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Moore JP, Kamino K, Kottou R, Shimizu TS, Emonet T. Signal Integration and Adaptive Sensory Diversity Tuning in Escherichia coli Chemotaxis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.08.527720. [PMID: 36798398 PMCID: PMC9934624 DOI: 10.1101/2023.02.08.527720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
In uncertain environments, phenotypic diversity can be advantageous for survival. However, as the environmental uncertainty decreases, the relative advantage of having diverse phenotypes decreases. Here, we show how populations of E. coli integrate multiple chemical signals to adjust sensory diversity in response to changes in the prevalence of each ligand in the environment. Measuring kinase activity in single cells, we quantified the sensitivity distribution to various chemoattractants in different mixtures of background stimuli. We found that when ligands bind uncompetitively, the population tunes sensory diversity to each signal independently, decreasing diversity when the signal ambient concentration increases. However, amongst competitive ligands the population can only decrease sensory diversity one ligand at a time. Mathematical modeling suggests that sensory diversity tuning benefits E. coli populations by modulating how many cells are committed to tracking each signal proportionally as their prevalence changes.
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Sherry DM, Graf IR, Bryant SJ, Emonet T, Machta BB. Lattice ultrasensitivity produces large gain in E. coli chemosensing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596300. [PMID: 38854030 PMCID: PMC11160650 DOI: 10.1101/2024.05.28.596300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
E. coli use a regular lattice of receptors and attached kinases to detect and amplify faint chemical signals. Kinase output is characterized by precise adaptation to a wide range of background ligand levels and large gain in response to small relative changes in ligand concentration. These characteristics are well described by models which achieve their gain through equilibrium cooperativity. But these models are challenged by two experimental results. First, neither adaptation nor large gain are present in receptor binding assays. Second, in cells lacking adaptation machinery, fluctuations can sometimes be enormous, with essentially all kinases transitioning together. Here we introduce a far-from equilibrium model in which receptors gate the spread of activity between neighboring kinases. This model achieves large gain through a mechanism we term lattice ultrasensitivity (LU). In our LU model, kinase and receptor states are separate degrees of freedom, and kinase kinetics are dominated by chemical rates far-from-equilibrium rather than by equilibrium allostery. The model recapitulates the successes of past models, but also matches the challenging experimental findings. Importantly, unlike past lattice critical models, our LU model does not require parameters to be fine tuned for function.
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Sagoo J, Abedrabbo S, Liu X, Ottemann KM. Helicobacter pylori cheV1 mutants recover semisolid agar migration due to loss of a previously uncharacterized Type IV filament membrane alignment complex homolog. J Bacteriol 2024; 206:e0040623. [PMID: 38446058 PMCID: PMC11025336 DOI: 10.1128/jb.00406-23] [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: 12/04/2023] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
The bacterial chemotaxis system is a well-understood signaling pathway that promotes bacterial success. Chemotaxis systems comprise chemoreceptors and the CheA kinase, linked by CheW or CheV scaffold proteins. Scaffold proteins provide connections between chemoreceptors and CheA and also between chemoreceptors to create macromolecular arrays. Chemotaxis is required for host colonization by many microbes, including the stomach pathogen Helicobacter pylori. This bacterium builds chemoreceptor-CheA contacts with two distinct scaffold proteins, CheW and CheV1. H. pylori cheW or cheV1 deletion mutants both lose chemoreceptor array formation, but show differing semisolid agar chemotaxis assay behaviors: ∆cheW mutants exhibit total migration failure, whereas ∆cheV1::cat mutants display a 50% reduction. On investigating these varied responses, we found that both mutants initially struggle with migration. However, over time, ∆cheV1::cat mutants develop a stable, enhanced migration capability, termed "migration-able" (Mig+). Whole-genome sequencing analysis of four distinct ∆cheV1::cat Mig+ strains identified single-nucleotide polymorphisms (SNPs) in hpg27_252 (hp0273) that were predicted to truncate the encoded protein. Computational analysis of the hpg27_252-encoded protein revealed it encoded a hypothetical protein that was a remote homolog of the PilO Type IV filament membrane alignment complex protein. Although H. pylori lacks Type IV filaments, our analysis showed it retains an operon of genes for homologs of PilO, PilN, and PilM. Deleting hpg27_252 in the ∆cheV1::cat or wild type strain resulted in enhanced migration in semisolid agar. Our study thus reveals that while cheV1 mutants initially have significant migration defects, they can recover the migration ability through genetic suppressors, highlighting a complex regulatory mechanism in bacterial migration. IMPORTANCE Chemotactic motility, present in over half of bacteria, depends on chemotaxis signaling systems comprising receptors, kinases, and scaffold proteins. In Helicobacter pylori, a stomach pathogen, chemotaxis is crucial for colonization, with CheV1 and CheW as key scaffold proteins. While both scaffolds are essential for building chemoreceptor complexes, their roles vary in other assays. Our research reexamines cheV1 mutants' behavior in semisolid agar, a standard chemotaxis test. Initially, cheV1 mutants exhibited defects similar to those of cheW mutants, but they evolved genetic suppressors that enhanced migration. These suppressors involve mutations in a previously uncharacterized gene, unknown in motility behavior. Our findings highlight the significant chemotaxis defects in cheV1 mutants and identify new elements influencing bacterial motility.
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Affiliation(s)
- Jashwin Sagoo
- Department of Microbiology and Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA
| | - Samar Abedrabbo
- Department of Microbiology and Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA
| | - Xiaolin Liu
- Department of Microbiology and Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA
| | - Karen M. Ottemann
- Department of Microbiology and Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA
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Koler M, Parkinson JS, Vaknin A. Signal integration in chemoreceptor complexes. Proc Natl Acad Sci U S A 2024; 121:e2312064121. [PMID: 38530894 PMCID: PMC10998596 DOI: 10.1073/pnas.2312064121] [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: 07/15/2023] [Accepted: 03/01/2024] [Indexed: 03/28/2024] Open
Abstract
Motile bacteria use large receptor arrays to detect chemical and physical stimuli in their environment, process this complex information, and accordingly bias their swimming in a direction they deem favorable. The chemoreceptor molecules form tripod-like trimers of receptor dimers through direct contacts between their cytoplasmic tips. A pair of trimers, together with a dedicated kinase enzyme, form a core signaling complex. Hundreds of core complexes network to form extended arrays. While considerable progress has been made in revealing the hierarchical structure of the array, the molecular properties underlying signal processing in these structures remain largely unclear. Here we analyzed the signaling properties of nonnetworked core complexes in live cells by following both conformational and kinase control responses to attractant stimuli and to output-biasing lesions at various locations in the receptor molecule. Contrary to the prevailing view that individual receptors are binary two-state devices, we demonstrate that conformational coupling between the ligand binding and the kinase-control receptor domains is, in fact, only moderate. In addition, we demonstrate communication between neighboring receptors through their trimer-contact domains that biases them to adopt similar signaling states. Taken together, these data suggest a view of signaling in receptor trimers that allows significant signal integration to occur within individual core complexes.
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Affiliation(s)
- Moriah Koler
- The Racah Institute of Physics, The Hebrew University, Jerusalem91904, Israel
| | - John S. Parkinson
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112
| | - Ady Vaknin
- The Racah Institute of Physics, The Hebrew University, Jerusalem91904, Israel
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5
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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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Cassidy CK, Qin Z, Frosio T, Gosink K, Yang Z, Sansom MSP, Stansfeld PJ, Parkinson JS, Zhang P. Structure of the native chemotaxis core signaling unit from phage E-protein lysed E. coli cells. mBio 2023; 14:e0079323. [PMID: 37772839 PMCID: PMC10653900 DOI: 10.1128/mbio.00793-23] [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: 03/28/2023] [Accepted: 08/09/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE Bacterial chemotaxis is a ubiquitous behavior that enables cell movement toward or away from specific chemicals. It serves as an important model for understanding cell sensory signal transduction and motility. Characterization of the molecular mechanisms underlying chemotaxis is of fundamental interest and requires a high-resolution structural picture of the sensing machinery, the chemosensory array. In this study, we combine cryo-electron tomography and molecular simulation to present the complete structure of the core signaling unit, the basic building block of chemosensory arrays, from Escherichia coli. Our results provide new insight into previously poorly-resolved regions of the complex and offer a structural basis for designing new experiments to test mechanistic hypotheses.
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Affiliation(s)
- C. Keith Cassidy
- Diamond Light Source, Didcot, United Kingdom
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri, USA
| | - Zhuan Qin
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Khoosheh Gosink
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - John S. Parkinson
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Peijun Zhang
- Diamond Light Source, Didcot, United Kingdom
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
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Muok AR, Kurniyati K, Cassidy CK, Olsthoorn FA, Ortega DR, Mabrouk AS, Li C, Briegel A. A new class of protein sensor links spirochete pleomorphism, persistence, and chemotaxis. mBio 2023; 14:e0159823. [PMID: 37607060 PMCID: PMC10653840 DOI: 10.1128/mbio.01598-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 08/24/2023] Open
Abstract
IMPORTANCE A new class of bacterial protein sensors monitors intracellular levels of S-adenosylmethionine to modulate cell morphology, chemotaxis, and biofilm formation. Simultaneous regulation of these behaviors enables bacterial pathogens to survive within their niche. This sensor, exemplified by Treponema denticola CheWS, is anchored to the chemotaxis array and its sensor domain is located below the chemotaxis rings. This position may allow the sensor to directly interact with the chemotaxis histidine kinase CheA. Collectively, these data establish a critical role of CheWS in pathogenesis and further illustrate the impact of studying non-canonical chemotaxis proteins.
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Affiliation(s)
- A. R. Muok
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - K. Kurniyati
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute for Oral Health, Virginia Commonwealth University, Richmond, Virginia, USA
| | - C. K. Cassidy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - F. A. Olsthoorn
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - D. R. Ortega
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - A. Sidi Mabrouk
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - C. Li
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute for Oral Health, Virginia Commonwealth University, Richmond, Virginia, USA
| | - A. Briegel
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
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Wang W, Xia J, Wang Z, Shao Z. Bacterial cell sensing and signaling pathway for external polycyclic aromatic hydrocarbons (PAHs). iScience 2023; 26:107912. [PMID: 37841585 PMCID: PMC10570129 DOI: 10.1016/j.isci.2023.107912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/19/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
The mechanism by which a bacterial cell senses external nutrients remains largely unknown. In this study, we identified a bacterial cell sensing system for polycyclic aromatic hydrocarbons (PAHs) in a common marine PAH-using bacterium, Cycloclasticus. It consists of an outer membrane receptor (PahS) and a periplasmic protein (PahP) in combination with a two-component sensing system (TCS) that ensures a rapid response to PAH occurrence by directly controlling serial reactions including chemotactic sensing and movement, PAH uptake and intracellular PAH metabolism. PahS protrudes from the cell and acts as a PAH sensor, transducing the PAH signal across the outer membrane to its periplasmic partner PahP, which in turn transduces the PAH signal across the periplasm to a specialized TCS. This sensing system plays a critical role in sensing and promoting the metabolism of PAHs, which can be scavenged by various hydrocarbon-degrading bacteria.
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Affiliation(s)
- Wanpeng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Jingyu Xia
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zining Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
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Tran T, Karunanayake Mudiyanselage APKK, Eyles SJ, Thompson LK. Bacterial chemoreceptor signaling complexes control kinase activity by stabilizing the catalytic domain of CheA. Proc Natl Acad Sci U S A 2023; 120:e2218467120. [PMID: 37523532 PMCID: PMC10410752 DOI: 10.1073/pnas.2218467120] [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: 10/28/2022] [Accepted: 07/10/2023] [Indexed: 08/02/2023] Open
Abstract
Motile bacteria have a chemotaxis system that enables them to sense their environment and direct their swimming toward favorable conditions. Chemotaxis involves a signaling process in which ligand binding to the extracellular domain of the chemoreceptor alters the activity of the histidine kinase, CheA, bound ~300 Å away to the distal cytoplasmic tip of the receptor, to initiate a phosphorylation cascade that controls flagellar rotation. The cytoplasmic domain of the receptor is thought to propagate this signal via changes in dynamics and/or stability, but it is unclear how these changes modulate the kinase activity of CheA. To address this question, we have used hydrogen deuterium exchange mass spectrometry to probe the structure and dynamics of CheA within functional signaling complexes of the Escherichia coli aspartate receptor cytoplasmic fragment, CheA, and CheW. Our results reveal that stabilization of the P4 catalytic domain of CheA correlates with kinase activation. Furthermore, differences in activation of the kinase that occur during sensory adaptation depend on receptor destabilization of the P3 dimerization domain of CheA. Finally, hydrogen exchange properties of the P1 domain that bears the phosphorylated histidine identify the dimer interface of P1/P1' in the CheA dimer and support an ordered sequential binding mechanism of catalysis, in which dimeric P1/P1' has productive interactions with P4 only upon nucleotide binding. Thus stabilization/destabilization of domains is a key element of the mechanism of modulating CheA kinase activity in chemotaxis, and may play a role in the control of other kinases.
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Affiliation(s)
- Thomas Tran
- Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA01003
| | | | - Stephen J. Eyles
- Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA01003
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA01003
| | - Lynmarie K. Thompson
- Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA01003
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA01003
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10
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Das S, Chatterjee A, Datta PP. Knockdown Experiment Reveals an Essential GTPase CgtA's Involvement in Growth, Viability, Motility, Morphology, and Persister Phenotypes in Vibrio cholerae. Microbiol Spectr 2023; 11:e0318122. [PMID: 36916969 PMCID: PMC10100748 DOI: 10.1128/spectrum.03181-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/13/2023] [Indexed: 03/16/2023] Open
Abstract
CgtA is an essential bacterial GTPase consisting of a highly conserved N-terminal Spo0B-associated GTP-binding protein (Obg) domain, a central GTPase domain, and a variable C-terminal domain (CTD). This study reports global changes in the proteome and transcriptome of wild-type (Wt) versus full-length CgtA-depleted Vibrio cholerae in minimal media. Comparative transcriptome sequencing (RNA-Seq), followed by comparative proteomic analyses, revealed that the knockdown of cgtA significantly altered expressions of 311 proteins involved in diverse cellular activities, many of which are associated with the survival of V. cholerae. Various intracellular functional roles of CgtA in growth, viability, motility, morphology, and persister phenotypes in V. cholerae are revealed based on subsequent confirmatory experiments. Furthermore, a more sustained mRNA expression pattern of cgtA in a minimal medium than in a rich medium was also observed for Wt V. cholerae, where the highest level of mRNA expression of cgtA was observed during the logarithmic growth phase. Thereby, we propose that minimal medium-associated reduced growth rate coupled with cgtA depletion aggravates the intracellular stress in V. cholerae, interrupting vital cellular processes. The functional role of the CTD in V. cholerae is not fully understood. Hence, to specifically investigate the intracellular role of the 57-amino-acid-long CTD of CgtAVC, the CTD-only portion of CgtA was deleted. Subsequent proteomics studies revealed an altered expression of 240 proteins in the CgtA(ΔCTD) mutant, having major overlap with the full-length cgtA-deleted condition. Overall, our study reveals an alternative facet of the survival mechanism of V. cholerae during nutritional downshift as per the concomitant consequences of cgtA depletion. IMPORTANCE It is very important that we must find new drug target proteins from multidrug-resistant human-pathogenic organisms like V. cholerae. CgtA is among such potential candidates, and here, we are reporting about some newly identified cellular roles of it that are important for the survival of V. cholerae. Briefly, we knocked down the full-length cgtA gene, as well as did a partial deletion of this gene from the V. cholerae genome followed by RNA-Seq and proteomics studies. Results from our study revealed up- and downregulation of several known and unknown genes and proteins as the effect of the cgtA knockdown experiment. Also, we have presented some interesting observations that are linked with cgtA for growth, viability, motility, morphology, and persister phenotypes in V. cholerae. Our study enhances the importance of CgtA and paves the way for further exploration based on our provided data.
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Affiliation(s)
- Sagarika Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, West Bengal, India
| | - Ananya Chatterjee
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, West Bengal, India
| | - Partha Pratim Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, West Bengal, India
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11
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Hadjidemetriou K, Kaur S, Cassidy CK, Zhang P. Mechanisms of E. coli chemotaxis signaling pathways visualized using cryoET and computational approaches. Biochem Soc Trans 2022; 50:1595-1605. [PMID: 36421737 PMCID: PMC9788364 DOI: 10.1042/bst20220191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 11/25/2022]
Abstract
Chemotaxis signaling pathways enable bacteria to sense and respond to their chemical environment and, in some species, are critical for lifestyle processes such as biofilm formation and pathogenesis. The signal transduction underlying chemotaxis behavior is mediated by large, highly ordered protein complexes known as chemosensory arrays. For nearly two decades, cryo-electron tomography (cryoET) has been used to image chemosensory arrays, providing an increasingly detailed understanding of their structure and function. In this mini-review, we provide an overview of the use of cryoET to study chemosensory arrays, including imaging strategies, key results, and outstanding questions. We further discuss the application of molecular modeling and simulation techniques to complement structure determination efforts and provide insight into signaling mechanisms. We close the review with a brief outlook, highlighting promising future directions for the field.
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Affiliation(s)
| | - Satinder Kaur
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - C. Keith Cassidy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - Peijun Zhang
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, U.K
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, U.K
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12
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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: 5] [Impact Index Per Article: 2.5] [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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13
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Effect of an inorganic nitrogen source (NH 4) 2SO 4 on the production of welan gum from Sphingomonas sp. mutant obtained through UV-ARTP compound mutagenesis. Int J Biol Macromol 2022; 210:630-638. [PMID: 35513098 DOI: 10.1016/j.ijbiomac.2022.04.219] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/24/2022] [Accepted: 04/28/2022] [Indexed: 12/14/2022]
Abstract
As one of the most expensive extracellular polysaccharides, welan gum is widely used in biomedicine, food products, and petroleum because of its unique structure and excellent rheological properties. To reduce the cost of welan gum fermentation, together with (NH4)2SO4, which served as the sole nitrogen source, a high-welan-gum-producing mutant, B-8, screened through UV-ARTP compound mutagenesis was used. Under optimum conditions (C:N ratio 25:1, sucrose 50 g/L, (NH4)2SO4 4 g/L, and adding 8 mM NaCl at 32 h fermentation), the yield of welan gum and sucrose conversion were 18.86 g/L and 0.38 g/g, respectively, which were 98.95% and 137.50% higher than those achieved with the parent strain FM01, respectively. After the same treatment process, IN-welan (obtained with (NH4)2SO4) consumed less 95% ethanol, had higher molecular weight, and exhibited better rheological properties than ON-welan (obtained with beef extract). Transcriptome analysis revealed that (NH4)2SO4 could affect the synthetic pathway and monosaccharide content of welan gum by increasing bacterial chemotaxis and the availability of key intermediates. The fermentation performance of Sphingomonas sp. mutants could further be improved by providing several target genes to the mutants through metabolic engineering.
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14
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Livne N, Vaknin A. Collective responses of bacteria to a local source of conflicting effectors. Sci Rep 2022; 12:4928. [PMID: 35322063 PMCID: PMC8943191 DOI: 10.1038/s41598-022-08762-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/09/2022] [Indexed: 12/18/2022] Open
Abstract
To cope in complex environments, motile bacteria have developed a chemosensory system that integrates multiple cues and directs their motion toward regions that it deems favorable. However, we have a limited understanding of the principles that govern bacterial behavior in complex stimuli fields. Here, we followed the spatial redistribution of E. coli cells in perplexing environments created by a local source of both beneficial (nutrients) and hazardous (low pH or indole) effectors. We identified two fundamentally distinct collective responses: a ‘trade-off’ response, in which bacteria sharply accumulated at a distance from the source that reflected a trade-off between the propagating effectors, and a ‘bet-hedging’ response, in which part of the bacteria accumulated away from the source, avoiding the hazardous effector, while the other part evaded the repulsive force and accumulated at the source. In addition, we demonstrate that cells lacking the Tsr sensor swim toward both repellents and, surprisingly, even toward pH values well below 7. Using a numerical analysis, we could correlate the collective bacterial responses with fundamentally distinct chemotactic force fields created along the channel by the propagation of the effectors and their unique perception by the chemosensory system.
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Affiliation(s)
- Nir Livne
- The Racah Institute of Physics, The Hebrew University, Edmond J. Safra Campus, 91904, Jerusalem, Israel
| | - Ady Vaknin
- The Racah Institute of Physics, The Hebrew University, Edmond J. Safra Campus, 91904, Jerusalem, Israel.
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15
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Thompson LK. Protein rings are critical to the remarkable signaling properties of bacterial chemotaxis nanoarrays. Sci Signal 2022; 15:eabn2056. [PMID: 35077200 DOI: 10.1126/scisignal.abn2056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacteria build an extensive sensory nanoarray to collect information that guides their swimming. In this issue of Science Signaling, Piñas et al. demonstrate that a key element of these arrays that enhances chemotaxis responses are hexameric rings of CheW, one of two types of rings that couple the responses of core signaling units to achieve remarkable signaling properties such as single-molecule detection.
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Affiliation(s)
- Lynmarie K Thompson
- Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
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16
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Piñas GE, DeSantis MD, Cassidy CK, Parkinson JS. Hexameric rings of the scaffolding protein CheW enhance response sensitivity and cooperativity in Escherichia coli chemoreceptor arrays. Sci Signal 2022; 15:eabj1737. [PMID: 35077199 DOI: 10.1126/scisignal.abj1737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Escherichia coli chemoreceptor array is a supramolecular assembly that enables cells to respond to extracellular cues dynamically and with great precision and sensitivity. In the array, transmembrane receptors organized as trimers of dimers are connected at their cytoplasmic tips by hexameric rings of alternating subunits of the kinase CheA and the scaffolding protein CheW (CheA-CheW rings). Interactions of CheW molecules with the members of receptor trimers not directly bound to CheA-CheW rings may lead to the formation of hexameric CheW rings in the chemoreceptor array. Here, we detected such CheW rings with a cellular cysteine-directed cross-linking assay and explored the requirements for their formation and their participation in array assembly. We found that CheW ring formation varied with cellular CheW abundance, depended on the presence of receptors capable of a trimer-of-dimers arrangement, and did not require CheA. Cross-linking studies of a CheA~CheW fusion protein incapable of forming homomeric CheW oligomers demonstrated that CheW rings were not essential for the assembly of CheA-containing arrays. Förster resonance energy transfer (FRET)-based kinase assays of arrays containing variable amounts of CheW rings revealed that CheW rings enhanced the cooperativity and the sensitivity of the responses to attractants. We propose that six-membered CheW rings provide the additional interconnectivity required for optimal signaling and gradient tracking performance by chemosensory arrays.
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Affiliation(s)
- Germán E Piñas
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael D DeSantis
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - John S Parkinson
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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17
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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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18
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Liu X, Liu Y, Wang Y, Wang D, Johnson KS, Xie Z. The Hypoxia-Associated Localization of Chemotaxis Protein CheZ in Azorhizorbium caulinodans. Front Microbiol 2021; 12:731419. [PMID: 34737727 PMCID: PMC8563088 DOI: 10.3389/fmicb.2021.731419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/22/2021] [Indexed: 11/15/2022] Open
Abstract
Spatial organization of chemotactic proteins is important for cooperative response to external stimuli. However, factors affecting the localization dynamics of chemotaxis proteins are less studied. According to some reports, the polar localization of chemotaxis system I is induced by hypoxia and starvation in Vibrio cholerae. However, in V. cholerae, the chemotaxis system I is not involved in flagellum-mediated chemotaxis, and it may play other alternative cellular functions. In this study, we found that the polar localization of CheZ, a phosphatase regulating chemotactic movement in Azorhizobium caulinodans ORS571, can also be affected by hypoxia and cellular energy-status. The conserved phosphatase active site D165 and the C-terminus of CheZ are essential for the energy-related localization, indicating a cross link between hypoxia-related localization changes and phosphatase activity of CheZ. Furthermore, three of five Aer-like chemoreceptors containing PAS domains participate in the cellular localization of CheZ. In contrast to carbon starvation, free-living nitrogen fixation can alleviate the role of nitrogen limitation and hypoxia on polar localization of CheZ. These results showed that the localization changes induced by hypoxia might be a strategy for bacteria to adapt to complex environment.
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Affiliation(s)
- Xiaolin Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yixuan Wang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Dandan Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Kevin Scot Johnson
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Zhihong Xie
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
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19
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Ryzhykau YL, Vlasov AV, Orekhov PS, Rulev MI, Rogachev AV, Vlasova AD, Kazantsev AS, Verteletskiy DP, Skoi VV, Brennich ME, Pernot P, Murugova TN, Gordeliy VI, Kuklin AI. Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II-transducer complex. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1386-1400. [PMID: 34726167 DOI: 10.1107/s2059798321009542] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/14/2021] [Indexed: 01/14/2023]
Abstract
Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complementary measurements are not performed and/or a priori information on the protein is not taken into account. Understanding the nature of the limitations may help to overcome these problems. One of the main problems of SAS data analysis of solubilized membrane proteins is the contribution of the detergent belt surrounding the MP. Here, a comprehensive analysis of how the detergent belt contributes to the SAS data of a membrane-protein complex of sensory rhodopsin II with its cognate transducer from Natronomonas pharaonis (NpSRII-NpHtrII) was performed. The influence of the polydispersity of NpSRII-NpHtrII oligomerization is the second problem that is addressed here. It is shown that inhomogeneity in the scattering length density of the detergent belt surrounding a membrane part of the complex and oligomerization polydispersity significantly impacts on SAXS and SANS profiles, and therefore on 3D ab initio structures. It is described how both problems can be taken into account to improve the quality of SAS data treatment. Since SAS data for MPs are usually obtained from solubilized proteins, and their detergent belt and, to a certain extent, oligomerization polydispersity are sufficiently common phenomena, the approaches proposed in this work might be used in SAS studies of different MPs.
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Affiliation(s)
- Yury L Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Alexey V Vlasov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Philipp S Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Maksim I Rulev
- Structural Biology Group, European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Andrey V Rogachev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Anastasia D Vlasova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Alexander S Kazantsev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Dmitry P Verteletskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Vadim V Skoi
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Martha E Brennich
- Synchrotron Crystallography Team, EMBL Grenoble Outstation, 38042 Grenoble, France
| | - Petra Pernot
- Structural Biology Group, European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Tatiana N Murugova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Alexander I Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
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20
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Moore JP, Kamino K, Emonet T. Non-Genetic Diversity in Chemosensing and Chemotactic Behavior. Int J Mol Sci 2021; 22:6960. [PMID: 34203411 PMCID: PMC8268644 DOI: 10.3390/ijms22136960] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 01/18/2023] Open
Abstract
Non-genetic phenotypic diversity plays a significant role in the chemotactic behavior of bacteria, influencing how populations sense and respond to chemical stimuli. First, we review the molecular mechanisms that generate phenotypic diversity in bacterial chemotaxis. Next, we discuss the functional consequences of phenotypic diversity for the chemosensing and chemotactic performance of single cells and populations. Finally, we discuss mechanisms that modulate the amount of phenotypic diversity in chemosensory parameters in response to changes in the environment.
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Affiliation(s)
- Jeremy Philippe Moore
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; (J.P.M.); (K.K.)
- Quantitative Biology Institute, Yale University, New Haven, CT 06511, USA
| | - Keita Kamino
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; (J.P.M.); (K.K.)
- Quantitative Biology Institute, Yale University, New Haven, CT 06511, USA
| | - Thierry Emonet
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; (J.P.M.); (K.K.)
- Quantitative Biology Institute, Yale University, New Haven, CT 06511, USA
- Department of Physics, Yale University, New Haven, CT 06511, USA
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21
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Burt A, Cassidy CK, Stansfeld PJ, Gutsche I. Alternative Architecture of the E. coli Chemosensory Array. Biomolecules 2021; 11:biom11040495. [PMID: 33806045 PMCID: PMC8064477 DOI: 10.3390/biom11040495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 11/16/2022] Open
Abstract
Chemotactic responses in motile bacteria are the result of sophisticated signal transduction by large, highly organized arrays of sensory proteins. Despite tremendous progress in the understanding of chemosensory array structure and function, a structural basis for the heightened sensitivity of networked chemoreceptors is not yet complete. Here, we present cryo-electron tomography visualisations of native-state chemosensory arrays in E. coli minicells. Strikingly, these arrays appear to exhibit a p2-symmetric array architecture that differs markedly from the p6-symmetric architecture previously described in E. coli. Based on this data, we propose molecular models of this alternative architecture and the canonical p6-symmetric assembly. We evaluate our observations and each model in the context of previously published data, assessing the functional implications of an alternative architecture and effects for future studies.
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Affiliation(s)
- Alister Burt
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France;
| | - C. Keith Cassidy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK;
| | - Phillip J. Stansfeld
- Department of Chemistry, School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK;
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France;
- Correspondence:
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22
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How an unusual chemosensory system forms arrays on the bacterial nucleoid. Biochem Soc Trans 2021; 48:347-356. [PMID: 32129822 DOI: 10.1042/bst20180450] [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: 10/25/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 11/17/2022]
Abstract
Chemosensory systems are signaling pathways elegantly organized in hexagonal arrays that confer unique functional features to these systems such as signal amplification. Chemosensory arrays adopt different subcellular localizations from one bacterial species to another, yet keeping their supramolecular organization unmodified. In the gliding bacterium Myxococcus xanthus, a cytoplasmic chemosensory system, Frz, forms multiple clusters on the nucleoid through the direct binding of the FrzCD receptor to DNA. A small CheW-like protein, FrzB, might be responsible for the formation of multiple (instead of just one) Frz arrays. In this review, we summarize what is known on Frz array formation on the bacterial chromosome and discuss hypotheses on how FrzB might contribute to the nucleation of multiple clusters. Finally, we will propose some possible biological explanations for this type of localization pattern.
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23
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Liu X, Liu Y, Johnson KS, Dong X, Xie Z. Protein Residues and a Novel Motif Involved in the Cellular Localization of CheZ in Azorhizobium caulinodans ORS571. Front Microbiol 2020; 11:585140. [PMID: 33365019 PMCID: PMC7750401 DOI: 10.3389/fmicb.2020.585140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 11/16/2020] [Indexed: 12/26/2022] Open
Abstract
Chemotaxis is essential for the competitiveness of motile bacteria in complex and harsh environments. The localization of chemotactic proteins in the cell is critical for coordinating a maximal response to chemotactic signals. One chemotaxis protein with a well-defined subcellular localization is the phosphatase CheZ. CheZ localizes to cell poles by binding with CheA in Escherichia coli and other enteric bacteria, or binding with a poorly understood protein called ChePep in epsilon-Proteobacteria. In alpha-Proteobacteria, CheZ lacks CheA-binding sites, and its cellular localization remains unknown. We therefore determined the localization of CheZ in the alpha-Proteobacteria Azorhizobium caulinodans ORS571. A. caulinodans CheZ, also termed as CheZAC, was found to be located to cell poles independently of CheA, and we suspect that either the N-terminal helix or the four-helix bundle of CheZAC is sufficient to locate to cell poles. We also found a novel motif, AXXFQ, which is adjacent to the phosphatase active motif DXXXQ, which effects the monopolar localization of CheZAC. This novel motif consisting of AXXFQ is conserved in CheZ and widely distributed among Proteobacteria. Finally, we found that the substitution of phosphatase active site affects the polar localization of CheZAC. In total, this work characterized the localization pattern of CheZ containing a novel motif, and we mapped the regions of CheZAC that are critical for its polar localization.
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Affiliation(s)
- Xiaolin Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kevin Scot Johnson
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Xiaoyan Dong
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zhihong Xie
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
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24
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Muok AR, Ortega DR, Kurniyati K, Yang W, Maschmann ZA, Sidi Mabrouk A, Li C, Crane BR, Briegel A. Atypical chemoreceptor arrays accommodate high membrane curvature. Nat Commun 2020; 11:5763. [PMID: 33188180 PMCID: PMC7666581 DOI: 10.1038/s41467-020-19628-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022] Open
Abstract
The prokaryotic chemotaxis system is arguably the best-understood signaling pathway in biology. In all previously described species, chemoreceptors organize into a hexagonal (P6 symmetry) extended array. Here, we report an alternative symmetry (P2) of the chemotaxis apparatus that emerges from a strict linear organization of the histidine kinase CheA in Treponema denticola cells, which possesses arrays with the highest native curvature investigated thus far. Using cryo-ET, we reveal that Td chemoreceptor arrays assume an unusual arrangement of the supra-molecular protein assembly that has likely evolved to accommodate the high membrane curvature. The arrays have several atypical features, such as an extended dimerization domain of CheA and a variant CheW-CheR-like fusion protein that is critical for maintaining an ordered chemosensory apparatus. Furthermore, the previously characterized Td oxygen sensor ODP influences CheA ordering. These results suggest a greater diversity of the chemotaxis signaling system than previously thought.
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Affiliation(s)
- Alise R Muok
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Davi R Ortega
- Department of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Kurni Kurniyati
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute for Oral Health, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Wen Yang
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Zachary A Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Adam Sidi Mabrouk
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Chunhao Li
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute for Oral Health, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Ariane Briegel
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands.
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25
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Muok AR, Chua TK, Srivastava M, Yang W, Maschmann Z, Borbat PP, Chong J, Zhang S, Freed JH, Briegel A, Crane BR. Engineered chemotaxis core signaling units indicate a constrained kinase-off state. Sci Signal 2020; 13:13/657/eabc1328. [PMID: 33172954 DOI: 10.1126/scisignal.abc1328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacterial chemoreceptors, the histidine kinase CheA, and the coupling protein CheW form transmembrane molecular arrays with remarkable sensing properties. The receptors inhibit or stimulate CheA kinase activity depending on the presence of attractants or repellants, respectively. We engineered chemoreceptor cytoplasmic regions to assume a trimer of receptor dimers configuration that formed well-defined complexes with CheA and CheW and promoted a CheA kinase-off state. These mimics of core signaling units were assembled to homogeneity and investigated by site-directed spin-labeling with pulse-dipolar electron-spin resonance spectroscopy (PDS), small-angle x-ray scattering, targeted protein cross-linking, and cryo-electron microscopy. The kinase-off state was especially stable, had relatively low domain mobility, and associated the histidine substrate and docking domains with the kinase core, thus preventing catalytic activity. Together, these data provide an experimentally restrained model for the inhibited state of the core signaling unit and suggest that chemoreceptors indirectly sequester the kinase and substrate domains to limit histidine autophosphorylation.
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Affiliation(s)
- Alise R Muok
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Teck Khiang Chua
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Wen Yang
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Zach Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Petr P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Jenna Chong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Sheng Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca, NY 14853, USA
| | - Ariane Briegel
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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26
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Kamino K, Keegstra JM, Long J, Emonet T, Shimizu TS. Adaptive tuning of cell sensory diversity without changes in gene expression. SCIENCE ADVANCES 2020; 6:6/46/eabc1087. [PMID: 33188019 PMCID: PMC7673753 DOI: 10.1126/sciadv.abc1087] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/30/2020] [Indexed: 05/24/2023]
Abstract
In the face of uncertainty, cell populations tend to diversify to enhance survival and growth. Previous studies established that cells can optimize such bet hedging upon environmental change by modulating gene expression to adapt both the average and diversity of phenotypes. Here, we demonstrate that cells can tune phenotypic diversity also using posttranslational modifications. In the chemotaxis network of Escherichia coli, we find, for both major chemoreceptors Tar and Tsr, that cell-to-cell variation in response sensitivity is dynamically modulated depending on the presence or absence of their cognate chemoeffector ligands in the environment. Combining experiments with mathematical modeling, we show that this diversity tuning requires only the environment-dependent covalent modification of chemoreceptors and a standing cell-to-cell variation in their allosteric coupling. Thus, when environmental cues are unavailable, phenotypic diversity enhances the population's readiness for many signals. However, once a signal is perceived, the population focuses on tracking that signal.
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Affiliation(s)
- K Kamino
- AMOLF Institute, Amsterdam, Netherlands
- Departments of Molecular, Cellular and Developmental Biology and Physics, Yale University, New Haven, CT, USA
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
| | | | - J Long
- Departments of Molecular, Cellular and Developmental Biology and Physics, Yale University, New Haven, CT, USA
| | - T Emonet
- Departments of Molecular, Cellular and Developmental Biology and Physics, Yale University, New Haven, CT, USA.
- Quantitative Biology Institute, Yale University, New Haven, CT, USA
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27
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Arapov TD, Saldaña RC, Sebastian AL, Ray WK, Helm RF, Scharf BE. Cellular Stoichiometry of Chemotaxis Proteins in Sinorhizobium meliloti. J Bacteriol 2020; 202:e00141-20. [PMID: 32393521 PMCID: PMC7317046 DOI: 10.1128/jb.00141-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/05/2020] [Indexed: 11/20/2022] Open
Abstract
Chemotaxis systems enable microbes to sense their immediate environment, moving toward beneficial stimuli and away from those that are harmful. In an effort to better understand the chemotaxis system of Sinorhizobium meliloti, a symbiont of the legume alfalfa, the cellular stoichiometries of all ten chemotaxis proteins in S. meliloti were determined. A combination of quantitative immunoblot and mass spectrometry revealed that the protein stoichiometries in S. meliloti varied greatly from those in Escherichia coli and Bacillus subtilis To compare protein ratios to other systems, values were normalized to the central kinase CheA. All S. meliloti chemotaxis proteins exhibited increased ratios to various degrees. The 10-fold higher molar ratio of adaptor proteins CheW1 and CheW2 to CheA might result in the formation of rings in the chemotaxis array that consist of only CheW instead of CheA and CheW in a 1:1 ratio. We hypothesize that the higher ratio of CheA to the main response regulator CheY2 is a consequence of the speed-variable motor in S. meliloti, instead of a switch-type motor. Similarly, proteins involved in signal termination are far more abundant in S. meliloti, which utilizes a phosphate sink mechanism based on CheA retrophosphorylation to inactivate the motor response regulator versus CheZ-catalyzed dephosphorylation as in E. coli and B. subtilis Finally, the abundance of CheB and CheR, which regulate chemoreceptor methylation, was increased compared to CheA, indicative of variations in the adaptation system of S. meliloti Collectively, these results mark significant differences in the composition of bacterial chemotaxis systems.IMPORTANCE The symbiotic soil bacterium Sinorhizobium meliloti contributes greatly to host-plant growth by fixing atmospheric nitrogen. The provision of nitrogen as ammonium by S. meliloti leads to increased biomass production of its legume host alfalfa and diminishes the use of environmentally harmful chemical fertilizers. To better understand the role of chemotaxis in host-microbe interaction, a comprehensive catalogue of the bacterial chemotaxis system is vital, including its composition, function, and regulation. The stoichiometry of chemotaxis proteins in S. meliloti has very few similarities to the systems in Escherichia coli and Bacillus subtilis In addition, total amounts of proteins are significantly lower. S. meliloti exhibits a chemotaxis system distinct from known models by incorporating new proteins as exemplified by the phosphate sink mechanism.
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Affiliation(s)
- Timofey D Arapov
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Amanda L Sebastian
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - W Keith Ray
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Birgit E Scharf
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
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28
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Jun SY, Pan W, Hazelbauer GL. ATP Binding as a Key Target for Control of the Chemotaxis Kinase. J Bacteriol 2020; 202:e00095-20. [PMID: 32341073 PMCID: PMC7283602 DOI: 10.1128/jb.00095-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/13/2020] [Indexed: 02/07/2023] Open
Abstract
In bacterial chemotaxis, chemoreceptors in signaling complexes modulate the activity of two-component histidine kinase CheA in response to chemical stimuli. CheA catalyzes phosphoryl transfer from ATP to a histidinyl residue of its P1 domain. That phosphoryl group is transferred to two response regulators. Receptor control is almost exclusively at autophosphorylation, but the aspect of enzyme action on which that control acts is unclear. We investigated this by a kinetic analysis of activated kinase in signaling complexes. We found that phosphoryl transfer from ATP to P1 is an ordered sequential reaction in which the binding of ATP to CheA is the necessary first step; the second substrate, the CheA P1 domain, binds only to an ATP-occupied enzyme; and phosphorylated P1 is released prior to the second product, namely, ADP. We confirmed the crucial features of this kinetically deduced ordered mechanism by assaying P1 binding to the enzyme. In the absence of a bound nucleotide, there was no physiologically significant binding, but the enzyme occupied with a nonhydrolyzable ATP analog bound P1. Previous structural and computational analyses indicated that ATP binding creates the P1-binding site by ordering the "ATP lid." This process identifies the structural basis for the ordered kinetic mechanism. Recent mathematical modeling of kinetic data identified ATP binding as a focus of receptor-mediated kinase control. The ordered kinetic mechanism provides the biochemical logic of that control. We conclude that chemoreceptors modulate kinase by controlling ATP binding. Structural similarities among two-component kinases, particularly the ATP lid, suggest that ordered mechanisms and control of ATP binding are general features of two-component signaling.IMPORTANCE Our work provides important new insights into the action of the chemotaxis signaling kinase CheA by identifying the kinetic mechanism of its autophosphorylation as an ordered sequential reaction, in which the required first step is binding of ATP. These insights provide a framework for integrating previous kinetic, mathematical modeling, structural, simulation, and docking observations to conclude that chemoreceptors control the activity of the chemotaxis kinase by regulating binding of the autophosphorylation substrate ATP. Previously observed conformational changes in the ATP lid of the enzyme active site provide a structural basis for the ordered mechanism. Such lids are characteristic of two-component histidine kinases in general, suggesting that ordered sequential mechanisms and regulation by controlling ATP binding are common features of these kinases.
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Affiliation(s)
- Se-Young Jun
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Wenlin Pan
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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Frutos-Grilo E, Marsal M, Irazoki O, Barbé J, Campoy S. The Interaction of RecA With Both CheA and CheW Is Required for Chemotaxis. Front Microbiol 2020; 11:583. [PMID: 32318049 PMCID: PMC7154110 DOI: 10.3389/fmicb.2020.00583] [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: 12/23/2019] [Accepted: 03/17/2020] [Indexed: 12/20/2022] Open
Abstract
Salmonella enterica is the most frequently reported cause of foodborne illness. As in other microorganisms, chemotaxis affords key physiological benefits, including enhanced access to growth substrates, but also plays an important role in infection and disease. Chemoreceptor signaling core complexes, consisting of CheA, CheW and methyl-accepting chemotaxis proteins (MCPs), modulate the switching of bacterial flagella rotation that drives cell motility. These complexes, through the formation of heterohexameric rings composed of CheA and CheW, form large clusters at the cell poles. RecA plays a key role in polar cluster formation, impairing the assembly when the SOS response is activated. In this study, we determined that RecA protein interacts with both CheW and CheA. The binding of these proteins to RecA is needed for wild-type polar cluster formation. In silico models showed that one RecA molecule, attached to one signaling unit, fits within a CheA-CheW ring without interfering with the complex formation or array assembly. Activation of the SOS response is followed by an increase in RecA, which rises up the number of signaling complexes associated with this protein. This suggests the presence of allosteric inhibition in the CheA-CheW interaction and thus of heterohexameric ring formation, impairing the array assembly. STED imaging demonstrated that all core unit components (CheA, CheW, and MPCs) have the same subcellular location as RecA. Activation of the SOS response promotes the RecA distribution along the cell instead of being at the cell poles. CheA- and CheW- RecA interactions are also crucial for chemotaxis, which is maintained when the SOS response is induced and the signaling units are dispersed. Our results provide new molecular-level insights into the function of RecA in chemoreceptor clustering and chemotaxis determining that the impaired chemoreceptor clustering not only inhibits swarming but also modulates chemotaxis in SOS-induced cells, thereby modifying bacterial motility in the presence of DNA-damaging compounds, such as antibiotics.
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Affiliation(s)
- Elisabet Frutos-Grilo
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Marsal
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Oihane Irazoki
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jordi Barbé
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Susana Campoy
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
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30
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Burt A, Cassidy CK, Ames P, Bacia-Verloop M, Baulard M, Huard K, Luthey-Schulten Z, Desfosses A, Stansfeld PJ, Margolin W, Parkinson JS, Gutsche I. Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain. Nat Commun 2020; 11:743. [PMID: 32029744 PMCID: PMC7005262 DOI: 10.1038/s41467-020-14350-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/21/2019] [Indexed: 12/01/2022] Open
Abstract
Motile bacteria sense chemical gradients with transmembrane receptors organised in supramolecular signalling arrays. Understanding stimulus detection and transmission at the molecular level requires precise structural characterisation of the array building block known as a core signalling unit. Here we introduce an Escherichia coli strain that forms small minicells possessing extended and highly ordered chemosensory arrays. We use cryo-electron tomography and subtomogram averaging to provide a three-dimensional map of a complete core signalling unit, with visible densities corresponding to the HAMP and periplasmic domains. This map, combined with previously determined high resolution structures and molecular dynamics simulations, yields a molecular model of the transmembrane core signalling unit and enables spatial localisation of its individual domains. Our work thus offers a solid structural basis for the interpretation of a wide range of existing data and the design of further experiments to elucidate signalling mechanisms within the core signalling unit and larger array.
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Affiliation(s)
- Alister Burt
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Peter Ames
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Maria Bacia-Verloop
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Megghane Baulard
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Karine Huard
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ambroise Desfosses
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - William Margolin
- Department of Microbiology & Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - John S Parkinson
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044, Grenoble, France.
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31
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Pedetta A, Studdert CA. Truncated, Non-networking Versions of the Coupling Protein CheW Retain Chemoreceptor Control of Kinase CheA. J Mol Biol 2020; 432:576-584. [PMID: 31626809 DOI: 10.1016/j.jmb.2019.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 11/18/2022]
Abstract
Bacterial chemoreceptors control the activity of the associated CheA kinase in response to chemical gradients and, consequently, regulate the swimming behavior of the cell. However, such control is not direct but requires the participation of the essential coupling protein CheW, which is structurally homologous to the carboxy-terminal domain of the kinase. The actual role of this small coupling protein is somehow intriguing. It has been demonstrated that it is absolutely essential for chemoreceptor control of the kinase, in spite of the occurrence of direct contacts between chemoreceptors and CheA. In addition, CheW plays an essential role in the assembly of the large macromolecular arrays that combine chemoreceptors of different specificities, and it is therefore responsible for molecular interactions that provide such arrays with remarkable signaling properties. In this work, we analyze truncated CheW derivatives that are still able to control the kinase but have lost the ability to connect signaling units. We demonstrate that these two activities can work separately and speculate about the significance of the roles of these two different activities in the context of the chemoreceptor cluster.
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Affiliation(s)
- Andrea Pedetta
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar Del Plata - CONICET, Mar Del Plata, Buenos Aires, Argentina
| | - Claudia Alicia Studdert
- Instituto de Agrobiotecnología Del Litoral, CONICET - Universidad Nacional Del Litoral, Santa Fe, Santa Fe, Argentina.
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32
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Cassidy CK, Himes BA, Sun D, Ma J, Zhao G, Parkinson JS, Stansfeld PJ, Luthey-Schulten Z, Zhang P. Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations. Commun Biol 2020; 3:24. [PMID: 31925330 PMCID: PMC6954272 DOI: 10.1038/s42003-019-0748-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/19/2019] [Indexed: 01/08/2023] Open
Abstract
To enable the processing of chemical gradients, chemotactic bacteria possess large arrays of transmembrane chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW, organized as coupled core-signaling units (CSU). Despite decades of study, important questions surrounding the molecular mechanisms of sensory signal transduction remain unresolved, owing especially to the lack of a high-resolution CSU structure. Here, we use cryo-electron tomography and sub-tomogram averaging to determine a structure of the Escherichia coli CSU at sub-nanometer resolution. Based on our experimental data, we use molecular simulations to construct an atomistic model of the CSU, enabling a detailed characterization of CheA conformational dynamics in its native structural context. We identify multiple, distinct conformations of the critical P4 domain as well as asymmetries in the localization of the P3 bundle, offering several novel insights into the CheA signaling mechanism.
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Affiliation(s)
- C Keith Cassidy
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Benjamin A Himes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Dapeng Sun
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Jun Ma
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Gongpu Zhao
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - John S Parkinson
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Zaida Luthey-Schulten
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemistry and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA.
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Electron Bio-Imaging Centre, Diamond Light Sources, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
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Guiseppi A, Vicente JJ, Herrou J, Byrne D, Barneoud A, Moine A, Espinosa L, Basse MJ, Molle V, Mignot T, Roche P, Mauriello EMF. A divergent CheW confers plasticity to nucleoid-associated chemosensory arrays. PLoS Genet 2019; 15:e1008533. [PMID: 31860666 PMCID: PMC6952110 DOI: 10.1371/journal.pgen.1008533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 01/09/2020] [Accepted: 11/22/2019] [Indexed: 11/30/2022] Open
Abstract
Chemosensory systems are highly organized signaling pathways that allow bacteria to adapt to environmental changes. The Frz chemosensory system from M. xanthus possesses two CheW-like proteins, FrzA (the core CheW) and FrzB. We found that FrzB does not interact with FrzE (the cognate CheA) as it lacks the amino acid region responsible for this interaction. FrzB, instead, acts upstream of FrzCD in the regulation of M. xanthus chemotaxis behaviors and activates the Frz pathway by allowing the formation and distribution of multiple chemosensory clusters on the nucleoid. These results, together, show that the lack of the CheA-interacting region in FrzB confers new functions to this small protein.
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Affiliation(s)
- Annick Guiseppi
- Laboratoire de Chimie Bactérienne, Aix Marseille Univ, CNRS, Marseille, France
| | - Juan Jesus Vicente
- Physiology & Biophysics, University of Washington, Seattle, WA, United States of America
| | - Julien Herrou
- Laboratoire de Chimie Bactérienne, Aix Marseille Univ, CNRS, Marseille, France
| | - Deborah Byrne
- Protein Purification Platform, Institut de Microbiologie de la Méditerranée, CNRS, Marseille, France
| | - Aurelie Barneoud
- Laboratoire de Chimie Bactérienne, Aix Marseille Univ, CNRS, Marseille, France
| | - Audrey Moine
- Laboratoire de Chimie Bactérienne, Aix Marseille Univ, CNRS, Marseille, France
| | - Leon Espinosa
- Laboratoire de Chimie Bactérienne, Aix Marseille Univ, CNRS, Marseille, France
| | - Marie-Jeanne Basse
- CRCM, Institute Paoli-Calmettes, CNRS, INSERM, Aix Marseille Univ, Marseille, France
| | - Virginie Molle
- Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologique, Montpellier II et I University, CNRS, France
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne, Aix Marseille Univ, CNRS, Marseille, France
| | - Philippe Roche
- CRCM, Institute Paoli-Calmettes, CNRS, INSERM, Aix Marseille Univ, Marseille, France
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34
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Identification of a Kinase-Active CheA Conformation in Escherichia coli Chemoreceptor Signaling Complexes. J Bacteriol 2019; 201:JB.00543-19. [PMID: 31501279 DOI: 10.1128/jb.00543-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/04/2019] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli chemotaxis relies on control of the autophosphorylation activity of the histidine kinase CheA by transmembrane chemoreceptors. Core signaling units contain two receptor trimers of dimers, one CheA homodimer, and two monomeric CheW proteins that couple CheA activity to receptor control. Core signaling units appear to operate as two-state devices, with distinct kinase-on and kinase-off CheA output states whose structural nature is poorly understood. A recent all-atom molecular dynamic simulation of a receptor core unit revealed two alternative conformations, "dipped" and "undipped," for the ATP-binding CheA.P4 domain that could be related to kinase activity states. To explore possible signaling roles for the dipped CheA.P4 conformation, we created CheA mutants with amino acid replacements at residues (R265, E368, and D372) implicated in promoting the dipped conformation and examined their signaling consequences with in vivo Förster resonance energy transfer (FRET)-based kinase assays. We used cysteine-directed in vivo cross-linking reporters for the dipped and undipped conformations to assess mutant proteins for these distinct CheA.P4 domain configurations. Phenotypic suppression analyses revealed functional interactions among the conformation-controlling residues. We found that structural interactions between R265, located at the N terminus of the CheA.P3 dimerization domain, and E368/D372 in the CheA.P4 domain played a critical role in stabilizing the dipped conformation and in producing kinase-on output. Charge reversal replacements at any of these residues abrogated the dipped cross-linking signal, CheA kinase activity, and chemotactic ability. We conclude that the dipped conformation of the CheA.P4 domain is critical to the kinase-active state in core signaling units.IMPORTANCE Regulation of CheA kinase in chemoreceptor arrays is critical for Escherichia coli chemotaxis. However, to date, little is known about the CheA conformations that lead to the kinase-on or kinase-off states. Here, we explore the signaling roles of a distinct conformation of the ATP-binding CheA.P4 domain identified by all-atom molecular dynamics simulation. Amino acid replacements at residues predicted to stabilize the so-called "dipped" CheA.P4 conformation abolished the kinase activity of CheA and its ability to support chemotaxis. Our findings indicate that the dipped conformation of the CheA.P4 domain is critical for reaching the kinase-active state in chemoreceptor signaling arrays.
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35
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Distinct Chemotaxis Protein Paralogs Assemble into Chemoreceptor Signaling Arrays To Coordinate Signaling Output. mBio 2019; 10:mBio.01757-19. [PMID: 31551333 PMCID: PMC6759762 DOI: 10.1128/mbio.01757-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The assembly of chemotaxis receptors and signaling proteins into polar arrays is universal in motile chemotactic bacteria. Comparative genome analyses indicate that most motile bacteria possess multiple chemotaxis signaling systems, and experimental evidence suggests that signaling from distinct chemotaxis systems is integrated. Here, we identify one such mechanism. We show that paralogs from two chemotaxis systems assemble together into chemoreceptor arrays, forming baseplates comprised of proteins from both chemotaxis systems. These mixed arrays provide a straightforward mechanism for signal integration and coordinated response output from distinct chemotaxis systems. Given that most chemotactic bacteria encode multiple chemotaxis systems and the propensity for these systems to be laterally transferred, this mechanism may be common to ensure chemotaxis signal integration occurs. Most chemotactic motile bacteria possess multiple chemotaxis signaling systems, the functions of which are not well characterized. Chemotaxis signaling is initiated by chemoreceptors that assemble as large arrays, together with chemotaxis coupling proteins (CheW) and histidine kinase proteins (CheA), which form a baseplate with the cytoplasmic tips of receptors. These cell pole-localized arrays mediate sensing, signaling, and signal amplification during chemotaxis responses. Membrane-bound chemoreceptors with different cytoplasmic domain lengths segregate into distinct arrays. Here, we show that a bacterium, Azospirillum brasilense, which utilizes two chemotaxis signaling systems controlling distinct motility parameters, coordinates its chemotactic responses through the production of two separate membrane-bound chemoreceptor arrays by mixing paralogs within chemotaxis baseplates. The polar localization of chemoreceptors of different length classes is maintained in strains that had baseplate signaling proteins from either chemotaxis system but was lost when both systems were deleted. Chemotaxis proteins (CheA and CheW) from each of the chemotaxis signaling systems (Che1 and Che4) could physically interact with one another, and chemoreceptors from both classes present in A. brasilense could interact with Che1 and Che4 proteins. The assembly of paralogs from distinct chemotaxis pathways into baseplates provides a straightforward mechanism for coordinating signaling from distinct pathways, which we predict is not unique to this system given the propensity of chemotaxis systems for horizontal gene transfer.
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Abstract
Prokaryotic organisms occupy the most diverse set of environments and conditions on our planet. Their ability to sense and respond to a broad range of external cues remain key research areas in modern microbiology, central to behaviors that underlie beneficial and pathogenic interactions of bacteria with multicellular organisms and within complex ecosystems. Advances in our understanding of the one- and two-component signal transduction systems that underlie these sensing pathways have been driven by advances in imaging the behavior of many individual bacterial cells, as well as visualizing individual proteins and protein arrays within living cells. Cryo-electron tomography continues to provide new insights into the structure and function of chemosensory receptors and flagellar motors, while advances in protein labeling and tracking are applied to understand information flow between receptor and motor. Sophisticated microfluidics allow simultaneous analysis of the behavior of thousands of individual cells, increasing our understanding of how variance between individuals is generated, regulated and employed to maximize fitness of a population. In vitro experiments have been complemented by the study of signal transduction and motility in complex in vivo models, allowing investigators to directly address the contribution of motility, chemotaxis and aggregation/adhesion on virulence during infection. Finally, systems biology approaches have demonstrated previously uncharted areas of protein space in which novel two-component signal transduction pathways can be designed and constructed de novo These exciting experimental advances were just some of the many novel findings presented at the 15th Bacterial Locomotion and Signal Transduction conference (BLAST XV) in January 2019.
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Yang W, Briegel A. Diversity of Bacterial Chemosensory Arrays. Trends Microbiol 2019; 28:68-80. [PMID: 31473052 DOI: 10.1016/j.tim.2019.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/15/2019] [Accepted: 08/01/2019] [Indexed: 02/01/2023]
Abstract
Chemotaxis is crucial for the survival of bacteria, and the signaling systems associated with it exhibit a high level of evolutionary conservation. The architecture of the chemosensory array and the signal transduction mechanisms have been extensively studied in Escherichia coli. More recent studies have revealed a vast diversity of the chemosensory system among bacteria. Unlike E. coli, some bacteria assemble more than one chemosensory array and respond to a broader spectrum of environmental and internal stimuli. These chemosensory arrays exhibit a great variability in terms of protein composition, cellular localization, and functional variability. Here, we present recent findings that emphasize the extent of diversity in chemosensory arrays and highlight the importance of studying chemosensory arrays in bacteria other than the common model organisms.
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Affiliation(s)
- Wen Yang
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Ariane Briegel
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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Muok AR, Briegel A, Crane BR. Regulation of the chemotaxis histidine kinase CheA: A structural perspective. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183030. [PMID: 31374212 DOI: 10.1016/j.bbamem.2019.183030] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 02/06/2023]
Abstract
Bacteria sense and respond to their environment through a highly conserved assembly of transmembrane chemoreceptors (MCPs), the histidine kinase CheA, and the coupling protein CheW, hereafter termed "the chemosensory array". In recent years, great strides have been made in understanding the architecture of the chemosensory array and how this assembly engenders sensitive and cooperative responses. Nonetheless, a central outstanding question surrounds how receptors modulate the activity of the CheA kinase, the enzymatic output of the sensory system. With a focus on recent advances, we summarize the current understanding of array structure and function to comment on the molecular mechanism by which CheA, receptors and CheW generate the high sensitivity, gain and dynamic range emblematic of bacterial chemotaxis. The complexity of the chemosensory arrays has motivated investigation with many different approaches. In particular, structural methods, genetics, cellular activity assays, nanodisc technology and cryo-electron tomography have provided advances that bridge length scales and connect molecular mechanism to cellular function. Given the high degree of component integration in the chemosensory arrays, we ultimately aim to understand how such networked molecular interactions generate a whole that is truly greater than the sum of its parts. This article is part of a Special Issue entitled: Molecular biophysics of membranes and membrane proteins.
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Affiliation(s)
- Alise R Muok
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Ariane Briegel
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, United States of America.
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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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Yang W, Cassidy CK, Ames P, Diebolder CA, Schulten K, Luthey-Schulten Z, Parkinson JS, Briegel A. In Situ Conformational Changes of the Escherichia coli Serine Chemoreceptor in Different Signaling States. mBio 2019; 10:e00973-19. [PMID: 31266867 PMCID: PMC6606802 DOI: 10.1128/mbio.00973-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 05/31/2019] [Indexed: 11/20/2022] Open
Abstract
Tsr, the serine chemoreceptor in Escherichia coli, transduces signals from a periplasmic ligand-binding site to its cytoplasmic tip, where it controls the activity of the CheA kinase. To function, Tsr forms trimers of homodimers (TODs), which associate in vivo with the CheA kinase and CheW coupling protein. Together, these proteins assemble into extended hexagonal arrays. Here, we use cryo-electron tomography and molecular dynamics simulation to study Tsr in the context of a near-native array, characterizing its signaling-related conformational changes at both the individual dimer and the trimer level. In particular, we show that individual Tsr dimers within a trimer exhibit asymmetric flexibilities that are a function of the signaling state, highlighting the effect of their different protein interactions at the receptor tips. We further reveal that the dimer compactness of the Tsr trimer changes between signaling states, transitioning at the glycine hinge from a compact conformation in the kinase-OFF state to an expanded conformation in the kinase-ON state. Hence, our results support a crucial role for the glycine hinge: to allow the receptor flexibility necessary to achieve different signaling states while also maintaining structural constraints imposed by the membrane and extended array architecture.IMPORTANCE In Escherichia coli, membrane-bound chemoreceptors, the histidine kinase CheA, and coupling protein CheW form highly ordered chemosensory arrays. In core signaling complexes, chemoreceptor trimers of dimers undergo conformational changes, induced by ligand binding and sensory adaptation, which regulate kinase activation. Here, we characterize by cryo-electron tomography the kinase-ON and kinase-OFF conformations of the E. coli serine receptor in its native array context. We found distinctive structural differences between the members of a receptor trimer, which contact different partners in the signaling unit, and structural differences between the ON and OFF signaling complexes. Our results provide new insights into the signaling mechanism of chemoreceptor arrays and suggest an important functional role for a previously postulated flexible region and glycine hinge in the receptor molecule.
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Affiliation(s)
- Wen Yang
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Department of Physics and Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Peter Ames
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | | | - Klaus Schulten
- Department of Physics and Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Zaida Luthey-Schulten
- Department of Chemistry and Center for the Physics of Living Cells, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - John S Parkinson
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Ariane Briegel
- Institute of Biology, Leiden University, Leiden, The Netherlands
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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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Abstract
Archaea are ubiquitous single cellular microorganisms that play important ecological roles in nature. The intracellular organization of archaeal cells is among the unresolved mysteries of archaeal biology. With this work, we show that cells of haloarchaea are polarized. The cellular positioning of proteins involved in chemotaxis and motility is spatially and temporally organized in these cells. This suggests the presence of a specific mechanism responsible for the positioning of macromolecular protein complexes in archaea. Bacteria and archaea exhibit tactical behavior and can move up and down chemical gradients. This tactical behavior relies on a motility structure, which is guided by a chemosensory system. Environmental signals are sensed by membrane-inserted chemosensory receptors that are organized in large ordered arrays. While the cellular positioning of the chemotaxis machinery and that of the flagellum have been studied in detail in bacteria, we have little knowledge about the localization of such macromolecular assemblies in archaea. Although the archaeal motility structure, the archaellum, is fundamentally different from the flagellum, archaea have received the chemosensory machinery from bacteria and have connected this system with the archaellum. Here, we applied a combination of time-lapse imaging and fluorescence and electron microscopy using the model euryarchaeon Haloferax volcanii and found that archaella were specifically present at the cell poles of actively dividing rod-shaped cells. The chemosensory arrays also had a polar preference, but in addition, several smaller arrays moved freely in the lateral membranes. In the stationary phase, rod-shaped cells became round and chemosensory arrays were disassembled. The positioning of archaella and that of chemosensory arrays are not interdependent and likely require an independent form of positioning machinery. This work showed that, in the rod-shaped haloarchaeal cells, the positioning of the archaellum and of the chemosensory arrays is regulated in time and in space. These insights into the cellular organization of H. volcanii suggest the presence of an active mechanism responsible for the positioning of macromolecular protein complexes in archaea.
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Bacterial chemotaxis coupling protein: Structure, function and diversity. Microbiol Res 2019; 219:40-48. [DOI: 10.1016/j.micres.2018.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 01/10/2023]
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44
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Abstract
The chemoreceptor array, a remarkably ordered supramolecular complex, is composed of hexagonally packed trimers of receptor dimers networked by a histidine kinase and one or more coupling proteins. Even though the receptor packing is universal among chemotactic bacteria and archaea, the array architecture has been extensively studied only in selected model organisms. Here, we show that even in the complete absence of the kinase, the cluster II arrays in Vibrio cholerae retain their native spatial localization and the iconic hexagonal packing of the receptors with 12-nm spacing. Our results demonstrate that the chemotaxis array is versatile in composition, a property that allows auxiliary chemotaxis proteins such as ParP and CheV to integrate directly into the assembly. Along with its compositional variability, cluster II arrays exhibit a low degree of structural stability compared with the ultrastable arrays in Escherichia coli We propose that the variability in chemoreceptor arrays is an important mechanism that enables the incorporation of chemotaxis proteins based on their availability.
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45
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Koler M, Peretz E, Aditya C, Shimizu TS, Vaknin A. Long-term positioning and polar preference of chemoreceptor clusters in E. coli. Nat Commun 2018; 9:4444. [PMID: 30361683 PMCID: PMC6202326 DOI: 10.1038/s41467-018-06835-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 09/26/2018] [Indexed: 11/09/2022] Open
Abstract
The bacterial chemosensory arrays are a notable model for studying the basic principles of receptor clustering and cellular organization. Here, we provide a new perspective regarding the long-term dynamics of these clusters in growing E. coli cells. We demonstrate that pre-existing lateral clusters tend to avoid translocation to pole regions and, therefore, continually shuttle between the cell poles for many generations while being static relative to the local cell-wall matrix. We also show that the polar preference of clusters results fundamentally from reduced clustering efficiency in the lateral region, rather than a developmental-like progression of clusters. Furthermore, polar preference is surprisingly robust to structural alterations designed to probe preference due to curvature sorting, perturbing the cell envelope physiology affects the cluster-size distribution, and the size-dependent mobility of receptor complexes differs between polar and lateral regions. Thus, distinct envelope physiology in the polar and lateral cell regions may contribute to polar preference. Bacterial chemoreceptors form clusters, preferably at the cell poles. Here, Koler et al. show that polar and lateral clusters exhibit distinct long-term positional dynamics and that polar bias may be due to differences in mobility of receptor complexes between the polar and lateral cell regions.
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Affiliation(s)
- Moriah Koler
- The Racah Institute of Physics, The Hebrew University, Jerusalem, 91904, Israel
| | - Eliran Peretz
- The Racah Institute of Physics, The Hebrew University, Jerusalem, 91904, Israel
| | | | | | - Ady Vaknin
- The Racah Institute of Physics, The Hebrew University, Jerusalem, 91904, Israel.
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46
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Orekhov P, Bothe A, Steinhoff HJ, Shaitan KV, Raunser S, Fotiadis D, Schlesinger R, Klare JP, Engelhard M. Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers. Photochem Photobiol 2018; 93:796-804. [PMID: 28500714 DOI: 10.1111/php.12763] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/02/2017] [Indexed: 12/28/2022]
Abstract
Archaeal photoreceptors consist of sensory rhodopsins in complex with their cognate transducers. After light excitation, a two-component signaling chain is activated, which is homologous to the chemotactic signaling cascades in enterobacteria. The latter system has been studied in detail. From structural and functional studies, a picture emerges which includes stable signaling complexes, which assemble to receptor arrays displaying hexagonal structural elements. At this higher order structural level, signal amplification and sensory adaptation occur. Here, we describe electron microscopy data, which show that also the archaeal phototaxis receptors sensory rhodopsin I and II in complex with their cognate transducers can form hexagonal lattices even in the presence of a detergent. This result could be confirmed by molecular dynamics calculations, which revealed similar structural elements. Calculations of the global modes of motion displayed one mode, which resembles the "U"-"V" transition of the NpSRII:NpHtrII complex, which was previously argued to represent a functionally relevant global conformational change accompanying the activation process [Ishchenko et al. (2013) J. Photochem. Photobiol. B 123, 55-58]. A model of cooperativity at the transmembrane level is discussed.
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Affiliation(s)
- Philipp Orekhov
- Department of Physics, University of Osnabrück, Osnabrück, Germany.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Arne Bothe
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | | | - Stefan Raunser
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Ramona Schlesinger
- Department of Physics, Institute of Experimental Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Johann P Klare
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - Martin Engelhard
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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Chavent M, Duncan AL, Rassam P, Birkholz O, Hélie J, Reddy T, Beliaev D, Hambly B, Piehler J, Kleanthous C, Sansom MSP. How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins. Nat Commun 2018; 9:2846. [PMID: 30030429 PMCID: PMC6054660 DOI: 10.1038/s41467-018-05255-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 06/15/2018] [Indexed: 01/07/2023] Open
Abstract
The spatiotemporal organisation of membranes is often characterised by the formation of large protein clusters. In Escherichia coli, outer membrane protein (OMP) clustering leads to OMP islands, the formation of which underpins OMP turnover and drives organisation across the cell envelope. Modelling how OMP islands form in order to understand their origin and outer membrane behaviour has been confounded by the inherent difficulties of simulating large numbers of OMPs over meaningful timescales. Here, we overcome these problems by training a mesoscale model incorporating thousands of OMPs on coarse-grained molecular dynamics simulations. We achieve simulations over timescales that allow direct comparison to experimental data of OMP behaviour. We show that specific interaction surfaces between OMPs are key to the formation of OMP clusters, that OMP clusters present a mesh of moving barriers that confine newly inserted proteins within islands, and that mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs. In Escherichia coli, outer membrane protein (OMP) cluster and form islands, but the origin and behaviour of those clusters remains poorly understood. Here authors use coarse grained molecular dynamics simulation and show that their mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs.
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Affiliation(s)
- Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 Route de Narbonne, Toulouse, 31400, France
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK
| | - Patrice Rassam
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74 Route du Rhin, 67401, Illkirch, France
| | - Oliver Birkholz
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Jean Hélie
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,SEMMLE, Blue Boar Court, 9 Alfred St, Oxford, OX1 4EH, UK
| | - Tyler Reddy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.,Theoretical Biology and Biophysics, T-6, Los Alamos National Laboratory, Los Alamos, NM, 87525, USA
| | - Dmitry Beliaev
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter (550), Woodstock Road, Oxford, OX2 6GG, UK
| | - Ben Hambly
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter (550), Woodstock Road, Oxford, OX2 6GG, UK
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 5RJ, UK.
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48
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Regulatory Role of an Interdomain Linker in the Bacterial Chemotaxis Histidine Kinase CheA. J Bacteriol 2018; 200:JB.00052-18. [PMID: 29483161 DOI: 10.1128/jb.00052-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 02/07/2018] [Indexed: 11/20/2022] Open
Abstract
The histidine kinase CheA plays a central role in signal integration, conversion, and amplification in the bacterial chemotaxis signal transduction pathway. The kinase activity is regulated in chemotaxis signaling complexes formed via the interactions among CheA's regulatory domain (P5), the coupling protein CheW, and transmembrane chemoreceptors. Despite recent advancements in the understanding of the architecture of the signaling complex, the molecular mechanism underlying this regulation remains elusive. An interdomain linker that connects the catalytic (P4) and regulatory domains of CheA may mediate regulatory signals from the P5-CheW-receptor interactions to the catalytic domain. To investigate whether this interdomain linker is capable of both activating and inhibiting CheA, we performed in vivo screens to search for P4-P5 linker mutations that result in different CheA autokinase activities. Several CheA variants were identified with kinase activities ranging from 30% to 670% of the activity of wild-type CheA. All of these CheA variants were defective in receptor-mediated kinase activation, indicating that the natural receptor-mediated signal transmission pathway was simultaneously affected by these mutations. The altered P4-P5 linkers were sufficient for making significant changes in the kinase activity even in the absence of the P5 domain. Therefore, the interdomain linker is an active module that has the ability to impose regulatory effects on the catalytic activity of the P4 domain. These results suggest that chemoreceptors may manipulate the conformation of the P4-P5 linker to achieve CheA regulation in the platform of the signaling complex.IMPORTANCE The molecular mechanism underlying kinase regulation in bacterial chemotaxis signaling complexes formed by the regulatory domain of the histidine kinase CheA, the coupling protein CheW, and chemoreceptors is still unknown. We isolated and characterized mutations in the interdomain linker that connects the catalytic and regulatory domains of CheA and found that the linker mutations resulted in different CheA autokinase activities in the absence and presence of the regulatory domain as well as a defect in receptor-mediated kinase activation. These results demonstrate that the interdomain linker is an active module that has the ability to impose regulatory effects on CheA activity. Chemoreceptors may manipulate the conformation of this interdomain linker to achieve CheA regulation in the platform of the signaling complex.
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49
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Gasperotti AF, Revuelta MV, Studdert CA, Herrera Seitz MK. Identification of two different chemosensory pathways in representatives of the genus Halomonas. BMC Genomics 2018; 19:266. [PMID: 29669514 PMCID: PMC5907407 DOI: 10.1186/s12864-018-4655-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 04/10/2018] [Indexed: 11/22/2022] Open
Abstract
Background Species of the genus Halomonas are salt-tolerant organisms that have a versatile metabolism and can degrade a variety of xenobiotic compounds, utilizing them as their sole carbon source. In this study, we examined the genome of a Halomonas isolate from a hydrocarbon-contaminated site to search for chemosensory genes that might be responsible for the observed chemotactic behavior of this organism as well as for other responses to environmental cues. Results Using genome-wide comparative tools, our isolate was identified as a strain of Halomonas titanicae (strain KHS3), together with two other Halomonas strains with available genomes that had not been previously identified at a species level. The search for the main components of chemosensory pathways resulted in the identification of two clusters of chemosensory genes and a total of twenty-five chemoreceptor genes. One of the gene clusters is very similar to the che cluster from Escherichia coli and, presumably, it is responsible for the chemotactic behavior towards a variety of compounds. This gene cluster is present in 47 out of 56 analyzed Halomonas strains with available genomes. A second che-like cluster includes a gene coding for a diguanylate cyclase with a phosphotransfer and two receiver domains, as well as a gene coding for a chemoreceptor with a longer cytoplasmic domain than the other twenty-four. This seemingly independent pathway resembles the wsp pathway from Pseudomonas aeruginosa although it also presents several differences in gene order and domain composition. This second chemosensory gene cluster is only present in a sub-group within the genus Halomonas. Moreover, remarkably similar gene clusters are also found in some orders of Proteobacteria phylogenetically more distant from the Oceanospirillales, suggesting the occurrence of lateral transfer events. Conclusions Chemosensory pathways were investigated within the genus Halomonas. A canonical chemotaxis pathway, controlled by a variable number of chemoreceptors, is widespread among Halomonas species. A second chemosensory pathway of unique organization that involves some type of c-di-GMP signaling was found to be present only in one branch of the genus, as well as in other proteobacterial lineages. Electronic supplementary material The online version of this article (10.1186/s12864-018-4655-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Florencia Gasperotti
- Instituto de Investigaciones Biológicas, CONICET - Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - María Victoria Revuelta
- Department of Medicine, Hematology and Oncology Division, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Claudia Alicia Studdert
- Instituto de Agrobiotecnología del Litoral, CONICET - Universidad Nacional del Litoral, Santa Fe, Argentina
| | - María Karina Herrera Seitz
- Instituto de Investigaciones Biológicas, CONICET - Universidad Nacional de Mar del Plata, Mar del Plata, Argentina.
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Huang Z, Zhou Q, Sun P, Yang J, Guo M. Two Agrobacterium tumefaciens CheW Proteins Are Incorporated into One Chemosensory Pathway with Different Efficiencies. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:460-470. [PMID: 29182466 DOI: 10.1094/mpmi-10-17-0255-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Agrobacterium tumefaciens is the agent that causes crown gall tumor disease on more than 140 species of dicotyledonous plants. Chemotaxis of A. tumefaciens toward the wound sites of the host plant is the first step to recognize the host. CheW is a coupling protein that bridges the histidine kinase CheA and the chemoreceptors to form the chemotaxis core signaling complex and plays a crucial role in the assembly and function of the large chemosensory array. Unlike all previously reported chemotaxis systems, A. tumefaciens has only one major che operon but two cheW homologs (atu2075 as cheW1 and atu2617 as cheW2) on unlinked loci. The in-frame deletion of either cheW gene significantly affects A. tumefaciens chemotaxis but does not abolish the chemotaxis, unless both cheW genes were deleted. The effect of cheW2 deletion on the chemotaxis is more severe than that of cheW1 deletion. Either CheW can interact with CheA and couple it to the cell poles. The promoter activity of cheW2 is always higher than that of cheW1 under all of the tested conditions. When two cheW genes were adjusted to the same expression level by using the identical promoter, the difference between the effects of two CheW proteins on the chemotaxis still existed. Therefore, we envision that both the different molecular ratio of two CheW proteins in cell and the different affinities of two CheW proteins with CheA and chemoreceptors result in the efficiency difference of two CheW proteins in functioning in the large chemosensory array.
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Affiliation(s)
- Zhiwei Huang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou City, Jiangsu 225009, P R China
| | - Qingxuan Zhou
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou City, Jiangsu 225009, P R China
| | - Pan Sun
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou City, Jiangsu 225009, P R China
| | - Jing Yang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou City, Jiangsu 225009, P R China
| | - Minliang Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou City, Jiangsu 225009, P R China
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