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Glenn SJ, Gentry-Lear Z, Shavlik M, Harms MJ, Asaki TJ, Baylink A. Bacterial vampirism mediated through taxis to serum. eLife 2024; 12:RP93178. [PMID: 38820052 PMCID: PMC11142651 DOI: 10.7554/elife.93178] [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] [Indexed: 06/02/2024] Open
Abstract
Bacteria of the family Enterobacteriaceae are associated with gastrointestinal (GI) bleeding and bacteremia and are a leading cause of death, from sepsis, for individuals with inflammatory bowel diseases. The bacterial behaviors and mechanisms underlying why these bacteria are prone to bloodstream entry remain poorly understood. Herein, we report that clinical isolates of non-typhoidal Salmonella enterica serovars, Escherichia coli, and Citrobacter koseri are rapidly attracted toward sources of human serum. To simulate GI bleeding, we utilized an injection-based microfluidics device and found that femtoliter volumes of human serum are sufficient to induce bacterial attraction to the serum source. This response is orchestrated through chemotaxis and the chemoattractant L-serine, an amino acid abundant in serum that is recognized through direct binding by the chemoreceptor Tsr. We report the first crystal structures of Salmonella Typhimurium Tsr in complex with L-serine and identify a conserved amino acid recognition motif for L-serine shared among Tsr orthologues. We find Tsr to be widely conserved among Enterobacteriaceae and numerous World Health Organization priority pathogens associated with bloodstream infections. Lastly, we find that Enterobacteriaceae use human serum as a source of nutrients for growth and that chemotaxis and the chemoreceptor Tsr provide a competitive advantage for migration into enterohemorrhagic lesions. We define this bacterial behavior of taxis toward serum, colonization of hemorrhagic lesions, and the consumption of serum nutrients as 'bacterial vampirism', which may relate to the proclivity of Enterobacteriaceae for bloodstream infections.
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Affiliation(s)
- Siena J Glenn
- Washington State University, Department of Veterinary Microbiology and PathologyPullmanUnited States
| | | | - Michael Shavlik
- University of Oregon, Institute of Molecular BiologyEugeneUnited States
| | - Michael J Harms
- University of Oregon, Institute of Molecular BiologyEugeneUnited States
- University of Oregon, Department of Chemistry & BiochemistryEugeneUnited States
| | - Thomas J Asaki
- Washington State University, Department of Mathematics and StatisticsPullmanUnited States
| | - Arden Baylink
- Washington State University, Department of Veterinary Microbiology and PathologyPullmanUnited States
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2
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Lee Upton S, Tay JW, Schwartz DK, Sousa MC. Similarly slow diffusion of BAM and SecYEG complexes in live E. coli cells observed with 3D spt-PALM. Biophys J 2023; 122:4382-4394. [PMID: 37853695 PMCID: PMC10698321 DOI: 10.1016/j.bpj.2023.10.017] [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: 04/19/2023] [Revised: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 10/20/2023] Open
Abstract
The β-barrel assembly machinery (BAM) complex is responsible for inserting outer membrane proteins (OMPs) into the Escherichia coli outer membrane. The SecYEG translocon inserts inner membrane proteins into the inner membrane and translocates both soluble proteins and nascent OMPs into the periplasm. Recent reports describe Sec possibly playing a direct role in OMP biogenesis through interactions with the soluble polypeptide transport-associated (POTRA) domains of BamA (the central OMP component of BAM). Here we probe the diffusion behavior of these protein complexes using photoactivatable super-resolution localization microscopy and single-particle tracking in live E. coli cells of BAM and SecYEG components BamA and SecE and compare them to other outer and inner membrane proteins. To accurately measure trajectories on the highly curved cell surface, three-dimensional tracking was performed using double-helix point-spread function microscopy. All proteins tested exhibit two diffusive modes characterized by "slow" and "fast" diffusion coefficients. We implement a diffusion coefficient analysis as a function of the measurement lag time to separate positional uncertainty from true mobility. The resulting true diffusion coefficients of the slow and fast modes showed a complete immobility of full-length BamA constructs in the time frame of the experiment, whereas the OMP OmpLA displayed a slow diffusion consistent with the high viscosity of the outer membrane. The periplasmic POTRA domains of BamA were found to anchor BAM to other cellular structures and render it immobile. However, deletion of individual distal POTRA domains resulted in increased mobility, suggesting that these domains are required for the full set of cellular interactions. SecE diffusion was much slower than that of the inner membrane protein PgpB and was more like OMPs and BamA. Strikingly, SecE diffused faster upon POTRA domain deletion. These results are consistent with the existence of a BAM-SecYEG trans-periplasmic assembly in live E. coli cells.
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Affiliation(s)
- Stephen Lee Upton
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado
| | - Jian Wei Tay
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Daniel Keith Schwartz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado
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3
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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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4
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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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5
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Chen EHL, Wang CH, Liao YT, Chan FY, Kanaoka Y, Uchihashi T, Kato K, Lai L, Chang YW, Ho MC, Chen RPY. Visualizing the membrane disruption action of antimicrobial peptides by cryo-electron tomography. Nat Commun 2023; 14:5464. [PMID: 37673860 PMCID: PMC10482868 DOI: 10.1038/s41467-023-41156-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/24/2023] [Indexed: 09/08/2023] Open
Abstract
The abuse of antibiotics has led to the emergence of multidrug-resistant microbial pathogens, presenting a pressing challenge in global healthcare. Membrane-disrupting antimicrobial peptides (AMPs) combat so-called superbugs via mechanisms different than conventional antibiotics and have good application prospects in medicine, agriculture, and the food industry. However, the mechanism-of-action of AMPs has not been fully characterized at the cellular level due to a lack of high-resolution imaging technologies that can capture cellular-membrane disruption events in the hydrated state. Previously, we reported PepD2M, a de novo-designed AMP with potent and wide-spectrum bactericidal and fungicidal activity. In this study, we use cryo-electron tomography (cryo-ET) and high-speed atomic force microscopy (HS-AFM) to directly visualize the pepD2M-induced disruption of the outer and inner membranes of the Gram-negative bacterium Escherichia coli, and compared with a well-known pore-forming peptide, melittin. Our high-resolution cryo-ET images reveal how pepD2M disrupts the E. coli membrane using a carpet/detergent-like mechanism. Our studies reveal the direct membrane-disrupting consequence of AMPs on the bacterial membrane by cryo-ET, and this information provides critical insights into the mechanisms of this class of antimicrobial agents.
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Affiliation(s)
- Eric H-L Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Ting Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Feng-Yueh Chan
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan
| | - Yui Kanaoka
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Nagoya, 464-8602, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8602, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Longsheng Lai
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan.
| | - Rita P-Y Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
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6
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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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7
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Riechmann C, Zhang P. Recent structural advances in bacterial chemotaxis signalling. Curr Opin Struct Biol 2023; 79:102565. [PMID: 36868078 PMCID: PMC10460253 DOI: 10.1016/j.sbi.2023.102565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 03/05/2023]
Abstract
Bacterial chemosensory arrays have served as a model system for in-situ structure determination, clearly cataloguing the improvement of cryo-electron tomography (cryoET) over the past decade. In recent years, this has culminated in an accurately fitted atomistic model for the full-length core signalling unit (CSU) and numerous insights into the function of the transmembrane receptors responsible for signal transduction. Here, we review the achievements of the latest structural advances in bacterial chemosensory arrays and the developments which have made such advances possible.
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Affiliation(s)
- Carlos Riechmann
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK.
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8
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Pan X, Tran T, Kirsch ZJ, Thompson LK, Vachet RW. Diethylpyrocarbonate-Based Covalent Labeling Mass Spectrometry of Protein Interactions in a Membrane Complex System. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:82-91. [PMID: 36475668 PMCID: PMC9812933 DOI: 10.1021/jasms.2c00262] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Membrane-associated proteins are important because they mediate interactions between a cell's external and internal environment and they are often targets of therapeutics. Characterizing their structures and binding interactions, however, is challenging because they typically must be solubilized using artificial membrane systems that can make measurements difficult. Mass spectrometry (MS) is emerging as a valuable tool for studying membrane-associated proteins, and covalent labeling MS has unique potential to provide higher order structure and binding information for these proteins in complicated membrane systems. Here, we demonstrate that diethylpyrocarbonate (DEPC) can be effectively used as a labeling reagent to characterize the binding interactions between a membrane-associated protein and its binding partners in an artificial membrane system. Using chemotaxis histidine kinase (CheA) as a model system, we demonstrate that DEPC-based covalent labeling MS can provide structural and binding information about the ternary complex of CheA with two other proteins that is consistent with structural models of this membrane-associated chemoreceptor system. Despite the moderate hydrophobicity of DEPC, we find that its reactivity with proteins is not substantially influenced by the presence of the artificial membranes. However, correct structural information for this multiprotein chemoreceptor system requires measurements of DEPC labeling at multiple reagent concentrations to enable an accurate comparison between CheA and its ternary complex in the chemoreceptor system. In addition to providing structural information that is consistent with the model of this complex system, the labeling data supplements structural information that is not sufficiently refined in the chemoreceptor model.
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Affiliation(s)
- Xiao Pan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
| | - Thomas Tran
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
| | - Zachary J. Kirsch
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
| | - Lynmarie K. Thompson
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
| | - Richard W. Vachet
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
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9
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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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10
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Maschmann Z, Chandrasekaran S, Chua TK, Crane BR. Interdomain Linkers Regulate Histidine Kinase Activity by Controlling Subunit Interactions. Biochemistry 2022; 61:2672-2686. [PMID: 36321948 PMCID: PMC10134573 DOI: 10.1021/acs.biochem.2c00326] [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] [Indexed: 11/06/2022]
Abstract
Bacterial chemoreceptors regulate the cytosolic multidomain histidine kinase CheA through largely unknown mechanisms. Residue substitutions in the peptide linkers that connect the P4 kinase domain to the P3 dimerization and P5 regulatory domain affect CheA basal activity and activation. To understand the role that these linkers play in CheA activity, the P3-to-P4 linker (L3) and P4-to-P5 linker (L4) were extended and altered in variants of Thermotoga maritima (Tm) CheA. Flexible extensions of the L3 and L4 linkers in CheA-LV1 (linker variant 1) allowed for a well-folded kinase domain that retained wild-type (WT)-like binding affinities for nucleotide and normal interactions with the receptor-coupling protein CheW. However, CheA-LV1 autophosphorylation activity registered ∼50-fold lower compared to WT. Neither a WT nor LV1 dimer containing a single P4 domain could autophosphorylate the P1 substrate domain. Autophosphorylation activity was rescued in variants with extended L3 and L4 linkers that favor helical structure and heptad spacing. Autophosphorylation depended on linker spacing and flexibility and not on sequence. Pulse-dipolar electron-spin resonance (ESR) measurements with spin-labeled adenosine 5'-triphosphate (ATP) analogues indicated that CheA autophosphorylation activity inversely correlated with the proximity of the P4 domains within the dimers of the variants. Despite their separation in primary sequence and space, the L3 and L4 linkers also influence the mobility of the P1 substrate domains. In all, interactions of the P4 domains, as modulated by the L3 and L4 linkers, affect domain dynamics and autophosphorylation of CheA, thereby providing potential mechanisms for receptors to regulate the kinase.
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Affiliation(s)
- Zachary Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850
| | - Siddarth Chandrasekaran
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850
- National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca NY 1485
| | - Teck Khiang Chua
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850
- National Biomedical Center for Advanced ESR Technologies, Cornell University, Ithaca NY 1485
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11
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Bacterial chemotaxis in human diseases. Trends Microbiol 2022; 31:453-467. [PMID: 36411201 DOI: 10.1016/j.tim.2022.10.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 11/21/2022]
Abstract
To infect and cause disease, bacterial pathogens must localize to specific regions of the host where they possess the metabolic and defensive acumen for survival. Motile flagellated pathogens exercise control over their localization through chemotaxis to direct motility based on the landscape of exogenous nutrients, toxins, and molecular cues sensed within the host. Here, we review advances in understanding the roles chemotaxis plays in human diseases. Chemotaxis drives pathogen colonization to sites of inflammation and injury and mediates fitness advantages through accessing host-derived nutrients from damaged tissue. Injury tropism may worsen clinical outcomes through instigating chronic inflammation and subsequent cancer development. Inhibiting bacterial chemotactic systems could act synergistically with antibacterial medicines for more effective and specific eradication.
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12
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Zhu Y, Koo CW, Cassidy CK, Spink MC, Ni T, Zanetti-Domingues LC, Bateman B, Martin-Fernandez ML, Shen J, Sheng Y, Song Y, Yang Z, Rosenzweig AC, Zhang P. Structure and activity of particulate methane monooxygenase arrays in methanotrophs. Nat Commun 2022; 13:5221. [PMID: 36064719 PMCID: PMC9445010 DOI: 10.1038/s41467-022-32752-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/16/2022] [Indexed: 01/29/2023] Open
Abstract
Methane-oxidizing bacteria play a central role in greenhouse gas mitigation and have potential applications in biomanufacturing. Their primary metabolic enzyme, particulate methane monooxygenase (pMMO), is housed in copper-induced intracytoplasmic membranes (ICMs), of which the function and biogenesis are not known. We show by serial cryo-focused ion beam (cryoFIB) milling/scanning electron microscope (SEM) volume imaging and lamellae-based cellular cryo-electron tomography (cryoET) that these ICMs are derived from the inner cell membrane. The pMMO trimer, resolved by cryoET and subtomogram averaging to 4.8 Å in the ICM, forms higher-order hexagonal arrays in intact cells. Array formation correlates with increased enzymatic activity, highlighting the importance of studying the enzyme in its native environment. These findings also demonstrate the power of cryoET to structurally characterize native membrane enzymes in the cellular context.
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Affiliation(s)
- Yanan Zhu
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christopher W. Koo
- grid.16753.360000 0001 2299 3507Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL USA
| | - C. Keith Cassidy
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, Oxford, UK
| | - Matthew C. Spink
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Tao Ni
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Laura C. Zanetti-Domingues
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Benji Bateman
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Marisa L. Martin-Fernandez
- grid.76978.370000 0001 2296 6998Central Laser Facility, Science and Technology Facility Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire UK
| | - Juan Shen
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuewen Sheng
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Yun Song
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Zhengyi Yang
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK ,grid.4709.a0000 0004 0495 846XPresent Address: Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Amy C. Rosenzweig
- grid.16753.360000 0001 2299 3507Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL USA
| | - Peijun Zhang
- grid.4991.50000 0004 1936 8948Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK ,grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK ,grid.4991.50000 0004 1936 8948Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
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13
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Joshi H, Prakash MK. Using Atomistic Simulations to Explore the Role of Methylation and ATP in Chemotaxis Signal Transduction. ACS OMEGA 2022; 7:27886-27895. [PMID: 35990422 PMCID: PMC9386827 DOI: 10.1021/acsomega.2c00792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
A bacterial chemotaxis mechanism is activated when nutrients bind to surface receptors. The sequence of intra- and interprotein events in this signal cascade from the receptors to the eventual molecular motors has been clearly identified. However, the atomistic details remain elusive, as in general may be expected of intraprotein signal transduction pathways, especially when fibrillar proteins are involved. We performed atomistic calculations of the methyl accepting chemoprotein (MCP)-CheA-CheW multidomain complex from Escherichia coli, simulating the methylated and unmethylated conditions in the chemoreceptors and the ATP-bound and apo conditions of the CheA. Our results indicate that these atomistic simulations, especially with one of the two force fields we tried, capture several relevant features of the downstream effects, such as the methylation favoring an intermediate structure that is more toward a dipped state and increases the chance of ATP hydrolysis. The results thus suggest the sensitivity of the model to reflect the nutrient signal response, a nontrivial validation considering the complexity of the system, encouraging even more detailed studies on the thermodynamic quantification of the effects and the identification of the signaling networks.
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14
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Gupta C, Sarkar D, Tieleman DP, Singharoy A. The ugly, bad, and good stories of large-scale biomolecular simulations. Curr Opin Struct Biol 2022; 73:102338. [PMID: 35245737 DOI: 10.1016/j.sbi.2022.102338] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/29/2021] [Accepted: 01/24/2022] [Indexed: 12/20/2022]
Abstract
Molecular modeling of large biomolecular assemblies exemplifies a disruptive area holding both promises and contentions. Propelled by peta and exascale computing, several simulation methodologies have now matured into user-friendly tools that are successfully employed for modeling viruses, membranous nano-constructs, and key pieces of the genetic machinery. We present three unifying biophysical themes that emanate from some of the most recent multi-million atom simulation endeavors. Despite connecting molecular changes with phenotypic outcomes, the quality measures of these simulations remain questionable. We discuss the existing and upcoming strategies for constructing representative ensembles of large systems, how new computing technologies will boost this area, and make a point that integrative modeling guided by experimental data is the future of biomolecular computations.
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Affiliation(s)
- Chitrak Gupta
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ, 85282, USA; Biodesign Institute, Tempe, AZ, 85281, USA. https://twitter.com/ChitrakGupta2
| | - Daipayan Sarkar
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ, 85282, USA; MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824-1319, USA. https://twitter.com/17Dsarkar
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada.
| | - Abhishek Singharoy
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University at Tempe, Tempe, AZ, 85282, USA; Biodesign Institute, Tempe, AZ, 85281, USA.
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15
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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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16
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Ni T, Frosio T, Mendonça L, Sheng Y, Clare D, Himes BA, Zhang P. High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity. Nat Protoc 2022; 17:421-444. [PMID: 35022621 DOI: 10.1038/s41596-021-00648-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022]
Abstract
Cryo-electron tomography and subtomogram averaging (STA) has developed rapidly in recent years. It provides structures of macromolecular complexes in situ and in cellular context at or below subnanometer resolution and has led to unprecedented insights into the inner working of molecular machines in their native environment, as well as their functional relevant conformations and spatial distribution within biological cells or tissues. Given the tremendous potential of cryo-electron tomography STA in in situ structural cell biology, we previously developed emClarity, a graphics processing unit-accelerated image-processing software that offers STA and classification of macromolecular complexes at high resolution. However, the workflow remains challenging, especially for newcomers to the field. In this protocol, we describe a detailed workflow, processing and parameters associated with each step, from initial tomography tilt-series data to the final 3D density map, with several features unique to emClarity. We use four different samples, including human immunodeficiency virus type 1 Gag assemblies, ribosome and apoferritin, to illustrate the procedure and results of STA and classification. Following the processing steps described in this protocol, along with a comprehensive tutorial and guidelines for troubleshooting and parameter optimization, one can obtain density maps up to 2.8 Å resolution from six tilt series by cryo-electron tomography STA.
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Affiliation(s)
- Tao Ni
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Thomas Frosio
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Luiza Mendonça
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuewen Sheng
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Daniel Clare
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Benjamin A Himes
- Howard Hughes Medical Institute, RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. .,Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
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17
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Timsit Y, Grégoire SP. Towards the Idea of Molecular Brains. Int J Mol Sci 2021; 22:ijms222111868. [PMID: 34769300 PMCID: PMC8584932 DOI: 10.3390/ijms222111868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
- Correspondence:
| | - Sergeant-Perthuis Grégoire
- Institut de Mathématiques de Jussieu—Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS-Université Paris Diderot, 75013 Paris, France;
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18
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Studying bacterial chemosensory array with CryoEM. Biochem Soc Trans 2021; 49:2081-2089. [PMID: 34495335 PMCID: PMC8589424 DOI: 10.1042/bst20210080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 12/30/2022]
Abstract
Bacteria direct their movement in respond to gradients of nutrients and other stimuli in the environment through the chemosensory system. The behavior is mediated by chemosensory arrays that are made up of thousands of proteins to form an organized array near the cell pole. In this review, we briefly introduce the architecture and function of the chemosensory array and its core signaling unit. We describe the in vivo and in vitro systems that have been used for structural studies of chemosensory array by cryoEM, including reconstituted lipid nanodiscs, 2D lipid monolayer arrays, lysed bacterial ghosts, bacterial minicells and native bacteria cells. Lastly, we review recent advances in structural analysis of chemosensory arrays using state-of-the-art cryoEM and cryoET methodologies, focusing on the latest developments and insights with a perspective on current challenges and future directions.
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19
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Multiscale simulations of large complexes in conjunction with cryo-EM analysis. Curr Opin Struct Biol 2021; 72:27-32. [PMID: 34399155 DOI: 10.1016/j.sbi.2021.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 11/21/2022]
Abstract
The cellular environment is highly crowded with most proteins and RNA/DNA forming homomeric and heteromeric complexes. Essential questions regarding how these complexes switch between functional, rest, and abnormal states with regulators or modifications remain challenging and complicated. Here, we review the recent progress integrating cryoelectron microscopy and multiscale molecular modeling to understand the dynamics and function-related mechanism in protein-RNA/DNA complexes, protein-protein complexes/assemblies, and membrane protein complexes. One future direction of multiscale simulations will be to interpret the large complex multibody regulation in assembly-induced function enhancement in conjunction with advanced atomic resolution structural-biology techniques and specialized computing architectures.
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20
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Gushchin I, Aleksenko VA, Orekhov P, Goncharov IM, Nazarenko VV, Semenov O, Remeeva A, Gordeliy V. Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity. Int J Mol Sci 2021; 22:5933. [PMID: 34072989 PMCID: PMC8199190 DOI: 10.3390/ijms22115933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/18/2022] Open
Abstract
Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.
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Affiliation(s)
- Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vladimir A. Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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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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de Pina LC, da Silva FSH, Galvão TC, Pauer H, Ferreira RBR, Antunes LCM. The role of two-component regulatory systems in environmental sensing and virulence in Salmonella. Crit Rev Microbiol 2021; 47:397-434. [PMID: 33751923 DOI: 10.1080/1040841x.2021.1895067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Adaptation to environments with constant fluctuations imposes challenges that are only overcome with sophisticated strategies that allow bacteria to perceive environmental conditions and develop an appropriate response. The gastrointestinal environment is a complex ecosystem that is home to trillions of microorganisms. Termed microbiota, this microbial ensemble plays important roles in host health and provides colonization resistance against pathogens, although pathogens have evolved strategies to circumvent this barrier. Among the strategies used by bacteria to monitor their environment, one of the most important are the sensing and signalling machineries of two-component systems (TCSs), which play relevant roles in the behaviour of all bacteria. Salmonella enterica is no exception, and here we present our current understanding of how this important human pathogen uses TCSs as an integral part of its lifestyle. We describe important aspects of these systems, such as the stimuli and responses involved, the processes regulated, and their roles in virulence. We also dissect the genomic organization of histidine kinases and response regulators, as well as the input and output domains for each TCS. Lastly, we explore how these systems may be promising targets for the development of antivirulence therapeutics to combat antibiotic-resistant infections.
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Affiliation(s)
- Lucindo Cardoso de Pina
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Biociências, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação Ciência para o Desenvolvimento, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Teca Calcagno Galvão
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Heidi Pauer
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil
| | | | - L Caetano M Antunes
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Rio de Janeiro, Brazil.,Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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23
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Bechtel W, Bich L. Grounding cognition: heterarchical control mechanisms in biology. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190751. [PMID: 33487110 PMCID: PMC7934967 DOI: 10.1098/rstb.2019.0751] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We advance an account that grounds cognition, specifically decision-making, in an activity all organisms as autonomous systems must perform to keep themselves viable—controlling their production mechanisms. Production mechanisms, as we characterize them, perform activities such as procuring resources from their environment, putting these resources to use to construct and repair the organism's body and moving through the environment. Given the variable nature of the environment and the continual degradation of the organism, these production mechanisms must be regulated by control mechanisms that select when a production is required and how it should be carried out. To operate on production mechanisms, control mechanisms need to procure information through measurement processes and evaluate possible actions. They are making decisions. In all organisms, these decisions are made by multiple different control mechanisms that are organized not hierarchically but heterarchically. In many cases, they employ internal models of features of the environment with which the organism must deal. Cognition, in the form of decision-making, is thus fundamental to living systems which must control their production mechanisms. This article is part of the theme issue ‘Basal cognition: conceptual tools and the view from the single cell’.
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Affiliation(s)
- William Bechtel
- Department of Philosophy, University of California San Diego, La Jolla, CA, USA
| | - Leonardo Bich
- IAS-Research Centre for Life, Mind and Society, Department of Philosophy, University of the Basque Country (UPV/EHU), Avenida de Tolosa 70, Donostia-San Sebastian 20018, Spain
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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: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Turk M, Baumeister W. The promise and the challenges of cryo-electron tomography. FEBS Lett 2020; 594:3243-3261. [PMID: 33020915 DOI: 10.1002/1873-3468.13948] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 01/11/2023]
Abstract
Structural biologists have traditionally approached cellular complexity in a reductionist manner in which the cellular molecular components are fractionated and purified before being studied individually. This 'divide and conquer' approach has been highly successful. However, awareness has grown in recent years that biological functions can rarely be attributed to individual macromolecules. Most cellular functions arise from their concerted action, and there is thus a need for methods enabling structural studies performed in situ, ideally in unperturbed cellular environments. Cryo-electron tomography (Cryo-ET) combines the power of 3D molecular-level imaging with the best structural preservation that is physically possible to achieve. Thus, it has a unique potential to reveal the supramolecular architecture or 'molecular sociology' of cells and to discover the unexpected. Here, we review state-of-the-art Cryo-ET workflows, provide examples of biological applications, and discuss what is needed to realize the full potential of Cryo-ET.
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Affiliation(s)
- Martin Turk
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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Abstract
Ethanol is a chemoattractant for Bacillus subtilis even though it is not metabolized and inhibits growth. B. subtilis likely uses ethanol to find ethanol-fermenting microorganisms to utilize as prey. Two chemoreceptors sense ethanol: HemAT and McpB. HemAT’s myoglobin-like sensing domain directly binds ethanol, but the heme group is not involved. McpB is a transmembrane receptor consisting of an extracellular sensing domain and a cytoplasmic signaling domain. While most attractants bind the extracellular sensing domain, we found that ethanol directly binds between intermonomer helices of the cytoplasmic signaling domain of McpB, using a mechanism akin to those identified in many mammalian ethanol-binding proteins. Our results indicate that the sensory repertoire of chemoreceptors extends beyond the sensing domain and can directly involve the signaling domain. Motile bacteria sense chemical gradients using chemoreceptors, which consist of distinct sensing and signaling domains. The general model is that the sensing domain binds the chemical and the signaling domain induces the tactic response. Here, we investigated the unconventional sensing mechanism for ethanol taxis in Bacillus subtilis. Ethanol and other short-chain alcohols are attractants for B. subtilis. Two chemoreceptors, McpB and HemAT, sense these alcohols. In the case of McpB, the signaling domain directly binds ethanol. We were further able to identify a single amino acid residue, Ala431, on the cytoplasmic signaling domain of McpB that, when mutated to serine, reduces taxis to alcohols. Molecular dynamics simulations suggest that the conversion of Ala431 to serine increases coiled-coil packing within the signaling domain, thereby reducing the ability of ethanol to bind between the helices of the signaling domain. In the case of HemAT, the myoglobin-like sensing domain binds ethanol, likely between the helices encapsulating the heme group. Aside from being sensed by an unconventional mechanism, ethanol also differs from many other chemoattractants because it is not metabolized by B. subtilis and is toxic. We propose that B. subtilis uses ethanol and other short-chain alcohols to locate prey, namely, alcohol-producing microorganisms.
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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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Crystal Structure of a Proteolytic Fragment of the Sensor Histidine Kinase NarQ. CRYSTALS 2020. [DOI: 10.3390/cryst10030149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Two-component signaling systems (TCSs) are a large and important class of sensory systems in bacteria, archaea, and some eukaryotes, yet their mechanism of action is still not fully understood from the structural point of view. Many TCS receptors are elongated flexible proteins with transmembrane (TM) regions, and are difficult to work with. Consequently, truncated fragments of the receptors are often used in structural studies. However, it is not fully clear whether the structures of the fragments correspond well to their native structures in the context of full-length proteins. Recently, we crystallized a fragment of Escherichia coli nitrate/nitrite sensor histidine kinase, NarQ, encompassing the sensor, TM, and HAMP domains. Here we report that a smaller proteolytic fragment consisting of the sensor and TM domains can also be crystallized using the in meso approach. The structure of the fragment is similar to the previously determined one, with minor differences in the vicinity of the truncation site. The results show that the crystallization of such sensor–TM fragments can be accomplished and can provide information on the packing of transmembrane helices, albeit limited, and that the proteolysis may or may not be a problem during crystallization.
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