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Yang X, Zhang J, Zhu J, Yang R, Tong Y. Molecular insights into FucR transcription factor to control the metabolism of L-fucose in Bifidobacterium longum subsp. infantis. Microbiol Res 2024; 283:127709. [PMID: 38593579 DOI: 10.1016/j.micres.2024.127709] [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: 12/13/2023] [Revised: 03/27/2024] [Accepted: 03/30/2024] [Indexed: 04/11/2024]
Abstract
Bifidobacterium longum subsp. infantis commonly colonizes the human gut and is capable of metabolizing L-fucose, which is abundant in the gut. Multiple studies have focused on the mechanisms of L-fucose utilization by B. longum subsp. infantis, but the regulatory pathways governing the expression of these catabolic processes are still unclear. In this study, we have conducted a structural and functional analysis of L-fucose metabolism transcription factor FucR derived from B. longum subsp. infantis Bi-26. Our results indicated that FucR is a L-fucose-sensitive repressor with more α-helices, fewer β-sheets, and β-turns. Transcriptional analysis revealed that FucR displays weak negative self-regulation, which is counteracted in the presence of L-fucose. Isothermal titration calorimetry indicated that FucR has a 2:1 stoichiometry with L-fucose. The key amino acid residues for FucR binding L-fucose are Asp280 and Arg331, with mutation of Asp280 to Ala resulting in a decrease in the affinity between FucR and L-fucose with the Kd value from 2.58 to 11.68 μM, and mutation of Arg331 to Ala abolishes the binding ability of FucR towards L-fucose. FucR specifically recognized and bound to a 20-bp incomplete palindrome sequence (5'-ACCCCAATTACGAAAATTTTT-3'), and the affinity of the L-fucose-loaded FucR for the DNA fragment was lower than apo-FucR. The results provided new insights into the regulating L-fucose metabolism by B. longum subsp. infantis.
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Affiliation(s)
- Xiaojun Yang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jing Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jing Zhu
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ruijin Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yanjun Tong
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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2
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Marshall A, McGrath JW, Mitchell M, Fanning S, McMullan G. One size does not fit all - Trehalose metabolism by Clostridioides difficile is variable across the five phylogenetic lineages. Microb Genom 2023; 9:001110. [PMID: 37768179 PMCID: PMC10569727 DOI: 10.1099/mgen.0.001110] [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: 05/25/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Clostridioides difficile, the leading cause of antibiotic-associated diarrhoea worldwide, is a genetically diverse species which can metabolise a number of nutrient sources upon colonising a dysbiotic gut environment. Trehalose, a disaccharide sugar consisting of two glucose molecules bonded by an α 1,1-glycosidic bond, has been hypothesised to be involved in the emergence of C. difficile hypervirulence due to its increased utilisation by the RT027 and RT078 strains. Here, growth in trehalose as the sole carbon source was shown to be non-uniform across representative C. difficile strains, even though the genes for its metabolism were induced. Growth in trehalose reduced the expression of genes associated with toxin production and sporulation in the C. difficile R20291 (RT027) and M120 (RT078) strains in vitro, suggesting an inhibitory effect on virulence factors. Interestingly, the R20291 TreR transcriptional regulatory protein appeared to possess an activator function as its DNA-binding ability was increased in the presence of its effector, trehalose-6-phosphate. Using RNA-sequencing analysis, we report the identification of a putative trehalose metabolism pathway which is induced during growth in trehalose: this has not been previously described within the C. difficile species. These data demonstrate the metabolic diversity exhibited by C. difficile which warrants further investigation to elucidate the molecular basis of trehalose metabolism within this important gut pathogen.
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Affiliation(s)
- Andrew Marshall
- School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - John W. McGrath
- School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Molly Mitchell
- University College Dublin-Centre for Food Safety University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- University College Dublin-Centre for Food Safety University College Dublin, Dublin, Ireland
| | - Geoff McMullan
- School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
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3
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Pawlik KJ, Zelkowski M, Biernacki M, Litwinska K, Jaworski P, Kotowska M. GntR-like SCO3932 Protein Provides a Link between Actinomycete Integrative and Conjugative Elements and Secondary Metabolism. Int J Mol Sci 2021; 22:ijms222111867. [PMID: 34769298 PMCID: PMC8584621 DOI: 10.3390/ijms222111867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 01/16/2023] Open
Abstract
Streptomyces bacteria produce a plethora of secondary metabolites including the majority of medically important antibiotics. The onset of secondary metabolism is correlated with morphological differentiation and controlled by a complex regulatory network involving numerous regulatory proteins. Control over these pathways at the molecular level has a medical and industrial importance. Here we describe a GntR-like DNA binding transcription factor SCO3932, encoded within an actinomycete integrative and conjugative element, which is involved in the secondary metabolite biosynthesis regulation. Affinity chromatography, electrophoresis mobility shift assay, footprinting and chromatin immunoprecipitation experiments revealed, both in vitro and in vivo, SCO3932 binding capability to its own promoter region shared with the neighboring gene SCO3933, as well as promoters of polyketide metabolite genes, such as cpkD, a coelimycin biosynthetic gene, and actII-orf4—an activator of actinorhodin biosynthesis. Increased activity of SCO3932 target promoters, as a result of SCO3932 overproduction, indicates an activatory role of this protein in Streptomyces coelicolor A3(2) metabolite synthesis pathways.
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4
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Li H, Ramia NE, Borges F, Revol-Junelles AM, Vogensen FK, Leisner JJ. Identification of Potential Citrate Metabolism Pathways in Carnobacterium maltaromaticum. Microorganisms 2021; 9:microorganisms9102169. [PMID: 34683489 PMCID: PMC8537297 DOI: 10.3390/microorganisms9102169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
In the present study, we describe the identification of potential citrate metabolism pathways for the lactic acid bacterium (LAB) Carnobacterium maltaromaticum. A phenotypic assay indicated that four of six C. maltaromaticum strains showed weak (Cm 6-1 and ATCC 35586) or even delayed (Cm 3-1 and Cm 5-1) citrate utilization activity. The remaining two strains, Cm 4-1 and Cm 1-2 gave negative results. Additional analysis showed no or very limited utilization of citrate in media containing 1% glucose and 22 or 30 mM citrate and inoculated with Cm 6-1 or ATCC 35586. Two potential pathways of citrate metabolism were identified by bioinformatics analyses in C. maltaromaticum including either oxaloacetate (pathway 1) or tricarboxylic compounds such as isocitrate and α-ketoglutarate (pathway 2) as intermediates. Genes encoding pathway 1 were present in two out of six strains while pathway 2 included genes present in all six strains. The two potential citrate metabolism pathways in C. maltaromaticum may potentially affect the sensory profiles of milk and soft cheeses subjected to growth with this species.
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Affiliation(s)
- Heng Li
- Pasteurien College, Soochow University, Suzhou 215123, China;
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark
| | - Nancy E. Ramia
- Laboratoire d’Ingénierie des Biomolécules (LIBio), Ecole Nationale Supérieure d’Agronomie et des Industries Alimentaires (ENSAIA), Université de Lorraine, LIBio, F-54000 Nancy, France; (N.E.R.); (F.B.); (A.-M.R.-J.)
| | - Frédéric Borges
- Laboratoire d’Ingénierie des Biomolécules (LIBio), Ecole Nationale Supérieure d’Agronomie et des Industries Alimentaires (ENSAIA), Université de Lorraine, LIBio, F-54000 Nancy, France; (N.E.R.); (F.B.); (A.-M.R.-J.)
| | - Anne-Marie Revol-Junelles
- Laboratoire d’Ingénierie des Biomolécules (LIBio), Ecole Nationale Supérieure d’Agronomie et des Industries Alimentaires (ENSAIA), Université de Lorraine, LIBio, F-54000 Nancy, France; (N.E.R.); (F.B.); (A.-M.R.-J.)
| | - Finn Kvist Vogensen
- Department of Food Science, Faculty of Science, University of Copenhagen, DK-1958 Frederiksberg, Denmark;
| | - Jørgen J. Leisner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark
- Correspondence:
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5
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Terán LC, Mortera P, Tubio G, Alarcón SH, Blancato VS, Espariz M, Esteban L, Magni C. Genomic analysis revealed conserved acid tolerance mechanisms from native micro-organisms in fermented feed. J Appl Microbiol 2021; 132:1152-1165. [PMID: 34487594 DOI: 10.1111/jam.15292] [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: 01/07/2021] [Revised: 07/28/2021] [Accepted: 08/30/2021] [Indexed: 11/27/2022]
Abstract
AIMS Fermented feed is an agricultural practice used in many regions of the world to improve the growth performance of farm animals. This study aimed to identify and evaluate the lactic acid bacteria and yeast involved in the production of fermented feed. METHODS AND RESULTS We isolated and described two micro-organisms from autochthonous microbiota origin present in a regional feed product, Lactobacillus paracasei IBR07 (Lacticaseibacillus paracasei) and Kazachstania unispora IBR014 (Saccharomyces unisporum). Genome sequence analyses were performed to characterize both micro-organisms. Potential pathways involved in the acid response, tolerance and persistence were predicted in both genomes. Although L. paracasei and K. unispora are considered safe for animal feed, we analysed the presence of virulence factors, antibiotic resistance and pathogenicity islands. Furthermore, the Galleria mellonella model was used to support the safety of both isolates. CONCLUSIONS We conclude that IBR07 and IBR014 strains are good candidates to be used as starter cultures for feed fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY The data presented here will be helpful to explore other biotechnological aspects and constitute a starting point for further studies to establish the consumption benefit of fermented feed in farm animal production.
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Affiliation(s)
- Lucrecia C Terán
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina.,Centro de Referencia para Lactobacilos, CERELA-CONICET, San Miguel de Tucuman, Tucumán, Argentina
| | - Pablo Mortera
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina
| | - Gisela Tubio
- Instituto de Procesos Biotecnológicos y Químicos Rosario, IPROByQ (CONICET-UNR), Rosario, Argentina
| | - Sergio H Alarcón
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina.,Instituto de Química de Rosario, IQUIR (CONICET-UNR), Rosario, Argentina
| | - Victor S Blancato
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina
| | - Martín Espariz
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina.,Área Estadística y Procesamiento de Datos, Departamento de Matemática y Estadística, FBioyF-UNR, Rosario, Argentina
| | - Luis Esteban
- Química Biológica, Facultad de Ciencias Médicas, UNR, Rosario, Argentina
| | - Christian Magni
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina
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6
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Matilla MA, Velando F, Martín-Mora D, Monteagudo-Cascales E, Krell T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol Rev 2021; 46:6356564. [PMID: 34424339 DOI: 10.1093/femsre/fuab043] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria have evolved many different signal transduction systems that sense signals and generate a variety of responses. Generally, most abundant are transcriptional regulators, sensor histidine kinases and chemoreceptors. Typically, these systems recognize their signal molecules with dedicated ligand-binding domains (LBDs), which, in turn, generate a molecular stimulus that modulates the activity of the output module. There are an enormous number of different LBDs that recognize a similarly diverse set of signals. To give a global perspective of the signals that interact with transcriptional regulators, sensor kinases and chemoreceptors, we manually retrieved information on the protein-ligand interaction from about 1,200 publications and 3D structures. The resulting 811 proteins were classified according to the Pfam family into 127 groups. These data permit a delineation of the signal profiles of individual LBD families as well as distinguishing between families that recognize signals in a promiscuous manner and those that possess a well-defined ligand range. A major bottleneck in the field is the fact that the signal input of many signaling systems is unknown. The signal repertoire reported here will help the scientific community design experimental strategies to identify the signaling molecules for uncharacterised sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
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7
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Almeida BC, Kaczmarek JA, Figueiredo PR, Prather KLJ, Carvalho ATP. Transcription factor allosteric regulation through substrate coordination to zinc. NAR Genom Bioinform 2021; 3:lqab033. [PMID: 33987533 PMCID: PMC8092373 DOI: 10.1093/nargab/lqab033] [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: 11/17/2020] [Revised: 03/30/2021] [Accepted: 04/08/2021] [Indexed: 11/14/2022] Open
Abstract
The development of new synthetic biology circuits for biotechnology and medicine requires deeper mechanistic insight into allosteric transcription factors (aTFs). Here we studied the aTF UxuR, a homodimer of two domains connected by a highly flexible linker region. To explore how ligand binding to UxuR affects protein dynamics we performed molecular dynamics simulations in the free protein, the aTF bound to the inducer D-fructuronate or the structural isomer D-glucuronate. We then validated our results by constructing a sensor plasmid for D-fructuronate in Escherichia coli and performed site-directed mutagenesis. Our results show that zinc coordination is necessary for UxuR function since mutation to alanines prevents expression de-repression by D-fructuronate. Analyzing the different complexes, we found that the disordered linker regions allow the N-terminal domains to display fast and large movements. When the inducer is bound, UxuR can sample an open conformation with a more pronounced negative charge at the surface of the N-terminal DNA binding domains. In opposition, in the free and D-glucuronate bond forms the protein samples closed conformations, with a more positive character at the surface of the DNA binding regions. These molecular insights provide a new basis to harness these systems for biological systems engineering.
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Affiliation(s)
- Beatriz C Almeida
- CNC-Center for Neuroscience and Cell Biology, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Jennifer A Kaczmarek
- MIT-Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Pedro R Figueiredo
- CNC-Center for Neuroscience and Cell Biology, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Kristala L J Prather
- MIT-Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexandra T P Carvalho
- CNC-Center for Neuroscience and Cell Biology, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3004-504 Coimbra, Portugal
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8
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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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9
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Arya G, Pal M, Sharma M, Singh B, Singh S, Agrawal V, Chaba R. Molecular insights into effector binding by DgoR, a GntR/FadR family transcriptional repressor of D-galactonate metabolism in Escherichia coli. Mol Microbiol 2020; 115:591-609. [PMID: 33068046 DOI: 10.1111/mmi.14625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 01/23/2023]
Abstract
Several GntR/FadR transcriptional regulators govern sugar acid metabolism in bacteria. Although effectors have been identified for a few sugar acid regulators, the mode of effector binding is unknown. Even in the overall FadR subfamily, there are limited details on effector-regulator interactions. Here, we identified the effector-binding cavity in Escherichia coli DgoR, a FadR subfamily transcriptional repressor of D-galactonate metabolism that employs D-galactonate as its effector. Using a genetic screen, we isolated several dgoR superrepressor alleles. Blind docking suggested eight amino acids corresponding to these alleles to form a part of the effector-binding cavity. In vivo and in vitro assays showed that these mutations compromise the inducibility of DgoR without affecting its oligomeric status or affinity for target DNA. Taking Bacillus subtilis GntR as a representative, we demonstrated that the effector-binding cavity is similar among FadR subfamily sugar acid regulators. Finally, a comparison of sugar acid regulators with other FadR members suggested conserved features of effector-regulator recognition within the FadR subfamily. Sugar acid metabolism is widely implicated in bacterial colonization and virulence. The present study sets the basis to investigate the influence of natural genetic variations in FadR subfamily regulators on their sensitivity to sugar acids and ultimately on host-bacterial interactions.
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Affiliation(s)
- Garima Arya
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Mohinder Pal
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, India
| | - Bhupinder Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Swati Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Vishal Agrawal
- Department of Biochemistry, Panjab University, Chandigarh, India
| | - Rachna Chaba
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
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10
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D'Angelo M, Martino GP, Blancato VS, Espariz M, Hartke A, Sauvageot N, Benachour A, Alarcón SH, Magni C. Diversity of volatile organic compound production from leucine and citrate in Enterococcus faecium. Appl Microbiol Biotechnol 2019; 104:1175-1186. [PMID: 31828406 DOI: 10.1007/s00253-019-10277-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/14/2019] [Accepted: 11/23/2019] [Indexed: 01/22/2023]
Abstract
Enterococcus faecium is frequently isolated from fermented food; in particular, they positively contribute to the aroma compound generation in traditional cheese. Citrate fermentation is a desirable property in these bacteria, but this feature is not uniformly distributed among E. faecium strains. In the present study, three selected E. faecium strains, IQ110 (cit-), GM70 (cit+ type I), and Com12 (cit+ type II), were analyzed in their production of aroma compounds in milk. End products and volatile organic compounds (VOCs) were determined by solid-phase micro-extraction combined with gas chromatography mass spectrometry (SPME-GC-MS). Principal component analysis (PCA) of aroma compound profiles revealed a different VOC composition for the three strains. In addition, resting cell experiments of E. faecium performed in the presence of leucine, citrate, or pyruvate as aroma compound precursors allowed us to determine metabolic differences between the studied strains. GM70 (cit+ type I) showed an active citrate metabolism, with increased levels of diacetyl and acetoin generation relative to Com12 or to citrate defective IQ110 strains. In addition, in the experimental conditions tested, a defective citrate-fermenting phenotype for the Com12 strain was found, while its leucine degradation and pyruvate metabolism were conserved. In conclusion, rational selection of E. faecium strains could be performed based on genotypic and phenotypic analyses. This would result in a performing strain, such as GM70, that could positively contribute to flavor, with typical notes of diacetyl, acetoin, 3-methyl butanal, and 3-methyl butanol in an adjuvant culture.
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Affiliation(s)
- Matilde D'Angelo
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Suipacha 590, Rosario, Argentina
- Instituto de Química de Rosario (IQUIR), FBioyF, UNR-CONICET, Suipacha 570, Rosario, Argentina
| | - Gabriela P Martino
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Suipacha 590, Rosario, Argentina
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Argentina
| | - Victor S Blancato
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Suipacha 590, Rosario, Argentina
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Argentina
- U2RM Stress/Virulence, Normandie Univ, UNICAEN, 14000, Caen, France
| | - Martín Espariz
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Suipacha 590, Rosario, Argentina
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Argentina
- U2RM Stress/Virulence, Normandie Univ, UNICAEN, 14000, Caen, France
| | - Axel Hartke
- U2RM Stress/Virulence, Normandie Univ, UNICAEN, 14000, Caen, France
| | | | | | - Sergio H Alarcón
- Instituto de Química de Rosario (IQUIR), FBioyF, UNR-CONICET, Suipacha 570, Rosario, Argentina
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Argentina
| | - Christian Magni
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Suipacha 590, Rosario, Argentina.
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Sede Suipacha 590, Rosario, Argentina.
- U2RM Stress/Virulence, Normandie Univ, UNICAEN, 14000, Caen, France.
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11
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Kotowska M, Świat M, Zarȩba-Pasławska J, Jaworski P, Pawlik K. A GntR-Like Transcription Factor HypR Regulates Expression of Genes Associated With L-Hydroxyproline Utilization in Streptomyces coelicolor A3(2). Front Microbiol 2019; 10:1451. [PMID: 31297104 PMCID: PMC6608401 DOI: 10.3389/fmicb.2019.01451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/11/2019] [Indexed: 11/13/2022] Open
Abstract
Bacteria from the genus Streptomyces have been long exploited as the most prolific producers of antibiotics, other secondary metabolites and enzymes. They are important members of soil microbial communities that can adapt to changing conditions thank to the fine regulation of gene expression in response to environmental signals. Streptomyces coelicolor A3(2) is a model organism for molecular studies with the most deeply recognized interactions within the complex metabolic and regulatory network. However, details about molecular signals recognized by specialized regulatory proteins as well as their direct targets are often missing. We describe here a zinc-binding protein HypR (SCO6294) which belongs to FadR subfamily of GntR-like regulators. The DNA sequence 5'-TACAATGTCAC-3' recognized by the HypR protein in its own promoter region was identified by DNase I footprinting. Binding of six DNA fragments containing similar sequences located in other promoter regions were confirmed by the electrophoretic mobility shift assay (EMSA). The sequences of 7 in vitro-determined binding sites were assembled to generate a logo of the HypR binding motif, 5'-CTNTGC(A/C)ATGTCAC-3'. Comparison of luciferase reporter genes expression under the control of cloned promoter regions in S. coelicolor A3(2) wild type and deletion mutant strains revealed, that the HypR protein acts as a repressor of its target genes. Genes belonging to the regulon of HypR code for enzymes putatively involved in collagen degradation and utilization of L-hydroxyproline (L-Hyp) as concluded from predicted structure and conserved domains. Their transcription is induced in the wild type strain by the addition of L-Hyp to the culture medium. Moreover, knockout of one of the genes from the predicted L-Hyp utilization operon abolished the ability of the strain to grow on L-Hyp as a sole source of carbon. To our knowledge, this work is the first indication of the existence of the pathway of L-hydroxyproline catabolism in Streptomycetes.
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Affiliation(s)
- Magdalena Kotowska
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | | | | | | | - Krzysztof Pawlik
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
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12
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Implications of the expression of Enterococcus faecalis citrate fermentation genes during infection. PLoS One 2018; 13:e0205787. [PMID: 30335810 PMCID: PMC6193673 DOI: 10.1371/journal.pone.0205787] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/02/2018] [Indexed: 12/05/2022] Open
Abstract
Citrate is an ubiquitous compound in nature. However, citrate fermentation is present only in a few pathogenic or nonpathogenic microorganisms. The citrate fermentation pathway includes a citrate transporter, a citrate lyase complex, an oxaloacetate decarboxylase and a regulatory system. Enterococcus faecalis is commonly present in the gastro-intestinal microbiota of warm-blooded animals and insect guts. These bacteria can also cause infection and disease in immunocompromised individuals. In the present study, we performed whole genome analysis in Enterococcus strains finding that the complete citrate pathway is present in all of the E. faecalis strains isolated from such diverse habitats as animals, hospitals, water, milk, plants, insects, cheese, etc. These results indicate the importance of this metabolic preservation for persistence and growth of E. faecalis in different niches. We also analyzed the role of citrate metabolism in the E. faecalis pathogenicity. We found that an E. faecalis citrate fermentation-deficient strain was less pathogenic for Galleria mellonella larvae than the wild type. Furthermore, strains with deletions in the oxaloacetate decarboxylase subunits or in the α-acetolactate synthase resulted also less virulent than the wild type strain. We also observed that citrate promoters are induced in blood, urine and also in the hemolymph of G. mellonella. In addition, we showed that citrate fermentation allows E. faecalis to grow better in blood, urine and G. mellonella. The results presented here clearly indicate that citrate fermentation plays an important role in E. faecalis opportunistic pathogenic behavior.
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13
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Quintana I, Espariz M, Villar SR, González FB, Pacini MF, Cabrera G, Bontempi I, Prochetto E, Stülke J, Perez AR, Marcipar I, Blancato V, Magni C. Genetic Engineering of Lactococcus lactis Co-producing Antigen and the Mucosal Adjuvant 3' 5'- cyclic di Adenosine Monophosphate (c-di-AMP) as a Design Strategy to Develop a Mucosal Vaccine Prototype. Front Microbiol 2018; 9:2100. [PMID: 30258417 PMCID: PMC6143824 DOI: 10.3389/fmicb.2018.02100] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/16/2018] [Indexed: 12/20/2022] Open
Abstract
Lactococcus lactis is a promising candidate for the development of mucosal vaccines. More than 20 years of experimental research supports this immunization approach. In addition, 3′ 5′- cyclic di-adenosine monophosphate (c-di-AMP) is a bacterial second messenger that plays a key role in the regulation of diverse physiological functions (potassium and cellular wall homeostasis, among others). Moreover, recent studies showed that c-di-AMP has a strong mucosal adjuvant activity that promotes both humoral and cellular immune responses. In this study, we report the development of a novel mucosal vaccine prototype based on a genetically engineered L. lactis strain. First, we demonstrate that homologous expression of cdaA gen in L. lactis is able to increase c-di-AMP levels. Thus, we hypothesized that in vivo synthesis of the adjuvant can be combined with production of an antigen of interest in a separate form or jointly in the same strain. Therefore, a specifically designed fragment of the trans-sialidase (TScf) enzyme from the Trypanosoma cruzi parasite, the etiological agent of Chagas disease, was selected to evaluate as proof of concept the immune response triggered by our vaccine prototypes. Consequently, we found that oral administration of a L. lactis strain expressing antigenic TScf combined with another L. lactis strain producing the adjuvant c-di-AMP could elicit a TS-specific immune response. Also, an additional L. lactis strain containing a single plasmid with both cdaA and tscf genes under the Pcit and Pnis promoters, respectively, was also able to elicit a specific immune response. Thus, the current report is the first one to describe an engineered L. lactis strain that simultaneously synthesizes the adjuvant c-di-AMP as well as a heterologous antigen in order to develop a simple and economical system for the formulation of vaccine prototypes using a food grade lactic acid bacterium.
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Affiliation(s)
- Ingrid Quintana
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET UNR), Universidad Nacional de Rosario, Rosario, Argentina.,Department of General Microbiology, GZMB, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Martín Espariz
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET UNR), Universidad Nacional de Rosario, Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas - Municipalidad de Granadero Baigorria (UNR), Rosario, Argentina
| | - Silvina R Villar
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER, CONICET UNR), Rosario, Argentina.,Facultad de Ciencias Médicas, Centro de Investigación y Producción de Reactivos Biológicos, Universidad Nacional de Rosario, Rosario, Argentina
| | - Florencia B González
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER, CONICET UNR), Rosario, Argentina
| | - Maria F Pacini
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER, CONICET UNR), Rosario, Argentina
| | - Gabriel Cabrera
- Laboratorio de Tecnología Inmunológica, Universidad Nacional del Litoral, Santa Fe, Argentina.,Facultad de Ciencias Médicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Iván Bontempi
- Laboratorio de Tecnología Inmunológica, Universidad Nacional del Litoral, Santa Fe, Argentina.,Facultad de Ciencias Médicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Estefanía Prochetto
- Laboratorio de Tecnología Inmunológica, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Jörg Stülke
- Department of General Microbiology, GZMB, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Ana R Perez
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER, CONICET UNR), Rosario, Argentina.,Facultad de Ciencias Médicas, Centro de Investigación y Producción de Reactivos Biológicos, Universidad Nacional de Rosario, Rosario, Argentina
| | - Iván Marcipar
- Laboratorio de Tecnología Inmunológica, Universidad Nacional del Litoral, Santa Fe, Argentina.,Facultad de Ciencias Médicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Victor Blancato
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET UNR), Universidad Nacional de Rosario, Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas - Municipalidad de Granadero Baigorria (UNR), Rosario, Argentina
| | - Christian Magni
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET UNR), Universidad Nacional de Rosario, Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Facultad de Ciencias Bioquímicas y Farmacéuticas - Municipalidad de Granadero Baigorria (UNR), Rosario, Argentina
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14
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Pan L, Gardner CL, Pagliai FA, Gonzalez CF, Lorca GL. Identification of the Tolfenamic Acid Binding Pocket in PrbP from Liberibacter asiaticus. Front Microbiol 2017; 8:1591. [PMID: 28878750 PMCID: PMC5572369 DOI: 10.3389/fmicb.2017.01591] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/04/2017] [Indexed: 12/31/2022] Open
Abstract
In Liberibacter asiaticus, PrbP is an important transcriptional accessory protein that was found to regulate gene expression through interactions with the RNA polymerase β-subunit and a specific sequence on the promoter region. It was found that inactivation of PrbP, using the inhibitor tolfenamic acid, resulted in a significant decrease in the overall transcriptional activity of L. asiaticus, and the suppression of L. asiaticus infection in HLB symptomatic citrus seedlings. The molecular interactions between PrbP and tolfenamic acid, however, were yet to be elucidated. In this study, we modeled the structure of PrbP and identified a ligand binding pocket, TaP, located at the interface of the predicted RNA polymerase interaction domain (N-terminus) and the DNA binding domain (C-terminus). The molecular interactions of PrbP with tolfenamic acid were predicted using in silico docking. Site-directed mutagenesis of specific amino acids was followed by electrophoresis mobility shift assays and in vitro transcription assays, where residues N107, G109, and E148 were identified as the primary amino acids involved in interactions with tolfenamic acid. These results provide insight into the binding mechanism of PrbP to a small inhibitory molecule, and a starting scaffold for the identification and development of therapeutics targeting PrbP and other homologs in the CarD_CdnL_TRCF family.
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Affiliation(s)
| | | | | | | | - Graciela L. Lorca
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Science, University of FloridaGainesville, FL, United States
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15
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Metallochaperones and metalloregulation in bacteria. Essays Biochem 2017; 61:177-200. [PMID: 28487396 DOI: 10.1042/ebc20160076] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/23/2017] [Accepted: 02/27/2017] [Indexed: 12/21/2022]
Abstract
Bacterial transition metal homoeostasis or simply 'metallostasis' describes the process by which cells control the intracellular availability of functionally required metal cofactors, from manganese (Mn) to zinc (Zn), avoiding both metal deprivation and toxicity. Metallostasis is an emerging aspect of the vertebrate host-pathogen interface that is defined by a 'tug-of-war' for biologically essential metals and provides the motivation for much recent work in this area. The host employs a number of strategies to starve the microbial pathogen of essential metals, while for others attempts to limit bacterial infections by leveraging highly competitive metals. Bacteria must be capable of adapting to these efforts to remodel the transition metal landscape and employ highly specialized metal sensing transcriptional regulators, termed metalloregulatory proteins,and metallochaperones, that allocate metals to specific destinations, to mediate this adaptive response. In this essay, we discuss recent progress in our understanding of the structural mechanisms and metal specificity of this adaptive response, focusing on energy-requiring metallochaperones that play roles in the metallocofactor active site assembly in metalloenzymes and metallosensors, which govern the systems-level response to metal limitation and intoxication.
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16
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Zuljan FA, Mortera P, Alarcón SH, Blancato VS, Espariz M, Magni C. Lactic acid bacteria decarboxylation reactions in cheese. Int Dairy J 2016. [DOI: 10.1016/j.idairyj.2016.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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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