene clusters in Streptomyces genomes. Most of these gene clusters are defined cryptic for unknown or undetectable natural products. In the synthetic biology era, activation of the cryptic gene clusters has been successfully achieved by manipulation of the regulatory genes. Chemical elicitors, rewiring regulatory gene and ribosomal engineering have been employed to crack the potential of cryptic gene clusters. These have been proposed as the most promising strategy to discover new antibiotics. For the complex of regulatory network in Streptomyces, we proposed that the discovery of new antibiotics and the optimization of industrial strains would be greatly promoted by further understanding the regulatory mechanism of antibiotic production.
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Affiliation(s)
- Haiyang Xia
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xiaofang Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Zhangqun Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xinqiao Zhan
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xuming Mao
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China.,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongquan Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China.,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
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11
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Xia H, Zhan X, Mao XM, Li YQ. The regulatory cascades of antibiotic production in Streptomyces. World J Microbiol Biotechnol 2020; 36:13. [PMID: 31897764 DOI: 10.1007/s11274-019-2789-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 12/18/2019] [Indexed: 01/27/2023]
Abstract
Streptomyces is famous for its capability to produce the most abundant antibiotics in all kingdoms. All Streptomyces antibiotics are natural products, whose biosynthesis from the so-called gene clusters are elaborately regulated by pyramidal transcriptional regulatory cascades. In the past decades, scientists have striven to unveil the regulatory mechanisms involved in antibiotic production in Streptomyces. Here we mainly focus on three aspects of the regulation on antibiotic production. 1. The onset of antibiotic production triggered by hormones and their coupled receptors as regulators; 2. The cascades of global and pathway-specific regulators governing antibiotic production; 3. The feedback regulation of antibiotics and/or intermediates on the gene cluster expression for their coordinated production. This review will summarize how the antibiotic production is stringently regulated in Streptomyces based on the signaling, and lay a theoretical foundation for improvement of antibiotic production and potentially drug discovery.
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Affiliation(s)
- Haiyang Xia
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, 318000, China
| | - Xinqiao Zhan
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, 318000, China
| | - Xu-Ming Mao
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, 318000, China. .,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
| | - Yong-Quan Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, 318000, China. .,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
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12
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Molecular Fingerprints for a Novel Enzyme Family in Actinobacteria with Glucosamine Kinase Activity. mBio 2019; 10:mBio.00239-19. [PMID: 31088917 PMCID: PMC6520443 DOI: 10.1128/mbio.00239-19] [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] [Indexed: 11/23/2022] Open
Abstract
The discovery of novel enzymes involved in antibiotic biosynthesis pathways is currently a topic of utmost importance. The high levels of antibiotic resistance detected worldwide threaten our ability to combat infections and other 20th-century medical achievements, namely, organ transplantation or cancer chemotherapy. We have identified and characterized a unique family of enzymes capable of phosphorylating glucosamine to glucosamine-6-phosphate, a crucial molecule directly involved in the activation of antibiotic production pathways in Actinobacteria, nature’s main source of antimicrobials. The consensus sequence identified for these glucosamine kinases will help establish a molecular fingerprint to reveal yet-uncharacterized sequences in antibiotic producers, which should have an important impact in biotechnological and biomedical applications, including the enhancement and optimization of antibiotic production. Actinobacteria have long been the main source of antibiotics, secondary metabolites with tightly controlled biosynthesis by environmental and physiological factors. Phosphorylation of exogenous glucosamine has been suggested as a mechanism for incorporation of this extracellular material into secondary metabolite biosynthesis, but experimental evidence of specific glucosamine kinases in Actinobacteria is lacking. Here, we present the molecular fingerprints for the identification of a unique family of actinobacterial glucosamine kinases. Structural and biochemical studies on a distinctive kinase from the soil bacterium Streptacidiphilus jiangxiensis unveiled its preference for glucosamine and provided structural evidence of a phosphoryl transfer to this substrate. Conservation of glucosamine-contacting residues across a large number of uncharacterized actinobacterial proteins unveiled a specific glucosamine binding sequence motif. This family of kinases and their genetic context may represent the missing link for the incorporation of environmental glucosamine into the antibiotic biosynthesis pathways in Actinobacteria and can be explored to enhance antibiotic production.
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13
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van der Heul HU, Bilyk BL, McDowall KJ, Seipke RF, van Wezel GP. Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era. Nat Prod Rep 2019; 35:575-604. [PMID: 29721572 DOI: 10.1039/c8np00012c] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2000 to 2018 The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described.
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14
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Iinuma C, Saito A, Ohnuma T, Tenconi E, Rosu A, Colson S, Mizutani Y, Liu F, Świątek-Połatyńska M, van Wezel GP, Rigali S, Fujii T, Miyashita K. NgcE Sco Acts as a Lower-Affinity Binding Protein of an ABC Transporter for the Uptake of N,N'-Diacetylchitobiose in Streptomyces coelicolor A3(2). Microbes Environ 2018; 33:272-281. [PMID: 30089751 PMCID: PMC6167110 DOI: 10.1264/jsme2.me17172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In the model species Streptomyces coelicolor A3(2), the uptake of chitin-degradation byproducts, mainly N,N′- diacetylchitobiose ([GlcNAc]2) and N-acetylglucosamine (GlcNAc), is performed by the ATP-binding cassette (ABC) transporter DasABC-MsiK and the sugar-phosphotransferase system (PTS), respectively. Studies on the S. coelicolor chromosome have suggested the occurrence of additional uptake systems of GlcNAc-related compounds, including the SCO6005–7 cluster, which is orthologous to the ABC transporter NgcEFG of S. olivaceoviridis. However, despite conserved synteny between the clusters in S. coelicolor and S. olivaceoviridis, homology between them is low, with only 35% of residues being identical between NgcE proteins, suggesting different binding specificities. Isothermal titration calorimetry experiments revealed that recombinant NgcESco interacts with GlcNAc and (GlcNAc)2, with Kd values (1.15 and 1.53 μM, respectively) that were higher than those of NgcE of S. olivaceoviridis (8.3 and 29 nM, respectively). The disruption of ngcESco delayed (GlcNAc)2 consumption, but did not affect GlcNAc consumption ability. The ngcESco-dasA double mutation severely decreased the ability to consume (GlcNAc)2 and abolished the induction of chitinase production in the presence of (GlcNAc)2, but did not affect the GlcNAc consumption rate. The results of these biochemical and reverse genetic analyses indicate that NgcESco acts as a (GlcNAc)2- binding protein of the ABC transporter NgcEFGSco-MsiK. Transcriptional and biochemical analyses of gene regulation demonstrated that the ngcESco gene was slightly induced by GlcNAc, (GlcNAc)2, and chitin, but repressed by DasR. Therefore, a model was proposed for the induction of the chitinolytic system and import of (GlcNAc)2, in which (GlcNAc)2 generated from chitin by chitinase produced leakily, is mainly transported via NgcEFG-MsiK and induces the expression of chitinase genes and dasABCD.
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Affiliation(s)
- Chiharu Iinuma
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University
| | - Akihiro Saito
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University.,Department of Materials and Life Science, Shizuoka Institute of Science and Technology
| | | | - Elodie Tenconi
- InBioS-Center for Protein Engineering, Institut de Chimie B6a, University of Liège
| | - Adeline Rosu
- InBioS-Center for Protein Engineering, Institut de Chimie B6a, University of Liège
| | - Séverine Colson
- InBioS-Center for Protein Engineering, Institut de Chimie B6a, University of Liège
| | - Yuuki Mizutani
- Department of Materials and Life Science, Shizuoka Institute of Science and Technology
| | - Feng Liu
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University
| | | | | | - Sébastien Rigali
- InBioS-Center for Protein Engineering, Institut de Chimie B6a, University of Liège
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15
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Rigali S, Anderssen S, Naômé A, van Wezel GP. Cracking the regulatory code of biosynthetic gene clusters as a strategy for natural product discovery. Biochem Pharmacol 2018; 153:24-34. [DOI: 10.1016/j.bcp.2018.01.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/03/2018] [Indexed: 12/19/2022]
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16
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Daniel-Ivad M, Pimentel-Elardo S, Nodwell JR. Control of Specialized Metabolism by Signaling and Transcriptional Regulation: Opportunities for New Platforms for Drug Discovery? Annu Rev Microbiol 2018; 72:25-48. [PMID: 29799791 DOI: 10.1146/annurev-micro-022618-042458] [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: 11/09/2022]
Abstract
Specialized metabolites are bacterially produced small molecules that have an extraordinary diversity of important biological activities. They are useful as biochemical probes of living systems, and they have been adapted for use as drugs for human afflictions ranging from infectious diseases to cancer. The biosynthetic genes for these molecules are controlled by a dense network of regulatory mechanisms: Cell-cell signaling and nutrient sensing are conspicuous features of this network. While many components of these mechanisms have been identified, important questions about their biological roles remain shrouded in mystery. In addition to identifying new molecules and solving their mechanisms of action (a central preoccupation in this field), we suggest that addressing questions of quorum sensing versus diffusion sensing and identifying the dominant nutritional and environmental cues for specialized metabolism are important directions for research.
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Affiliation(s)
- M Daniel-Ivad
- Department of Biochemistry, University of Toronto, Ontario M5G 1M1, Canada;
| | - S Pimentel-Elardo
- Department of Biochemistry, University of Toronto, Ontario M5G 1M1, Canada;
| | - J R Nodwell
- Department of Biochemistry, University of Toronto, Ontario M5G 1M1, Canada;
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17
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Labella JI, Obrebska A, Espinosa J, Salinas P, Forcada-Nadal A, Tremiño L, Rubio V, Contreras A. Expanding the Cyanobacterial Nitrogen Regulatory Network: The GntR-Like Regulator PlmA Interacts with the PII-PipX Complex. Front Microbiol 2016; 7:1677. [PMID: 27840625 PMCID: PMC5083789 DOI: 10.3389/fmicb.2016.01677] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/06/2016] [Indexed: 11/17/2022] Open
Abstract
Cyanobacteria, phototrophic organisms that perform oxygenic photosynthesis, perceive nitrogen status by sensing 2-oxoglutarate levels. PII, a widespread signaling protein, senses and transduces nitrogen and energy status to target proteins, regulating metabolism and gene expression. In cyanobacteria, under conditions of low 2-oxoglutarate, PII forms complexes with the enzyme N-acetyl glutamate kinase, increasing arginine biosynthesis, and with PII-interacting protein X (PipX), making PipX unavailable for binding and co-activation of the nitrogen regulator NtcA. Both the PII-PipX complex structure and in vivo functional data suggested that this complex, as such, could have regulatory functions in addition to PipX sequestration. To investigate this possibility we performed yeast three-hybrid screening of genomic libraries from Synechococcus elongatus PCC7942, searching for proteins interacting simultaneously with PII and PipX. The only prey clone found in the search expressed PlmA, a member of the GntR family of transcriptional regulators proven here by gel filtration to be homodimeric. Interactions analyses further confirmed the simultaneous requirement of PII and PipX, and showed that the PlmA contacts involve PipX elements exposed in the PII-PipX complex, specifically the C-terminal helices and one residue of the tudor-like body. In contrast, PII appears not to interact directly with PlmA, possibly being needed indirectly, to induce an extended conformation of the C-terminal helices of PipX and for modulating the surface polarity at the PII-PipX boundary, two elements that appear crucial for PlmA binding. Attempts to inactive plmA confirmed that this gene is essential in S. elongatus. Western blot assays revealed that S. elongatus PlmA, irrespective of the nitrogen regime, is a relatively abundant transcriptional regulator, suggesting the existence of a large PlmA regulon. In silico studies showed that PlmA is universally and exclusively found in cyanobacteria. Based on interaction data, on the relative amounts of the proteins involved in PII-PipX-PlmA complexes, determined in western assays, and on the restrictions imposed by the symmetries of trimeric PII and dimeric PlmA molecules, a structural and regulatory model for PlmA function is discussed in the context of the cyanobacterial nitrogen interaction network.
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Affiliation(s)
- Jose I Labella
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | - Anna Obrebska
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | - Javier Espinosa
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | - Paloma Salinas
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | | | - Lorena Tremiño
- Instituto de Biomedicina de Valencia of the CSIC Valencia, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia of the CSICValencia, Spain; Group 739, CIBER de Enfermedades Raras (CIBERER-ISCIII)Valencia, Spain
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
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18
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Urem M, Świątek-Połatyńska MA, Rigali S, van Wezel GP. Intertwining nutrient-sensory networks and the control of antibiotic production inStreptomyces. Mol Microbiol 2016; 102:183-195. [DOI: 10.1111/mmi.13464] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Mia Urem
- Molecular Biotechnology, Institute of Biology, Leiden University; Sylviusweg 72 Leiden 2333BE The Netherlands
| | - Magdalena A. Świątek-Połatyńska
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Strasse 10 Marburg 35043 Germany
| | - Sébastien Rigali
- InBioS, Centre for Protein Engineering; University of Liège; Liège B-4000 Belgium
| | - Gilles P. van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University; Sylviusweg 72 Leiden 2333BE The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW); Droevendaalsesteeg 10 Wageningen 6708 PB The Netherlands
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