1
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Winski A, Ludwiczak J, Orlowska M, Madaj R, Kaminski K, Dunin‐Horkawicz S. AlphaFold2 captures the conformational landscape of the HAMP signaling domain. Protein Sci 2024; 33:e4846. [PMID: 38010737 PMCID: PMC10731501 DOI: 10.1002/pro.4846] [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: 05/23/2023] [Revised: 10/30/2023] [Accepted: 11/19/2023] [Indexed: 11/29/2023]
Abstract
In this study, we present a conformational landscape of 5000 AlphaFold2 models of the Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases (HAMP) domain, a short helical bundle that transduces signals from sensors to effectors in two-component signaling proteins such as sensory histidine kinases and chemoreceptors. The landscape reveals the conformational variability of the HAMP domain, including rotations, shifts, displacements, and tilts of helices, many combinations of which have not been observed in experimental structures. HAMP domains belonging to a single family tend to occupy a defined region of the landscape, even when their sequence similarity is low, suggesting that individual HAMP families have evolved to operate in a specific conformational range. The functional importance of this structural conservation is illustrated by poly-HAMP arrays, in which HAMP domains from families with opposite conformational preferences alternate, consistent with the rotational model of signal transduction. The only poly-HAMP arrays that violate this rule are predicted to be of recent evolutionary origin and structurally unstable. Finally, we identify a family of HAMP domains that are likely to be dynamic due to the presence of a conserved pi-helical bulge. All code associated with this work, including a tool for rapid sequence-based prediction of the rotational state in HAMP domains, is deposited at https://github.com/labstructbioinf/HAMPpred.
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Affiliation(s)
- Aleksander Winski
- Laboratory of Structural Bioinformatics, Centre of New TechnologiesUniversity of WarsawWarsawPoland
| | - Jan Ludwiczak
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
- Present address:
Prescient Design, Genentech Research & Early DevelopmentRoche GroupBaselSwitzerland
| | - Malgorzata Orlowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
| | - Rafal Madaj
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
| | - Kamil Kaminski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
| | - Stanislaw Dunin‐Horkawicz
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
- Department of Protein EvolutionMax Planck Institute for Biology TübingenTübingenGermany
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2
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Guo L, Wang YH, Cui R, Huang Z, Hong Y, Qian JW, Ni B, Xu AM, Jiang CY, Zhulin IB, Liu SJ, Li DF. Attractant and repellent induce opposing changes in the four-helix bundle ligand-binding domain of a bacterial chemoreceptor. PLoS Biol 2023; 21:e3002429. [PMID: 38079456 PMCID: PMC10735184 DOI: 10.1371/journal.pbio.3002429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/21/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
Motile bacteria navigate toward favorable conditions and away from unfavorable environments using chemotaxis. Mechanisms of sensing attractants are well understood; however, molecular aspects of how bacteria sense repellents have not been established. Here, we identified malate as a repellent recognized by the MCP2201 chemoreceptor in a bacterium Comamonas testosteroni and showed that it binds to the same site as an attractant citrate. Binding determinants for a repellent and an attractant had only minor differences, and a single amino acid substitution in the binding site inverted the response to malate from a repellent to an attractant. We found that malate and citrate affect the oligomerization state of the ligand-binding domain in opposing way. We also observed opposing effects of repellent and attractant binding on the orientation of an alpha helix connecting the sensory domain to the transmembrane helix. We propose a model to illustrate how positive and negative signals might be generated.
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Affiliation(s)
- Lu Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun-Hao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Rui Cui
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhou Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuan Hong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jia-Wei Qian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bin Ni
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - An-Ming Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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3
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Riechmann C, Zhang P. Recent structural advances in bacterial chemotaxis signalling. Curr Opin Struct Biol 2023; 79:102565. [PMID: 36868078 PMCID: PMC10460253 DOI: 10.1016/j.sbi.2023.102565] [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: 10/16/2022] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 03/05/2023]
Abstract
Bacterial chemosensory arrays have served as a model system for in-situ structure determination, clearly cataloguing the improvement of cryo-electron tomography (cryoET) over the past decade. In recent years, this has culminated in an accurately fitted atomistic model for the full-length core signalling unit (CSU) and numerous insights into the function of the transmembrane receptors responsible for signal transduction. Here, we review the achievements of the latest structural advances in bacterial chemosensory arrays and the developments which have made such advances possible.
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Affiliation(s)
- Carlos Riechmann
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK.
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4
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Woolfson DN. Understanding a protein fold: the physics, chemistry, and biology of α-helical coiled coils. J Biol Chem 2023; 299:104579. [PMID: 36871758 PMCID: PMC10124910 DOI: 10.1016/j.jbc.2023.104579] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023] Open
Abstract
Protein science is being transformed by powerful computational methods for structure prediction and design: AlphaFold2 can predict many natural protein structures from sequence, and other AI methods are enabling the de novo design of new structures. This raises a question: how much do we understand the underlying sequence-to-structure/function relationships being captured by these methods? This perspective presents our current understanding of one class of protein assembly, the α-helical coiled coils. At first sight, these are straightforward: sequence repeats of hydrophobic (h) and polar (p) residues, (hpphppp)n, direct the folding and assembly of amphipathic α helices into bundles. However, many different bundles are possible: they can have two or more helices (different oligomers); the helices can have parallel, antiparallel or mixed arrangements (different topologies); and the helical sequences can be the same (homomers) or different (heteromers). Thus, sequence-to-structure relationships must be present within the hpphppp repeats to distinguish these states. I discuss the current understanding of this problem at three levels: First, physics gives a parametric framework to generate the many possible coiled-coil backbone structures. Second, chemistry provides a means to explore and deliver sequence-to-structure relationships. Third, biology shows how coiled coils are adapted and functionalized in nature, inspiring applications of coiled coils in synthetic biology. I argue that the chemistry is largely understood; the physics is partly solved, though the considerable challenge of predicting even relative stabilities of different coiled-coil states remains; but there is much more to explore in the biology and synthetic biology of coiled coils.
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, United Kingdom; School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, United Kingdom; BrisEngBio, School of Chemistry, University of Bristol, Bristol, United Kingdom; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, United Kingdom.
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5
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Wong AI, Beites T, Planck KA, Fieweger RA, Eckartt KA, Li S, Poulton NC, VanderVen BC, Rhee KY, Schnappinger D, Ehrt S, Rock J. Cyclic AMP is a critical mediator of intrinsic drug resistance and fatty acid metabolism in M. tuberculosis. eLife 2023; 12:e81177. [PMID: 36810158 PMCID: PMC9995111 DOI: 10.7554/elife.81177] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/22/2023] [Indexed: 02/24/2023] Open
Abstract
Cyclic AMP (cAMP) is a ubiquitous second messenger that transduces signals from cellular receptors to downstream effectors. Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, devotes a considerable amount of coding capacity to produce, sense, and degrade cAMP. Despite this fact, our understanding of how cAMP regulates Mtb physiology remains limited. Here, we took a genetic approach to investigate the function of the sole essential adenylate cyclase in Mtb H37Rv, Rv3645. We found that a lack of rv3645 resulted in increased sensitivity to numerous antibiotics by a mechanism independent of substantial increases in envelope permeability. We made the unexpected observation that rv3645 is conditionally essential for Mtb growth only in the presence of long-chain fatty acids, a host-relevant carbon source. A suppressor screen further identified mutations in the atypical cAMP phosphodiesterase rv1339 that suppress both fatty acid and drug sensitivity phenotypes in strains lacking rv3645. Using mass spectrometry, we found that Rv3645 is the dominant source of cAMP under standard laboratory growth conditions, that cAMP production is the essential function of Rv3645 in the presence of long-chain fatty acids, and that reduced cAMP levels result in increased long-chain fatty acid uptake and metabolism and increased antibiotic susceptibility. Our work defines rv3645 and cAMP as central mediators of intrinsic multidrug resistance and fatty acid metabolism in Mtb and highlights the potential utility of small molecule modulators of cAMP signaling.
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Affiliation(s)
- Andrew I Wong
- Laboratory of Host-Pathogen Biology, The Rockefeller UniversityNew YorkUnited States
| | - Tiago Beites
- Department of Microbiology and Immunology, Weill Cornell MedicineNew YorkUnited States
| | - Kyle A Planck
- Department of Microbiology and Immunology, Weill Cornell MedicineNew YorkUnited States
- Division of Infectious Diseases, Department of Medicine, Weill Cornell MedicineNew YorkUnited States
| | - Rachael A Fieweger
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
| | - Kathryn A Eckartt
- Laboratory of Host-Pathogen Biology, The Rockefeller UniversityNew YorkUnited States
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller UniversityNew YorkUnited States
| | - Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller UniversityNew YorkUnited States
| | - Brian C VanderVen
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
| | - Kyu Y Rhee
- Department of Microbiology and Immunology, Weill Cornell MedicineNew YorkUnited States
- Division of Infectious Diseases, Department of Medicine, Weill Cornell MedicineNew YorkUnited States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell MedicineNew YorkUnited States
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell MedicineNew YorkUnited States
| | - Jeremy Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller UniversityNew YorkUnited States
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Cervimycin-Resistant Staphylococcus aureus Strains Display Vancomycin-Intermediate Resistant Phenotypes. Microbiol Spectr 2022; 10:e0256722. [PMID: 36173303 PMCID: PMC9603734 DOI: 10.1128/spectrum.02567-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Resistance to antibiotics is an increasing problem and necessitates novel antibacterial therapies. The polyketide antibiotics cervimycin A to D are natural products of Streptomyces tendae HKI 0179 with promising activity against multidrug-resistant staphylococci and vancomycin-resistant enterococci. To initiate mode of action studies, we selected cervimycin C- and D-resistant (CmR) Staphylococcus aureus strains. Genome sequencing of CmR mutants revealed amino acid exchanges in the essential histidine kinase WalK, the Clp protease proteolytic subunit ClpP or the Clp ATPase ClpC, and the heat shock protein DnaK. Interestingly, all characterized CmR mutants harbored a combination of mutations in walK and clpP or clpC. In vitro and in vivo analyses showed that the mutations in the Clp proteins abolished ClpP or ClpC activity, and the deletion of clpP rendered S. aureus but not all Bacillus subtilis strains cervimycin-resistant. The essential gene walK was the second mutational hotspot in the CmR S. aureus strains, which decreased WalK activity in vitro and generated a vancomycin-intermediate resistant phenotype, with a thickened cell wall, a lower growth rate, and reduced cell lysis. Transcriptomic and proteomic analyses revealed massive alterations in the CmR strains compared to the parent strain S. aureus SG511, with major shifts in the heat shock regulon, the metal ion homeostasis, and the carbohydrate metabolism. Taken together, mutations in the heat shock genes clpP, clpC, and dnaK, and the walK kinase gene in CmR mutants induced a vancomycin-intermediate resistant phenotype in S. aureus, suggesting cell wall metabolism or the Clp protease system as primary target of cervimycin. IMPORTANCE Staphylococcus aureus is a frequent cause of infections in both the community and hospital setting. Resistance development of S. aureus to various antibiotics is a severe problem for the treatment of this pathogen worldwide. New powerful antimicrobial agents against Gram-positives are needed, since antibiotics like vancomycin fail to cure vancomycin-intermediate resistant S. aureus (VISA) and vancomycin-resistant enterococci (VRE) infections. One candidate substance with promising activity against these organisms is cervimycin, which is an antibiotic complex with a yet unknown mode of action. In our study, we provide first insights into the mode of action of cervimycins. By characterizing cervimycin-resistant S. aureus strains, we revealed the Clp system and the essential kinase WalK as mutational hotspots for cervimycin resistance in S. aureus. It further emerged that cervimycin-resistant S. aureus strains show a VISA phenotype, indicating a role of cervimycin in perturbing the bacterial cell envelope.
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7
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New Roles for HAMP Domains: the Tri-HAMP Region of Pseudomonas aeruginosa Aer2 Controls Receptor Signaling and Cellular Localization. J Bacteriol 2022; 204:e0022522. [PMID: 35916529 PMCID: PMC9487508 DOI: 10.1128/jb.00225-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Aer2 chemoreceptor from Pseudomonas aeruginosa is an O2 sensor involved in stress responses, virulence, and tuning the behavior of the chemotaxis (Che) system. Aer2 is the sole receptor of the Che2 system. It is soluble, but membrane associated, and forms complexes at the cell pole during stationary phase. The domain arrangement of Aer2 is unusual, with a PAS sensing domain sandwiched between five HAMP domains, followed by a C-terminal kinase-control output domain. The first three HAMP domains form a poly-HAMP chain N-terminal to the PAS sensing domain. HAMP domains are often located between signal input and output domains, where they transduce signals. Given that HAMP1 to 3 reside N-terminal to the input-output pathway, we undertook a systematic examination of their function in Aer2. We found that HAMP1 to 3 influence PAS signaling over a considerable distance, as the majority of HAMP1, 2 and 3 mutations, and deletions of helical phase stutters, led to nonresponsive signal-off or off-biased receptors. PAS signal-on lesions that mimic activated Aer2 also failed to override N-terminal HAMP signal-off replacements. This indicates that HAMP1 to 3 are critical coupling partners for PAS signaling and likely function as a cohesive unit and moveable scaffold to correctly orient and poise PAS dimers for O2-mediated signaling in Aer2. HAMP1 additionally controlled the clustering and polar localization of Aer2 in P. aeruginosa. Localization was not driven by HAMP1 charge, and HAMP1 signal-off mutants still localized. Employing HAMP as a clustering and localization determinant, as well as a facilitator of PAS signaling, are newly recognized roles for HAMP domains. IMPORTANCE P. aeruginosa is an opportunistic pathogen that interprets environmental stimuli via 26 chemoreceptors that signal through 4 distinct chemosensory systems. The second chemosensory system, Che2, contains a receptor named Aer2 that senses O2 and mediates stress responses and virulence and tunes chemotactic behavior. Aer2 is membrane associated, but soluble, and has three N-terminal HAMP domains (HAMP1 to 3) that reside outside the signal input-output pathway of Aer2. In this study, we determined that HAMP1 to 3 facilitate O2-dependent signaling from the PAS sensing domain and that HAMP1 controls the formation of Aer2-containing polar foci in P. aeruginosa. Both of these are newly recognized roles for HAMP domains that may be applicable to other non-signal-transducing HAMP domains and poly-HAMP chains.
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8
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Sun S, Wang R, Pandelia ME. Vibrio cholerae V-cGAP3 Is an HD-GYP Phosphodiesterase with a Metal Tunable Substrate Selectivity. Biochemistry 2022; 61:1801-1809. [PMID: 35901269 DOI: 10.1021/acs.biochem.2c00269] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclic dinucleotides (CDNs) are signaling molecules involved in the immune response and virulence factor production. CDN cellular levels are fine-tuned by metal-dependent phosphodiesterases (PDEs), among which HD-GYPs make up a subclass of the larger HD-domain protein superfamily. The human pathogen Vibrio cholerae (Vc) encodes nine HD-GYPs, one of which is V-cGAP3 (or VCA0931). V-cGAP3 acts on c-di-GMP and 3'3'c-GAMP, and this activity is related to bacterial infectivity. However, the extant chemical makeup of the V-cGAP3 cofactor and steady state parameters have not been established. Employing electron paramagnetic resonance and Mössbauer spectroscopy in tandem with elemental analyses and activity assays, we demonstrate that V-cGAP3 coordinates different dimetal cofactors with variable activities. MnII and FeII afford c-di-GMP hydrolysis with the highest observed rates, while c-GAMP hydrolysis is selectively dependent on Mn. V-cGAP3 has a single functional domain, and this simple architecture allows us to examine the roles of characteristic conserved residues in catalysis. Substitution of the adjacent to the active site GYP residue triad and the specifically conserved in HD-domain PDEs fifth histidine ligand (i.e., H371 in V-cGAP3) with alanines severely compromises CDN hydrolysis but only modestly affects cofactor incorporation. Our data are consistent with V-cGAP3 being the major regulator of 3'3'c-GAMP hydrolysis in Vc and delineate the importance of specific residues in tuning activity in HD-GYPs in general. We propose that HD-GYPs exhibit diversity in their metallocofactors and substrates, which may serve to increase their functional potential in regulatory pathways or allow for PDE activity upon adaptation of the parent organism to diverse environmental niches.
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Affiliation(s)
- Sining Sun
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Richard Wang
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
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Structural signatures of Escherichia coli chemoreceptor signaling states revealed by cellular crosslinking. Proc Natl Acad Sci U S A 2022; 119:e2204161119. [PMID: 35787052 PMCID: PMC9282233 DOI: 10.1073/pnas.2204161119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The chemotaxis machinery of Escherichia coli has served as a model for exploring the molecular signaling mechanisms of transmembrane chemoreceptors known as methyl-accepting chemotaxis proteins (MCPs). Yet, fundamental questions about signal transmission through MCP molecules remain unanswered. Our work with the E. coli serine chemoreceptor Tsr has developed in vivo reporters that distinguish kinase-OFF and kinase-ON structures in the cytoplasmic methylation helix (MH) cap, which receives stimulus signals from an adjoining, membrane-proximal histidine kinase, adenylyl cyclases, MCPs, and phosphatases (HAMP) domain. The cytoplasmic helices of the Tsr homodimer interact mainly through packing interactions of hydrophobic residues at a and d heptad positions. We investigated the in vivo crosslinking properties of Tsr molecules bearing cysteine replacements at functionally tolerant g heptad positions in the N-terminal and C-terminal cap helices. Upon treatment of cells with bismaleimidoethane (BMOE), a bifunctional thiol-reagent, Tsr-G273C/Q504C readily formed a doubly crosslinked product in the presence of serine but not in its absence. Moreover, a serine stimulus combined with BMOE treatment during in vivo Förster resonance energy transfer-based kinase assays locked Tsr-G273C/Q504C in kinase-OFF output. An OFF-shifting lesion in MH1 (D269P) promoted the formation of the doubly crosslinked species in the absence of serine, whereas an ON-shifting lesion (G268P) suppressed the formation of the doubly crosslinked species. Tsr-G273C/Q504C also showed output-dependent crosslinking patterns in combination with ON-shifting and OFF-shifting adaptational modifications. Our results are consistent with a helix breathing-axial rotation-bundle repacking signaling mechanism and imply that in vivo crosslinking tools could serve to probe helix-packing transitions and their output consequences in other regions of the receptor molecule.
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Ramos AL, Aquino M, García G, Gaspar M, de la Cruz C, Saavedra-Flores A, Brom S, Cervantes-Rivera R, Galindo-Sánchez CE, Hernandez R, Puhar A, Lupas AN, Sepulveda E. RpuS/R Is a Novel Two-Component Signal Transduction System That Regulates the Expression of the Pyruvate Symporter MctP in Sinorhizobium fredii NGR234. Front Microbiol 2022; 13:871077. [PMID: 35572670 PMCID: PMC9100948 DOI: 10.3389/fmicb.2022.871077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/11/2022] [Indexed: 11/16/2022] Open
Abstract
The SLC5/STAC histidine kinases comprise a recently identified family of sensor proteins in two-component signal transduction systems (TCSTS), in which the signaling domain is fused to an SLC5 solute symporter domain through a STAC domain. Only two members of this family have been characterized experimentally, the CrbS/R system that regulates acetate utilization in Vibrio and Pseudomonas, and the CbrA/B system that regulates the utilization of histidine in Pseudomonas and glucose in Azotobacter. In an attempt to expand the characterized members of this family beyond the Gammaproteobacteria, we identified two putative TCSTS in the Alphaproteobacterium Sinorhizobium fredii NGR234 whose sensor histidine kinases belong to the SLC5/STAC family. Using reverse genetics, we were able to identify the first TCSTS as a CrbS/R homolog that is also needed for growth on acetate, while the second TCSTS, RpuS/R, is a novel system required for optimal growth on pyruvate. Using RNAseq and transcriptional fusions, we determined that in S. fredii the RpuS/R system upregulates the expression of an operon coding for the pyruvate symporter MctP when pyruvate is the sole carbon source. In addition, we identified a conserved DNA sequence motif in the putative promoter region of the mctP operon that is essential for the RpuR-mediated transcriptional activation of genes under pyruvate-utilizing conditions. Finally, we show that S. fredii mutants lacking these TCSTS are affected in nodulation, producing fewer nodules than the parent strain and at a slower rate.
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Affiliation(s)
| | - Maria Aquino
- Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - Gema García
- Facultad de Biología, Universidad Autónoma de Sinaloa, Culiacan, Mexico
| | - Miriam Gaspar
- Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - Cristina de la Cruz
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Anaid Saavedra-Flores
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ramón Cervantes-Rivera
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Clara Elizabeth Galindo-Sánchez
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Rufina Hernandez
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Andrea Puhar
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Andrei N. Lupas
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Edgardo Sepulveda
- CONACYT-Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
- *Correspondence: Edgardo Sepulveda,
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11
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Li L, He Z, Liang T, Sheng T, Zhang F, Wu D, Ma F. Colonization of biofilm in wastewater treatment: A review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 293:118514. [PMID: 34808308 DOI: 10.1016/j.envpol.2021.118514] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 10/28/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
The attachment and colonization process of microorganisms on a carrier is an interdisciplinary research field. Through a series of physical, chemical, and biological actions, the microorganisms can eventually reproduce on the carrier. This article introduces biofilm start-up and its applications, and explores the current issues to look forward to future development directions. Firstly, the mechanism of microbial film formation is analyzed from the microbial community colonization and reproduction process. Secondly, when analyzing the factors influencing microbial membrane formation, the effect of microbial properties (e.g., genes, proteins, lipids) and external conditions (i.e., carrier, operating environment, and regulation mechanism among microbial communities) were discussed in depth. Aimed at exploring the mechanisms and influencing factors of biofilm start-up, this article proposes the application measures to strengthen this process. Finally, the problems encountered and the future development direction of the technology are analyzed and prospected.
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Affiliation(s)
- Lixin Li
- School of Environment and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, 150022, China.
| | - Zhengming He
- School of Environment and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, 150022, China
| | - Taojie Liang
- School of Environment and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, 150022, China
| | - Tao Sheng
- School of Environment and Chemical Engineering, Heilongjiang University of Science and Technology, Harbin, 150022, China
| | - Fugui Zhang
- Longjiang Environmental Protection Group Co. Ltd., Harbin, 150050, China
| | - Dan Wu
- Longjiang Environmental Protection Group Co. Ltd., Harbin, 150050, China
| | - Fang Ma
- State Key Lab of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
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12
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Mensa B, Polizzi NF, Molnar KS, Natale AM, Lemmin T, DeGrado WF. Allosteric mechanism of signal transduction in the two-component system histidine kinase PhoQ. eLife 2021; 10:73336. [PMID: 34904568 PMCID: PMC8719878 DOI: 10.7554/elife.73336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/13/2021] [Indexed: 12/05/2022] Open
Abstract
Transmembrane signaling proteins couple extracytosolic sensors to cytosolic effectors. Here, we examine how binding of Mg2+ to the sensor domain of an E. coli two component histidine kinase (HK), PhoQ, modulates its cytoplasmic kinase domain. We use cysteine-crosslinking and reporter-gene assays to simultaneously and independently probe the signaling state of PhoQ’s sensor and autokinase domains in a set of over 30 mutants. Strikingly, conservative single-site mutations distant from the sensor or catalytic site strongly influence PhoQ’s ligand-sensitivity as well as the magnitude and direction of the signal. Data from 35 mutants are explained by a semi-empirical three-domain model in which the sensor, intervening HAMP, and catalytic domains can adopt kinase-promoting or inhibiting conformations that are in allosteric communication. The catalytic and sensor domains intrinsically favor a constitutively ‘kinase-on’ conformation, while the HAMP domain favors the ‘off’ state; when coupled, they create a bistable system responsive to physiological concentrations of Mg2+. Mutations alter signaling by locally modulating domain intrinsic equilibrium constants and interdomain couplings. Our model suggests signals transmit via interdomain allostery rather than propagation of a single concerted conformational change, explaining the diversity of signaling structural transitions observed in individual HK domains.
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Affiliation(s)
- Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Chemistry and Chemical Biology PhD program, University of California, San Francisco, San Francisco, United States
| | - Nicholas F Polizzi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | | | - Andrew M Natale
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Biophysics PhD program, University of California, San Francisco, San Francisco, United States
| | - Thomas Lemmin
- Euler Institute, Università della Svizzera Italiana, Lugano, Switzerland
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
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13
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Kryshtafovych A, Moult J, Albrecht R, Chang GA, Chao K, Fraser A, Greenfield J, Hartmann MD, Herzberg O, Josts I, Leiman PG, Linden SB, Lupas AN, Nelson DC, Rees SD, Shang X, Sokolova ML, Tidow H. Computational models in the service of X-ray and cryo-electron microscopy structure determination. Proteins 2021; 89:1633-1646. [PMID: 34449113 PMCID: PMC8616789 DOI: 10.1002/prot.26223] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 01/20/2023]
Abstract
Critical assessment of structure prediction (CASP) conducts community experiments to determine the state of the art in computing protein structure from amino acid sequence. The process relies on the experimental community providing information about not yet public or about to be solved structures, for use as targets. For some targets, the experimental structure is not solved in time for use in CASP. Calculated structure accuracy improved dramatically in this round, implying that models should now be much more useful for resolving many sorts of experimental difficulties. To test this, selected models for seven unsolved targets were provided to the experimental groups. These models were from the AlphaFold2 group, who overall submitted the most accurate predictions in CASP14. Four targets were solved with the aid of the models, and, additionally, the structure of an already solved target was improved. An a posteriori analysis showed that, in some cases, models from other groups would also be effective. This paper provides accounts of the successful application of models to structure determination, including molecular replacement for X-ray crystallography, backbone tracing and sequence positioning in a cryo-electron microscopy structure, and correction of local features. The results suggest that, in future, there will be greatly increased synergy between computational and experimental approaches to structure determination.
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Affiliation(s)
| | - John Moult
- Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular genetics, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Reinhard Albrecht
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Geoffrey A. Chang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA, 92093, USA
- Department of Pharmacology, University of California-San Diego, La Jolla, CA, 92093, USA
| | - Kinlin Chao
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Alec Fraser
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (SCSB), The University of Texas Medical Branch at Galveston, TX 77555, USA
| | - Julia Greenfield
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Marcus D. Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Osnat Herzberg
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Inokentijs Josts
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR) & Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Petr G. Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (SCSB), The University of Texas Medical Branch at Galveston, TX 77555, USA
| | - Sara B. Linden
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Andrei N. Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Daniel C. Nelson
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
- Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Steven D. Rees
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA, 92093, USA
| | - Xiaoran Shang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Maria L. Sokolova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Henning Tidow
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR) & Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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14
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Gordon JB, Hoffman MC, Troiano JM, Li M, Hazelbauer GL, Schlau-Cohen GS. Concerted Differential Changes of Helical Dynamics and Packing upon Ligand Occupancy in a Bacterial Chemoreceptor. ACS Chem Biol 2021; 16:2472-2480. [PMID: 34647725 PMCID: PMC9990816 DOI: 10.1021/acschembio.1c00576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Transmembrane receptors are central components of the chemosensory systems by which motile bacteria detect and respond to chemical gradients. An attractant bound to the receptor periplasmic domain generates conformational signals that regulate a histidine kinase interacting with its cytoplasmic domain. Ligand-induced signaling through the periplasmic and transmembrane domains of the receptor involves a piston-like helical displacement, but the nature of this signaling through the >200 Å four-helix coiled coil of the cytoplasmic domain had not yet been identified. We performed single-molecule Förster resonance energy transfer measurements on Escherichia coli aspartate receptor homodimers inserted into native phospholipid bilayers enclosed in nanodiscs. The receptors were labeled with fluorophores at diagnostic positions near the middle of the cytoplasmic coiled coil. At these positions, we found that the two N-helices of the homodimer were more distant, that is, less tightly packed and more dynamic than the companion C-helix pair, consistent with previous deductions that the C-helices form a stable scaffold and the N-helices are dynamic. Upon ligand binding, the scaffold pair compacted further, while separation and dynamics of the dynamic pair increased. Thus, ligand binding had asymmetric effects on the two helical pairs, shifting mean distances in opposite directions and increasing the dynamics of one pair. We suggest that this reflects a conformational change in which differential alterations to the packing and dynamics of the two helical pairs are coupled. These coupled changes could represent a previously unappreciated mode of conformational signaling that may well occur in other coiled-coil signaling proteins.
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Affiliation(s)
- Jesse B Gordon
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, 6-225, Cambridge, Massachusetts 02139, United States
| | - Mikaila C Hoffman
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, 6-225, Cambridge, Massachusetts 02139, United States
| | - Julianne M Troiano
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, 6-225, Cambridge, Massachusetts 02139, United States
| | - Mingshan Li
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Gerald L Hazelbauer
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, 6-225, Cambridge, Massachusetts 02139, United States
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15
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Li T, Xiu Q, Wang Q, Wang J, Duan Y, Zhou M. Functional dissection of individual domains in group III histidine kinase Sshk1p from the phytopathogenic fungus Sclerotinia sclerotiorum. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 178:104914. [PMID: 34446190 DOI: 10.1016/j.pestbp.2021.104914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/19/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
A conserved kinase domain and phosphoryl group receiver domain at the C-terminus and poly-HAMP domains at the N-terminus comprise the structural components of the group III HK which was considered as a potential antifungal target. However, the roles of individual domains in the function of group III HKs have rarely been dissected in fungi. In this study, we dissected the roles of individual domains to better understand the function of Sshk1p, a group III HK from Sclerotinia sclerotiorum. The results suggest that individual domains play different roles in the functionality of Sshk1p and are implicated in the regulation of mycelial growth, sclerotia formation, pathogenicity. And the mutants of each domain in Sshk1 showed significantly increased sensitivity to hyperosmotic stress. However, the mutants of each domain in Sshk1 showed high resistance to fludioxonil and dimethachlon which suggested that all nine domains of Sshk1p were indispensable for susceptibility to fludioxonil and dimethachlon. Moreover, deletion of each individual domain in Sshk1 cancelled intracellular glycerol accumulation and increased SsHog1p phosphorylation level triggered by NaCl and fludioxonil, suggesting that all the domains of Sshk1 were essential for Sshk1-mediated SsHog1p phosphorylation and subsequent polyol accumulation in response to fludioxonil and hyperosmotic stress.
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Affiliation(s)
- Tao Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Qian Xiu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiao Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianxin Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Research Center of Pesticide Resistance & Management Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yabing Duan
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Research Center of Pesticide Resistance & Management Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Mingguo Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Research Center of Pesticide Resistance & Management Technology, Nanjing Agricultural University, Nanjing 210095, China.
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16
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Protein design-scapes generated by microfluidic DNA assembly elucidate domain coupling in the bacterial histidine kinase CpxA. Proc Natl Acad Sci U S A 2021; 118:2017719118. [PMID: 33723045 PMCID: PMC8000134 DOI: 10.1073/pnas.2017719118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The randomization and screening of combinatorial DNA libraries is a powerful technique for understanding sequence-function relationships and optimizing biosynthetic pathways. Although it can be difficult to predict a priori which sequence combinations encode functional units, it is often possible to omit undesired combinations that inflate library size and screening effort. However, defined library generation is difficult when a complex scan through sequence space is needed. To overcome this challenge, we designed a hybrid valve- and droplet-based microfluidic system that deterministically assembles DNA parts in picoliter droplets, reducing reagent consumption and bias. Using this system, we built a combinatorial library encoding an engineered histidine kinase (HK) based on bacterial CpxA. Our library encodes designed transmembrane (TM) domains that modulate the activity of the cytoplasmic domain of CpxA and variants of the structurally distant "S helix" located near the catalytic domain. We find that the S helix sets a basal activity further modulated by the TM domain. Surprisingly, we also find that a given TM motif can elicit opposing effects on the catalytic activity of different S-helix variants. We conclude that the intervening HAMP domain passively transmits signals and shapes the signaling response depending on subtle changes in neighboring domains. This flexibility engenders a richness in functional outputs as HKs vary in response to changing evolutionary pressures.
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17
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Silva MA, Salgueiro CA. Multistep Signaling in Nature: A Close-Up of Geobacter Chemotaxis Sensing. Int J Mol Sci 2021; 22:ijms22169034. [PMID: 34445739 PMCID: PMC8396549 DOI: 10.3390/ijms22169034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/30/2021] [Accepted: 08/09/2021] [Indexed: 11/23/2022] Open
Abstract
Environmental changes trigger the continuous adaptation of bacteria to ensure their survival. This is possible through a variety of signal transduction pathways involving chemoreceptors known as methyl-accepting chemotaxis proteins (MCP) that allow the microorganisms to redirect their mobility towards favorable environments. MCP are two-component regulatory (or signal transduction) systems (TCS) formed by a sensor and a response regulator domain. These domains synchronize transient protein phosphorylation and dephosphorylation events to convert the stimuli into an appropriate cellular response. In this review, the variability of TCS domains and the most common signaling mechanisms are highlighted. This is followed by the description of the overall cellular topology, classification and mechanisms of MCP. Finally, the structural and functional properties of a new family of MCP found in Geobacter sulfurreducens are revisited. This bacterium has a diverse repertoire of chemosensory systems, which represents a striking example of a survival mechanism in challenging environments. Two G. sulfurreducens MCP—GSU0582 and GSU0935—are members of a new family of chemotaxis sensor proteins containing a periplasmic PAS-like sensor domain with a c-type heme. Interestingly, the cellular location of this domain opens new routes to the understanding of the redox potential sensing signaling transduction pathways.
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Affiliation(s)
- Marta A. Silva
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carlos A. Salgueiro
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- Correspondence:
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18
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Orillard E, Anaya S, Johnson MS, Watts KJ. Oxygen-Induced Conformational Changes in the PAS-Heme Domain of the Pseudomonas aeruginosa Aer2 Receptor. Biochemistry 2021; 60:2610-2622. [PMID: 34383467 DOI: 10.1021/acs.biochem.1c00452] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Aer2 receptor from Pseudomonas aeruginosa has an O2-binding PAS-heme domain that stabilizes O2 via a Trp residue in the distal heme pocket. Trp rotates ∼90° to bond with the ligand and initiate signaling. Although the isolated PAS domain is monomeric, both in solution and in a cyanide-bound crystal structure, an unliganded structure forms a dimer. An overlay of the two structures suggests possible signaling motions but also predicts implausible clashes at the dimer interface when the ligand is bound. Moreover, in a full-length Aer2 dimer, PAS is sandwiched between multiple N- and C-terminal HAMP domains, which would feasibly restrict PAS motions. To explore the PAS dimer interface and signal-induced motions in full-length Aer2, we introduced Cys substitutions and used thiol-reactive probes to examine in vivo accessibility and residue proximities under both aerobic and anaerobic conditions. In vivo, PAS dimers were retained in full-length Aer2 in the presence and absence of O2, and the dimer interface was consistent with the isolated PAS dimer structure. O2-mediated changes were also consistent with structural predictions in which the PAS N-terminal caps move apart and the C-terminal DxT region moves closer together. The DxT motif links PAS to the C-terminal HAMP domains and was critical for PAS-HAMP signaling. Removing the N-terminal HAMP domains altered the distal PAS dimer interface and prevented signaling, even after signal-on lesions were introduced into PAS. The N-terminal HAMP domains thus facilitate the O2-dependent shift of PAS to the signal-on conformation, clarifying their role upstream of the PAS-sensing domain.
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Affiliation(s)
- Emilie Orillard
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, California 92350, United States
| | - Selina Anaya
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, California 92350, United States
| | - Mark S Johnson
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, California 92350, United States
| | - Kylie J Watts
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, California 92350, United States
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19
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Woolfson DN. A Brief History of De Novo Protein Design: Minimal, Rational, and Computational. J Mol Biol 2021; 433:167160. [PMID: 34298061 DOI: 10.1016/j.jmb.2021.167160] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/26/2022]
Abstract
Protein design has come of age, but how will it mature? In the 1980s and the 1990s, the primary motivation for de novo protein design was to test our understanding of the informational aspect of the protein-folding problem; i.e., how does protein sequence determine protein structure and function? This necessitated minimal and rational design approaches whereby the placement of each residue in a design was reasoned using chemical principles and/or biochemical knowledge. At that time, though with some notable exceptions, the use of computers to aid design was not widespread. Over the past two decades, the tables have turned and computational protein design is firmly established. Here, I illustrate this progress through a timeline of de novo protein structures that have been solved to atomic resolution and deposited in the Protein Data Bank. From this, it is clear that the impact of rational and computational design has been considerable: More-complex and more-sophisticated designs are being targeted with many being resolved to atomic resolution. Furthermore, our ability to generate and manipulate synthetic proteins has advanced to a point where they are providing realistic alternatives to natural protein functions for applications both in vitro and in cells. Also, and increasingly, computational protein design is becoming accessible to non-specialists. This all begs the questions: Is there still a place for minimal and rational design approaches? And, what challenges lie ahead for the burgeoning field of de novo protein design as a whole?
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
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20
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Ishikawa K, Chubachi C, Tochigi S, Hoshi N, Kojima S, Hyodo M, Hayakawa Y, Furuta T, Kera K, Uozumi N. Functional characterization of multiple PAS domain-containing diguanylate cyclases in Synechocystis sp. PCC 6803. MICROBIOLOGY-SGM 2021; 166:659-668. [PMID: 32478657 DOI: 10.1099/mic.0.000929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is a second messenger known to control a variety of bacterial processes. The model cyanobacterium, Synechocystis sp. PCC 6803, has a score of genes encoding putative enzymes for c-di-GMP synthesis and degradation. However, most of them have not been functionally characterized. Here, we chose four genes in Synechocystis (dgcA-dgcD), which encode proteins with a GGDEF, diguanylate cyclase (DGC) catalytic domain and multiple Per-ARNT-Sim (PAS) conserved regulatory motifs, for detailed analysis. Purified DgcA, DgcB and DgcC were able to catalyze synthesis of c-di-GMP from two GTPs in vitro. DgcA had the highest activity, compared with DgcB and DgcC. DgcD did not show detectable activity. DgcA activity was specific for GTP and stimulated by the divalent cations, magnesium or manganese. Full activity of DgcA required the presence of the multiple PAS domains, probably because of their role in protein dimerization or stability. Synechocystis mutants carrying single deletions of dgcA-dgcD were not affected in their growth rate or biofilm production during salt stress, suggesting that there was functional redundancy in vivo. In contrast, overexpression of dgcA resulted in increased biofilm formation in the absence of salt stress. In this study, we characterize the enzymatic and physiological function of DgcA-DgcD, and propose that the PAS domains in DgcA function in maintaining the enzyme in its active form.
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Affiliation(s)
- Ko Ishikawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan
| | - Chihiro Chubachi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan
| | - Saeko Tochigi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan
| | - Naomi Hoshi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan
| | - Seiji Kojima
- Panasonic corporation, Technology Innovation Division, Hikaridai 3-4, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan
| | - Mamoru Hyodo
- Department of Applied Chemistry, Faculty of Engineering, Aichi Institute of Technology, Toyota 470-0392, Japan
| | - Yoshihiro Hayakawa
- Department of Applied Chemistry, Faculty of Engineering, Aichi Institute of Technology, Toyota 470-0392, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, B-62 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Kota Kera
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan
| | - Nobuyuki Uozumi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan
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21
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Gushchin I, Aleksenko VA, Orekhov P, Goncharov IM, Nazarenko VV, Semenov O, Remeeva A, Gordeliy V. Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity. Int J Mol Sci 2021; 22:5933. [PMID: 34072989 PMCID: PMC8199190 DOI: 10.3390/ijms22115933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/18/2022] Open
Abstract
Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.
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Affiliation(s)
- Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vladimir A. Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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Qian X, Gunturu S, Guo J, Chai B, Cole JR, Gu J, Tiedje JM. Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems. MICROBIOME 2021; 9:108. [PMID: 33990222 PMCID: PMC8122544 DOI: 10.1186/s40168-021-01047-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/11/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic approach and datasets with well-characterized metadata to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively. RESULTS High diversity (242 ARG subtypes) and abundance (0.184-0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance and efflux pump the dominant class and mechanism. Ten regulatory genes were identified and they accounted for 13-35% of resistome abundances in soils, among them arlR, cpxR, ompR, vanR, and vanS were dominant and observed in all studied soils. We identified 55 non-regulatory ARGs shared by all 26 soil metagenomes of the three ecosystems, which accounted for more than 81% of non-regulatory resistome abundance. Proteobacteria, Firmicutes, and Actinobacteria were primary ARG hosts, 7 of 10 most abundant ARGs were found in all of them. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition. CONCLUSIONS Our results identify candidate background ARGs (shared in all 26 soils), classify ARG hosts, quantify resistance classes, and provide quantitative and sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future. Video abstract.
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Affiliation(s)
- Xun Qian
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Santosh Gunturu
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - Jiarong Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - James R. Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - Jie Gu
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - James M. Tiedje
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
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Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae- A Hairpin-swapped Dimer and its Conformational Change. J Bacteriol 2021; 203:JB.00643-20. [PMID: 33753465 PMCID: PMC8117521 DOI: 10.1128/jb.00643-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
VxrA and VxrB are cognate histidine kinase (HK) - response regulator (RR) pairs of a two-component signaling system (TCS) found in Vibrio cholerae, a bacterial pathogen that causes cholera. The VxrAB TCS positively regulates virulence, the Type VI Secretion System, biofilm formation, and cell wall homeostasis in V. cholerae, providing protection from environmental stresses and contributing to the transmission and virulence of the pathogen. The VxrA HK has a unique periplasmic sensor domain (SD) and, remarkably, lacks a cytoplasmic linker domain between the second transmembrane helix and the dimerization and histidine phosphotransfer (DHp) domain, indicating that this system may utilize a potentially unique signal sensing and transmission TCS mechanism. In this study, we have determined several crystal structures of VxrA-SD and its mutants. These structures reveal a novel structural fold forming an unusual β hairpin-swapped dimer. A conformational change caused by relative rotation of the two monomers in a VxrA-SD dimer could potentially change the association of transmembrane helices and, subsequently, the pairing of cytoplasmic DHp domains. Based on the structural observation, we propose a putative scissor-like closing regulation mechanism for the VxrA HK.IMPORTANCE V. cholerae has a dynamic life cycle, which requires rapid adaptation to changing external conditions. Two-component signal transduction (TCS) systems allow V. cholerae to sense and respond to these environmental changes. The VxrAB TCS positively regulates a number of important V. cholerae phenotypes, including virulence, the Type Six Secretion System, biofilm formation, and cell wall homeostasis. Here, we provide the crystal structure of the VxrA sensor histidine kinase sensing domain and propose a mechanism for signal transduction. The cognate signal for VxrAB remains unknown, however, in this work we couple our structural analysis with functional assessments of key residues to further our understanding of this important TCS.
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24
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Teixeira RD, Holzschuh F, Schirmer T. Activation mechanism of a small prototypic Rec-GGDEF diguanylate cyclase. Nat Commun 2021; 12:2162. [PMID: 33846343 PMCID: PMC8041772 DOI: 10.1038/s41467-021-22492-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/15/2021] [Indexed: 01/24/2023] Open
Abstract
Diguanylate cyclases synthesising the bacterial second messenger c-di-GMP are found to be regulated by a variety of sensory input domains that control the activity of their catalytical GGDEF domain, but how activation proceeds mechanistically is, apart from a few examples, still largely unknown. As part of two-component systems, they are activated by cognate histidine kinases that phosphorylate their Rec input domains. DgcR from Leptospira biflexa is a constitutively dimeric prototype of this class of diguanylate cyclases. Full-length crystal structures reveal that BeF3- pseudo-phosphorylation induces a relative rotation of two rigid halves in the Rec domain. This is coupled to a reorganisation of the dimeric structure with concomitant switching of the coiled-coil linker to an alternative heptad register. Finally, the activated register allows the two substrate-loaded GGDEF domains, which are linked to the end of the coiled-coil via a localised hinge, to move into a catalytically competent dimeric arrangement. Bioinformatic analyses suggest that the binary register switch mechanism is utilised by many diguanylate cyclases with N-terminal coiled-coil linkers. As part of two-component systems, diguanylate cyclases (DGCs) are activated by phosphorylation. Structural and computational analyses of DgcR, a model DGC, reveal the phosphorylation-induced conformational changes and the activation mechanism likely shared by many DGCs with N-terminal coiled-coil linkers.
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Affiliation(s)
| | - Fabian Holzschuh
- Structural Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Tilman Schirmer
- Structural Biology, Biozentrum, University of Basel, Basel, Switzerland.
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25
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Szczepaniak K, Bukala A, da Silva Neto AM, Ludwiczak J, Dunin-Horkawicz S. A library of coiled-coil domains: from regular bundles to peculiar twists. Bioinformatics 2021; 36:5368-5376. [PMID: 33325494 PMCID: PMC8016460 DOI: 10.1093/bioinformatics/btaa1041] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/30/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022] Open
Abstract
MOTIVATION Coiled coils are widespread protein domains involved in diverse processes ranging from providing structural rigidity to the transduction of conformational changes. They comprise two or more α-helices that are wound around each other to form a regular supercoiled bundle. Owing to this regularity, coiled-coil structures can be described with parametric equations, thus enabling the numerical representation of their properties, such as the degree and handedness of supercoiling, rotational state of the helices, and the offset between them. These descriptors are invaluable in understanding the function of coiled coils and designing new structures of this type. The existing tools for such calculations require manual preparation of input and are therefore not suitable for the high-throughput analyses. RESULTS To address this problem, we developed SamCC-Turbo, a software for fully automated, per-residue measurement of coiled coils. By surveying Protein Data Bank with SamCC-Turbo, we generated a comprehensive atlas of ∼50 000 coiled-coil regions. This machine learning-ready dataset features precise measurements as well as decomposes coiled-coil structures into fragments characterized by various degrees of supercoiling. The potential applications of SamCC-Turbo are exemplified by analyses in which we reveal general structural features of coiled coils involved in functions requiring conformational plasticity. Finally, we discuss further directions in the prediction and modeling of coiled coils. AVAILABILITY AND IMPLEMENTATION SamCC-Turbo is available as a web server (https://lbs.cent.uw.edu.pl/samcc_turbo) and as a Python library (https://github.com/labstructbioinf/samcc_turbo), whereas the results of the Protein Data Bank scan can be browsed and downloaded at https://lbs.cent.uw.edu.pl/ccdb. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Krzysztof Szczepaniak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Adriana Bukala
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Antonio Marinho da Silva Neto
- Molecular Prospecting and Bioinformatics Group, Laboratory of Immunopathology Keizo Asami, Federal University of Pernambuco, 50670-901 Recife, Brazil
| | - Jan Ludwiczak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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26
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Arroyo-Pérez EE, Ringgaard S. Interdependent Polar Localization of FlhF and FlhG and Their Importance for Flagellum Formation of Vibrio parahaemolyticus. Front Microbiol 2021; 12:655239. [PMID: 33815347 PMCID: PMC8009987 DOI: 10.3389/fmicb.2021.655239] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/23/2021] [Indexed: 11/14/2022] Open
Abstract
Failure of the cell to properly regulate the number and intracellular positioning of their flagella, has detrimental effects on the cells’ swimming ability. The flagellation pattern of numerous bacteria is regulated by the NTPases FlhF and FlhG. In general, FlhG controls the number of flagella produced, whereas FlhF coordinates the position of the flagella. In the human pathogen Vibrio parahaemolyticus, its single flagellum is positioned and formed at the old cell pole. Here, we describe the spatiotemporal localization of FlhF and FlhG in V. parahaemolyticus and their effect on swimming motility. Absence of either FlhF or FlhG caused a significant defect in swimming ability, resulting in absence of flagella in a ΔflhF mutant and an aberrant flagellated phenotype in ΔflhG. Both proteins localized to the cell pole in a cell cycle-dependent manner, but displayed different patterns of localization throughout the cell cycle. FlhF transitioned from a uni- to bi-polar localization, as observed in other polarly flagellated bacteria. Localization of FlhG was strictly dependent on the cell pole-determinant HubP, while polar localization of FlhF was HubP independent. Furthermore, localization of FlhF and FlhG was interdependent and required for each other’s proper intracellular localization and recruitment to the cell pole. In the absence of HubP or FlhF, FlhG forms non-polar foci in the cytoplasm of the cell, suggesting the possibility of a secondary localization site within the cell besides its recruitment to the cell poles.
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Affiliation(s)
- Erick Eligio Arroyo-Pérez
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Simon Ringgaard
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
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27
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Gopinath T, Weber D, Wang S, Larsen E, Veglia G. Solid-State NMR of Membrane Proteins in Lipid Bilayers: To Spin or Not To Spin? Acc Chem Res 2021; 54:1430-1439. [PMID: 33655754 DOI: 10.1021/acs.accounts.0c00670] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Membrane proteins mediate a plethora of cellular functions and represent important targets for drug development. Unlike soluble proteins, membrane proteins require native-like environments to fold correctly and be active. Therefore, modern structural biology techniques have aimed to determine the structure and dynamics of these membrane proteins at physiological temperature and in liquid crystalline lipid bilayers. With the flourishing of new NMR methodologies and improvements in sample preparations, magic angle spinning (MAS) and oriented sample solid-state NMR (OS-ssNMR) spectroscopy of membrane proteins is experiencing a new renaissance. Born as antagonistic approaches, these techniques nowadays offer complementary information on the structural topology and dynamics of membrane proteins reconstituted in lipid membranes. By spinning biosolid samples at the magic angle (θ = 54.7°), MAS NMR experiments remove the intrinsic anisotropy of the NMR interactions, increasing spectral resolution. Internuclear spin interactions (spin exchange) are reintroduced by RF pulses, providing distances and torsion angles to determine secondary, tertiary, and quaternary structures of membrane proteins. OS-ssNMR, on the other hand, directly detects anisotropic NMR parameters such as dipolar couplings (DC) and anisotropic chemical shifts (CS), providing orientational constraints to determine the architecture (i.e., topology) of membrane proteins relative to the lipid membrane. Defining the orientation of membrane proteins and their interactions with lipid membranes is of paramount importance since lipid-protein interactions can shape membrane protein conformations and ultimately define their functional states.In this Account, we report selected studies from our group integrating MAS and OS-ssNMR techniques to give a comprehensive view of the biological processes occurring at cellular membranes. We focus on the main experiments for both techniques, with an emphasis on new implementation to increase both sensitivity and spectral resolution. We also describe how the structural constraints derived from both isotropic and anisotropic NMR parameters are integrated into dynamic structural modeling using replica-averaged orientational-restrained molecular dynamics simulations (RAOR-MD). We showcase small membrane proteins that are involved in Ca2+ transport and regulate cardiac and skeletal muscle contractility: phospholamban (PLN, 6 kDa), sarcolipin (SLN, 4 kDa), and DWORF (4 kDa). We summarize our results for the structures of these polypeptides free and in complex with the sarcoplasmic reticulum (SR) Ca2+-ATPase (SERCA, 110 kDa). Additionally, we illustrate the progress toward the determination of the structural topology of a six transmembrane protein associated with succinate and acetate transport (SatP, hexamer 120 kDa). From these examples, the integrated MAS and OS-ssNMR approach, in combination with modern computational methods, emerges as a way to overcome the challenges posed by studying large membrane protein systems.
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Structural resolution of switchable states of a de novo peptide assembly. Nat Commun 2021; 12:1530. [PMID: 33750792 PMCID: PMC7943578 DOI: 10.1038/s41467-021-21851-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/12/2021] [Indexed: 12/18/2022] Open
Abstract
De novo protein design is advancing rapidly. However, most designs are for single states. Here we report a de novo designed peptide that forms multiple α-helical-bundle states that are accessible and interconvertible under the same conditions. Usually in such designs amphipathic α helices associate to form compact structures with consolidated hydrophobic cores. However, recent rational and computational designs have delivered open α-helical barrels with functionalisable cavities. By placing glycine judiciously in the helical interfaces of an α-helical barrel, we obtain both open and compact states in a single protein crystal. Molecular dynamics simulations indicate a free-energy landscape with multiple and interconverting states. Together, these findings suggest a frustrated system in which steric interactions that maintain the open barrel and the hydrophobic effect that drives complete collapse are traded-off. Indeed, addition of a hydrophobic co-solvent that can bind within the barrel affects the switch between the states both in silico and experimentally. So far most of the de novo designed proteins are for single states only. Here, the authors present the de novo design and crystal structure determination of a coiled-coil peptide that assembles into multiple, distinct conformational states under the same conditions and further characterise its properties with biophysical experiments, NMR and MD simulations.
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29
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Orientational Ambiguity in Septin Coiled Coils and its Structural Basis. J Mol Biol 2021; 433:166889. [PMID: 33639214 DOI: 10.1016/j.jmb.2021.166889] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/25/2021] [Accepted: 02/17/2021] [Indexed: 12/21/2022]
Abstract
Septins are an example of subtle molecular recognition whereby different paralogues must correctly assemble into functional filaments important for essential cellular events such as cytokinesis. Most possess C-terminal domains capable of forming coiled coils which are believed to be involved in filament formation and bundling. Here, we report an integrated structural approach which aims to unravel their architectural diversity and in so doing provide direct structural information for the coiled-coil regions of five human septins. Unexpectedly, we encounter dimeric structures presenting both parallel and antiparallel arrangements which are in consonance with molecular modelling suggesting that both are energetically accessible. These sequences therefore code for two metastable states of different orientations which employ different but overlapping interfaces. The antiparallel structures present a mixed coiled-coil interface, one side of which is dominated by a continuous chain of core hydrophilic residues. This unusual type of coiled coil could be used to expand the toolkit currently available to the protein engineer for the design of previously unforeseen coiled-coil based assemblies. Within a physiological context, our data provide the first atomic details related to the assumption that the parallel orientation is likely formed between septin monomers from the same filament whilst antiparallelism may participate in the widely described interfilament cross bridges necessary for higher order structures and thereby septin function.
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30
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Zhu J, Liu B, Shu X, Sun B. A novel mutation of walK confers vancomycin-intermediate resistance in methicillin-susceptible Staphylococcus aureus. Int J Med Microbiol 2021; 311:151473. [PMID: 33445057 DOI: 10.1016/j.ijmm.2021.151473] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 10/22/2022] Open
Abstract
With the treatment failure by vancomycin and poor clinical outcomes, the emergence and spread of vancomycin intermediate-resistant Staphylococcus aureus (VISA) has raised more concerns in recent years. While most VISA strains are isolated from methicillin-resistant S. aureus (MRSA), the mechanism underlying the generation of VISA from methicillin-susceptible S. aureus (MSSA) is still largely unknown. Here, we identified a total of 10 mutations in 9 genes through comparative genome analysis from laboratory-derived VISA strain. We verified the role of a novel mutation of WalK (I237T) and our results further indicated that the introduction of WalK (I237T) by allelic replacement can confer vancomycin resistance in MSSA with common VISA characteristics, including thickened cell walls, reduced autolysis, and attenuated virulence. Consistent with these phenotypes, real-time quantitative reverse transcription-PCR revealed the altered expression of several genes associated with cell wall metabolism and virulence control. In addition, electrophoretic mobility shift assay indicated that WalR can directly bind to the promoter regions of oatA, sle1, and mgt, fluorescence-based promoter activity and β-galactosidase assays revealed WalK (I237T) can alter promoter activities of oatA, mgt, and sle1, thus regulating genes expression. These findings broaden our understanding of the regulatory network by WalKR system and decipher the molecular mechanisms of developmental VISA resistance in MSSA with point mutations.
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Affiliation(s)
- Jiade Zhu
- Department of Oncology, The First Affiliated Hospital, CAS Key Laboratory of Innate Immunity and Chronic Disease, and Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Banghui Liu
- Department of Oncology, The First Affiliated Hospital, CAS Key Laboratory of Innate Immunity and Chronic Disease, and Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Xueqin Shu
- Department of Oncology, The First Affiliated Hospital, CAS Key Laboratory of Innate Immunity and Chronic Disease, and Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China
| | - Baolin Sun
- Department of Oncology, The First Affiliated Hospital, CAS Key Laboratory of Innate Immunity and Chronic Disease, and Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, 230027, China.
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31
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Pi H, Chu ML, Ivan SJ, Latario CJ, Toth AM, Carlin SM, Hillebrand GH, Lin HK, Reppart JD, Stauff DL, Skaar EP. Directed evolution reveals the mechanism of HitRS signaling transduction in Bacillus anthracis. PLoS Pathog 2020; 16:e1009148. [PMID: 33362282 PMCID: PMC7790381 DOI: 10.1371/journal.ppat.1009148] [Citation(s) in RCA: 3] [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: 09/13/2020] [Revised: 01/07/2021] [Accepted: 11/11/2020] [Indexed: 12/03/2022] Open
Abstract
Two component systems (TCSs) are a primary mechanism of signal sensing and response in bacteria. Systematic characterization of an entire TCS could provide a mechanistic understanding of these important signal transduction systems. Here, genetic selections were employed to dissect the molecular basis of signal transduction by the HitRS system that detects cell envelope stress in the pathogen Bacillus anthracis. Numerous point mutations were isolated within HitRS, 17 of which were in a 50-residue HAMP domain. Mutational analysis revealed the importance of hydrophobic interactions within the HAMP domain and highlighted its essentiality in TCS signaling. In addition, these data defined residues critical for activities intrinsic to HitRS, uncovered specific interactions among individual domains and between the two signaling proteins, and revealed that phosphotransfer is the rate-limiting step for signal transduction. Furthermore, this study establishes the use of unbiased genetic selections to study TCS signaling and provides a comprehensive mechanistic understanding of an entire TCS. Bacterial TCSs are a primary strategy for stress sensing and niche adaptation. Although individual domains and proteins of these systems have been extensively studied, systematic characterization of an entire TCS is rare. In this study, through unbiased genetic selections and rigorous biochemical analysis, we provide a detailed characterization and structure-function analysis of an entire TCS and extend our understanding of the molecular basis of signal transduction through TCSs. Moreover, this study provides a comprehensive map of point-mutations in these well-conserved signaling proteins, which will be broadly useful for studying other TCSs. The described genetic selection strategies are applicable to any TCS, providing a powerful tool for researchers interested in microbial signal transduction.
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Affiliation(s)
- Hualiang Pi
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Infection, Immunology, & Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Michelle L. Chu
- Department of Biology, Grove City College, Grove City, Pennsylvania, United States of America
| | - Samuel J. Ivan
- Department of Biology, Grove City College, Grove City, Pennsylvania, United States of America
| | - Casey J. Latario
- Department of Biology, Grove City College, Grove City, Pennsylvania, United States of America
| | - Allen M. Toth
- Department of Biology, Grove City College, Grove City, Pennsylvania, United States of America
| | - Sophia M. Carlin
- Department of Biology, Grove City College, Grove City, Pennsylvania, United States of America
| | - Gideon H. Hillebrand
- Department of Biology, Grove City College, Grove City, Pennsylvania, United States of America
| | - Hannah K. Lin
- Department of Biology, Grove City College, Grove City, Pennsylvania, United States of America
| | - Jared D. Reppart
- Department of Biology, Grove City College, Grove City, Pennsylvania, United States of America
| | - Devin L. Stauff
- Department of Biology, Grove City College, Grove City, Pennsylvania, United States of America
| | - Eric P. Skaar
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Infection, Immunology, & Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- * E-mail:
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Stopp M, Steinmetz PA, Schubert C, Griesinger C, Schneider D, Unden G. Transmembrane signaling and cytoplasmic signal conversion by dimeric transmembrane helix 2 and a linker domain of the DcuS sensor kinase. J Biol Chem 2020; 296:100148. [PMID: 33277358 PMCID: PMC7857512 DOI: 10.1074/jbc.ra120.015999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 01/16/2023] Open
Abstract
Transmembrane (TM) signaling is a key process of membrane-bound sensor kinases. The C4-dicarboxylate (fumarate) responsive sensor kinase DcuS of Escherichia coli is anchored by TM helices TM1 and TM2 in the membrane. Signal transmission across the membrane relies on the piston-type movement of the periplasmic part of TM2. To define the role of TM2 in TM signaling, we use oxidative Cys cross-linking to demonstrate that TM2 extends over the full distance of the membrane and forms a stable TM homodimer in both the inactive and fumarate-activated state of DcuS. An S186xxxGxxxG194 motif is required for the stability and function of the TM2 homodimer. The TM2 helix further extends on the periplasmic side into the α6-helix of the sensory PASP domain and on the cytoplasmic side into the α1-helix of PASC. PASC has to transmit the signal to the C-terminal kinase domain. A helical linker on the cytoplasmic side connecting TM2 with PASC contains an LxxxLxxxL sequence. The dimeric state of the linker was relieved during fumarate activation of DcuS, indicating structural rearrangements in the linker. Thus, DcuS contains a long α-helical structure reaching from the sensory PASP (α6) domain across the membrane to α1(PASC). Taken together, the results suggest piston-type TM signaling by the TM2 homodimer from PASP across the full TM region, whereas the fumarate-destabilized linker dimer converts the signal on the cytoplasmic side for PASC and kinase regulation.
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Affiliation(s)
- Marius Stopp
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Philipp Aloysius Steinmetz
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Christopher Schubert
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Gottfried Unden
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany.
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Identification of Uncharacterized Components of Prokaryotic Immune Systems and Their Diverse Eukaryotic Reformulations. J Bacteriol 2020; 202:JB.00365-20. [PMID: 32868406 DOI: 10.1128/jb.00365-20] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/25/2020] [Indexed: 12/19/2022] Open
Abstract
Nucleotide-activated effector deployment, prototyped by interferon-dependent immunity, is a common mechanistic theme shared by immune systems of several animals and prokaryotes. Prokaryotic versions include CRISPR-Cas with the CRISPR polymerase domain, their minimal variants, and systems with second messenger oligonucleotide or dinucleotide synthetase (SMODS). Cyclic or linear oligonucleotide signals in these systems help set a threshold for the activation of potentially deleterious downstream effectors in response to invader detection. We establish such a regulatory mechanism to be a more general principle of immune systems, which can also operate independently of such messengers. Using sensitive sequence analysis and comparative genomics, we identify 12 new prokaryotic immune systems, which we unify by this principle of threshold-dependent effector activation. These display regulatory mechanisms paralleling physiological signaling based on 3'-5' cyclic mononucleotides, NAD+-derived messengers, two- and one-component signaling that includes histidine kinase-based signaling, and proteolytic activation. Furthermore, these systems allowed the identification of multiple new sensory signal sensory components, such as a tetratricopeptide repeat (TPR) scaffold predicted to recognize NAD+-derived signals, unreported versions of the STING domain, prokaryotic YEATS domains, and a predicted nucleotide sensor related to receiver domains. We also identify previously unrecognized invader detection components and effector components, such as prokaryotic versions of the Wnt domain. Finally, we show that there have been multiple acquisitions of unidentified STING domains in eukaryotes, while the TPR scaffold was incorporated into the animal immunity/apoptosis signal-regulating kinase (ASK) signalosome.IMPORTANCE Both prokaryotic and eukaryotic immune systems face the dangers of premature activation of effectors and degradation of self-molecules in the absence of an invader. To mitigate this, they have evolved threshold-setting regulatory mechanisms for the triggering of effectors only upon the detection of a sufficiently strong invader signal. This work defines general templates for such regulation in effector-based immune systems. Using this, we identify several previously uncharacterized prokaryotic immune mechanisms that accomplish the regulation of downstream effector deployment by using nucleotide, NAD+-derived, two-component, and one-component signals paralleling physiological homeostasis. This study has also helped identify several previously unknown sensor and effector modules in these systems. Our findings also augment the growing evidence for the emergence of key animal immunity and chromatin regulatory components from prokaryotic progenitors.
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R 93P Substitution in the PmrB HAMP Domain Contributes to Colistin Heteroresistance in Escherichia coli Isolates from Swine. Antimicrob Agents Chemother 2020; 64:AAC.01509-20. [PMID: 32868331 DOI: 10.1128/aac.01509-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/19/2020] [Indexed: 02/04/2023] Open
Abstract
Here, the mechanisms of colistin heteroresistance (CHR) were assessed in 12 Escherichia coli isolates from swine in China. CHR was investigated by population analysis profile tests. CHR stability was studied by culturing isolates for five overnight incubation periods in colistin-free medium. Subsequently, the mcr-1 gene and mutations in PmrAB, PhoPQ, and MgrB were screened in parental isolates and resistant subpopulations. Additionally, the expression levels of phoPQ, its target gene pagP, and its negative regulator gene mgrB, as well as pmrAB and its target genes pmrHFIJKLM and pmrC, were determined by real-time relative quantitative PCR. Eleven of the 12 isolates were confirmed to show CHR, with 17 resistant subpopulations. Also, 11 of the 17 subpopulations (64.71%) harbored point mutations in PmrB and/or PhoQ, differing from their parental isolates. However, only one stable resistant subpopulation (EPF42-4) was identified; it harbored an arginine-to-proline substitution at position 93 (R93P) within the PmrB HAMP (histidine kinase, adenylyl cyclase, methyl-binding protein, and phosphatase) domain. Compared to the pmrB expression levels in the parental isolate EPF42 and E. coli K-12 MG1655, remarkable pmrB overexpression was observed in EPF42-4, which showed upregulated pmrA, pmrK, and pmrC expression. Structural analysis demonstrated that the R93P substitution promotes conformational changes in the HAMP domain, leading to an acceleration in its signal transduction ability and the activation of PmrB expression. In conclusion, point mutations in PmrB and/or PhoQ were primarily associated with CHR. The R93P substitution resulted in the establishment of stable resistant subpopulations in E. coli showing CHR.
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Koh A, Gibbon MJ, Van der Kamp MW, Pudney CR, Gebhard S. Conformation control of the histidine kinase BceS of Bacillus subtilis by its cognate ABC-transporter facilitates need-based activation of antibiotic resistance. Mol Microbiol 2020; 115:157-174. [PMID: 32955745 DOI: 10.1111/mmi.14607] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 12/15/2022]
Abstract
Bacteria closely control gene expression to ensure optimal physiological responses to their environment. Such careful gene expression can minimize the fitness cost associated with antibiotic resistance. We previously described a novel regulatory logic in Bacillus subtilis enabling the cell to directly monitor its need for detoxification. This cost-effective strategy is achieved via a two-component regulatory system (BceRS) working in a sensory complex with an ABC-transporter (BceAB), together acting as a flux-sensor where signaling is proportional to transport activity. How this is realized at the molecular level has remained unknown. Using experimentation and computation we here show that the histidine kinase is activated by piston-like displacements in the membrane, which are converted to helical rotations in the catalytic core via an intervening HAMP-like domain. Intriguingly, the transporter was not only required for kinase activation, but also to actively maintain the kinase in its inactive state in the absence of antibiotics. Such coupling of kinase activity to that of the transporter ensures the complete control required for transport flux-dependent signaling. Moreover, we show that the transporter likely conserves energy by signaling with sub-maximal sensitivity. These results provide the first mechanistic insights into transport flux-dependent signaling, a unique strategy for energy-efficient decision making.
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Affiliation(s)
- Alan Koh
- Department of Biology and Biochemistry, University of Bath, Bath, UK.,Milner Centre for Evolution, University of Bath, Bath, UK
| | - Marjorie J Gibbon
- Department of Biology and Biochemistry, University of Bath, Bath, UK.,Milner Centre for Evolution, University of Bath, Bath, UK
| | | | | | - Susanne Gebhard
- Department of Biology and Biochemistry, University of Bath, Bath, UK.,Milner Centre for Evolution, University of Bath, Bath, UK
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36
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Kumar S, Gillilan RE, Yernool DA. Structure and function of the juxtamembrane GAF domain of potassium biosensor KdpD. Protein Sci 2020; 29:2009-2021. [PMID: 32713093 DOI: 10.1002/pro.3920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 11/10/2022]
Abstract
KdpD/KdpE two-component signaling system regulates expression of a high affinity potassium transporter responsible for potassium homeostasis. The C-terminal module of KdpD consists of a GAF domain linked to a histidine kinase domain. Whereas certain GAF domains act as regulators by binding cyclic nucleotides, the role of the juxtamembrane GAF domain in KdpD is unknown. We report the high-resolution crystal structure of KdpD GAF domain (KdpDG ) consisting of five α-helices, four β-sheets and two large loops. KdpDG forms a symmetry-related dimer, wherein parallelly arranged monomers contribute to a four-helix bundle at the dimer-interface, SAXS analysis of KdpD C-terminal module reveals an elongated structure that is a dimer in solution. Substitution of conserved residues with various residues that disrupt the dimer interface produce a range of effects on gene expression demonstrating the importance of the interface in inactive to active transitions during signaling. Comparison of ligand binding site of the classic cyclic nucleotide-binding GAF domains to KdpDG reveals structural differences arising from naturally occurring substitutions in primary sequence of KdpDG that modifies the canonical NKFDE sequence motif required for cyclic nucleotide binding. Together these results suggest a structural role for KdpDG in dimerization and transmission of signal to the kinase domain.
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Affiliation(s)
- Shivesh Kumar
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Richard E Gillilan
- Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source (MacCHESS), Cornell University, Ithaca, New York, USA
| | - Dinesh A Yernool
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
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Gushchin I, Orekhov P, Melnikov I, Polovinkin V, Yuzhakova A, Gordeliy V. Sensor Histidine Kinase NarQ Activates via Helical Rotation, Diagonal Scissoring, and Eventually Piston-Like Shifts. Int J Mol Sci 2020; 21:E3110. [PMID: 32354084 PMCID: PMC7247690 DOI: 10.3390/ijms21093110] [Citation(s) in RCA: 8] [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: 03/25/2020] [Revised: 04/19/2020] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
Membrane-embedded sensor histidine kinases (HKs) and chemoreceptors are used ubiquitously by bacteria and archaea to percept the environment, and are often crucial for their survival and pathogenicity. The proteins can transmit the signal from the sensor domain to the catalytic kinase domain reliably over the span of several hundreds of angstroms, and regulate the activity of the cognate response regulator proteins, with which they form two-component signaling systems (TCSs). Several mechanisms of transmembrane signal transduction in TCS receptors have been proposed, dubbed (swinging) piston, helical rotation, and diagonal scissoring. Yet, despite decades of studies, there is no consensus on whether these mechanisms are common for all TCS receptors. Here, we extend our previous work on Escherichia coli nitrate/nitrite sensor kinase NarQ. We determined a crystallographic structure of the sensor-TM-HAMP fragment of the R50S mutant, which, unexpectedly, was found in a ligand-bound-like conformation, despite an inability to bind nitrate. Subsequently, we reanalyzed the structures of the ligand-free and ligand-bound NarQ and NarX sensor domains, and conducted extensive molecular dynamics simulations of ligand-free and ligand-bound wild type and mutated NarQ. Based on the data, we show that binding of nitrate to NarQ causes, first and foremost, helical rotation and diagonal scissoring of the α-helices at the core of the sensor domain. These conformational changes are accompanied by a subtle piston-like motion, which is amplified by a switch in the secondary structure of the linker between the sensor and TM domains. We conclude that helical rotation, diagonal scissoring, and piston are simply different degrees of freedom in coiled-coil proteins and are not mutually exclusive in NarQ, and likely in other nitrate sensors and TCS proteins as well.
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Affiliation(s)
- Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Institute of Personalized Medicine, Sechenov University, 119146 Moscow, Russia
| | - Igor Melnikov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Vitaly Polovinkin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
| | - Anastasia Yuzhakova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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38
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Horx P, Geyer A. Defining the mobility range of a hinge-type connection using molecular dynamics and metadynamics. PLoS One 2020; 15:e0230962. [PMID: 32282813 PMCID: PMC7153902 DOI: 10.1371/journal.pone.0230962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 03/12/2020] [Indexed: 01/29/2023] Open
Abstract
A designed disulfide-rich β-hairpin peptide that dimerizes spontaneously served as a hinge-type connection between proteins. Here, we analyze the range of dynamics of this hinge dimer with the aim of proposing new applications for the DNA-encodable peptide and establishing guidelines for the computational analysis of other disulfide hinges. A recent structural analysis based on nuclear magnetic resonance spectroscopy and ion mobility spectrometry revealed an averaged conformation in the hinge region which motivated us to investigate the dynamic behavior using a combination of molecular dynamics simulation, metadynamics and free energy surface analysis to characterize the conformational space available to the hinge. Principal component analysis uncovered two slow modes of the peptide, namely, the opening and closing motion and twisting of the two β-hairpins assembling the hinge. Applying a collective variable (CV) that mimics the first dominating mode, led to a major expansion of the conformational space. The description of the dynamics could be achieved by analysis of the opening angle and the twisting of the β-hairpins and, thus, offers a methodology that can also be transferred to other derivatives. It has been demonstrated that the hinge peptide’s lowest energy conformation consists of a large opening angle and strong twist but is separated by small energy barriers and can, thus, adopt a closed and untwisted structure. With the aim of proposing further applications for the hinge peptide, we simulated its behavior in the sterically congested environment of a four-helix bundle. Preliminary investigations show that one helix is pushed out and a three-helix bundle forms. The insights gained into the dynamics of the tetra-disulfide peptide and analytical guidelines developed in this study may contribute to the understanding of the structure and function of more complex hinge-type proteins, such as the IgG antibody family.
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Affiliation(s)
- Philip Horx
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Armin Geyer
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
- * E-mail:
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39
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Huang J, Li C, Song J, Velkov T, Wang L, Zhu Y, Li J. Regulating polymyxin resistance in Gram-negative bacteria: roles of two-component systems PhoPQ and PmrAB. Future Microbiol 2020; 15:445-459. [PMID: 32250173 DOI: 10.2217/fmb-2019-0322] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Polymyxins (polymyxin B and colistin) are last-line antibiotics against multidrug-resistant Gram-negative pathogens. Polymyxin resistance is increasing worldwide, with resistance most commonly regulated by two-component systems such as PmrAB and PhoPQ. This review discusses the regulatory mechanisms of PhoPQ and PmrAB in mediating polymyxin resistance, from receiving an external stimulus through to activation of genes responsible for lipid A modifications. By analyzing the reported nonsynonymous substitutions in each two-component system, we identified the domains that are critical for polymyxin resistance. Notably, for PmrB 71% of resistance-conferring nonsynonymous mutations occurred in the HAMP (present in histidine kinases, adenylate cyclases, methyl accepting proteins and phosphatase) linker and DHp (dimerization and histidine phosphotransfer) domains. These results enhance our understanding of the regulatory mechanisms underpinning polymyxin resistance and may assist with the development of new strategies to minimize resistance emergence.
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Affiliation(s)
- Jiayuan Huang
- Biomedicine Discovery Institute & Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Chen Li
- Biomedicine Discovery Institute & Department of Biochemistry & Molecular Biology, Monash University, Melbourne 3800, Australia.,Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Jiangning Song
- Biomedicine Discovery Institute & Department of Biochemistry & Molecular Biology, Monash University, Melbourne 3800, Australia
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry & Health Sciences, The University of Melbourne, Melbourne 3010, Australia
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yan Zhu
- Biomedicine Discovery Institute & Department of Microbiology, Monash University, Melbourne 3800, Australia
| | - Jian Li
- Biomedicine Discovery Institute & Department of Microbiology, Monash University, Melbourne 3800, Australia
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40
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Lockey C, Edwards RJ, Roper DI, Dixon AM. The Extracellular Domain of Two-component System Sensor Kinase VanS from Streptomyces coelicolor Binds Vancomycin at a Newly Identified Binding Site. Sci Rep 2020; 10:5727. [PMID: 32235931 PMCID: PMC7109055 DOI: 10.1038/s41598-020-62557-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/11/2020] [Indexed: 11/24/2022] Open
Abstract
The glycopeptide antibiotic vancomycin has been widely used to treat infections of Gram-positive bacteria including Clostridium difficile and methicillin-resistant Staphylococcus aureus. However, since its introduction, high level vancomycin resistance has emerged. The genes responsible require the action of the two-component regulatory system VanSR to induce expression of resistance genes. The mechanism of detection of vancomycin by this two-component system has yet to be elucidated. Diverging evidence in the literature supports activation models in which the VanS protein binds either vancomycin, or Lipid II, to induce resistance. Here we investigated the interaction between vancomycin and VanS from Streptomyces coelicolor (VanSSC), a model Actinomycete. We demonstrate a direct interaction between vancomycin and purified VanSSC, and traced these interactions to the extracellular region of the protein, which we reveal adopts a predominantly α-helical conformation. The VanSSC-binding epitope within vancomycin was mapped to the N-terminus of the peptide chain, distinct from the binding site for Lipid II. In targeting a separate site on vancomycin, the effective VanS ligand concentration includes both free and lipid-bound molecules, facilitating VanS activation. This is the first molecular description of the VanS binding site within vancomycin, and could direct engineering of future therapeutics.
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Affiliation(s)
- Christine Lockey
- MOAC Doctoral Training Centre, University of Warwick, Coventry, CV4 7AL, UK
| | - Richard J Edwards
- Medical Research Council Doctoral Training Centre, University of Warwick, Coventry, CV4 7AL, UK
| | - David I Roper
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Ann M Dixon
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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41
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Kenney LJ, Anand GS. EnvZ/OmpR Two-Component Signaling: An Archetype System That Can Function Noncanonically. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0001-2019. [PMID: 32003321 PMCID: PMC7192543 DOI: 10.1128/ecosalplus.esp-0001-2019] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Indexed: 01/09/2023]
Abstract
Two-component regulatory systems represent the major paradigm for signal transduction in prokaryotes. The simplest systems are composed of a sensor kinase and a response regulator. The sensor is often a membrane protein that senses a change in environmental conditions and is autophosphorylated by ATP on a histidine residue. The phosphoryl group is transferred onto an aspartate of the response regulator, which activates the regulator and alters its output, usually resulting in a change in gene expression. In this review, we present a historical view of the archetype EnvZ/OmpR two-component signaling system, and then we provide a new view of signaling based on our recent experiments. EnvZ responds to cytoplasmic signals that arise from changes in the extracellular milieu, and OmpR acts canonically (requiring phosphorylation) to regulate the porin genes and noncanonically (without phosphorylation) to activate the acid stress response. Herein, we describe how insights gleaned from stimulus recognition and response in EnvZ are relevant to nearly all sensor kinases and response regulators.
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Affiliation(s)
- Linda J Kenney
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
- Mechanobiology Institute, T-Lab, National University of Singapore, Singapore
| | - Ganesh S Anand
- Department of Biological Sciences, National University of Singapore, Singapore
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42
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Li Z, Lou Y, Ding J, Liu BF, Xie GJ, Ren NQ, Xing D. Metabolic regulation of ethanol-type fermentation of anaerobic acidogenesis at different pH based on transcriptome analysis of Ethanoligenens harbinense. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:101. [PMID: 32518589 PMCID: PMC7268672 DOI: 10.1186/s13068-020-01740-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/25/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Ethanol-type fermentation, one of the fermentation types in mixed cultures of acidogenesis with obvious advantages such as low pH tolerance and high efficiency of H2 production, has attracted widespread attentions. pH level greatly influences the establishment of the fermentation of carbohydrate acidogenesis by shaping community assembly and the metabolic activity of keystone populations. To explore the adaptation mechanisms of ethanol-type fermentation to low pH, we report the effects of initial pH on the physiological metabolism and transcriptomes of Ethanoligenens harbinense-a representative species of ethanol-type fermentation. RESULTS Different initial pH levels significantly changed the cell growth and fermentation products of E. harbinense. Using transcriptomic analysis, we identified and functionally categorized 1753 differentially expressed genes (DEGs). By mining information on metabolic pathways, we probed the transcriptional regulation of ethanol-H2 metabolism relating to pH responses. Multiple pathways of E. harbinense were co-regulated by changing gene expression patterns. Low initial pH down-regulated the expression of cell growth- and acidogenesis-related genes but did not affect the expression of H2 evolution-related hydrogenase and ferredoxin genes. High pH down-regulated the expression of H2 evolution- and acidogenesis-related genes. Multiple resistance mechanisms, including chemotaxis, the phosphotransferase system (PTS), and the antioxidant system, were regulated at the transcriptional level under pH stress. CONCLUSIONS Ethanoligenens adapted to low pH by regulating the gene expression networks of cell growth, basic metabolism, chemotaxis and resistance but not H2 evolution-related genes. Regulation based on pH shifts can represent an important approach to establish and enhance ethanol-type fermentation. The complete gene expression network of ethanol fermentative bacteria for pH response provides valuable insights into the acidogenic fermentation, and offers an effective regulation strategy for the sustainable energy recovery from wastewater and solid waste.
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Affiliation(s)
- Zhen Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District, P.O. Box 2614, Harbin, Heilongjiang 150090 China
| | - Yu Lou
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District, P.O. Box 2614, Harbin, Heilongjiang 150090 China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District, P.O. Box 2614, Harbin, Heilongjiang 150090 China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District, P.O. Box 2614, Harbin, Heilongjiang 150090 China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District, P.O. Box 2614, Harbin, Heilongjiang 150090 China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District, P.O. Box 2614, Harbin, Heilongjiang 150090 China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District, P.O. Box 2614, Harbin, Heilongjiang 150090 China
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Soules KR, Dmitriev A, LaBrie SD, Dimond ZE, May BH, Johnson DK, Zhang Y, Battaile KP, Lovell S, Hefty PS. Structural and ligand binding analyses of the periplasmic sensor domain of RsbU in Chlamydia trachomatis support a role in TCA cycle regulation. Mol Microbiol 2020; 113:68-88. [PMID: 31637787 PMCID: PMC7007330 DOI: 10.1111/mmi.14401] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2019] [Indexed: 12/17/2022]
Abstract
Chlamydia trachomatis is an obligate intracellular bacteria that undergo dynamic morphologic and physiologic conversions upon gaining an access to a eukaryotic cell. These conversions likely require the detection of key environmental conditions and regulation of metabolic activity. Chlamydia encodes homologs to proteins in the Rsb phosphoregulatory partner-switching pathway, best described in Bacillus subtilis. ORF CT588 has a strong sequence similarity to RsbU cytoplasmic phosphatase domain but also contains a unique periplasmic sensor domain that is expected to control the phosphatase activity. A 1.7 Å crystal structure of the periplasmic domain of the RsbU protein from C. trachomatis (PDB 6MAB) displays close structural similarity to DctB from Vibrio and Sinorhizobium. DctB has been shown, both structurally and functionally, to specifically bind to the tricarboxylic acid (TCA) cycle intermediate succinate. Surface plasmon resonance and differential scanning fluorimetry of TCA intermediates and potential metabolites from a virtual screen of RsbU revealed that alpha-ketoglutarate, malate and oxaloacetate bound to the RsbU periplasmic domain. Substitutions in the putative binding site resulted in reduced binding capabilities. An RsbU null mutant showed severe growth defects which could be restored through genetic complementation. Chemical inhibition of ATP synthesis by oxidative phosphorylation phenocopied the growth defect observed in the RsbU null strain. Altogether, these data support a model with the Rsb system responding differentially to TCA cycle intermediates to regulate metabolism and key differentiation processes.
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Affiliation(s)
- Katelyn R Soules
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Aidan Dmitriev
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Scott D LaBrie
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Zoë E Dimond
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Benjamin H May
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - David K Johnson
- Computational Chemical Biology Core Facility, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66047, USA
| | - Yang Zhang
- Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, IL, 60439, USA
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66047, USA
| | - P Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
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44
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Möglich A. Signal transduction in photoreceptor histidine kinases. Protein Sci 2019; 28:1923-1946. [PMID: 31397927 PMCID: PMC6798134 DOI: 10.1002/pro.3705] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/06/2019] [Accepted: 08/06/2019] [Indexed: 12/14/2022]
Abstract
Two-component systems (TCS) constitute the predominant means by which prokaryotes read out and adapt to their environment. Canonical TCSs comprise a sensor histidine kinase (SHK), usually a transmembrane receptor, and a response regulator (RR). In signal-dependent manner, the SHK autophosphorylates and in turn transfers the phosphoryl group to the RR which then elicits downstream responses, often in form of altered gene expression. SHKs also catalyze the hydrolysis of the phospho-RR, hence, tightly adjusting the overall degree of RR phosphorylation. Photoreceptor histidine kinases are a subset of mostly soluble, cytosolic SHKs that sense light in the near-ultraviolet to near-infrared spectral range. Owing to their experimental tractability, photoreceptor histidine kinases serve as paradigms and provide unusually detailed molecular insight into signal detection, decoding, and regulation of SHK activity. The synthesis of recent results on receptors with light-oxygen-voltage, bacteriophytochrome and microbial rhodopsin sensor units identifies recurring, joint signaling strategies. Light signals are initially absorbed by the sensor module and converted into subtle rearrangements of α helices, mostly through pivoting and rotation. These conformational transitions propagate through parallel coiled-coil linkers to the effector unit as changes in left-handed superhelical winding. Within the effector, subtle conformations are triggered that modulate the solvent accessibility of residues engaged in the kinase and phosphatase activities. Taken together, a consistent view of the entire trajectory from signal detection to regulation of output emerges. The underlying allosteric mechanisms could widely apply to TCS signaling in general.
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Affiliation(s)
- Andreas Möglich
- Department of BiochemistryUniversität BayreuthBayreuthGermany
- Bayreuth Center for Biochemistry & Molecular BiologyUniversität BayreuthBayreuthGermany
- North‐Bavarian NMR CenterUniversität BayreuthBayreuthGermany
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45
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Heal JW, Bartlett GJ, Wood CW, Thomson AR, Woolfson DN. Applying graph theory to protein structures: an Atlas of coiled coils. Bioinformatics 2019; 34:3316-3323. [PMID: 29722888 PMCID: PMC6157074 DOI: 10.1093/bioinformatics/bty347] [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: 12/12/2017] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
Motivation To understand protein structure, folding and function fully and to design proteins de novo reliably, we must learn from natural protein structures that have been characterized experimentally. The number of protein structures available is large and growing exponentially, which makes this task challenging. Indeed, computational resources are becoming increasingly important for classifying and analyzing this resource. Here, we use tools from graph theory to define an Atlas classification scheme for automatically categorizing certain protein substructures. Results Focusing on the α-helical coiled coils, which are ubiquitous protein-structure and protein-protein interaction motifs, we present a suite of computational resources designed for analyzing these assemblies. iSOCKET enables interactive analysis of side-chain packing within proteins to identify coiled coils automatically and with considerable user control. Applying a graph theory-based Atlas classification scheme to structures identified by iSOCKET gives the Atlas of Coiled Coils, a fully automated, updated overview of extant coiled coils. The utility of this approach is illustrated with the first formal classification of an emerging subclass of coiled coils called α-helical barrels. Furthermore, in the Atlas, the known coiled-coil universe is presented alongside a partial enumeration of the 'dark matter' of coiled-coil structures; i.e. those coiled-coil architectures that are theoretically possible but have not been observed to date, and thus present defined targets for protein design. Availability and implementation iSOCKET is available as part of the open-source GitHub repository associated with this work (https://github.com/woolfson-group/isocket). This repository also contains all the data generated when classifying the protein graphs. The Atlas of Coiled Coils is available at: http://coiledcoils.chm.bris.ac.uk/atlas/app.
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Affiliation(s)
- Jack W Heal
- School of Chemistry, University of Bristol, Bristol, UK
| | | | | | - Andrew R Thomson
- School of Chemistry, University of Bristol, Bristol, UK.,School of Chemistry, University of Glasgow, Glasgow, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Life Sciences Building, Bristol, UK
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Hong Y, Huang Z, Guo L, Ni B, Jiang CY, Li XJ, Hou YJ, Yang WS, Wang DC, Zhulin IB, Liu SJ, Li DF. The ligand-binding domain of a chemoreceptor from Comamonas testosteroni has a previously unknown homotrimeric structure. Mol Microbiol 2019; 112:906-917. [PMID: 31177588 PMCID: PMC6736725 DOI: 10.1111/mmi.14326] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2019] [Indexed: 01/01/2023]
Abstract
Transmembrane chemoreceptors are widely present in Bacteria and Archaea. They play a critical role in sensing various signals outside and transmitting to the cell interior. Here, we report the structure of the periplasmic ligand-binding domain (LBD) of the transmembrane chemoreceptor MCP2201, which governs chemotaxis to citrate and other organic compounds in Comamonas testosteroni. The apo-form LBD crystal revealed a typical four-helix bundle homodimer, similar to previously well-studied chemoreceptors such as Tar and Tsr of Escherichia coli. However, the citrate-bound LBD revealed a four-helix bundle homotrimer that had not been observed in bacterial chemoreceptor LBDs. This homotrimer was further confirmed with size-exclusion chromatography, analytical ultracentrifugation and cross-linking experiments. The physiological importance of the homotrimer for chemotaxis was demonstrated with site-directed mutations of key amino acid residues in C. testosteroni mutants.
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Affiliation(s)
- Yuan Hong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhou Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Bin Ni
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Xiao-Jing Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Yan-Jie Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Si Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Da-Cheng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Igor B. Zhulin
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China,For correspondence. (D.-F.L.); (S.-J.L.); Tel. (+86) 10 64807423; Fax (+86) 10 64807421
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China,For correspondence. (D.-F.L.); (S.-J.L.); Tel. (+86) 10 64807423; Fax (+86) 10 64807421
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Jacob-Dubuisson F, Mechaly A, Betton JM, Antoine R. Structural insights into the signalling mechanisms of two-component systems. Nat Rev Microbiol 2019; 16:585-593. [PMID: 30008469 DOI: 10.1038/s41579-018-0055-7] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Two-component systems reprogramme diverse aspects of microbial physiology in response to environmental cues. Canonical systems are composed of a transmembrane sensor histidine kinase and its cognate response regulator. They catalyse three reactions: autophosphorylation of the histidine kinase, transfer of the phosphoryl group to the regulator and dephosphorylation of the phosphoregulator. Elucidating signal transduction between sensor and output domains is highly challenging given the size, flexibility and dynamics of histidine kinases. However, recent structural work has provided snapshots of the catalytic mechanisms of the three enzymatic reactions and described the conformation and dynamics of the enzymatic moiety in the kinase-competent and phosphatase-competent states. Insight into signalling mechanisms across the membrane is also starting to emerge from new crystal structures encompassing both sensor and transducer domains of sensor histidine kinases. In this Progress article, we highlight such important advances towards understanding at the molecular level the signal transduction mechanisms mediated by these fascinating molecular machines.
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Affiliation(s)
- Françoise Jacob-Dubuisson
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204 - Center for Infection and Immunity of Lille, Lille, France.
| | - Ariel Mechaly
- Institut Pasteur, Plateforme de Cristallographie, CNRS-UMR3528, Paris, France
| | - Jean-Michel Betton
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS-UMR3528, Paris, France
| | - Rudy Antoine
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204 - Center for Infection and Immunity of Lille, Lille, France
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48
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Conformational shifts in a chemoreceptor helical hairpin control kinase signaling in Escherichia coli. Proc Natl Acad Sci U S A 2019; 116:15651-15660. [PMID: 31315979 PMCID: PMC6681711 DOI: 10.1073/pnas.1902521116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Motile bacteria use chemoreceptor signaling arrays to track chemical gradients with high precision. The Escherichia coli chemotaxis system offers an ideal model for probing the molecular mechanisms of transmembrane and intracellular signaling. In this study, we characterized the signaling properties of mutant E. coli receptors that had amino acid replacements in residues that form a salt-bridge connection between the cytoplasmic tips of receptor molecules. The mutant signaling defects suggested that the chemoreceptor tip operates as a two-state device with discrete active and inactive conformations and that the level of output activity modulates connections between receptor signaling units that produce highly cooperative responses to attractant stimuli. These findings shed important light on the nature and control of receptor signaling states. Motile Escherichia coli cells use chemoreceptor signaling arrays to track chemical gradients with exquisite precision. Highly conserved residues in the cytoplasmic hairpin tip of chemoreceptor molecules promote assembly of trimer-based signaling complexes and modulate the activity of their CheA kinase partners. To explore hairpin tip output states in the serine receptor Tsr, we characterized the signaling consequences of amino acid replacements at the salt-bridge residue pair E385-R388. All mutant receptors assembled trimers and signaling complexes, but most failed to support serine chemotaxis in soft agar assays. Small side-chain replacements at either residue produced OFF- or ON-shifted outputs that responded to serine stimuli in wild-type fashion, suggesting that these receptors, like the wild-type, operate as two-state signaling devices. Larger aliphatic or aromatic side chains caused slow or partial kinase control responses that proved dependent on the connections between core signaling units that promote array cooperativity. In a mutant lacking one of two key adapter-kinase contacts (interface 2), those mutant receptors exhibited more wild-type behaviors. Lastly, mutant receptors with charged amino acid replacements assembled signaling complexes that were locked in kinase-ON (E385K|R) or kinase-OFF (R388D|E) output. The hairpin tips of mutant receptors with these more aberrant signaling properties probably have nonnative structures or dynamic behaviors. Our results suggest that chemoeffector stimuli and adaptational modifications influence the cooperative connections between core signaling units. This array remodeling process may involve activity-dependent changes in the relative strengths of interface 1 and 2 interactions between the CheW and CheA.P5 components of receptor core signaling complexes.
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49
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Stalla D, Akkaladevi N, White TA, Hazelbauer GL. Spatial Restrictions in Chemotaxis Signaling Arrays: A Role for Chemoreceptor Flexible Hinges across Bacterial Diversity. Int J Mol Sci 2019; 20:ijms20122989. [PMID: 31248079 PMCID: PMC6628036 DOI: 10.3390/ijms20122989] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/15/2019] [Accepted: 06/17/2019] [Indexed: 01/02/2023] Open
Abstract
The chemotactic sensory system enables motile bacteria to move toward favorable environments. Throughout bacterial diversity, the chemoreceptors that mediate chemotaxis are clustered into densely packed arrays of signaling complexes. In these arrays, rod-shaped receptors are in close proximity, resulting in limited options for orientations. A recent geometric analysis of these limitations in Escherichia coli, using published dimensions and angles, revealed that in this species, straight chemoreceptors would not fit into the available space, but receptors bent at one or both of the recently-documented flexible hinges would fit, albeit over a narrow window of shallow bend angles. We have now expanded our geometric analysis to consider variations in receptor length, orientation and placement, and thus to species in which those parameters are known to be, or might be, different, as well as to the possibility of dynamic variation in those parameters. The results identified significant limitations on the allowed combinations of chemoreceptor dimensions, orientations and placement. For most combinations, these limitations excluded straight chemoreceptors, but allowed receptors bent at a flexible hinge. Thus, our analysis identifies across bacterial diversity a crucial role for chemoreceptor flexible hinges, in accommodating the limitations of molecular crowding in chemotaxis core signaling complexes and their arrays.
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Affiliation(s)
- David Stalla
- Electron Microscopy Core Facility, W117 Veterinary Medicine Building, 1600 East Rollins St., University of Missouri, Columbia, MO 65211, USA.
| | - Narahari Akkaladevi
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, MO 65211, USA.
| | - Tommi A White
- Electron Microscopy Core Facility, W117 Veterinary Medicine Building, 1600 East Rollins St., University of Missouri, Columbia, MO 65211, USA.
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, MO 65211, USA.
| | - Gerald L Hazelbauer
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, MO 65211, USA.
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50
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Rhys GG, Wood CW, Beesley JL, Zaccai NR, Burton AJ, Brady RL, Thomson AR, Woolfson DN. Navigating the Structural Landscape of De Novo α-Helical Bundles. J Am Chem Soc 2019; 141:8787-8797. [PMID: 31066556 DOI: 10.1021/jacs.8b13354] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The association of amphipathic α helices in water leads to α-helical-bundle protein structures. However, the driving force for this-the hydrophobic effect-is not specific and does not define the number or the orientation of helices in the associated state. Rather, this is achieved through deeper sequence-to-structure relationships, which are increasingly being discerned. For example, for one structurally extreme but nevertheless ubiquitous class of bundle-the α-helical coiled coils-relationships have been established that discriminate between all-parallel dimers, trimers, and tetramers. Association states above this are known, as are antiparallel and mixed arrangements of the helices. However, these alternative states are less well understood. Here, we describe a synthetic-peptide system that switches between parallel hexamers and various up-down-up-down tetramers in response to single-amino-acid changes and solution conditions. The main accessible states of each peptide variant are characterized fully in solution and, in most cases, to high resolution with X-ray crystal structures. Analysis and inspection of these structures helps rationalize the different states formed. This navigation of the structural landscape of α-helical coiled coils above the dimers and trimers that dominate in nature has allowed us to design rationally a well-defined and hyperstable antiparallel coiled-coil tetramer (apCC-Tet). This robust de novo protein provides another scaffold for further structural and functional designs in protein engineering and synthetic biology.
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Affiliation(s)
- Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Christopher W Wood
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Joseph L Beesley
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Nathan R Zaccai
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
| | - Antony J Burton
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- Frick Chemistry Laboratory , Princeton University , Princeton , New Jersey 08544 , United States
| | - R Leo Brady
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
| | - Andrew R Thomson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- School of Chemistry , University of Glasgow , Glasgow G12 8QQ , United Kingdom
| | - Derek N Woolfson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
- BrisSynBio , University of Bristol , Life Sciences Building, Tyndall Avenue , Bristol BS8 1TQ , United Kingdom
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