1
|
The Regulations of Essential WalRK Two-Component System on Enterococcus faecalis. J Clin Med 2023; 12:jcm12030767. [PMID: 36769415 PMCID: PMC9917794 DOI: 10.3390/jcm12030767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
Enterococcus faecalis (E. faecalis) is a Gram-positive, facultative anaerobic bacterium that is highly adaptable to its environment. In humans, it can cause serious infections with biofilm formation. With increasing attention on its health threat, prevention and control of biofilm formation in E. faecalis have been observed. Many factors including polysaccharides as well as autolysis, proteases, and eDNA regulate biofilm formation. Those contributors are regulated by several important regulatory systems involving the two-component signal transduction system (TCS) for its adaptation to the environment. Highly conserved WalRK as one of 17 TCSs is the only essential TCS in E. faecalis. In addition to biofilm formation, various metabolisms, including cell wall construction, drug resistance, as well as interactions among regulatory systems and resistance to the host immune system, can be modulated by the WalRK system. Therefore, WalRK has been identified as a key target for E. faecalis infection control. In the present review, the regulation of WalRK on E. faecalis pathogenesis and associated therapeutic strategies are demonstrated.
Collapse
|
2
|
Ke N, Bauer CE. The Response Regulator RegA Is a Copper Binding Protein That Covalently Dimerizes When Exposed to Oxygen. Microorganisms 2022; 10:microorganisms10050934. [PMID: 35630378 PMCID: PMC9147068 DOI: 10.3390/microorganisms10050934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 01/27/2023] Open
Abstract
In Rhodobacter capsulatus, the histidine kinase RegB is believed to phosphorylate its cognate transcriptional factor RegA only under anaerobic conditions. However, transcriptome evidence indicates that RegA regulates 47 genes involved in energy storage, energy production, signaling and transcription, under aerobic conditions. In this study, we provide evidence that RegA is a copper binding protein and that copper promotes the dimerization of RegA under aerobic conditions. Inductively coupled plasma mass spectrometry (ICP-MS) analysis indicates that RegA binds Cu1+ and Cu2+ in a 1:1 and 2:1 ratio, respectively. Through LC-MS/MS, ESI-MS and non-reducing SDS-PAGE gels, we show that Cu2+ stimulates disulfide bond formation in RegA at Cys156 in the presence of oxygen. Finally, we used DNase I footprint analysis to demonstrate that Cu2+-mediated covalent dimerized RegA is capable of binding to the ccoN promoter, which drives the expression of cytochrome cbb3 oxidase subunits. This study provides a new model of aerobic regulation of gene expression by RegA involving the formation of an intermolecular disulfide bond.
Collapse
|
3
|
Ma P, Phillips-Jones MK. Membrane Sensor Histidine Kinases: Insights from Structural, Ligand and Inhibitor Studies of Full-Length Proteins and Signalling Domains for Antibiotic Discovery. Molecules 2021; 26:molecules26165110. [PMID: 34443697 PMCID: PMC8399564 DOI: 10.3390/molecules26165110] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/02/2021] [Accepted: 08/19/2021] [Indexed: 12/19/2022] Open
Abstract
There is an urgent need to find new antibacterial agents to combat bacterial infections, including agents that inhibit novel, hitherto unexploited targets in bacterial cells. Amongst novel targets are two-component signal transduction systems (TCSs) which are the main mechanism by which bacteria sense and respond to environmental changes. TCSs typically comprise a membrane-embedded sensory protein (the sensor histidine kinase, SHK) and a partner response regulator protein. Amongst promising targets within SHKs are those involved in environmental signal detection (useful for targeting specific SHKs) and the common themes of signal transmission across the membrane and propagation to catalytic domains (for targeting multiple SHKs). However, the nature of environmental signals for the vast majority of SHKs is still lacking, and there is a paucity of structural information based on full-length membrane-bound SHKs with and without ligand. Reasons for this lack of knowledge lie in the technical challenges associated with investigations of these relatively hydrophobic membrane proteins and the inherent flexibility of these multidomain proteins that reduces the chances of successful crystallisation for structural determination by X-ray crystallography. However, in recent years there has been an explosion of information published on (a) methodology for producing active forms of full-length detergent-, liposome- and nanodisc-solubilised membrane SHKs and their use in structural studies and identification of signalling ligands and inhibitors; and (b) mechanisms of signal sensing and transduction across the membrane obtained using sensory and transmembrane domains in isolation, which reveal some commonalities as well as unique features. Here we review the most recent advances in these areas and highlight those of potential use in future strategies for antibiotic discovery. This Review is part of a Special Issue entitled “Interactions of Bacterial Molecules with Their Ligands and Other Chemical Agents” edited by Mary K. Phillips-Jones.
Collapse
Affiliation(s)
- Pikyee Ma
- Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen, Switzerland;
| | - Mary K. Phillips-Jones
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
- Correspondence:
| |
Collapse
|
4
|
Jeong EL, Broad S, Moody R, Phillips-Jones M. The adherence-associated Fdp fasciclin I domain protein of the biohydrogen producer Rhodobacter sphaeroides is regulated by the global Prr pathway. INTERNATIONAL JOURNAL OF HYDROGEN ENERGY 2020; 45:26840-26854. [PMID: 33093750 PMCID: PMC7561615 DOI: 10.1016/j.ijhydene.2020.07.108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 07/07/2020] [Accepted: 07/12/2020] [Indexed: 05/23/2023]
Abstract
Expression of fdp, encoding a fasciclin I domain protein important for adherence in the hydrogen-producing bacterium Rhodobacter sphaeroides, was investigated under a range of conditions to gain insights into optimization of adherence for immobilization strategies suitable for H2 production. The fdp promoter was linked to a lacZ reporter and expressed in wild type and in PRRB and PRRA mutant strains of the Prr regulatory pathway. Expression was significantly negatively regulated by Prr under all conditions of aerobiosis tested including anaerobic conditions (required for H2 production), and aerobically regardless of growth phase, growth medium complexity or composition, carbon source, heat and cold shock and dark/light conditions. Negative fdp regulation by Prr was reflected in cellular levels of translated Fdp protein. Since Prr is required directly for nitrogenase expression, we propose optimization of Fdp-based adherence in R. sphaeroides for immobilized biohydrogen production by inactivation of the PrrA binding site(s) upstream of fdp.
Collapse
Affiliation(s)
- E.-L. Jeong
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - S.J. Broad
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - R.G. Moody
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, United Kingdom
- Department of Molecular Biology & Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - M.K. Phillips-Jones
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, United Kingdom
| |
Collapse
|
5
|
Masukagami Y, Nijagal B, Mahdizadeh S, Tseng CW, Dayalan S, Tivendale KA, Markham PF, Browning GF, Sansom FM. A combined metabolomic and bioinformatic approach to investigate the function of transport proteins of the important pathogen Mycoplasma bovis. Vet Microbiol 2019; 234:8-16. [PMID: 31213276 DOI: 10.1016/j.vetmic.2019.05.008] [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: 11/27/2018] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 02/05/2023]
Abstract
Mycoplasma bovis is an economically important pathogen of the cattle industry worldwide, and there is an urgent need for a more effective vaccine to control the diseases caused by this organism. Although the M. bovis genome sequence is available, very few gene functions of M. bovis have been experimentally determined, and a better understanding of the genes involved in pathogenesis are required for vaccine development. In this study, we compared the metabolite profiles of wild type M. bovis to a number of strains that each contained a transposon insertion into a putative transporter gene. Transport systems are thought to play an important role in survival of mycoplasmas, as they rely on the host for many nutrients. We also performed 13C-stable isotope labelling on strains with transposon insertions into putative glycerol transporters. Integration of metabolomic and bioinformatic analyses revealed unexpected results (when compared to genome annotation) for two mutants, with a putative amino acid transporter (MBOVPG45_0533) appearing more likely to transport nucleotide sugars, and a second mutant, a putative dicarboxylate/amino acid:cation (Na+ or H+) symporter (DAACS), more likely to function as a biopterin/folate transporter. This study also highlighted the apparent redundancy in some transport and metabolic pathways, such as the glycerol transport systems, even in an organism with a reduced genome. Overall, this study highlights the value of metabolomics for revealing the likely function of a number of transporters of M. bovis.
Collapse
Affiliation(s)
- Yumiko Masukagami
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Brunda Nijagal
- Metabolomics Australia, The Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Victoria, Australia
| | - Sara Mahdizadeh
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Chi-Wen Tseng
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Saravanan Dayalan
- Metabolomics Australia, The Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Victoria, Australia
| | - Kelly A Tivendale
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Philip F Markham
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Fiona M Sansom
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia.
| |
Collapse
|
6
|
Reyes Ruiz LM, Fiebig A, Crosson S. Regulation of bacterial surface attachment by a network of sensory transduction proteins. PLoS Genet 2019; 15:e1008022. [PMID: 31075103 PMCID: PMC6530869 DOI: 10.1371/journal.pgen.1008022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/22/2019] [Accepted: 04/26/2019] [Indexed: 11/25/2022] Open
Abstract
Bacteria are often attached to surfaces in natural ecosystems. A surface-associated lifestyle can have advantages, but shifts in the physiochemical state of the environment may result in conditions in which attachment has a negative fitness impact. Therefore, bacteria employ numerous mechanisms to control the transition from an unattached to a sessile state. The Caulobacter crescentus protein HfiA is a potent developmental inhibitor of the secreted polysaccharide adhesin known as the holdfast, which enables permanent attachment to surfaces. Multiple environmental cues influence expression of hfiA, but mechanisms of hfiA regulation remain largely undefined. Through a forward genetic selection, we have discovered a multi-gene network encoding a suite of two-component system (TCS) proteins and transcription factors that coordinately control hfiA transcription, holdfast development and surface adhesion. The hybrid HWE-family histidine kinase, SkaH, is central among these regulators and forms heteromeric complexes with the kinases, LovK and SpdS. The response regulator SpdR indirectly inhibits hfiA expression by activating two XRE-family transcription factors that directly bind the hfiA promoter to repress its transcription. This study provides evidence for a model in which a consortium of environmental sensors and transcriptional regulators integrate environmental cues at the hfiA promoter to control the attachment decision. Living on a surface within a community of cells confers a number of advantages to a bacterium. However, the transition from a free-living, planktonic state to a surface-attached lifestyle should be tightly regulated to ensure that cells avoid adhering to toxic or resource-limited niches. Many bacteria build adhesive structures on the surface of their cell envelopes that enable attachment. We sought to discover genes that control development of the Caulobacter crescentus surface adhesin known as the holdfast. Our studies uncovered a network of signal transduction proteins that coordinately control the biosynthesis of the holdfast by regulating transcription of the holdfast inhibitor, hfiA. We conclude that C. crescentus uses a multi-component regulatory system to sense and integrate environmental information to determine whether to attach to a surface, or to remain in an unattached state.
Collapse
Affiliation(s)
- Leila M Reyes Ruiz
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Aretha Fiebig
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois United States of America
| | - Sean Crosson
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois United States of America.,Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| |
Collapse
|
7
|
Lee SJ, Kim DG, Lee KY, Koo JS, Lee BJ. Regulatory mechanisms of thiol-based redox sensors: lessons learned from structural studies on prokaryotic redox sensors. Arch Pharm Res 2018; 41:583-593. [PMID: 29777359 DOI: 10.1007/s12272-018-1036-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/01/2018] [Indexed: 01/29/2023]
Abstract
Oxidative stresses, such as reactive oxygen species, reactive electrophilic species, reactive nitrogen species, and reactive chlorine species, can damage cellular components, leading to cellular malfunction and death. In response to oxidative stress, bacteria have evolved redox-responsive sensors that enable them to simultaneously monitor and eradicate potential oxidative stress. Specifically, redox-sensing transcription regulators react to oxidative stress by means of modifying the thiol groups of cysteine residues, functioning as part of an efficient survival mechanism for many bacteria. In general, oxidative molecules can induce changes in the three-dimensional structures of redox sensors, which, in turn, affects the transcription of specific genes in detoxification pathways and defense mechanisms. Moreover, pathogenic bacteria utilize these redox sensors for adaptation and to evade subsequent oxidative attacks from host immune defense. For this reason, the redox sensors of pathogenic bacteria are potential antibiotic targets. Understanding the regulatory mechanisms of thiol-based redox sensors in bacteria will provide insight and knowledge into the discovery of new antibiotics.
Collapse
Affiliation(s)
- Sang Jae Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Dong-Gyun Kim
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Kyu-Yeon Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Ji Sung Koo
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
| |
Collapse
|
8
|
CbbR and RegA regulate cbb operon transcription in Ralstonia eutropha H16. J Biotechnol 2017; 257:78-86. [DOI: 10.1016/j.jbiotec.2017.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 07/03/2017] [Accepted: 07/03/2017] [Indexed: 11/23/2022]
|
9
|
Le Laz S, kpebe A, Bauzan M, Lignon S, Rousset M, Brugna M. Expression of terminal oxidases under nutrient-starved conditions in Shewanella oneidensis: detection of the A-type cytochrome c oxidase. Sci Rep 2016; 6:19726. [PMID: 26815910 PMCID: PMC4728554 DOI: 10.1038/srep19726] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 12/17/2015] [Indexed: 11/12/2022] Open
Abstract
Shewanella species are facultative anaerobic bacteria that colonize redox-stratified habitats where O2 and nutrient concentrations fluctuate. The model species Shewanella oneidensis MR-1 possesses genes coding for three terminal oxidases that can perform O2 respiration: a bd-type quinol oxidase and cytochrome c oxidases of the cbb3-type and the A-type. Whereas the bd- and cbb3-type oxidases are routinely detected, evidence for the expression of the A-type enzyme has so far been lacking. Here, we investigated the effect of nutrient starvation on the expression of these terminal oxidases under different O2 tensions. Our results reveal that the bd-type oxidase plays a significant role under nutrient starvation in aerobic conditions. The expression of the cbb3-type oxidase is also modulated by the nutrient composition of the medium and increases especially under iron-deficiency in exponentially growing cells. Most importantly, under conditions of carbon depletion, high O2 and stationary-growth, we report for the first time the expression of the A-type oxidase in S. oneidensis, indicating that this terminal oxidase is not functionally lost. The physiological role of the A-type oxidase in energy conservation and in the adaptation of S. oneidensis to redox-stratified environments is discussed.
Collapse
Affiliation(s)
- Sébastien Le Laz
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, IMM, 13402 Marseille Cedex 20, France
| | - Arlette kpebe
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, IMM, 13402 Marseille Cedex 20, France
| | - Marielle Bauzan
- CNRS, Aix-Marseille Université, Unité de fermentation, FR3479, IMM, 13402 Marseille Cedex 20, France
| | - Sabrina Lignon
- CNRS, Aix-Marseille Université, Plate-forme Protéomique, FR3479, IMM, MaP IBiSA, 13402 Marseille Cedex 20, France
| | - Marc Rousset
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, IMM, 13402 Marseille Cedex 20, France
| | - Myriam Brugna
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, IMM, 13402 Marseille Cedex 20, France
| |
Collapse
|
10
|
Greive SJ, Fung HKH, Chechik M, Jenkins HT, Weitzel SE, Aguiar PM, Brentnall AS, Glousieau M, Gladyshev GV, Potts JR, Antson AA. DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif. Nucleic Acids Res 2015; 44:776-89. [PMID: 26673721 PMCID: PMC4737164 DOI: 10.1093/nar/gkv1467] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/30/2015] [Indexed: 11/14/2022] Open
Abstract
The helix-turn-helix (HTH) motif features frequently in protein DNA-binding assemblies. Viral pac site-targeting small terminase proteins possess an unusual architecture in which the HTH motifs are displayed in a ring, distinct from the classical HTH dimer. Here we investigate how such a circular array of HTH motifs enables specific recognition of the viral genome for initiation of DNA packaging during virus assembly. We found, by surface plasmon resonance and analytical ultracentrifugation, that individual HTH motifs of the Bacillus phage SF6 small terminase bind the packaging regions of SF6 and related SPP1 genome weakly, with little local sequence specificity. Nuclear magnetic resonance chemical shift perturbation studies with an arbitrary single-site substrate suggest that the HTH motif contacts DNA similarly to how certain HTH proteins contact DNA non-specifically. Our observations support a model where specificity is generated through conformational selection of an intrinsically bent DNA segment by a ring of HTHs which bind weakly but cooperatively. Such a system would enable viral gene regulation and control of the viral life cycle, with a minimal genome, conferring a major evolutionary advantage for SPP1-like viruses.
Collapse
Affiliation(s)
- Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Herman K H Fung
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK Department of Biology, University of York, York YO10 5DD, UK
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Huw T Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Stephen E Weitzel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Pedro M Aguiar
- Department of Chemistry, University of York, York YO10 5DD, UK
| | | | - Matthieu Glousieau
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Grigory V Gladyshev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russian Federation
| | | | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| |
Collapse
|
11
|
An integrated approach to reconstructing genome-scale transcriptional regulatory networks. PLoS Comput Biol 2015; 11:e1004103. [PMID: 25723545 PMCID: PMC4344238 DOI: 10.1371/journal.pcbi.1004103] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 12/23/2014] [Indexed: 11/24/2022] Open
Abstract
Transcriptional regulatory networks (TRNs) program cells to dynamically alter their gene expression in response to changing internal or environmental conditions. In this study, we develop a novel workflow for generating large-scale TRN models that integrates comparative genomics data, global gene expression analyses, and intrinsic properties of transcription factors (TFs). An assessment of this workflow using benchmark datasets for the well-studied γ-proteobacterium Escherichia coli showed that it outperforms expression-based inference approaches, having a significantly larger area under the precision-recall curve. Further analysis indicated that this integrated workflow captures different aspects of the E. coli TRN than expression-based approaches, potentially making them highly complementary. We leveraged this new workflow and observations to build a large-scale TRN model for the α-Proteobacterium Rhodobacter sphaeroides that comprises 120 gene clusters, 1211 genes (including 93 TFs), 1858 predicted protein-DNA interactions and 76 DNA binding motifs. We found that ~67% of the predicted gene clusters in this TRN are enriched for functions ranging from photosynthesis or central carbon metabolism to environmental stress responses. We also found that members of many of the predicted gene clusters were consistent with prior knowledge in R. sphaeroides and/or other bacteria. Experimental validation of predictions from this R. sphaeroides TRN model showed that high precision and recall was also obtained for TFs involved in photosynthesis (PpsR), carbon metabolism (RSP_0489) and iron homeostasis (RSP_3341). In addition, this integrative approach enabled generation of TRNs with increased information content relative to R. sphaeroides TRN models built via other approaches. We also show how this approach can be used to simultaneously produce TRN models for each related organism used in the comparative genomics analysis. Our results highlight the advantages of integrating comparative genomics of closely related organisms with gene expression data to assemble large-scale TRN models with high-quality predictions. The ever growing amount of genomic data enables the assembly of large-scale network models that can provide important new insights into living systems. However, assembly and validation of such large-scale models can be challenging, since we often lack sufficient information to make accurate predictions. This work describes a new approach for constructing large-scale transcriptional regulatory networks of individual cells. We show that the reconstructed network captures a significantly larger fraction of cellular regulatory processes than networks generated by other existing approaches. We predict this approach, with appropriate refinements, will allow reconstruction of large-scale transcriptional network models for a variety of other organisms. As we work towards modeling the function of cells or complex ecosystems, individually reconstructed network models of signaling, information transfer and metabolism, can be integrated to provide high information predictions and insights not otherwise obtainable.
Collapse
|
12
|
Imam S, Noguera DR, Donohue TJ. Global analysis of photosynthesis transcriptional regulatory networks. PLoS Genet 2014; 10:e1004837. [PMID: 25503406 PMCID: PMC4263372 DOI: 10.1371/journal.pgen.1004837] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 10/20/2014] [Indexed: 12/18/2022] Open
Abstract
Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888), which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabolism and regulation of sRNA synthesis. Using global gene expression analysis combined with ChIP-seq, we mapped the regulons of PrrA, CrpK and MppG. PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis. Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant. We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA. Our results reveal a previously unrealized, high degree of combinatorial regulation of photosynthetic genes and significant cross-talk between their transcriptional regulators, while illustrating previously unidentified links between photosynthesis and the maintenance of iron homeostasis. Photosynthetic organisms are among the most abundant life forms on earth. Their unique ability to harvest solar energy and use it to fix atmospheric carbon dioxide is at the foundation of the global food chain. This paper reports the first comprehensive analysis of networks that control expression of photosynthesis genes using Rhodobacter sphaeroides, a microbe that has been studied for decades as a model of solar energy capture and other aspects of the photosynthetic lifestyle. We find a previously unappreciated complexity in the level of control of photosynthetic genes, while identifying new links between photosynthesis and central processes like iron availability. This organism is an ancestor of modern day plants, so our data can inform studies in other photosynthetic organisms and improve our ability to harness solar energy for food and industrial processes.
Collapse
Affiliation(s)
- Saheed Imam
- Program in Cellular and Molecular Biology, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin – Madison, Wisconsin Energy Institute, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Daniel R. Noguera
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- Department of Civil and Environmental Engineering, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Timothy J. Donohue
- Department of Bacteriology, University of Wisconsin – Madison, Wisconsin Energy Institute, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- * E-mail:
| |
Collapse
|
13
|
Amino acid residues of RegA important for interactions with the CbbR-DNA complex of Rhodobacter sphaeroides. J Bacteriol 2014; 196:3179-90. [PMID: 24957624 DOI: 10.1128/jb.01842-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
CbbR and RegA (PrrA) are transcriptional regulators of the Calvin-Benson-Bassham (CBB) CO2 fixation pathway (cbbI and cbbII) operons of Rhodobacter sphaeroides. The CbbR and RegA proteins interact, but CbbR must be bound to the promoter DNA in order for RegA-CbbR protein-protein interactions to occur. RegA greatly enhances the ability of CbbR to bind the cbbI promoter or greatly enhances the stability of the CbbR/promoter complex. The N-terminal receiver domain and the DNA binding domain of RegA were shown to interact with CbbR. Residues in α-helix 7 and α-helix 8 of the DNA binding domain (helix-turn-helix) of RegA directly interacted with CbbR, with α-helix 7 positioned immediately above the DNA and α-helix 8 located in the major groove of the DNA. A CbbR protein containing only the DNA binding motif and the linker helix was capable of binding to RegA. In contrast, a truncated CbbR containing only the linker helix and recognition domains I and II (required for effector binding) was not able to interact with RegA. The accumulated results strongly suggest that the DNA binding domains of both proteins interact to facilitate optimal transcriptional control over the cbb operons. In vivo analysis, using constitutively active mutant CbbR proteins, further indicated that CbbR must interact with phosphorylated RegA in order to accomplish transcriptional activation.
Collapse
|
14
|
The C-terminal domain of the Uup protein is a DNA-binding coiled coil motif. J Struct Biol 2012; 180:577-84. [DOI: 10.1016/j.jsb.2012.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 09/07/2012] [Accepted: 09/08/2012] [Indexed: 11/21/2022]
|
15
|
Bueno E, Mesa S, Bedmar EJ, Richardson DJ, Delgado MJ. Bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control. Antioxid Redox Signal 2012; 16:819-52. [PMID: 22098259 PMCID: PMC3283443 DOI: 10.1089/ars.2011.4051] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 11/16/2011] [Accepted: 11/18/2011] [Indexed: 12/22/2022]
Abstract
Under a shortage of oxygen, bacterial growth can be faced mainly by two ATP-generating mechanisms: (i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to use traces of oxygen or (ii) by utilizing other substrates as final electron acceptors such as nitrate, which can be reduced to dinitrogen gas through denitrification or to ammonium. This bacterial respiratory shift from oxic to microoxic and anoxic conditions requires a regulatory strategy which ensures that cells can sense and respond to changes in oxygen tension and to the availability of other electron acceptors. Bacteria can sense oxygen by direct interaction of this molecule with a membrane protein receptor (e.g., FixL) or by interaction with a cytoplasmic transcriptional factor (e.g., Fnr). A third type of oxygen perception is based on sensing changes in redox state of molecules within the cell. Redox-responsive regulatory systems (e.g., ArcBA, RegBA/PrrBA, RoxSR, RegSR, ActSR, ResDE, and Rex) integrate the response to multiple signals (e.g., ubiquinone, menaquinone, redox active cysteine, electron transport to terminal oxidases, and NAD/NADH) and activate or repress target genes to coordinate the adaptation of bacterial respiration from oxic to anoxic conditions. Here, we provide a compilation of the current knowledge about proteins and regulatory networks involved in the redox control of the respiratory adaptation of different bacterial species to microxic and anoxic environments.
Collapse
Affiliation(s)
- Emilio Bueno
- Estación Experimental del Zaidín, CSIC, Granada, Spain
| | | | | | | | | |
Collapse
|
16
|
Sahota G, Stormo GD. Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. ACTA ACUST UNITED AC 2010; 26:2672-7. [PMID: 20807838 DOI: 10.1093/bioinformatics/btq501] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Computational techniques for microbial genomic sequence analysis are becoming increasingly important. With next-generation sequencing technology and the human microbiome project underway, current sequencing capacity is significantly greater than the speed at which organisms of interest can be studied experimentally. Most related computational work has been focused on sequence assembly, gene annotation and metabolic network reconstruction. We have developed a method that will primarily use available sequence data in order to determine prokaryotic transcription factor (TF) binding specificities. RESULTS Specificity determining residues (critical residues) were identified from crystal structures of DNA-protein complexes and TFs with the same critical residues were grouped into specificity classes. The putative binding regions for each class were defined as the set of promoters for each TF itself (autoregulatory) and the immediately upstream and downstream operons. MEME was used to find putative motifs within each separate class. Tests on the LacI and TetR TF families, using RegulonDB annotated sites, showed the sensitivity of prediction 86% and 80%, respectively. AVAILABILITY http://ural.wustl.edu/∼gsahota/HTHmotif/
Collapse
Affiliation(s)
- Gurmukh Sahota
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | | |
Collapse
|
17
|
Petrova LP, Varshalomidze OE, Shelud’ko AV, Katsy EI. Localization of denitrification genes in plasmid DNA of bacteria Azospirillum brasilense. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410070045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
18
|
Ma P, Ma P, Yuille HM, Ma P, Yuille HM, Blessie V, Göhring N, Iglói Z, Nishiguchi K, Nakayama J, Henderson PJF, Phillips-Jones MK. Expression, purification and activities of the entire family of intact membrane sensor kinases fromEnterococcus faecalis. Mol Membr Biol 2009; 25:449-73. [DOI: 10.1080/09687680802359885] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
19
|
Regulation of gene expression by PrrA in Rhodobacter sphaeroides 2.4.1: role of polyamines and DNA topology. J Bacteriol 2009; 191:4341-52. [PMID: 19411327 DOI: 10.1128/jb.00243-09] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the present study, we show in vitro binding of PrrA, a global regulator in Rhodobacter sphaeroides 2.4.1, to the PrrA site 2, within the RSP3361 locus. Specific binding, as shown by competition experiments, requires the phosphorylation of PrrA. The binding affinity of PrrA for site 2 was found to increase 4- to 10-fold when spermidine was added to the binding reaction. The presence of extracellular concentrations of spermidine in growing cultures of R. sphaeroides gave rise to a twofold increase in the expression of the photosynthesis genes pucB and pufB, as well as the RSP3361 gene, under aerobic growth conditions, as shown by the use of lacZ transcriptional fusions, and led to the production of light-harvesting spectral complexes. In addition, we show that negative supercoiling positively regulates the expression of the RSP3361 gene, as well as pucB. We show the importance of supercoiling through an evaluation of the regulation of gene expression in situ by supercoiling, in the case of the former gene, as well as using the DNA gyrase inhibitor novobiocin. We propose that polyamines and DNA supercoiling act synergistically to regulate expression of the RSP3361 gene, partly by affecting the affinity of PrrA binding to the PrrA site 2 within the RSP3361 gene.
Collapse
|
20
|
Half-Site DNA sequence and spacing length contributions to PrrA binding to PrrA site 2 of RSP3361 in Rhodobacter sphaeroides 2.4.1. J Bacteriol 2009; 191:4353-64. [PMID: 19411326 DOI: 10.1128/jb.00244-09] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The consensus DNA binding sequence for PrrA, a global regulator in Rhodobacter sphaeroides 2.4.1, is poorly defined. We have performed mutational analysis of PrrA site 2, of the RSP3361 gene, to which PrrA binds in vitro (J. M. Eraso and S. Kaplan, J. Bacteriol. 191:4341-4352, 2009), to further define the consensus sequence for DNA binding. Two half-sites of equal length, containing 6 nucleotides each, were required for PrrA binding to this DNA sequence. Systematic nucleotide substitutions in both inverted half-sites led to a decrease in binding affinity of phosphorylated PrrA in vitro, the level of which was dependent on the substitution. The reduced binding affinities were confirmed by competition experiments and led to proportional decreases in the expression of lacZ transcriptional fusions to the RSP3361 gene in vivo. The 5-nucleotide spacer region between the half-sites was found to be optimal for PrrA binding to the wild-type half-sites, as shown by decreased PrrA DNA binding affinities to synthetic DNA sequences without spacer regions or with spacer regions ranging from 1 to 10 nucleotides. The synthetic spacer region alleles also showed decreased gene expression in vivo when analyzed using lacZ transcriptional fusions. We have studied three additional DNA sequences to which PrrA binds in vitro. They are located in the regulatory regions of genes positively regulated by PrrA and contain spacer regions with 5 or 8 nucleotides. We demonstrate that PrrA can bind in vitro to DNA sequences with different lengths in the spacer regions between the half-sites.
Collapse
|
21
|
Bauer CE, Setterdahl A, Wu J, Robinson BR. Regulation of Gene Expression in Response to Oxygen Tension. THE PURPLE PHOTOTROPHIC BACTERIA 2009. [DOI: 10.1007/978-1-4020-8815-5_35] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
22
|
Dangel AW, Tabita FR. Protein-protein interactions between CbbR and RegA (PrrA), transcriptional regulators of the cbb operons of Rhodobacter sphaeroides. Mol Microbiol 2008; 71:717-29. [PMID: 19077171 DOI: 10.1111/j.1365-2958.2008.06558.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CbbR and RegA (PrrA) are transcriptional regulators of the cbb(I) and cbb(II) (Calvin-Benson-Bassham CO(2) fixation pathway) operons of Rhodobacter sphaeroides. Both proteins interact specifically with promoter sequences of the cbb operons. RegA has four DNA binding sites within the cbb(I) promoter region, with the CbbR binding site and RegA binding site 1 overlapping each other. This study demonstrated that CbbR and RegA interact and form a discrete complex in vitro, as illustrated by gel mobility shift experiments, direct isolation of the proteins from DNA complexes, and chemical cross-linking analyses. For CbbR/RegA interactions to occur, CbbR must be bound to the DNA, with the ability of CbbR to bind the cbb(I) promoter enhanced by RegA. Conversely, interactions with CbbR did not require RegA to bind the cbb(I) promoter. RegA itself formed incrementally larger multimeric complexes with DNA as the concentration of RegA increased. The presence of RegA binding sites 1, 2 and 3 promoted RegA/DNA binding at significantly lower concentrations of RegA than when RegA binding site 3 was not present in the cbb(I) promoter. These studies support the premise that both CbbR and RegA are necessary for optimal transcription of the cbb(I) operon genes of R. sphaeroides.
Collapse
Affiliation(s)
- Andrew W Dangel
- Department of Microbiology and Plant Molecular Biology/Biotechnology Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210-1292, USA
| | | |
Collapse
|
23
|
RegB/RegA, A Global Redox-Responding Two-Component System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 631:131-48. [DOI: 10.1007/978-0-387-78885-2_9] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
24
|
Hierarchical regulation of photosynthesis gene expression by the oxygen-responsive PrrBA and AppA-PpsR systems of Rhodobacter sphaeroides. J Bacteriol 2008; 190:8106-14. [PMID: 18931128 DOI: 10.1128/jb.01094-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the facultatively phototrophic proteobacterium Rhodobacter sphaeroides, formation of the photosynthetic apparatus is oxygen dependent. When oxygen tension decreases, the response regulator PrrA of the global two-component PrrBA system is believed to directly activate transcription of the puf, puh, and puc operons, encoding structural proteins of the photosynthetic complexes, and to indirectly upregulate the photopigment biosynthesis genes bch and crt. Decreased oxygen also results in inactivation of the photosynthesis-specific repressor PpsR, bringing about derepression of the puc, bch, and crt operons. We uncovered a hierarchical relationship between these two regulatory systems, earlier thought to function independently. We also more accurately assessed the spectrum of gene targets of the PrrBA system. First, expression of the appA gene, encoding the PpsR antirepressor, is PrrA dependent, which establishes one level of hierarchical dominance of the PrrBA system over AppA-PpsR. Second, restoration of the appA transcript to the wild-type level is insufficient for rescuing phototrophic growth impairment of the prrA mutant, whereas inactivation of ppsR is sufficient. This suggests that in addition to controlling appA transcription, PrrA affects the activity of the AppA-PpsR system via an as yet unidentified mechanism(s). Third, PrrA directly activates several bch and crt genes, traditionally considered to be the PpsR targets. Therefore, in R. sphaeroides, the global PrrBA system regulates photosynthesis gene expression (i) by rigorous control over the photosynthesis-specific AppA-PpsR regulatory system and (ii) by extensive direct transcription activation of genes encoding structural proteins of photosynthetic complexes as well as genes encoding photopigment biosynthesis enzymes.
Collapse
|
25
|
Abstract
Part of the oxygen responsiveness of Rhodobacter sphaeroides 2.4.1 tetrapyrrole production involves changes in transcription of the hemA gene, which codes for one of two isoenzymes catalyzing 5-aminolevulinic acid synthesis. Regulation of hemA transcription from its two promoters is mediated by the DNA binding proteins FnrL and PrrA. The two PrrA binding sites, binding sites I and II, which are located upstream of the more-5' hemA promoter (P1), are equally important to transcription under aerobic conditions, while binding site II is more important under anaerobic conditions. By using phosphoprotein affinity chromatography and immunoblot analyses, we showed that the phosphorylated PrrA levels in the cell increase with decreasing oxygen tensions. Then, using both in vivo and in vitro methods, we demonstrated that the relative affinities of phosphorylated and unphosphorylated PrrA for the two binding sites differ and that phosphorylated PrrA has greater affinity for site II. We also showed that PrrA regulation is directed toward the P1 promoter. We propose that the PrrA component of anaerobic induction of P1 transcription is attributable to higher affinity of phosphorylated PrrA than of unphosphorylated PrrA for binding site II. Anaerobic activation of the more-3' hemA promoter (P2) is thought to involve FnrL binding to an FNR consensuslike sequence located upstream of the P2 promoter, but the contribution of FnrL to P1 induction may be indirect since the P1 transcription start is within the putative FnrL binding site. We present evidence suggesting that the indirect action of FnrL works through PrrA and discuss possible mechanisms.
Collapse
|
26
|
Mackenzie C, Eraso JM, Choudhary M, Roh JH, Zeng X, Bruscella P, Puskás A, Kaplan S. Postgenomic adventures with Rhodobacter sphaeroides. Annu Rev Microbiol 2007; 61:283-307. [PMID: 17506668 DOI: 10.1146/annurev.micro.61.080706.093402] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review describes some of the recent highlights taken from the studies of Rhodobacter sphaeroides 2.4.1. The review is not intended to be comprehensive, but to reflect the bias of the authors as to how the availability of a sequenced and annotated genome, a gene-chip, and proteomic profile as well as comparative genomic analyses can direct the progress of future research in this system.
Collapse
Affiliation(s)
- Chris Mackenzie
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030, USA.
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Han Y, Meyer MHF, Keusgen M, Klug G. A haem cofactor is required for redox and light signalling by the AppA protein of Rhodobacter sphaeroides. Mol Microbiol 2007; 64:1090-104. [PMID: 17501930 DOI: 10.1111/j.1365-2958.2007.05724.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The AppA protein of Rhodobacter sphaeroides is unique in its ability to sense and transmit redox signals as well as light signals. By functioning as antagonist to the PpsR transcriptional repressor, it regulates the expression of photosynthesis genes in response to these environmental stimuli. Here we show binding of the cofactor haem to a domain in the C-terminal part of AppA and redox activity of bound haem. This is supported by the findings that: (i) the C-terminal domain of AppA (AppADeltaN) binds to haemin agarose, (ii) AppADeltaN isolated from Escherichia coli shows absorbance at 411 nm and absorbances at 424 nm and 556 nm after reduction with dithionite and (iii) AppADeltaN can be reconstituted with haem in vitro. Expression of AppA variants in R. sphaeroides reveals that the haem binding domain is important for normal expression levels of photosynthesis genes and for normal light regulation in the presence of oxygen. The haem cofactor affects the interaction of the C-terminal part of AppA to PpsR but also its interaction to the N-terminal light sensing AppA-BLUF domain. Based on this we present a model for the transmission of light and redox signals by AppA.
Collapse
Affiliation(s)
- Yuchen Han
- Institut für Mikrobiologie und Molekularbiologie, University of Giessen, D-35392 Giessen, Germany
| | | | | | | |
Collapse
|
28
|
Agrobacterium tumefaciens C58 uses ActR and FnrN to control nirK and nor expression. J Bacteriol 2007; 190:78-86. [PMID: 17981975 DOI: 10.1128/jb.00792-07] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agrobacterium tumefaciens can grow anaerobically via denitrification. To learn more about how cells regulate production of nitrite and nitric oxide, experiments were carried out to identify proteins involved in regulating expression and activity of nitrite and nitric oxide reductase. Transcription of NnrR, required for expression of these two reductases, was found to be under control of FnrN. Insertional inactivation of the response regulator actR significantly reduced nirK expression and Nir activity but not nnrR expression. Purified ActR bound to the nirK promoter but not the nor or nnrR promoter. A putative ActR binding site was identified in the nirK promoter region using mutational analysis and an in vitro binding assay. A nirK promoter containing mutations preventing the binding of ActR showed delayed expression but eventually reached about 65% of the activity of an equivalent wild-type promoter lacZ fusion. Truncation of the nirK promoter revealed that truncation up to and within the ActR binding site reduced expression, but fragments lacking the ActR binding site and retaining the NnrR binding site showed expression as high as or higher than the full-length fragment. Additional experiments revealed that expression of paz, encoding the copper protein pseudoazurin, was highly reduced in the actR or fnrN mutants and that ActR binds to the paz promoter. Inactivation of paz reduced Nir activity by 55%. These results help explain why Nir activity is very low in the actR mutant even though a nirK promoter with mutations in the ActR binding site showed significant expression.
Collapse
|
29
|
Tavano CL, Donohue TJ. Development of the bacterial photosynthetic apparatus. Curr Opin Microbiol 2006; 9:625-31. [PMID: 17055774 PMCID: PMC2765710 DOI: 10.1016/j.mib.2006.10.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 10/11/2006] [Indexed: 11/29/2022]
Abstract
Anoxygenic photosynthetic bacteria have provided us with crucial insights into the process of solar energy capture, pathways of metabolic and societal importance, specialized differentiation of membrane domains, function or assembly of bioenergetic enzymes, and into the genetic control of these and other activities. Recent insights into the organization of this bioenergetic membrane system, the genetic control of this specialized domain of the inner membrane and the process by which potentially photosynthetic and non-photosynthetic cells protect themselves from an important class of reactive oxygen species will provide an unparalleled understanding of solar energy capture and facilitate the design of solar-powered microbial biorefineries.
Collapse
Affiliation(s)
- Christine L Tavano
- Bacteriology Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | |
Collapse
|
30
|
Beller HR, Letain TE, Chakicherla A, Kane SR, Legler TC, Coleman MA. Whole-genome transcriptional analysis of chemolithoautotrophic thiosulfate oxidation by Thiobacillus denitrificans under aerobic versus denitrifying conditions. J Bacteriol 2006; 188:7005-15. [PMID: 16980503 PMCID: PMC1595532 DOI: 10.1128/jb.00568-06] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with key chemolithoautotrophic functions (such as sulfur compound oxidation and CO2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately 10% of the genome) as differentially expressed using RMA (robust multiarray average) statistical analysis and a twofold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated, respectively, with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription-quantitative PCR analysis was used to validate these trends.
Collapse
Affiliation(s)
- Harry R Beller
- Lawrence Livermore National Laboratory, P. O. Box 808, L-542, Livermore, CA 94551-0808, USA.
| | | | | | | | | | | |
Collapse
|
31
|
Seok JS, Kaplan S, Oh JI. Interacting specificity of a histidine kinase and its cognate response regulator: the PrrBA system of Rhodobacter sphaeroides. MICROBIOLOGY-SGM 2006; 152:2479-2490. [PMID: 16849810 DOI: 10.1099/mic.0.28961-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Using a yeast two-hybrid assay system, it was demonstrated that the four-helix bundle of the Rhodobacter sphaeroides PrrB histidine kinase both serves as the interaction site for the regulatory domain of its cognate response regulator PrrA and is the primary determinant of the interaction specificity. The alpha-helix 1 and its flanking turn region within the dimerization domain (DD) of the PrrB histidine kinase appear to play an important role in conferring the recognition specificity for the PrrA response regulator on the DD. The catalytic ATP-binding domain of the histidine kinase, which functions as the catalytic unit for the phosphotransfer reaction from ATP to the conserved histidine residue in the DD, also appears to contribute to the enhancement of the recognition specificity conferred by the DD. It was also revealed that replacement of Asp-63 and Lys-113 of the PrrA response regulator by alanine abolished protein-protein interactions between PrrA and its cognate histidine kinase PrrB, whereas mutations of Asp-19, Asp-20 and Thr-87 to alanine did not affect protein-protein interactions, indicating that among the active site residues of PrrA, Asp-63 and Lys-113 are important not only in the function of PrrA but also for protein-protein interactions between PrrA and PrrB.
Collapse
Affiliation(s)
- Jin-Sook Seok
- Department of Microbiology, Pusan National University, 609-735 Busan, South Korea
| | - Samuel Kaplan
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center Medical School, 6431 Fannin, Houston, TX 77030, USA
| | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, 609-735 Busan, South Korea
| |
Collapse
|
32
|
Williamson M, Suzuki Y, Bourne N, Asakura T. Binding of amyloid beta-peptide to ganglioside micelles is dependent on histidine-13. Biochem J 2006; 397:483-90. [PMID: 16626304 PMCID: PMC1533309 DOI: 10.1042/bj20060293] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Amyloid beta-peptide (Abeta) is a major component of plaques in Alzheimer's disease, and formation of senile plaques has been suggested to originate from regions of neuronal membrane rich in gangliosides. Here we demonstrate using NMR on 15N-labelled Abeta-(1-40) and Abeta-(1-42) that the interaction with ganglioside G(M1) micelles is localized to the N-terminal region of the peptide, particularly residues His13 to Leu17, which become more helical when bound. The key interaction is with His13, which undergoes a G(M1)-specific conformational change. The sialic acid residue of the ganglioside headgroup is important for determining the nature of the conformational change. The isolated pentasaccharide headgroup of G(M1) is not bound, suggesting the need for a polyanionic surface. Binding to heparin confirms this suggestion, since binding is of similar affinity but does not produce the same conformational changes in the peptide. A comparison of Abeta-(1-40) and Abeta-(1-42) indicates that binding to G(M1) micelles is not related to oligomerization, which occurs at the C-terminal end. These results imply that binding to ganglioside micelles causes a transition from random coil to alpha-helix in the N-terminal region, leaving the C-terminal region unstructured.
Collapse
Affiliation(s)
- Mike P. Williamson
- *Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, U.K
- To whom correspondence should be addressed (email )
| | - Yu Suzuki
- †Department of Biotechnology, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Nathan T. Bourne
- *Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, U.K
| | - Tetsuo Asakura
- †Department of Biotechnology, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| |
Collapse
|
33
|
Laguri C, Stenzel RA, Donohue TJ, Phillips-Jones MK, Williamson MP. Activation of the global gene regulator PrrA (RegA) from Rhodobacter sphaeroides. Biochemistry 2006; 45:7872-81. [PMID: 16784239 PMCID: PMC2517121 DOI: 10.1021/bi060683g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PrrA is a global transcription regulator activated upon phosphorylation by its cognate kinase PrrB in response to low oxygen levels in Rhodobacter sphaeroides. Here we show by gel filtration, analytical ultracentrifugation, and NMR diffusion measurements that treatment of PrrA with a phosphate analogue, BeF(3)(-), results in dimerization of the protein, producing a protein that binds DNA. No dimeric species was observed in the absence of BeF(3)(-). Upon addition of BeF(3)(-), the inhibitory activity of the N-terminal domain on the C-terminal DNA-binding domain is relieved, after which PrrA becomes capable of binding DNA as a dimer. The interaction surface of the DNA-binding domain with the regulatory domain of PrrA is identified by NMR as being a well-conserved region centered on helix alpha6, which is on the face opposite from the DNA recognition helix. This suggests that there is no direct blockage of DNA binding in the inactive state but rather that PrrA dimerization promotes a correct arrangement of two adjacent DNA-binding domains that recognizes specific DNA binding sequences.
Collapse
Affiliation(s)
- Cédric Laguri
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, UK
| | | | | | | | | |
Collapse
|
34
|
Ranson-Olson B, Jones DF, Donohue TJ, Zeilstra-Ryalls JH. In vitro and in vivo analysis of the role of PrrA in Rhodobacter sphaeroides 2.4.1 hemA gene expression. J Bacteriol 2006; 188:3208-18. [PMID: 16621813 PMCID: PMC1447469 DOI: 10.1128/jb.188.9.3208-3218.2006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hemA gene codes for one of two synthases in Rhodobacter sphaeroides 2.4.1 which catalyze the formation of 5-aminolevulinic acid. We have examined the role of PrrA, a DNA binding protein that is associated with the metabolic switch between aerobic growth and anoxygenic photosynthetic growth, in hemA expression and found that hemA transcription is directly activated by PrrA. Using electrophoretic mobility shift assays and DNase I protection assays, we have mapped two binding sites for PrrA within the hemA upstream sequences, each of which contains an identical 9-bp motif. Using lacZ transcription reporter plasmids in wild-type strain 2.4.1 and PrrA- mutant strain PRRA2, we showed that PrrA was required for maximal expression. We also found that the relative impacts of altering DNA sequences within the two binding sites are different depending on whether cells are growing aerobically or anaerobically. This reveals a greater level of complexity associated with PrrA-mediated regulation of transcription than has been heretofore described. Our findings are of particular importance with respect to those genes regulated by PrrA having more than one upstream binding site. In the case of the hemA gene, we discuss possibilities as to how these new insights can be accommodated within the context of what has already been established for hemA transcription regulation in R. sphaeroides.
Collapse
Affiliation(s)
- Britton Ranson-Olson
- Department of Biological Sciences, 374 Dodge Hall, Oakland University, Rochester, Michigan 48309, USA
| | | | | | | |
Collapse
|
35
|
Galperin MY. Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J Bacteriol 2006; 188:4169-82. [PMID: 16740923 PMCID: PMC1482966 DOI: 10.1128/jb.01887-05] [Citation(s) in RCA: 372] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Accepted: 03/28/2006] [Indexed: 11/20/2022] Open
Abstract
CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. In this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. Previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. Transcriptional regulators of the OmpR, NarL, and NtrC families were found to comprise almost 60% of all response regulators; transcriptional regulators with other DNA-binding domains (LytTR, AraC, Spo0A, Fis, YcbB, RpoE, and MerR) account for an additional 6%. The remaining one-third is represented by the stand-alone REC domain (approximately 14%) and its combinations with a variety of enzymatic (GGDEF, EAL, HD-GYP, CheB, CheC, PP2C, and HisK), RNA-binding (ANTAR and CsrA), protein- or ligand-binding (PAS, GAF, TPR, CAP_ED, and HPt) domains, or newly described domains of unknown function. The diversity of domain architectures and the abundance of alternative domain combinations suggest that fusions between the REC domain and various output domains is a widespread evolutionary mechanism that allows bacterial cells to regulate transcription, enzyme activity, and/or protein-protein interactions in response to environmental challenges. The complete list of response regulators encoded in each of the 200 analyzed genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html.
Collapse
Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| |
Collapse
|
36
|
Potter CA, Jeong EL, Williamson MP, Henderson PJF, Phillips-Jones MK. Redox-responsive in vitro modulation of the signalling state of the isolated PrrB sensor kinase of Rhodobacter sphaeroides NCIB 8253. FEBS Lett 2006; 580:3206-10. [PMID: 16684526 DOI: 10.1016/j.febslet.2006.04.079] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Revised: 04/25/2006] [Accepted: 04/28/2006] [Indexed: 11/26/2022]
Abstract
Prr is a global regulatory system that controls a large and diverse range of genes in Rhodobacter sphaeroides in response to changing conditions of environmental redox potential. PrrB is the membrane-bound sensor kinase and previously we showed that the purified, detergent-solubilised intact membrane protein is functional in autophosphorylation, phosphotransfer and phosphatase activities. Here we confirm that it also senses and responds directly to its environmental signal, redox potential; strong autophosphorylation of PrrB occurred in response to dithiothreitol (DTT)-induced reducing conditions (and levels increased in response to a wide 0.1-100 mM DTT range), whilst under oxidising conditions, PrrB exhibited low, just detectable levels of autophosphorylation. The clear response of PrrB to changes in reducing conditions confirmed its suitability for in vitro studies to identify modulators of its phosphorylation signalling state, and was used here to investigate whether PrrB might sense more than one redox-related signal, such as signals of cell energy status. NADH, ATP and AMP were found to exert no detectable effect on maintenance of the PrrB-P signalling state. By contrast, adenosine diphosphate produced a very strong increase in PrrB-P dephosphorylation rate, presumably through the back-conversion of PrrB-P to PrrB.
Collapse
Affiliation(s)
- Christopher A Potter
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | | | | | | | | |
Collapse
|
37
|
Jones DF, Stenzel RA, Donohue TJ. Mutational analysis of the C-terminal domain of the Rhodobacter sphaeroides response regulator PrrA. MICROBIOLOGY-SGM 2006; 151:4103-4110. [PMID: 16339955 PMCID: PMC2800098 DOI: 10.1099/mic.0.28300-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Rhodobacter sphaeroides response regulator PrrA directly activates transcription of genes necessary for energy conservation at low O2 tensions and under anaerobic conditions. It is proposed that PrrA homologues contain a C-terminal DNA-binding domain (PrrA-CTD) that lacks significant amino acid sequence similarity to those found in other response regulators. To test this hypothesis, single amino acid substitutions were created at 12 residues in the PrrA-CTD. These mutant PrrA proteins were purified and tested for the ability to be phosphorylated by the low-molecular-mass phosphate donor acetyl phosphate, to activate transcription and to bind promoter DNA. Each mutant PrrA protein accepted phosphate from 32P-labelled acetyl phosphate. At micromolar concentrations of acetyl phosphate-treated wild-type PrrA, a single 20 bp region in the PrrA-dependent cycA P2 promoter was protected from DNase I digestion. Of the mutant PrrA proteins tested, only acetyl phosphate-treated PrrA-N168A and PrrA-I177A protected cycA P2 from DNase I digestion at similar protein concentrations compared to wild-type PrrA. The use of in vitro transcription assays with the PrrA-dependent cycA P2 and puc promoters showed that acetyl phosphate-treated PrrA-N168A produced transcript levels similar to that of wild-type PrrA at comparable protein concentrations. Using concentrations of acetyl phosphate-treated PrrA that are saturating for the wild-type protein, PrrA-H170A and PrrA-I177A produced <45 % as much transcript as wild-type PrrA. Under identical conditions, the remaining mutant PrrA proteins produced little or no detectable transcripts from either promoter in vitro. Explanations are presented for why these amino acid side chains in the PrrA-CTD are important for its ability to activate transcription.
Collapse
Affiliation(s)
- Denise F Jones
- Department of Bacteriology, University of Wisconsin-Madison, Room 390B, 420 Henry Mall, Madison, WI 53706, USA
| | - Rachelle A Stenzel
- Department of Bacteriology, University of Wisconsin-Madison, Room 390B, 420 Henry Mall, Madison, WI 53706, USA
| | - Timothy J Donohue
- Department of Bacteriology, University of Wisconsin-Madison, Room 390B, 420 Henry Mall, Madison, WI 53706, USA
| |
Collapse
|
38
|
Zeilstra-Ryalls JH, Schornberg KL. Analysis of hemF gene function and expression in Rhodobacter sphaeroides 2.4.1. J Bacteriol 2006; 188:801-4. [PMID: 16385070 PMCID: PMC1347313 DOI: 10.1128/jb.188.2.801-804.2006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hemF gene of Rhodobacter sphaeroides 2.4.1 is predicted to code for an oxygen-dependent coproporphyrinogen III oxidase. We found that a HemF- mutant strain is unable to grow under aerobic conditions. We also determined that hemF expression is controlled by oxygen, which is mediated, at least in part, by the response regulatory protein PrrA.
Collapse
Affiliation(s)
- Jill H Zeilstra-Ryalls
- Department of Biological Sciences, 374 Dodge Hall, Oakland University, Rochester, MI 48309, USA.
| | | |
Collapse
|
39
|
Hauser F, Lindemann A, Vuilleumier S, Patrignani A, Schlapbach R, Fischer HM, Hennecke H. Design and validation of a partial-genome microarray for transcriptional profiling of the Bradyrhizobium japonicum symbiotic gene region. Mol Genet Genomics 2005; 275:55-67. [PMID: 16328374 DOI: 10.1007/s00438-005-0059-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Accepted: 10/08/2005] [Indexed: 10/25/2022]
Abstract
The design and use of a pilot microarray for transcriptome analysis of the symbiotic, nitrogen-fixing Bradyrhizobium japonicum is reported here. The custom-synthesized chip (Affymetrix GeneChip) features 738 genes, more than half of which belong to a 400-kb chromosomal segment strongly associated with symbiosis-related functions. RNA was isolated following an optimized protocol from wild-type cells grown aerobically and microaerobically, and from cells of aerobically grown regR mutant and microaerobically grown nifA mutant. Comparative microarray analyses thus revealed genes that are transcribed in either a RegR- or a NifA-dependent manner plus genes whose expression depends on the cellular oxygen status. Several genes were newly identified as members of the RegR and NifA regulons, beyond genes, which had been known from previous work. A comprehensive transcription analysis was performed with one of the new RegR-controlled genes (id880). Expression levels determined by microarray analysis of selected NifA- and RegR-controlled genes corresponded well with quantitative real-time PCR data, demonstrating the high complementarity of microarray analysis to classical methods of gene expression analysis in B. japonicum. Nevertheless, several previously established members of the NifA regulon were not detected as transcribed genes by microarray analysis, confirming the potential pitfalls of this approach also observed by other authors. By and large, this pilot study has paved the way towards the genome-wide transcriptome analysis of the 9.1-Mb B. japonicum genome.
Collapse
Affiliation(s)
- F Hauser
- Institute of Microbiology, Eidgenössische Technische Hochschule, ETH-Hönggerberg, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
| | | | | | | | | | | | | |
Collapse
|
40
|
Mao L, Mackenzie C, Roh JH, Eraso JM, Kaplan S, Resat H. Combining microarray and genomic data to predict DNA binding motifs. Microbiology (Reading) 2005; 151:3197-3213. [PMID: 16207904 DOI: 10.1099/mic.0.28167-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to detect regulatory elements within genome sequences is important in understanding how gene expression is controlled in biological systems. In this work, microarray data analysis is combined with genome sequence analysis to predict DNA sequences in the photosynthetic bacterium Rhodobacter sphaeroides that bind the regulators PrrA, PpsR and FnrL. These predictions were made by using hierarchical clustering to detect genes that share similar expression patterns. The DNA sequences upstream of these genes were then searched for possible transcription factor recognition motifs that may be involved in their co-regulation. The approach used promises to be widely applicable for the prediction of cis-acting DNA binding elements. Using this method the authors were independently able to detect and extend the previously described consensus sequences that have been suggested to bind FnrL and PpsR. In addition, sequences that may be recognized by the global regulator PrrA were predicted. The results support the earlier suggestions that the DNA binding sequence of PrrA may have a variable-sized gap between its conserved block elements. Using the predicted DNA binding sequences, a whole-genome-scale analysis was performed to determine the relative importance of the interplay between the three regulators PpsR, FnrL and PrrA. Results of this analysis showed that, compared to the regulation by PpsR and FnrL, a much larger number of genes are candidates to be regulated by PrrA. The study demonstrates by example that integration of multiple data types can be a powerful approach for inferring transcriptional regulatory patterns in microbial systems, and it allowed the detection of photosynthesis-related regulatory patterns in R. sphaeroides.
Collapse
Affiliation(s)
- Linyong Mao
- Pacific Northwest National Laboratory, Computational Biology and Bioinformatics Group, PO Box 999, MS: K7-90, Richland, WA 99352, USA
| | - Chris Mackenzie
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Medical School, Houston, TX 77030, USA
| | - Jung H Roh
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Medical School, Houston, TX 77030, USA
| | - Jesus M Eraso
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Medical School, Houston, TX 77030, USA
| | - Samuel Kaplan
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Medical School, Houston, TX 77030, USA
| | - Haluk Resat
- Pacific Northwest National Laboratory, Computational Biology and Bioinformatics Group, PO Box 999, MS: K7-90, Richland, WA 99352, USA
| |
Collapse
|
41
|
McLaughlin WA, Kulp DW, de la Cruz J, Lu XJ, Lawson CL, Berman HM. A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction. ACTA ACUST UNITED AC 2005; 5:255-65. [PMID: 15704013 DOI: 10.1007/s10969-005-4902-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2004] [Accepted: 11/17/2004] [Indexed: 01/11/2023]
Abstract
A classification model of a DNA-binding protein chain was created based on identification of alpha helices within the chain likely to bind to DNA. Using the model, all chains in the Protein Data Bank were classified. For many of the chains classified with high confidence, previous documentation for DNA-binding was found, yet no sequence homology to the structures used to train the model was detected. The result indicates that the chain model can be used to supplement sequence based methods for annotating the function of DNA-binding. Four new candidates for DNA-binding were found, including two structures solved through structural genomics efforts. For each of the candidate structures, possible sites of DNA-binding are indicated by listing the residue ranges of alpha helices likely to interact with DNA.
Collapse
Affiliation(s)
- William A McLaughlin
- Department of Chemistry and Chemical Biology, Rutgers-The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
| | | | | | | | | | | |
Collapse
|
42
|
Smart JL, Willett JW, Bauer CE. Regulation of hem gene expression in Rhodobacter capsulatus by redox and photosystem regulators RegA, CrtJ, FnrL, and AerR. J Mol Biol 2004; 342:1171-86. [PMID: 15351643 DOI: 10.1016/j.jmb.2004.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2004] [Revised: 08/02/2004] [Accepted: 08/03/2004] [Indexed: 11/18/2022]
Abstract
Biosynthetic pathways for heme and chlorophyll share common intermediates from 5-aminolevulinic acid through protoporphyrin IX. To obtain a better understanding of how photosynthetic organisms coordinate heme and chlorophyll biosynthesis, we have undertaken detailed analysis of the expression pattern of numerous heme biosynthesis genes in the purple photosynthetic bacterium Rhodobacter capsulatus. beta-Galactosidase reporter assays demonstrated that expression of hemA, hemB, hemC, hemE and hemZ genes is elevated under conditions that give rise to elevated bacteriochlorophyll synthesis. Heme gene expression is shown to be affected by mutations in previously identified transcriptional regulators RegA, FnrL, CrtJ, and AerR, which also control expression of genes involved in bacteriochlorophyll and carotenoid synthesis, and synthesis of the apoprotein subunits of the photosynthetic and electron transport apparatus. High-resolution primer extension analysis of hem mRNA reveals the presence of numerous putative RegA, FnrL and CrtJ binding sites in several hem promoter regions.
Collapse
Affiliation(s)
- James L Smart
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | | |
Collapse
|
43
|
López-Marqués RL, Pérez-Castiñeira JR, Losada M, Serrano A. Differential regulation of soluble and membrane-bound inorganic pyrophosphatases in the photosynthetic bacterium Rhodospirillum rubrum provides insights into pyrophosphate-based stress bioenergetics. J Bacteriol 2004; 186:5418-26. [PMID: 15292143 PMCID: PMC490873 DOI: 10.1128/jb.186.16.5418-5426.2004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Soluble and membrane-bound inorganic pyrophosphatases (sPPase and H(+)-PPase, respectively) of the purple nonsulfur bacterium Rhodospirillum rubrum are differentially regulated by environmental growth conditions. Both proteins and their transcripts were found in cells of anaerobic phototrophic batch cultures along all growth phases, although they displayed different time patterns. However, in aerobic cells that grow in the dark, which exhibited the highest growth rates, Northern and Western blot analyses as well as activity assays demonstrated high sPPase levels but no H(+)-PPase. It is noteworthy that H(+)-PPase is highly expressed in aerobic cells under acute salt stress (1 M NaCl). H(+)-PPase was also present in anaerobic cells growing at reduced rates in the dark under either fermentative or anaerobic respiratory conditions. Since H(+)-PPase was detected not only under all anaerobic growth conditions but also under salt stress in aerobiosis, the corresponding gene is not invariably repressed by oxygen. Primer extension analyses showed that, under all anaerobic conditions tested, the R. rubrum H(+)-PPase gene utilizes two activator-dependent tandem promoters, one with an FNR-like sequence motif and the other with a RegA motif, whereas in aerobiosis under salt stress, the H(+)-PPase gene is transcribed from two further tandem promoters involving other transcription factors. These results demonstrate a tight transcriptional regulation of the H(+)-PPase gene, which appears to be induced in response to a variety of environmental conditions, all of which constrain cell energetics.
Collapse
MESH Headings
- Adaptation, Physiological
- Aerobiosis
- Anaerobiosis
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/metabolism
- Base Sequence
- Blotting, Northern
- Blotting, Western
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- Diphosphates/metabolism
- Energy Metabolism
- Gene Expression Regulation, Bacterial
- Inorganic Pyrophosphatase/biosynthesis
- Inorganic Pyrophosphatase/genetics
- Inorganic Pyrophosphatase/metabolism
- Light
- Membrane Proteins/biosynthesis
- Membrane Proteins/metabolism
- Molecular Sequence Data
- Osmotic Pressure
- Promoter Regions, Genetic
- RNA, Bacterial/analysis
- RNA, Bacterial/biosynthesis
- RNA, Messenger/analysis
- RNA, Messenger/biosynthesis
- Rhodospirillum rubrum/genetics
- Rhodospirillum rubrum/growth & development
- Rhodospirillum rubrum/metabolism
- Sequence Analysis, DNA
- Transcription Initiation Site
- Transcription, Genetic
- Transcriptional Activation
Collapse
Affiliation(s)
- Rosa L López-Marqués
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, 41092 Seville, Spain
| | | | | | | |
Collapse
|
44
|
Elsen S, Swem LR, Swem DL, Bauer CE. RegB/RegA, a highly conserved redox-responding global two-component regulatory system. Microbiol Mol Biol Rev 2004; 68:263-79. [PMID: 15187184 PMCID: PMC419920 DOI: 10.1128/mmbr.68.2.263-279.2004] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Reg regulon from Rhodobacter capsulatus and Rhodobacter sphaeroides encodes proteins involved in numerous energy-generating and energy-utilizing processes such as photosynthesis, carbon fixation, nitrogen fixation, hydrogen utilization, aerobic and anaerobic respiration, denitrification, electron transport, and aerotaxis. The redox signal that is detected by the membrane-bound sensor kinase, RegB, appears to originate from the aerobic respiratory chain, given that mutations in cytochrome c oxidase result in constitutive RegB autophosphorylation. Regulation of RegB autophosphorylation also involves a redox-active cysteine that is present in the cytosolic region of RegB. Both phosphorylated and unphosphorylated forms of the cognate response regulator RegA are capable of activating or repressing a variety of genes in the regulon. Highly conserved homologues of RegB and RegA have been found in a wide number of photosynthetic and nonphotosynthetic bacteria, with evidence suggesting that RegB/RegA plays a fundamental role in the transcription of redox-regulated genes in many bacterial species.
Collapse
Affiliation(s)
- Sylvie Elsen
- Laboratoire de Biochimie et de Biophysique des Systèmes Intégrés (UMR 5092 CNRS-CEA-UJF), Grenoble, France
| | | | | | | |
Collapse
|