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Bacterial Chemoreceptors
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Bacterial Chemoreceptors

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (20 July 2020) | Viewed by 18430

Special Issue Editors

Dr. Tino Krell

E-Mail Website
Guest Editor
Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
Interests: bacterial signal transduction; chemoreceptor; chemotaxis; Pseudomonas; two-component systems; molecular recognition; microcalorimetry; structural biology
Special Issues, Collections and Topics in MDPI journals
Dr. Miguel A. Matilla

E-Mail Website
Guest Editor
Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
Interests: molecular microbiology; chemosignaling; chemotaxis; chemoreceptor; rhizosphere colonization; plant-associated bacteria; antibiotics synthesis and regulation; Pseudomona; enterobacteria
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

A chemotactic response is initiated by the chemoeffector-mediated stimulation of chemoreceptors. Although chemoreceptors are essential for chemotaxis, many of their features remain poorly understood. Bacterial genome analysis and experimental data show that chemoreceptors form a highly diverse protein super-family that differs in size, topology, domain composition, cellular location, function, or the mechanism of action. Much research is still needed to describe and understand the physiological and evolutionary relevance of this diversity. Thus, for the large majority of chemoreceptors, the function or the corresponding chemoeffectors are unknown, and such information will help to identify the forces that have shaped the evolution of chemoreceptors. Contrary to a wide-spread misconception within the scientific community, not all chemoreceptors are involved in chemotaxis, and there is paucity of information on receptors that carry out alternative cellular functions. Most of what we know on chemoreceptor function derives from the study of Escherichia coli proteins. However, research over mainly the last decade has expanded chemoreceptor research into a variety of different bacterial species with different lifestyles. As a result, a more global picture of chemoreceptor function is emerging. These studies show that chemotaxis and chemoreceptor function is frequently important for virulence, plant root colonization, or biodegradation efficiency. In this context, the goal of this Special Issue is to further expand our knowledge of the chemoeffector function as well as the selective pressures that have shaped its evolution. We welcome the submission of original research and reviews.

Dr. Tino Krell
Dr. Miguel A. Matilla
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • bacteria
  • motility
  • chemoreceptor
  • chemoeffector
  • chemotaxis
  • aerotaxis/energy taxis
  • signal sensing
  • signal transduction
  • virulence
  • host colonization

Published Papers (5 papers)

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Research

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18 pages, 4336 KiB  
Article
Sensor Histidine Kinase NarQ Activates via Helical Rotation, Diagonal Scissoring, and Eventually Piston-Like Shifts
by Ivan Gushchin, Philipp Orekhov, Igor Melnikov, Vitaly Polovinkin, Anastasia Yuzhakova and Valentin Gordeliy
Int. J. Mol. Sci. 2020, 21(9), 3110; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21093110 - 28 Apr 2020
Cited by 9 | Viewed by 3608
Abstract
Membrane-embedded sensor histidine kinases (HKs) and chemoreceptors are used ubiquitously by bacteria and archaea to percept the environment, and are often crucial for their survival and pathogenicity. The proteins can transmit the signal from the sensor domain to the catalytic kinase domain reliably [...] Read more.
Membrane-embedded sensor histidine kinases (HKs) and chemoreceptors are used ubiquitously by bacteria and archaea to percept the environment, and are often crucial for their survival and pathogenicity. The proteins can transmit the signal from the sensor domain to the catalytic kinase domain reliably over the span of several hundreds of angstroms, and regulate the activity of the cognate response regulator proteins, with which they form two-component signaling systems (TCSs). Several mechanisms of transmembrane signal transduction in TCS receptors have been proposed, dubbed (swinging) piston, helical rotation, and diagonal scissoring. Yet, despite decades of studies, there is no consensus on whether these mechanisms are common for all TCS receptors. Here, we extend our previous work on Escherichia coli nitrate/nitrite sensor kinase NarQ. We determined a crystallographic structure of the sensor-TM-HAMP fragment of the R50S mutant, which, unexpectedly, was found in a ligand-bound-like conformation, despite an inability to bind nitrate. Subsequently, we reanalyzed the structures of the ligand-free and ligand-bound NarQ and NarX sensor domains, and conducted extensive molecular dynamics simulations of ligand-free and ligand-bound wild type and mutated NarQ. Based on the data, we show that binding of nitrate to NarQ causes, first and foremost, helical rotation and diagonal scissoring of the α-helices at the core of the sensor domain. These conformational changes are accompanied by a subtle piston-like motion, which is amplified by a switch in the secondary structure of the linker between the sensor and TM domains. We conclude that helical rotation, diagonal scissoring, and piston are simply different degrees of freedom in coiled-coil proteins and are not mutually exclusive in NarQ, and likely in other nitrate sensors and TCS proteins as well. Full article
(This article belongs to the Special Issue Bacterial Chemoreceptors)
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21 pages, 3300 KiB  
Article
Determination of Ligand Profiles for Pseudomonas aeruginosa Solute Binding Proteins
by Matilde Fernández, Miriam Rico-Jiménez, Álvaro Ortega, Abdelali Daddaoua, Ana Isabel García García, David Martín-Mora, Noel Mesa Torres, Ana Tajuelo, Miguel A. Matilla and Tino Krell
Int. J. Mol. Sci. 2019, 20(20), 5156; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20205156 - 17 Oct 2019
Cited by 19 | Viewed by 3496
Abstract
Solute binding proteins (SBPs) form a heterogeneous protein family that is found in all kingdoms of life. In bacteria, the ligand-loaded forms bind to transmembrane transporters providing the substrate. We present here the SBP repertoire of Pseudomonas aeruginosa PAO1 that is composed of [...] Read more.
Solute binding proteins (SBPs) form a heterogeneous protein family that is found in all kingdoms of life. In bacteria, the ligand-loaded forms bind to transmembrane transporters providing the substrate. We present here the SBP repertoire of Pseudomonas aeruginosa PAO1 that is composed of 98 proteins. Bioinformatic predictions indicate that many of these proteins have a redundant ligand profile such as 27 SBPs for proteinogenic amino acids, 13 proteins for spermidine/putrescine, or 9 proteins for quaternary amines. To assess the precision of these bioinformatic predictions, we have purified 17 SBPs that were subsequently submitted to high-throughput ligand screening approaches followed by isothermal titration calorimetry studies, resulting in the identification of ligands for 15 of them. Experimentation revealed that PA0222 was specific for γ-aminobutyrate (GABA), DppA2 for tripeptides, DppA3 for dipeptides, CysP for thiosulphate, OpuCC for betaine, and AotJ for arginine. Furthermore, RbsB bound D-ribose and D-allose, ModA bound molybdate, tungstate, and chromate, whereas AatJ recognized aspartate and glutamate. The majority of experimentally identified ligands were found to be chemoattractants. Data show that the ligand class recognized by SPBs can be predicted with confidence using bioinformatic methods, but experimental work is necessary to identify the precise ligand profile. Full article
(This article belongs to the Special Issue Bacterial Chemoreceptors)
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18 pages, 2911 KiB  
Article
Mechanism of Signalling and Adaptation through the Rhodobacter sphaeroides Cytoplasmic Chemoreceptor Cluster
by Jennifer A. de Beyer, Andrea Szöllössi, Elaine Byles, Roman Fischer and Judith P. Armitage
Int. J. Mol. Sci. 2019, 20(20), 5095; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20205095 - 14 Oct 2019
Cited by 7 | Viewed by 2778
Abstract
Rhodobacter sphaeroides has two chemotaxis clusters, an Escherichia coli-like cluster with membrane-spanning chemoreceptors and a less-understood cytoplasmic cluster. The cytoplasmic CheA is split into CheA4, a kinase, and CheA3, a His-domain phosphorylated by CheA4 and a phosphatase [...] Read more.
Rhodobacter sphaeroides has two chemotaxis clusters, an Escherichia coli-like cluster with membrane-spanning chemoreceptors and a less-understood cytoplasmic cluster. The cytoplasmic CheA is split into CheA4, a kinase, and CheA3, a His-domain phosphorylated by CheA4 and a phosphatase domain, which together phosphorylate and dephosphorylate motor-stopping CheY6. In bacterial two-hybrid analysis, one major cytoplasmic chemoreceptor, TlpT, interacted with CheA4, while the other, TlpC, interacted with CheA3. Both clusters have associated adaptation proteins. Deleting their methyltransferases and methylesterases singly and together removed chemotaxis, but with opposite effects. The cytoplasmic cluster signal overrode the membrane cluster signal. Methylation and demethylation of specific chemoreceptor glutamates controls adaptation. Tandem mass spectroscopy and bioinformatics identified four putative sites on TlpT, three glutamates and a glutamine. Mutating each glutamate to alanine resulted in smooth swimming and loss of chemotaxis, unlike similar mutations in E. coli chemoreceptors. Cells with two mutated glutamates were more stoppy than wild-type and responded and adapted to attractant addition, not removal. Mutating all four sites amplified the effect. Cells were non-motile, began smooth swimming on attractant addition, and rapidly adapted back to non-motile before attractant removal. We propose that TlpT responds and adapts to the cell’s metabolic state, generating the steady-state concentration of motor-stopping CheY6~P. Membrane-cluster signalling produces a pulse of CheY3/CheY4~P that displaces CheY6~P and allows flagellar rotation and smooth swimming before both clusters adapt. Full article
(This article belongs to the Special Issue Bacterial Chemoreceptors)
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14 pages, 4097 KiB  
Article
Spatial Restrictions in Chemotaxis Signaling Arrays: A Role for Chemoreceptor Flexible Hinges across Bacterial Diversity
by David Stalla, Narahari Akkaladevi, Tommi A. White and Gerald L. Hazelbauer
Int. J. Mol. Sci. 2019, 20(12), 2989; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20122989 - 19 Jun 2019
Cited by 5 | Viewed by 3155
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Bacterial Chemoreceptors)
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Review

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13 pages, 2906 KiB  
Review
Chemotaxis Towards Aromatic Compounds: Insights from Comamonas testosteroni
by Yun-Hao Wang, Zhou Huang and Shuang-Jiang Liu
Int. J. Mol. Sci. 2019, 20(11), 2701; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20112701 - 01 Jun 2019
Cited by 31 | Viewed by 4768
Abstract
Chemotaxis is an important physiological adaptation that allows many motile bacteria to orientate themselves for better niche adaptation. Chemotaxis is best understood in Escherichia coli. Other representative bacteria, such as Rhodobacter sphaeroides, Pseudomonas species, Helicobacter pylori, and Bacillus subtilis, [...] Read more.
Chemotaxis is an important physiological adaptation that allows many motile bacteria to orientate themselves for better niche adaptation. Chemotaxis is best understood in Escherichia coli. Other representative bacteria, such as Rhodobacter sphaeroides, Pseudomonas species, Helicobacter pylori, and Bacillus subtilis, also have been deeply studied and systemically summarized. These bacteria belong to α-, γ-, ε-Proteobacteria, or Firmicutes. However, β-Proteobacteria, of which many members have been identified as holding chemotactic pathways, lack a summary of chemotaxis. Comamonas testosteroni, belonging to β-Proteobacteria, grows with and chemotactically responds to a range of aromatic compounds. This paper summarizes the latest research on chemotaxis towards aromatic compounds, mainly from investigations of C. testosteroni and other Comamonas species. Full article
(This article belongs to the Special Issue Bacterial Chemoreceptors)
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