1
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Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL. Structure of mycobacterial respiratory complex I. Proc Natl Acad Sci U S A 2023; 120:e2214949120. [PMID: 36952383 PMCID: PMC10068793 DOI: 10.1073/pnas.2214949120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/10/2023] [Indexed: 03/24/2023] Open
Abstract
Oxidative phosphorylation, the combined activity of the electron transport chain (ETC) and adenosine triphosphate synthase, has emerged as a valuable target for the treatment of infection by Mycobacterium tuberculosis and other mycobacteria. The mycobacterial ETC is highly branched with multiple dehydrogenases transferring electrons to a membrane-bound pool of menaquinone and multiple oxidases transferring electrons from the pool. The proton-pumping type I nicotinamide adenine dinucleotide (NADH) dehydrogenase (Complex I) is found in low abundance in the plasma membranes of mycobacteria in typical in vitro culture conditions and is often considered dispensable. We found that growth of Mycobacterium smegmatis in carbon-limited conditions greatly increased the abundance of Complex I and allowed isolation of a rotenone-sensitive preparation of the enzyme. Determination of the structure of the complex by cryoEM revealed the "orphan" two-component response regulator protein MSMEG_2064 as a subunit of the assembly. MSMEG_2064 in the complex occupies a site similar to the proposed redox-sensing subunit NDUFA9 in eukaryotic Complex I. An apparent purine nucleoside triphosphate within the NuoG subunit resembles the GTP-derived molybdenum cofactor in homologous formate dehydrogenase enzymes. The membrane region of the complex binds acyl phosphatidylinositol dimannoside, a characteristic three-tailed lipid from the mycobacterial membrane. The structure also shows menaquinone, which is preferentially used over ubiquinone by gram-positive bacteria, in two different positions along the quinone channel, comparable to ubiquinone in other structures and suggesting a conserved quinone binding mechanism.
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Affiliation(s)
- Yingke Liang
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
- Department of Biochemistry, University of Toronto, TorontoM5S 1A8, Canada
| | - Alicia Plourde
- Department of Molecular and Cellular Biology, University of Guelph, TorontoN1G 2W1, Canada
| | - Stephanie A. Bueler
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, TorontoM5S 1A8, Canada
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91Stockholm, Sweden
| | - Siavash Vahidi
- Department of Molecular and Cellular Biology, University of Guelph, TorontoN1G 2W1, Canada
| | - John L. Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
- Department of Biochemistry, University of Toronto, TorontoM5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, TorontoM5G 1L7, Canada
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2
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Silversmith RE, Bourret RB. Fluorescence Measurement of Kinetics of CheY Autophosphorylation with Small Molecule Phosphodonors. Methods Mol Biol 2018; 1729:321-335. [PMID: 29429101 DOI: 10.1007/978-1-4939-7577-8_25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The Escherichia coli chemotaxis protein CheY is a model receiver domain containing a native tryptophan residue that serves as a fluorescent probe for CheY autophosphorylation with small molecule phosphodonors. Here we describe fluorescence measurement of apparent bimolecular rate constants for reaction of wild type and mutant CheY with phosphodonors acetyl phosphate, phosphoramidate, or monophosphoimidazole. Step-by-step protocols to synthesize phosphoramidate (K+ salt) and monophosphoimidazole (Na+ salt), which are not commercially available, are provided. Key factors to consider in developing autophosphorylation assays for other response regulators are also discussed.
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Affiliation(s)
- Ruth E Silversmith
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Robert B Bourret
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA.
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3
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Vandecan Y, Biondi E, Blossey R. Core-oscillator model of Caulobacter crescentus. Phys Rev E 2016; 93:062413. [PMID: 27415304 DOI: 10.1103/physreve.93.062413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Indexed: 11/07/2022]
Abstract
The gram-negative bacterium Caulobacter crescentus is a powerful model organism for studies of bacterial cell cycle regulation. Although the major regulators and their connections in Caulobacter have been identified, it still is a challenge to properly understand the dynamics of its circuitry which accounts for both cell cycle progression and arrest. We show that the key decision module in Caulobacter is built from a limit cycle oscillator which controls the DNA replication program. The effect of an induced cell cycle arrest is demonstrated to be a key feature to classify the underlying dynamics.
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Affiliation(s)
- Yves Vandecan
- Université de Lille 1, CNRS, UGSF UMR 8576, 59000 Lille, France
| | - Emanuele Biondi
- Aix-Marseille Université, CNRS, LCB UMR 7283, 13009 Marseille, France
| | - Ralf Blossey
- Université de Lille 1, CNRS, UGSF UMR 8576, 59000 Lille, France
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4
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Zea DJ, Monzon AM, Gonzalez C, Fornasari MS, Tosatto SCE, Parisi G. Disorder transitions and conformational diversity cooperatively modulate biological function in proteins. Protein Sci 2016; 25:1138-46. [PMID: 27038125 DOI: 10.1002/pro.2931] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/30/2016] [Accepted: 03/31/2016] [Indexed: 12/20/2022]
Abstract
Structural differences between conformers sustain protein biological function. Here, we studied in a large dataset of 745 intrinsically disordered proteins, how ordered-disordered transitions modulate structural differences between conformers as derived from crystallographic data. We found that almost 50% of the proteins studied show no transitions and have low conformational diversity while the rest show transitions and a higher conformational diversity. In this last subset, 60% of the proteins become more ordered after ligand binding, while 40% more disordered. As protein conformational diversity is inherently connected with protein function our analysis suggests differences in structure-function relationships related to order-disorder transitions.
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Affiliation(s)
- Diego Javier Zea
- Structural Bioinformatics Group, Department of Science and Technology, National University of Quilmes, Argentina
| | - Alexander Miguel Monzon
- Structural Bioinformatics Group, Department of Science and Technology, National University of Quilmes, Argentina
| | - Claudia Gonzalez
- Structural Bioinformatics Group, Department of Science and Technology, National University of Quilmes, Argentina
| | - María Silvina Fornasari
- Structural Bioinformatics Group, Department of Science and Technology, National University of Quilmes, Argentina
| | - Silvio C E Tosatto
- Biocomputing up, Department of Biomedical Sciences, University of Padova, Italy
| | - Gustavo Parisi
- Structural Bioinformatics Group, Department of Science and Technology, National University of Quilmes, Argentina
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5
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Khosa S, Hoeppner A, Gohlke H, Schmitt L, Smits SHJ. Structure of the Response Regulator NsrR from Streptococcus agalactiae, Which Is Involved in Lantibiotic Resistance. PLoS One 2016; 11:e0149903. [PMID: 26930060 PMCID: PMC4773095 DOI: 10.1371/journal.pone.0149903] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/05/2016] [Indexed: 01/22/2023] Open
Abstract
Lantibiotics are antimicrobial peptides produced by Gram-positive bacteria. Interestingly, several clinically relevant and human pathogenic strains are inherently resistant towards lantibiotics. The expression of the genes responsible for lantibiotic resistance is regulated by a specific two-component system consisting of a histidine kinase and a response regulator. Here, we focused on a response regulator involved in lantibiotic resistance, NsrR from Streptococcus agalactiae, and determined the crystal structures of its N-terminal receiver domain and C-terminal DNA-binding effector domain. The C-terminal domain exhibits a fold that classifies NsrR as a member of the OmpR/PhoB subfamily of regulators. Amino acids involved in phosphorylation, dimerization, and DNA-binding were identified and demonstrated to be conserved in lantibiotic resistance regulators. Finally, a model of the full-length NsrR in the active and inactive state provides insights into protein dimerization and DNA-binding.
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Affiliation(s)
- Sakshi Khosa
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Astrid Hoeppner
- X-Ray Facility and Crystal Farm, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
| | - Sander H. J. Smits
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany
- * E-mail:
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6
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Walsh PS, Dean JC, McBurney C, Kang H, Gellman SH, Zwier TS. Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences. Phys Chem Chem Phys 2016; 18:11306-22. [PMID: 27054830 DOI: 10.1039/c6cp01062h] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase.
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Affiliation(s)
| | - Jacob C. Dean
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Carl McBurney
- Department of Chemistry
- University of Wisconsin-Madison
- Madison
- USA
| | - Hyuk Kang
- Department of Chemistry
- Ajou University
- Republic of Korea
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7
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Joseph AP, de Brevern AG. From local structure to a global framework: recognition of protein folds. J R Soc Interface 2014; 11:20131147. [PMID: 24740960 DOI: 10.1098/rsif.2013.1147] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Protein folding has been a major area of research for many years. Nonetheless, the mechanisms leading to the formation of an active biological fold are still not fully apprehended. The huge amount of available sequence and structural information provides hints to identify the putative fold for a given sequence. Indeed, protein structures prefer a limited number of local backbone conformations, some being characterized by preferences for certain amino acids. These preferences largely depend on the local structural environment. The prediction of local backbone conformations has become an important factor to correctly identifying the global protein fold. Here, we review the developments in the field of local structure prediction and especially their implication in protein fold recognition.
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Affiliation(s)
- Agnel Praveen Joseph
- Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford, , Didcot OX11 0QX, UK
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8
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He K, Marden JN, Quardokus EM, Bauer CE. Phosphate flow between hybrid histidine kinases CheA₃ and CheS₃ controls Rhodospirillum centenum cyst formation. PLoS Genet 2013; 9:e1004002. [PMID: 24367276 PMCID: PMC3868531 DOI: 10.1371/journal.pgen.1004002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 10/21/2013] [Indexed: 01/21/2023] Open
Abstract
Genomic and genetic analyses have demonstrated that many species contain multiple chemotaxis-like signal transduction cascades that likely control processes other than chemotaxis. The Che3 signal transduction cascade from Rhodospirillum centenum is one such example that regulates development of dormant cysts. This Che-like cascade contains two hybrid response regulator-histidine kinases, CheA3 and CheS3, and a single-domain response regulator CheY3. We demonstrate that cheS3 is epistatic to cheA3 and that only CheS3∼P can phosphorylate CheY3. We further show that CheA3 derepresses cyst formation by phosphorylating a CheS3 receiver domain. These results demonstrate that the flow of phosphate as defined by the paradigm E. coli chemotaxis cascade does not necessarily hold true for non-chemotactic Che-like signal transduction cascades. Bacteria use chemotaxis and chemotaxis-like signal transduction pathways to quickly sense and adapt to a constantly changing environment. The purple photosynthetic bacterium Rhodospirillum centenum is able to withstand long periods of desiccation by forming metabolically dormant cyst cells, the development of which is regulated by the Che3 chemotaxis-like pathway. Using a combination of genetic and biochemical approaches, we demonstrate that hybrid histidine kinase (HHK) CheA3 encoded in the che3 gene cluster is essential for cyst formation while another HHK CheS3 inhibits cyst formation. We further show that the appended receiver domains of these kinases regulate their respective histidine kinase domains and are critical in controlling the timing of cyst formation. Finally, we demonstrate that CheA3 functions upstream of CheS3 and promotes cyst formation by phosphorylating CheS3.
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Affiliation(s)
- Kuang He
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, United States of America
| | - Jeremiah N. Marden
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, United States of America
| | - Ellen M. Quardokus
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Carl E. Bauer
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
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9
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Tsokos CG, Perchuk BS, Laub MT. A dynamic complex of signaling proteins uses polar localization to regulate cell-fate asymmetry in Caulobacter crescentus. Dev Cell 2011; 20:329-41. [PMID: 21397844 DOI: 10.1016/j.devcel.2011.01.007] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 01/06/2011] [Accepted: 01/07/2011] [Indexed: 11/15/2022]
Abstract
Cellular asymmetry is critical to metazoan development and the life cycle of many microbes. In Caulobacter, cell cycle progression and the formation of asymmetric daughter cells depend on the polarly-localized histidine kinase CckA. How CckA is regulated and why activity depends on localization are unknown. Here, we demonstrate that the unorthodox kinase DivL promotes CckA activity and that the phosphorylated regulator DivK inhibits CckA by binding to DivL. Early in the cell cycle, CckA is activated by the dephosphorylation of DivK throughout the cell. However, in later stages, when phosphorylated DivK levels are high, CckA activation relies on polar localization with a DivK phosphatase. Localization thus creates a protected zone for CckA within the cell, without the use of membrane-enclosed compartments. Our results reveal the mechanisms by which CckA is regulated in a cell-type-dependent manner. More generally, our findings reveal how cells exploit subcellular localization to orchestrate sophisticated regulatory processes.
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Affiliation(s)
- Christos G Tsokos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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10
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Getting in the loop: regulation of development in Caulobacter crescentus. Microbiol Mol Biol Rev 2010; 74:13-41. [PMID: 20197497 DOI: 10.1128/mmbr.00040-09] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Caulobacter crescentus is an aquatic Gram-negative alphaproteobacterium that undergoes multiple changes in cell shape, organelle production, subcellular distribution of proteins, and intracellular signaling throughout its life cycle. Over 40 years of research has been dedicated to this organism and its developmental life cycles. Here we review a portion of many developmental processes, with particular emphasis on how multiple processes are integrated and coordinated both spatially and temporally. While much has been discovered about Caulobacter crescentus development, areas of potential future research are also highlighted.
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11
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Wrabl JO, Hilser VJ. Investigating homology between proteins using energetic profiles. PLoS Comput Biol 2010; 6:e1000722. [PMID: 20361049 PMCID: PMC2845653 DOI: 10.1371/journal.pcbi.1000722] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 02/25/2010] [Indexed: 11/19/2022] Open
Abstract
Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding) and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved local stability, may provide guidance for a future thermodynamically informed classification of protein homology. Protein structure and function are fundamentally determined by thermodynamics. However, for technical as well as historical reasons, current evolutionary classification schemes and bioinformatics tools do not fully utilize thermodynamic information to describe or analyze proteins. In this work, we address this deficiency by computationally estimating the position-specific thermodynamic quantities of stability (ΔG), enthalpy (ΔH), and entropy (TΔS) for a large and diverse representative sample of protein structures. The sample was drawn from an expertly curated database, such that accepted evolutionary relationships existed for all protein pairs. Importantly, trivial relationships between pairs highly similar in amino acid sequence were explicitly excluded. We found that all position-specific thermodynamic quantities ΔG, ΔH, and TΔS were more similar between proteins that were evolutionarily related (i.e., homologous), and were less similar between proteins that were not evolutionarily related (i.e., non-homologous), with stability being particularly similar between homologous proteins. However, interesting statistically significant exceptions to these trends were observed, exceptions that could indicate novel processes of functional adaptation or evolutionary fold change, mediated by thermodynamics, for the proteins involved. Taken together, these results expand our understanding of the role of thermodynamics in protein evolution and suggest an organizational framework for a future thermodynamically-informed classification of protein homology.
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Affiliation(s)
- James O. Wrabl
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Vincent J. Hilser
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- * E-mail:
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12
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Bourret RB. Receiver domain structure and function in response regulator proteins. Curr Opin Microbiol 2010; 13:142-9. [PMID: 20211578 DOI: 10.1016/j.mib.2010.01.015] [Citation(s) in RCA: 186] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 01/22/2010] [Indexed: 10/19/2022]
Abstract
During signal transduction by two-component regulatory systems, sensor kinases detect and encode input information while response regulators (RRs) control output. Most receiver domains function as phosphorylation-mediated switches within RRs, but some transfer phosphoryl groups in multistep phosphorelays. Conserved features of receiver domain amino acid sequence correlate with structure and hence function. Receiver domains catalyze their own phosphorylation and dephosphorylation in reactions requiring a divalent cation. Molecular dynamics simulations are supplementing structural investigation of the conformational changes that underlie receiver domain switch function. As understanding of features shared by all receiver domains matures, factors conferring differences (e.g. in reaction rate or specificity) are receiving increased attention. Numerous examples of atypical receiver or pseudo-receiver domains that function without phosphorylation have recently been characterized.
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Affiliation(s)
- Robert B Bourret
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA.
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13
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Measurement of Response Regulator Autodephosphorylation Rates Spanning Six Orders of Magnitude. Methods Enzymol 2010; 471:89-114. [DOI: 10.1016/s0076-6879(10)71006-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Yamada S, Shiro Y. Structural Basis of the Signal Transduction in the Two-Component System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 631:22-39. [DOI: 10.1007/978-0-387-78885-2_3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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15
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Yamada S, Akiyama S, Sugimoto H, Kumita H, Ito K, Fujisawa T, Nakamura H, Shiro Y. The Signaling Pathway in Histidine Kinase and the Response Regulator Complex Revealed by X-ray Crystallography and Solution Scattering. J Mol Biol 2006; 362:123-39. [PMID: 16890956 DOI: 10.1016/j.jmb.2006.07.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Revised: 07/05/2006] [Accepted: 07/06/2006] [Indexed: 11/16/2022]
Abstract
The structure of a histidine kinase (ThkA) complexed with a response regulator (TrrA) in the two-component regulatory system from hyperthermophile Thermotoga maritima was determined by a combination of X-ray crystallography at a resolution of 4.2 A and small-angle X-ray scattering (SAXS). The boundary of the three component domains (PAS-sensor, dimerization and catalytic domains) of ThkA and the bound TrrA molecule were unambiguously assigned in the electron density map at 4.2 A resolution. ThkA forms a dimer with crystallographic 2-fold symmetry and two monomeric TrrAs bind to the ThkA dimer. SAXS experiments also confirmed this association state in solution and specific binding between ThkA and TrrA (Kd=8.2x10(-11) M(-2)). The association interface between ThkA and TrrA contains the phosphotransfer His residue in the ThkA, indicative of an efficient receipt of the phosphoryl group. One Per-Arnt-Sim (PAS) domain does not interact with the other PAS domain, but with the catalytic domain of the same polypeptide chain and with one TrrA molecule. Observed inter-domain and inter-molecular interactions reveal a definite pathway of signal transduction in the kinase/regulator complex. In addition, we propose a responsible role of TrrA for the feedback regulation of sensing and/or kinase activities of ThkA.
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Affiliation(s)
- Seiji Yamada
- Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
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16
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Abstract
Three-dimensional structures have been determined for 13 different enzymes that use thiamine diphosphate (ThDP) as a cofactor. These enzymes fall into five families, where members within a family have similar structures. In different families, there are similarities between some domains that clearly point to a common ancestor for all of these enzymes. Where the enzyme structures differ, evolutionary relationships between families can be discerned. Here, I present an analysis of these families and propose an evolutionary pathway to explain the diversity of structures that are now known.
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Affiliation(s)
- Ronald G Duggleby
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.
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17
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Nowak E, Panjikar S, Konarev P, Svergun DI, Tucker PA. The Structural Basis of Signal Transduction for the Response Regulator PrrA from Mycobacterium tuberculosis. J Biol Chem 2006; 281:9659-66. [PMID: 16434396 DOI: 10.1074/jbc.m512004200] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structure of the two-domain response regulator PrrA from Mycobacterium tuberculosis shows a compact structure in the crystal with a well defined interdomain interface. The interface, which does not include the interdomain linker, makes the recognition helix and the trans-activation loop of the effector domain inaccessible for interaction with DNA. Part of the interface involves hydrogen-bonding interactions of a tyrosine residue in the receiver domain that is believed to be involved in signal transduction, which, if disrupted, would destabilize the interdomain interface, allowing a more extended conformation of the molecule, which would in turn allow access to the recognition helix. In solution, there is evidence for an equilibrium between compact and extended forms of the protein that is far toward the compact form when the protein is inactivated but moves toward a more extended form when activated by the cognate sensor kinase PrrB.
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Affiliation(s)
- Elzbieta Nowak
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22603 Hamburg, Germany
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18
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Ausmees N, Jacobs-Wagner C. Spatial and temporal control of differentiation and cell cycle progression in Caulobacter crescentus. Annu Rev Microbiol 2004; 57:225-47. [PMID: 14527278 DOI: 10.1146/annurev.micro.57.030502.091006] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The dimorphic and intrinsically asymmetric bacterium Caulobacter crescentus has become an important model organism to study the bacterial cell cycle, cell polarity, and polar differentiation. A multifaceted regulatory network orchestrates the precise coordination between the development of polar organelles and the cell cycle. One master response regulator, CtrA, directly controls the initiation of chromosome replication as well as several aspects of polar morphogenesis and cell division. CtrA activity is temporally and spatially regulated by multiple partially redundant control mechanisms, such as transcription, phosphorylation, and targeted proteolysis. A multicomponent signal transduction network upstream CtrA, containing histidine kinases CckA, PleC, DivJ, and DivL and the essential response regulator DivK, contributes to the control of CtrA activity in response to cell cycle and developmental cues. An intriguing feature of this signaling network is the dynamic cell cycle-dependent polar localization of its components, which is believed to have a novel regulatory function.
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Affiliation(s)
- Nora Ausmees
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
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19
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Quardokus EM, Brun YV. Cell cycle timing and developmental checkpoints in Caulobacter crescentus. Curr Opin Microbiol 2003; 6:541-9. [PMID: 14662348 DOI: 10.1016/j.mib.2003.10.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Development in Caulobacter reflects a level of complexity once thought only to exist in eukaryotic cells. The cell cycle and development are not isolated from each other, but are interdependent processes. Checkpoints are in place to ensure that both cell cycle and developmental processes are completed accurately before the next stage is initiated. The timing of these processes is regulated by signal transduction networks that integrate signals from DNA replication, cell division and development. These signal transduction networks achieve precise timing of the cell cycle and development by regulating temporal gene expression, and protein activity by dynamic spatial localization within the cell and timed proteolysis.
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Affiliation(s)
- Ellen M Quardokus
- Department of Biology, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA
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Ohta N, Newton A. The core dimerization domains of histidine kinases contain recognition specificity for the cognate response regulator. J Bacteriol 2003; 185:4424-31. [PMID: 12867451 PMCID: PMC165744 DOI: 10.1128/jb.185.15.4424-4431.2003] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Histidine kinases DivJ and PleC initiate signal transduction pathways that regulate an early cell division cycle step and the gain of motility later in the Caulobacter crescentus cell cycle, respectively. The essential single-domain response regulator DivK functions downstream of these kinases to catalyze phosphotransfer from DivJ and PleC. We have used a yeast two-hybrid screen to investigate the molecular basis of DivJ and PleC interaction with DivK and to identify other His-Asp signal transduction proteins that interact with DivK. The only His-Asp proteins identified in the two-hybrid screen were five members of the histidine kinase superfamily. The finding that most of the kinase clones isolated correspond to either DivJ or PleC supports the previous conclusion that DivJ and PleC are cognate DivK kinases. A 66-amino-acid sequence common to all cloned DivJ and PleC fragments contains the conserved helix 1, helix 2 sequence that forms a four-helix bundle in histidine kinases required for dimerization, autophosphorylation and phosphotransfer. We present results that indicate that the four-helix bundle subdomain is not only necessary for binding of the response regulator but also sufficient for in vivo recognition specificity between DivK and its cognate histidine kinases. The other three kinases identified in this study correspond to DivL, an essential tyrosine kinase belonging to the same kinase subfamily as DivJ and PleC, and the two previously uncharacterized, soluble histidine kinases CckN and CckO. We discuss the significance of these results as they relate to kinase response regulator recognition specificity and the fidelity of phosphotransfer in signal transduction pathways.
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Affiliation(s)
- Noriko Ohta
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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Affiliation(s)
- Lee Kroos
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA.
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Abstract
In Caulobacter crescentus, a complex regulatory network integrates temporal and spatial information to control the ordered progression of the cell cycle, and to synchronize cell proliferation with development. Periodicity includes the timed synthesis, activation or destruction of key regulatory proteins, which activate a large number of genes at the appropriate time of the cell cycle. Checkpoints serve to couple cell division and polar development to the replication and segregation state of the chromosome. Asymmetrically positioned regulatory components are involved in the sequential positioning of polar organelles. New work sheds light on the spatial organization of cellular components involved in cell cycle progression and polar differentiation, and starts to define the molecular nature of checkpoints involved in cell cycle control and development.
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Affiliation(s)
- Urs Jenal
- Biozentrum, University of Basel, Klingelbergstrasse 70 4054, Basel, Switzerland.
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