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Raghunandanan S, Zhang K, Zhang Y, Sze CW, Priya R, Luo Y, Lynch MJ, Crane BR, Li C, Yang XF. MCP5, a methyl-accepting chemotaxis protein regulated by both the Hk1-Rrp1 and Rrp2-RpoN-RpoS pathways, is required for the immune evasion of Borrelia burgdorferi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598185. [PMID: 38915556 PMCID: PMC11195095 DOI: 10.1101/2024.06.10.598185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Borrelia (or Borreliella) burgdorferi, the causative agent of Lyme disease, is a motile and invasive zoonotic pathogen, adept at navigating between its arthropod vector and mammalian host. While motility and chemotaxis are well established as essential for its enzootic cycle, the function of methyl-accepting chemotaxis proteins (MCPs) in the infectious cycle of B. burgdorferi remains unclear. In this study, we demonstrate that MCP5, one of the most abundant MCPs in B. burgdorferi, is differentially expressed in response to environmental signals as well as at different stages of the pathogen's enzootic cycle. Specifically, the expression of mcp5 is regulated by the Hk1-Rrp1 and Rrp2-RpoN-RpoS pathways, which are critical for the spirochete's colonization of the tick vector and mammalian host, respectively. Infection experiments with an mcp5 mutant revealed that spirochetes lacking MCP5 could not establish infections in either C3H/HeN mice or Severe Combined Immunodeficiency (SCID) mice, which are defective in adaptive immunity, indicating the essential role of MCP5 in mammalian infection. However, the mcp5 mutant could establish infection and disseminate in NOD SCID Gamma (NSG) mice, which are deficient in both adaptive and most innate immune responses, suggesting a crucial role of MCP5 in evading host innate immunity. In the tick vector, the mcp5 mutants survived feeding but failed to transmit to mice, highlighting the importance of MCP5 in transmission. Our findings reveal that MCP5, regulated by the Rrp1 and Rrp2 pathways, is critical for the establishment of infection in mammalian hosts by evading host innate immunity and is important for the transmission of spirochetes from ticks to mammalian hosts, underscoring its potential as a target for intervention strategies.
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Affiliation(s)
- Sajith Raghunandanan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Kai Zhang
- Department of Oral Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, 23298
| | - Yan Zhang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China, 325035
| | - Ching Wooen Sze
- Department of Oral Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, 23298
| | - Raj Priya
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Yongliang Luo
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China, 325035
| | - Michael J Lynch
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Chunhao Li
- Department of Oral Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, 23298
| | - X. Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202
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2
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Chouhan U, Gamad U, Choudhari JK. Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease. J Genet Eng Biotechnol 2023; 21:84. [PMID: 37584775 PMCID: PMC10429481 DOI: 10.1186/s43141-023-00535-4] [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: 02/02/2023] [Accepted: 07/27/2023] [Indexed: 08/17/2023]
Abstract
BACKGROUND Soil metagenomics is a cultivation-independent molecular strategy for investigating and exploiting the diversity of soil microbial communities. Soil microbial diversity is essential because it is critical to sustaining soil health for agricultural productivity and protection against harmful organisms. This study aimed to perform a metagenomic analysis of the soybean endosphere (all microbial communities found in plant leaves) to reveal signatures of microbes for health and disease. RESULTS The dataset is based on the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) release "microbial diversity in soybean". The quality control process rejected 21 of the evaluated sequences (0.03% of the total sequences). Dereplication determined that 68,994 sequences were artificial duplicate readings, and removed them from consideration. Ribosomal Ribonucleic acid (RNA) genes were present in 72,747 sequences that successfully passed quality control (QC). Finally, we found that hierarchical classification for taxonomic assignment was conducted using MG-RAST, and the considered dataset of the metagenome domain of bacteria (99.68%) dominated the other groups. In Eukaryotes (0.31%) and unclassified sequence 2 (0.00%) in the taxonomic classification of bacteria in the genus group, Streptomyces, Chryseobacterium, Ppaenibacillus, Bacillus, and Mitsuaria were found. We also found some biological pathways, such as CMP-KDO biosynthesis II (from D-arabinose 5-phosphate), tricarboxylic acid cycle (TCA) cycle (plant), citrate cycle (TCA cycle), fatty acid biosynthesis, and glyoxylate and dicarboxylate metabolism. Gene prediction uncovered 1,180 sequences, 15,172 of which included gene products, with the shortest sequence being 131 bases and maximum length 3829 base pairs. The gene list was additionally annotated using Integrated Microbial Genomes and Microbiomes. The annotation process yielded a total of 240 genes found in 177 bacterial strains. These gene products were found in the genome of strain 7598. Large volumes of data are generated using modern sequencing technology to sample all genes in all species present in a given complex sample. CONCLUSIONS These data revealed that it is a rich source of potential biomarkers for soybean plants. The results of this study will help us to understand the role of the endosphere microbiome in plant health and identify the microbial signatures of health and disease. The MG-RAST is a public resource for the automated phylogenetic and functional study of metagenomes. This is a powerful tool for investigating the diversity and function of microbial communities.
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Affiliation(s)
- Usha Chouhan
- Department of Mathematics, Bioinformatics & Computer Applications, Maulana Azad National Institute of Technology, Bhopal, 462051, MP, India
| | - Umesh Gamad
- School of Biotechnology, Devi Ahilya Vishwavidyalaya, Indore, MP, 452001, India
| | - Jyoti Kant Choudhari
- Department of Mathematics, Bioinformatics & Computer Applications, Maulana Azad National Institute of Technology, Bhopal, 462051, MP, India.
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Comparative Genomic Insights into Chemoreceptor Diversity and Habitat Adaptation of Archaea. Appl Environ Microbiol 2022; 88:e0157422. [DOI: 10.1128/aem.01574-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Archaea are capable of sensing and responding to environmental changes by several signal transduction systems with different mechanisms. Much attention is paid to model organisms with complex signaling networks to understand their composition and function, but general principles regarding how an archaeal species organizes its chemoreceptor diversity and habitat adaptation are poorly understood.
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4
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Liu X, Liu Y, Wang Y, Wang D, Johnson KS, Xie Z. The Hypoxia-Associated Localization of Chemotaxis Protein CheZ in Azorhizorbium caulinodans. Front Microbiol 2021; 12:731419. [PMID: 34737727 PMCID: PMC8563088 DOI: 10.3389/fmicb.2021.731419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/22/2021] [Indexed: 11/15/2022] Open
Abstract
Spatial organization of chemotactic proteins is important for cooperative response to external stimuli. However, factors affecting the localization dynamics of chemotaxis proteins are less studied. According to some reports, the polar localization of chemotaxis system I is induced by hypoxia and starvation in Vibrio cholerae. However, in V. cholerae, the chemotaxis system I is not involved in flagellum-mediated chemotaxis, and it may play other alternative cellular functions. In this study, we found that the polar localization of CheZ, a phosphatase regulating chemotactic movement in Azorhizobium caulinodans ORS571, can also be affected by hypoxia and cellular energy-status. The conserved phosphatase active site D165 and the C-terminus of CheZ are essential for the energy-related localization, indicating a cross link between hypoxia-related localization changes and phosphatase activity of CheZ. Furthermore, three of five Aer-like chemoreceptors containing PAS domains participate in the cellular localization of CheZ. In contrast to carbon starvation, free-living nitrogen fixation can alleviate the role of nitrogen limitation and hypoxia on polar localization of CheZ. These results showed that the localization changes induced by hypoxia might be a strategy for bacteria to adapt to complex environment.
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Affiliation(s)
- Xiaolin Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yixuan Wang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Dandan Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Kevin Scot Johnson
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Zhihong Xie
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
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5
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Lamb E, Trimble MJ, McCarter LL. Cell-cell communication, chemotaxis and recruitment in Vibrio parahaemolyticus. Mol Microbiol 2019; 112:99-113. [PMID: 30938898 DOI: 10.1111/mmi.14256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2019] [Indexed: 01/16/2023]
Abstract
Motile bacteria are proficient at finding optimal environments for colonization. Often, they use chemotaxis to sense nutrient availability and dangerous concentrations of toxic chemicals. For many bacteria, the repertoire of chemoreceptors is large, suggesting they possess a broad palate with respect to sensing. However, knowledge of the molecules detected by chemotaxis signal transduction systems is limited. Some bacteria, like Vibrio parahaemolyticus, are social and swarm in groups on surfaces. This marine bacterium and human pathogen secretes the S signal autoinducer, which cues degradation of intracellular c-di-GMP leading to transcription of the swarming program. Here, we report that the S signal also directs motility at a behavioral level by serving as a chemoattractant. The data demonstrate that V. parahaemolyticus senses the S signal using SscL and SscS, homologous methyl-accepting chemotaxis proteins. SscL is required by planktonic bacteria for S signal chemotaxis. SscS plays a role during swarming, and mutants lacking this chemoreceptor swarm faster and produce colonies with more deeply branched swarming fronts than the wild type or the sscL mutant. Other Vibrio species can swim toward the S signal, suggesting a recruitment role for this cell-cell communication molecule in the context of polymicrobial marine communities.
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Affiliation(s)
- Evan Lamb
- The Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Michael J Trimble
- The Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Linda L McCarter
- The Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA
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Phototaxis in a wild isolate of the cyanobacterium Synechococcus elongatus. Proc Natl Acad Sci U S A 2018; 115:E12378-E12387. [PMID: 30552139 DOI: 10.1073/pnas.1812871115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many cyanobacteria, which use light as an energy source via photosynthesis, have evolved the ability to guide their movement toward or away from a light source. This process, termed "phototaxis," enables organisms to localize in optimal light environments for improved growth and fitness. Mechanisms of phototaxis have been studied in the coccoid cyanobacterium Synechocystis sp. strain PCC 6803, but the rod-shaped Synechococcus elongatus PCC 7942, studied for circadian rhythms and metabolic engineering, has no phototactic motility. In this study we report a recent environmental isolate of S. elongatus, the strain UTEX 3055, whose genome is 98.5% identical to that of PCC 7942 but which is motile and phototactic. A six-gene operon encoding chemotaxis-like proteins was confirmed to be involved in phototaxis. Environmental light signals are perceived by a cyanobacteriochrome, PixJSe (Synpcc7942_0858), which carries five GAF domains that are responsive to blue/green light and resemble those of PixJ from Synechocystis Plate-based phototaxis assays indicate that UTEX 3055 uses PixJSe to sense blue and green light. Mutation of conserved functional cysteine residues in different GAF domains indicates that PixJSe controls both positive and negative phototaxis, in contrast to the multiple proteins that are employed for implementing bidirectional phototaxis in Synechocystis.
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Ringgaard S, Yang W, Alvarado A, Schirner K, Briegel A. Chemotaxis arrays in Vibrio species and their intracellular positioning by the ParC/ParP system. J Bacteriol 2018; 200:e00793-17. [PMID: 29531180 PMCID: PMC6040185 DOI: 10.1128/jb.00793-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Most motile bacteria are able to bias their movement towards more favorable environments or to escape from obnoxious substances by a process called chemotaxis. Chemotaxis depends on a chemosensory system that is able to sense specific environmental signals and generate a behavioral response. Typically, the signal is transmitted to the bacterial flagellum, ultimately regulating the swimming behavior of individual cells. Chemotaxis is mediated by proteins that assemble into large, highly ordered arrays. It is imperative for successful chemotactic behavior and cellular competitiveness that chemosensory arrays form and localize properly within the cell. Here we review how chemotaxis arrays form and localize in Vibrio cholerae and Vibrio parahaemolyticus We focus on how the ParC/ParP-system mediates cell cycle-dependent polar localization of chemotaxis arrays and thus ensures proper cell pole development and array inheritance upon cell division.
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Affiliation(s)
- Simon Ringgaard
- Departmet of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
| | - Wen Yang
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - Alejandra Alvarado
- Departmet of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Ariane Briegel
- Institute of Biology, Leiden University, Leiden, Netherlands
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8
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Maslov I, Bogorodskiy A, Mishin A, Okhrimenko I, Gushchin I, Kalenov S, Dencher NA, Fahlke C, Büldt G, Gordeliy V, Gensch T, Borshchevskiy V. Efficient non-cytotoxic fluorescent staining of halophiles. Sci Rep 2018; 8:2549. [PMID: 29416075 PMCID: PMC5803262 DOI: 10.1038/s41598-018-20839-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 01/19/2018] [Indexed: 11/09/2022] Open
Abstract
Research on halophilic microorganisms is important due to their relation to fundamental questions of survival of living organisms in a hostile environment. Here we introduce a novel method to stain halophiles with MitoTracker fluorescent dyes in their growth medium. The method is based on membrane-potential sensitive dyes, which were originally used to label mitochondria in eukaryotic cells. We demonstrate that these fluorescent dyes provide high staining efficiency and are beneficial for multi-staining purposes due to the spectral range covered (from orange to deep red). In contrast with other fluorescent dyes used so far, MitoTracker does not affect growth rate, and remains in cells after several washing steps and several generations in cell culture. The suggested dyes were tested on three archaeal (Hbt. salinarum, Haloferax sp., Halorubrum sp.) and two bacterial (Salicola sp., Halomonas sp.) strains of halophilic microorganisms. The new staining approach provides new insights into biology of Hbt. salinarum. We demonstrated the interconversion of rod-shaped cells of Hbt. salinarium to spheroplasts and submicron-sized spheres, as well as the cytoplasmic integrity of giant rod Hbt. salinarum species. By expanding the variety of tools available for halophile detection, MitoTracker dyes overcome long-standing limitations in fluorescence microscopy studies of halophiles.
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Affiliation(s)
- Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Sergei Kalenov
- Mendeleyev University of Chemical Technology of Russia, 125047, Moscow, Russia
| | - Norbert A Dencher
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
- CSI Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Christoph Fahlke
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
- Institute of Complex Systems (ICS), ICS-4: Cellular Biophysics, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Georg Büldt
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Thomas Gensch
- Institute of Complex Systems (ICS), ICS-4: Cellular Biophysics, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia.
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9
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Neeli-Venkata R, Startceva S, Annila T, Ribeiro AS. Polar Localization of the Serine Chemoreceptor of Escherichia coli Is Nucleoid Exclusion-Dependent. Biophys J 2017; 111:2512-2522. [PMID: 27926852 DOI: 10.1016/j.bpj.2016.10.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/28/2016] [Accepted: 10/19/2016] [Indexed: 11/17/2022] Open
Abstract
We studied whether nucleoid exclusion contributes to the segregation and retention of Tsr chemoreceptor clusters at the cell poles. Using live time-lapse, single-cell microscopy measurements, we show that the single-cell spatial distributions of Tsr clusters have heterogeneities and asymmetries that are consistent with nucleoid exclusion and cannot be explained by the diffusion-and-capture mechanism supported by Tol-Pal complexes at the poles. Also, in cells subjected to ampicillin, which enhances relative nucleoid lengths, Tsr clusters locate relatively closer to the cell extremities, whereas in anucleated cells (deletion mutants for mukB), the Tsr clusters are closer to midcell. In addition, we find that the fraction of Tsr clusters at the poles is smaller in deletion mutants for Tol-Pal than in wild-type cells, although it is still larger than would be expected by chance. Also in deletion mutants, the distribution of Tsr clusters differs widely between cells with relatively small and large nucleoids, in a manner consistent with nucleoid exclusion from midcell. This comparison further showed that diffusion-and-capture by Tol-Pal complexes and nucleoid exclusion from the midcell have complementary effects. Subsequently, we subjected deletion mutants to suboptimal temperatures that are known to enhance cytoplasm viscosity, which hampers nucleoid exclusion effects. As the temperature was lowered, the fraction of clusters at the poles decreased linearly. Finally, a stochastic model including nucleoid exclusion at midcell and diffusion-and-capture due to Tol-Pal at the poles is shown to exhibit a cluster dynamics that is consistent with the empirical data. We conclude that nucleoid exclusion also contributes to the preference of Tsr clusters for polar localization.
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Affiliation(s)
- Ramakanth Neeli-Venkata
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Sofia Startceva
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Teppo Annila
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Andre S Ribeiro
- Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, Tampere, Finland.
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10
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Heering J, Ringgaard S. Differential Localization of Chemotactic Signaling Arrays during the Lifecycle of Vibrio parahaemolyticus. Front Microbiol 2016; 7:1767. [PMID: 27853457 PMCID: PMC5090175 DOI: 10.3389/fmicb.2016.01767] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/21/2016] [Indexed: 11/13/2022] Open
Abstract
When encountering new environments or changes to their external milieu, bacteria use elaborate mechanisms to respond accordingly. Here, we describe how Vibrio parahaemolyticus coordinates two such mechanisms - differentiation and chemotaxis. V. parahaemolyticus differentiates between two distinct cell types: short rod-shaped swimmer cells and highly elongated swarmer cells. We show that the intracellular organization of chemotactic signaling arrays changes according to the differentiation state. In swimmer cells chemotaxis arrays are strictly polarly localized, but in swarmer cells arrays form both at the cell poles and at irregular intervals along the entire cell length. Furthermore, the formation of lateral arrays increases with cell length of swarmer cells. Occurrence of lateral signaling arrays is not simply a consequence of the elongated state of swarmer cells, but is instead differentiation state-specific. Moreover, our data suggest that swarmer cells employ two distinct mechanisms for localization of polar and lateral signaling arrays, respectively. Furthermore, cells show a distinct differentiation and localization pattern of chemosensory arrays, depending on their location within swarm colonies, which likely allows for the organism to simultaneously swarm across surfaces while sustaining a pool of swimmers immediately capable of exploring new liquid surroundings.
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Affiliation(s)
- Jan Heering
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Simon Ringgaard
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
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11
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Barlag B, Beutel O, Janning D, Czarniak F, Richter CP, Kommnick C, Göser V, Kurre R, Fabiani F, Erhardt M, Piehler J, Hensel M. Single molecule super-resolution imaging of proteins in living Salmonella enterica using self-labelling enzymes. Sci Rep 2016; 6:31601. [PMID: 27534893 PMCID: PMC4989173 DOI: 10.1038/srep31601] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 07/20/2016] [Indexed: 12/23/2022] Open
Abstract
The investigation of the subcellular localization, dynamics and interaction of proteins and protein complexes in prokaryotes is complicated by the small size of the cells. Super-resolution microscopy (SRM) comprise various new techniques that allow light microscopy with a resolution that can be up to ten-fold higher than conventional light microscopy. Application of SRM techniques to living prokaryotes demands the introduction of suitable fluorescent probes, usually by fusion of proteins of interest to fluorescent proteins with properties compatible to SRM. Here we describe an approach that is based on the genetically encoded self-labelling enzymes HaloTag and SNAP-tag. Proteins of interest are fused to HaloTag or SNAP-tag and cell permeable substrates can be labelled with various SRM-compatible fluorochromes. Fusions of the enzyme tags to subunits of a type I secretion system (T1SS), a T3SS, the flagellar rotor and a transcription factor were generated and analysed in living Salmonella enterica. The new approach is versatile in tagging proteins of interest in bacterial cells and allows to determine the number, relative subcellular localization and dynamics of protein complexes in living cells.
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Affiliation(s)
- Britta Barlag
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Oliver Beutel
- Abt. Biophysik, Universität Osnabrück, Osnabrück, Germany
| | - Dennis Janning
- Abt. Neurobiologie, Universität Osnabrück, Osnabrück, Germany
| | | | | | - Carina Kommnick
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Vera Göser
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Rainer Kurre
- CALMOS, Universität Osnabrück, Osnabrück, Germany
| | - Florian Fabiani
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marc Erhardt
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jacob Piehler
- Abt. Biophysik, Universität Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
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12
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SOS System Induction Inhibits the Assembly of Chemoreceptor Signaling Clusters in Salmonella enterica. PLoS One 2016; 11:e0146685. [PMID: 26784887 PMCID: PMC4718596 DOI: 10.1371/journal.pone.0146685] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/21/2015] [Indexed: 01/08/2023] Open
Abstract
Swarming, a flagellar-driven multicellular form of motility, is associated with bacterial virulence and increased antibiotic resistance. In this work we demonstrate that activation of the SOS response reversibly inhibits swarming motility by preventing the assembly of chemoreceptor-signaling polar arrays. We also show that an increase in the concentration of the RecA protein, generated by SOS system activation, rather than another function of this genetic network impairs chemoreceptor polar cluster formation. Our data provide evidence that the molecular balance between RecA and CheW proteins is crucial to allow polar cluster formation in Salmonella enterica cells. Thus, activation of the SOS response by the presence of a DNA-injuring compound increases the RecA concentration, thereby disturbing the equilibrium between RecA and CheW and resulting in the cessation of swarming. Nevertheless, when the DNA-damage decreases and the SOS response is no longer activated, basal RecA levels and thus polar cluster assembly are reestablished. These results clearly show that bacterial populations moving over surfaces make use of specific mechanisms to avoid contact with DNA-damaging compounds.
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13
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Xie L, Lu C, Wu XL. Marine bacterial chemoresponse to a stepwise chemoattractant stimulus. Biophys J 2015; 108:766-74. [PMID: 25650943 DOI: 10.1016/j.bpj.2014.11.3479] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 11/20/2014] [Accepted: 11/24/2014] [Indexed: 02/03/2023] Open
Abstract
We found recently that polar flagellated marine bacterium Vibrio alginolyticus is capable of exhibiting taxis toward a chemical source in both forward and backward swimming directions. How the microorganism coordinates these two swimming intervals, however, is not known. The work presented herein is aimed at determining the response functions of the bacterium by applying a stepwise chemoattractant stimulus while it is swimming forward or backward. The important finding of our experiment is that the bacterium responds to an identical chemical signal similarly during the two swimming intervals. For weak stimuli, the difference is mainly in the amplitudes of the response functions while the reaction and adaptation times remain unchanged. In this linear-response regime, the amplitude in the forward swimming interval is approximately a factor of two greater than in the backward direction. Our observation suggests that the cell processes chemical signals identically in both swimming intervals, but the responses of the flagellar motor to the output of the chemotaxis network, the regulator CheY-P concentration, are different. The biological significance of this asymmetrical response in polar flagellated marine bacteria is discussed.
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Affiliation(s)
- Li Xie
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Chunliang Lu
- Department of Radiology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Xiao-Lun Wu
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania.
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Santos TMA, Lin TY, Rajendran M, Anderson SM, Weibel DB. Polar localization of Escherichia coli chemoreceptors requires an intact Tol-Pal complex. Mol Microbiol 2014; 92:985-1004. [PMID: 24720726 DOI: 10.1111/mmi.12609] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2014] [Indexed: 11/29/2022]
Abstract
Subcellular biomolecular localization is critical for the metabolic and structural properties of the cell. The functional implications of the spatiotemporal distribution of protein complexes during the bacterial cell cycle have long been acknowledged; however, the molecular mechanisms for generating and maintaining their dynamic localization in bacteria are not completely understood. Here we demonstrate that the trans-envelope Tol-Pal complex, a widely conserved component of the cell envelope of Gram-negative bacteria, is required to maintain the polar positioning of chemoreceptor clusters in Escherichia coli. Localization of the chemoreceptors was independent of phospholipid composition of the membrane and the curvature of the cell wall. Instead, our data indicate that chemoreceptors interact with components of the Tol-Pal complex and that this interaction is required to polarly localize chemoreceptor clusters. We found that disruption of the Tol-Pal complex perturbs the polar localization of chemoreceptors, alters cell motility, and affects chemotaxis. We propose that the E. coli Tol-Pal complex restricts mobility of the chemoreceptor clusters at the cell poles and may be involved in regulatory mechanisms that co-ordinate cell division and segregation of the chemosensory machinery.
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Affiliation(s)
- Thiago M A Santos
- Department of Biochemistry, University of Wisconsin-Madison, 440 Henry Mall, Madison, WI, 53706, USA
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15
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Proteomic analysis of the purple sulfur bacterium Candidatus “Thiodictyon syntrophicum” strain Cad16T isolated from Lake Cadagno. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2013.11.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Karttunen J, Mäntynen S, Ihalainen TO, Lehtivuori H, Tkachenko NV, Vihinen-Ranta M, Ihalainen JA, Bamford JKH, Oksanen HM. Subcellular localization of bacteriophage PRD1 proteins in Escherichia coli. Virus Res 2014; 179:44-52. [PMID: 24291253 DOI: 10.1016/j.virusres.2013.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/19/2013] [Accepted: 11/19/2013] [Indexed: 11/19/2022]
Abstract
Bacteria possess an intricate internal organization resembling that of the eukaryotes. The complexity is especially prominent at the bacterial cell poles, which are also known to be the preferable sites for some bacteriophages to infect. Bacteriophage PRD1 is a well-known model serving as an ideal system to study structures and functions of icosahedral internal membrane-containing viruses. Our aim was to analyze the localization and interactions of individual PRD1 proteins in its native host Escherichia coli. This was accomplished by constructing a vector library for production of fluorescent fusion proteins. Analysis of solubility and multimericity of the fusion proteins, as well as their localization in living cells by confocal microscopy, indicated that multimeric PRD1 proteins were prone to localize in the cell poles. Furthermore, PRD1 spike complex proteins P5 and P31, as fusion proteins, were shown to be functional in the virion assembly. In addition, they were shown to co-localize in the specific polar area of the cells, which might have a role in the multimerization and formation of viral protein complexes.
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Affiliation(s)
- Jenni Karttunen
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Sari Mäntynen
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Teemu O Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Heli Lehtivuori
- Nanoscience Center, Department of Biological and Environmental Science, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Nikolai V Tkachenko
- Department of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, 33101 Tampere, Finland
| | - Maija Vihinen-Ranta
- Nanoscience Center, Department of Biological and Environmental Science, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Janne A Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Jaana K H Bamford
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Hanna M Oksanen
- Institute of Biotechnology and Department of Biosciences, P.O. Box 56, 00014 University of Helsinki, Finland.
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Chiu SW, Roberts MAJ, Leake MC, Armitage JP. Positioning of chemosensory proteins and FtsZ through the Rhodobacter sphaeroides cell cycle. Mol Microbiol 2013; 90:322-37. [PMID: 23944351 DOI: 10.1111/mmi.12366] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2013] [Indexed: 12/28/2022]
Abstract
Bacterial chemotaxis depends on signalling through large protein complexes. Each cell must inherit a complex on division, suggesting some co-ordination with cell division. In Escherichia coli the membrane-spanning chemosensory complexes are polar and new static complexes form at pre-cytokinetic sites, ensuring positioning at the new pole after division and suggesting a role for the bacterial cytoskeleton. Rhodobacter sphaeroides has both membrane-associated and cytoplasmic, chromosome-associated chemosensory complexes. We followed the relative positions of the two chemosensory complexes, FtsZ and MreB in aerobic and in photoheterotrophic R. sphaeroides cells using fluorescence microscopy. FtsZ forms polar spots after cytokinesis, which redistribute to the midcell forming nodes from which FtsZ extends circumferentially to form the Z-ring. Membrane-associated chemosensory proteins form a number of dynamic unit-clusters with mature clusters containing about 1000 CheW(3) proteins. Individual clusters diffuse randomly within the membrane, accumulating at new poles after division but not colocalizing with either FtsZ or MreB. The cytoplasmic complex colocalizes with FtsZ at midcells in new-born cells. Before cytokinesis one complex moves to a daughter cell, followed by the second moving to the other cell. These data indicate that two homologous complexes use different mechanisms to ensure partitioning, and neither complex utilizes FtsZ or MreB for positioning.
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Affiliation(s)
- Sheng-Wen Chiu
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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Dunlap WC, Starcevic A, Baranasic D, Diminic J, Zucko J, Gacesa R, van Oppen MJH, Hranueli D, Cullum J, Long PF. KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome. BMC Genomics 2013; 14:509. [PMID: 23889801 PMCID: PMC3750612 DOI: 10.1186/1471-2164-14-509] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. DESCRIPTION Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics. CONCLUSIONS We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives.
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Affiliation(s)
- Walter C Dunlap
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Antonio Starcevic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Damir Baranasic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Janko Diminic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Jurica Zucko
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ranko Gacesa
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Madeleine JH van Oppen
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
| | - Daslav Hranueli
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - John Cullum
- Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany
| | - Paul F Long
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
- Department of Chemistry King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
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20
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Schlesner M, Miller A, Besir H, Aivaliotis M, Streif J, Scheffer B, Siedler F, Oesterhelt D. The protein interaction network of a taxis signal transduction system in a halophilic archaeon. BMC Microbiol 2012; 12:272. [PMID: 23171228 PMCID: PMC3579733 DOI: 10.1186/1471-2180-12-272] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/20/2012] [Indexed: 11/28/2022] Open
Abstract
Background The taxis signaling system of the extreme halophilic archaeon Halobacterium (Hbt.) salinarum differs in several aspects from its model bacterial counterparts Escherichia coli and Bacillus subtilis. We studied the protein interactions in the Hbt. salinarum taxis signaling system to gain an understanding of its structure, to gain knowledge about its known components and to search for new members. Results The interaction analysis revealed that the core signaling proteins are involved in different protein complexes and our data provide evidence for dynamic interchanges between them. Fifteen of the eighteen taxis receptors (halobacterial transducers, Htrs) can be assigned to four different groups depending on their interactions with the core signaling proteins. Only one of these groups, which contains six of the eight Htrs with known signals, shows the composition expected for signaling complexes (receptor, kinase CheA, adaptor CheW, response regulator CheY). From the two Hbt. salinarum CheW proteins, only CheW1 is engaged in signaling complexes with Htrs and CheA, whereas CheW2 interacts with Htrs but not with CheA. CheY connects the core signaling structure to a subnetwork consisting of the two CheF proteins (which build a link to the flagellar apparatus), CheD (the hub of the subnetwork), two CheC complexes and the receptor methylesterase CheB. Conclusions Based on our findings, we propose two hypotheses. First, Hbt. salinarum might have the capability to dynamically adjust the impact of certain Htrs or Htr clusters depending on its current needs or environmental conditions. Secondly, we propose a hypothetical feedback loop from the response regulator to Htr methylation made from the CheC proteins, CheD and CheB, which might contribute to adaptation analogous to the CheC/CheD system of B. subtilis.
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Affiliation(s)
- Matthias Schlesner
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
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21
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Li G, Young KD. Isolation and identification of new inner membrane-associated proteins that localize to cell poles inEscherichia coli. Mol Microbiol 2012; 84:276-95. [DOI: 10.1111/j.1365-2958.2012.08021.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Massazza DA, Izzo SA, Gasperotti AF, Herrera Seitz MK, Studdert CA. Functional and structural effects of seven-residue deletions on the coiled-coil cytoplasmic domain of a chemoreceptor. Mol Microbiol 2011; 83:224-39. [DOI: 10.1111/j.1365-2958.2011.07928.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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23
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Satti R, Deakin G, Tanaka RJ, Faisal A. Genes for adaptation and learning spanning evolution: computational comparison between synaptic transmission and chemo-tactic signaling protein networks. BMC Neurosci 2011. [PMCID: PMC3240569 DOI: 10.1186/1471-2202-12-s1-p97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Chemoreceptors and flagellar motors are subterminally located in close proximity at the two cell poles in spirochetes. J Bacteriol 2011; 193:2652-6. [PMID: 21441520 DOI: 10.1128/jb.01530-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Green fluorescent protein (GFP) fusions, immunofluorescence microscopy, and cryo-electron tomography revealed that the chemoreceptors of the Lyme disease spirochete Borrelia burgdorferi form long, thin arrays near both cell poles. These arrays are in close proximity to the flagellar motors. This information provides a basis for further understanding motility, chemotaxis, and protein localization in spirochetes.
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25
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Li M, Khursigara CM, Subramaniam S, Hazelbauer GL. Chemotaxis kinase CheA is activated by three neighbouring chemoreceptor dimers as effectively as by receptor clusters. Mol Microbiol 2010; 79:677-85. [PMID: 21255111 DOI: 10.1111/j.1365-2958.2010.07478.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Chemoreceptors are central to bacterial chemotaxis. These transmembrane homodimers form trimers of dimers. Trimers form clusters of a few to thousands of receptors. A crucial receptor function is 100-fold activation, in signalling complexes, of sensory histidine kinase CheA. Significant activation has been shown to require more than one receptor dimer but the number required for full activation was unknown. We investigated this issue using Nanodiscs, soluble, nanoscale (∼10 nm diameter) plugs of lipid bilayer, to limit the number of neighbouring receptors contributing to activation. Utilizing size-exclusion chromatography, we separated primary preparations of receptor-containing Nanodiscs, otherwise heterogeneous for number and orientation of inserted receptors, into fractions enriched for specific numbers of dimers per disc. Fractionated, clarified Nanodiscs carrying approximately five dimers per disc were as effective in activating kinase as native membrane vesicles containing many neighbouring dimers. At five independently inserted dimers per disc, every disc would have at least three dimers oriented in parallel and thus able act together as they would in native membrane. We conclude full kinase activation involves interaction of CheA with groups of three receptor dimers, presumably as a trimer of dimers, and that more extensive interactions among receptors are not necessary for full kinase activation.
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Affiliation(s)
- Mingshan Li
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri-Columbia, Columbia, MO 65211, USA
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Kentner D, Sourjik V. Use of Fluorescence Microscopy to Study Intracellular Signaling in Bacteria. Annu Rev Microbiol 2010; 64:373-90. [DOI: 10.1146/annurev.micro.112408.134205] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David Kentner
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;
| | - Victor Sourjik
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany;
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Alexandre G. Coupling metabolism and chemotaxis-dependent behaviours by energy taxis receptors. MICROBIOLOGY-SGM 2010; 156:2283-2293. [PMID: 20558508 DOI: 10.1099/mic.0.039214-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bacteria have evolved the ability to monitor changes in various physico-chemical parameters and to adapt their physiology and metabolism by implementing appropriate cellular responses to these changes. Energy taxis is a metabolism-dependent form of taxis and is the directed movement of motile bacteria in gradients of physico-chemical parameters that affect metabolism. Energy taxis has been described in diverse bacterial species and several dedicated energy sensors have been identified. The molecular mechanism of energy taxis has not been studied in as much detail as chemotaxis, but experimental evidence indicates that this behaviour differs from metabolism-independent taxis only by the presence of dedicated energy taxis receptors. Energy taxis receptors perceive changes in energy-related parameters, including signals related to the redox and/or intracellular energy status of the cell. The best-characterized energy taxis receptors are those that sense the redox state of the electron transport chain via non-covalently bound FAD cofactors. Other receptors shown to mediate energy taxis lack any recognizable redox cofactor or conserved energy-sensing motif, and some have been suggested to monitor changes in the proton motive force. The exact energy-sensing mechanism(s) involved are yet to be elucidated for most of these energy sensors. By monitoring changes in energy-related parameters, energy taxis receptors allow cells to couple motility behaviour with metabolism under diverse environmental conditions. Energy taxis receptors thus provide fruitful models to decipher how cells integrate sensory behaviours with metabolic activities.
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Affiliation(s)
- Gladys Alexandre
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, 1414 W. Cumberland Ave, Knoxville, TN 37996, USA
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Streif S, Oesterhelt D, Marwan W. A predictive computational model of the kinetic mechanism of stimulus-induced transducer methylation and feedback regulation through CheY in archaeal phototaxis and chemotaxis. BMC SYSTEMS BIOLOGY 2010; 4:27. [PMID: 20298562 PMCID: PMC2857822 DOI: 10.1186/1752-0509-4-27] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 03/18/2010] [Indexed: 11/10/2022]
Abstract
Background Photo- and chemotaxis of the archaeon Halobacterium salinarum is based on the control of flagellar motor switching through stimulus-specific methyl-accepting transducer proteins that relay the sensory input signal to a two-component system. Certain members of the transducer family function as receptor proteins by directly sensing specific chemical or physical stimuli. Others interact with specific receptor proteins like the phototaxis photoreceptors sensory rhodopsin I and II, or require specific binding proteins as for example some chemotaxis transducers. Receptor activation by light or a change in receptor occupancy by chemical stimuli results in reversible methylation of glutamate residues of the transducer proteins. Both, methylation and demethylation reactions are involved in sensory adaptation and are modulated by the response regulator CheY. Results By mathematical modeling we infer the kinetic mechanisms of stimulus-induced transducer methylation and adaptation. The model (deterministic and in the form of ordinary differential equations) correctly predicts experimentally observed transducer demethylation (as detected by released methanol) in response to attractant and repellent stimuli of wildtype cells, a cheY deletion mutant, and a mutant in which the stimulated transducer species is methylation-deficient. Conclusions We provide a kinetic model for signal processing in photo- and chemotaxis in the archaeon H. salinarum suggesting an essential role of receptor cooperativity, antagonistic reversible methylation, and a CheY-dependent feedback on transducer demethylation.
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Affiliation(s)
- Stefan Streif
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Network Analysis Group, Sandtorstr, 1, Magdeburg, Germany.
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García Véscovi E, Sciara MI, Castelli ME. Two component systems in the spatial program of bacteria. Curr Opin Microbiol 2010; 13:210-8. [PMID: 20138002 DOI: 10.1016/j.mib.2009.12.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 12/29/2009] [Accepted: 12/31/2009] [Indexed: 11/26/2022]
Abstract
Despite being considered a relatively simple form of life, bacteria have revealed a high degree of structural organization, with the spatial destination of their components precisely regulated within the cell. Nevertheless, the primary signals that dictate differential distribution of cellular building blocks and physiological processes remain in most cases largely undisclosed. Signal transduction systems are no exception within this three-dimensional organization and two-component systems (TCS) involved in controlling cell division, differentiation, chemotaxis and virulence show specific and/or dynamic localization, engaging in the spatial program of the bacterial cell.
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Affiliation(s)
- Eleonora García Véscovi
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina.
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30
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The chemoreceptor dimer is the unit of conformational coupling and transmembrane signaling. J Bacteriol 2010; 192:1193-200. [PMID: 20061469 DOI: 10.1128/jb.01391-09] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transmembrane chemoreceptors are central components in bacterial chemotaxis. Receptors couple ligand binding and adaptational modification to receptor conformation in processes that create transmembrane signaling. Homodimers, the fundamental receptor structural units, associate in trimers and localize in patches of thousands. To what degree do conformational coupling and transmembrane signaling require higher-order interactions among dimers? To what degree are they altered by such interactions? To what degree are they inherent features of homodimers? We addressed these questions using nanodiscs to create membrane environments in which receptor dimers had few or no potential interaction partners. Receptors with many, few, or no interaction partners were tested for conformational changes and transmembrane signaling in response to ligand occupancy and adaptational modification. Conformation was assayed by measuring initial rates of receptor methylation, a parameter independent of receptor-receptor interactions. Coupling of ligand occupancy and adaptational modification to receptor conformation and thus to transmembrane signaling occurred with essentially the same sensitivity and magnitude in isolated dimers as for dimers with many neighbors. Thus, we conclude that the chemoreceptor dimer is the fundamental unit of conformational coupling and transmembrane signaling. This implies that in signaling complexes, coupling and transmembrane signaling occur through individual dimers and that changes between dimers in a receptor trimer or among trimer-based signaling complexes are subsequent steps in signaling.
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31
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Gao Z, Schaller GE. The role of receptor interactions in regulating ethylene signal transduction. PLANT SIGNALING & BEHAVIOR 2009; 4:1152-3. [PMID: 20514232 PMCID: PMC2819442 DOI: 10.4161/psb.4.12.9943] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 08/27/2009] [Indexed: 05/20/2023]
Abstract
The phytohormone ethylene is perceived in Arabidopsis by a five-member receptor family. Earlier work has demonstrated that the basic functional unit for an ethylene receptor is a disulfide-linked homodimer. We recently reported in The Journal of Biological Chemistry that the ethylene-receptor ETR1 physically associates with other ethylene receptors through higher order interactions, suggesting the existence of receptor clusters. Here we consider the implications of such clusters upon the mechanism of ethylene signal transduction. In particular, we consider how such clustering provides a cooperative mechanism, akin to what has been found for the prokaryotic chemoreceptors, by which plant sensitivity to ethylene may be increased. In addition, we consider how the dominant ethylene insensitivity conferred by some receptor mutations, such as etr1-1, may also be propagated by interactions among members of the ethylene receptor family.
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Affiliation(s)
- Zhiyong Gao
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
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32
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Lamanna AC, Kiessling LL. Flow cytometry reveals that multivalent chemoattractants effect swarmer cell dedifferentiation. ACS Chem Biol 2009; 4:828-33. [PMID: 19691338 DOI: 10.1021/cb900132e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial cells can differentiate into states that allow them to respond efficiently to their environment. An example of such a transformation is the differentiation of planktonic bacteria into highly motile swarmer cells. The hyperflagellated, filamentous swarmer cells can use coordinated movement to seek out and colonize new sites for pathogenic infection. Because the chemotaxis proteins are essential for swarmer differentiation, we sought to probe the relationship between differentiation and chemoattractants. To this end, we developed a method to screen large populations of swarmer cells using flow cytometry. Using this approach, we found that highly potent multivalent chemoattractants can induce the dedifferentiation of swarmer cells. Our results indicate that chemotactic signaling functions as a target for agents that interfere with bacterial swarming. In addition, the identification of ligands that promote the dedifferentiation of swarmer cells offers new strategies for modulating this multicellular behavior.
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Affiliation(s)
| | - Laura L. Kiessling
- Departments of
Biochemistry
- Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706
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Abstract
Phototaxis in the broadest sense means positive or negative displacement along a light gradient or vector. Prokaryotes most often use a biased random walk strategy, employing type I sensory rhodopsin photoreceptors and two-component signalling to regulate flagellar reversal. This strategy only allows phototaxis along steep light gradients, as found in microbial mats or sediments. Some filamentous cyanobacteria evolved the ability to steer towards a light vector. Even these cyanobacteria, however, can only navigate in two dimensions, gliding on a surface. In contrast, eukaryotes evolved the capacity to follow a light vector in three dimensions in open water. This strategy requires a polarized organism with a stable form, helical swimming with cilia and a shading or focusing body adjacent to a light sensor to allow for discrimination of light direction. Such arrangement and the ability of three-dimensional phototactic navigation evolved at least eight times independently in eukaryotes. The origin of three-dimensional phototaxis often followed a transition from a benthic to a pelagic lifestyle and the acquisition of chloroplasts either via primary or secondary endosymbiosis. Based on our understanding of the mechanism of phototaxis in single-celled eukaryotes and animal larvae, it is possible to define a series of elementary evolutionary steps, each of potential selective advantage, which can lead to pelagic phototactic navigation. We can conclude that it is relatively easy to evolve phototaxis once cell polarity, ciliary swimming and a stable cell shape are present.
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Affiliation(s)
- Gáspár Jékely
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
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34
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Equilibrium mechanisms of receptor clustering. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2009; 100:18-24. [DOI: 10.1016/j.pbiomolbio.2009.08.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Endres RG, Wingreen NS. Accuracy of direct gradient sensing by cell-surface receptors. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2009; 100:33-9. [DOI: 10.1016/j.pbiomolbio.2009.06.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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36
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Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy. PLoS Biol 2009; 7:e1000137. [PMID: 19547746 PMCID: PMC2691949 DOI: 10.1371/journal.pbio.1000137] [Citation(s) in RCA: 277] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 05/14/2009] [Indexed: 11/19/2022] Open
Abstract
Photoactivated localization microscopy analysis of chemotaxis receptors in bacteria suggests that the non-random organization of these proteins results from random self-assembly of clusters without direct cytoskeletal involvement or active transport. The Escherichia coli chemotaxis network is a model system for biological signal processing. In E. coli, transmembrane receptors responsible for signal transduction assemble into large clusters containing several thousand proteins. These sensory clusters have been observed at cell poles and future division sites. Despite extensive study, it remains unclear how chemotaxis clusters form, what controls cluster size and density, and how the cellular location of clusters is robustly maintained in growing and dividing cells. Here, we use photoactivated localization microscopy (PALM) to map the cellular locations of three proteins central to bacterial chemotaxis (the Tar receptor, CheY, and CheW) with a precision of 15 nm. We find that cluster sizes are approximately exponentially distributed, with no characteristic cluster size. One-third of Tar receptors are part of smaller lateral clusters and not of the large polar clusters. Analysis of the relative cellular locations of 1.1 million individual proteins (from 326 cells) suggests that clusters form via stochastic self-assembly. The super-resolution PALM maps of E. coli receptors support the notion that stochastic self-assembly can create and maintain approximately periodic structures in biological membranes, without direct cytoskeletal involvement or active transport. Cells arrange their components—proteins, lipids, and nucleic acids—in organized and reproducible ways to optimize the activities of these components and, therefore, to improve cell efficiency and survival. Eukaryotic cells have a complex arrangement of subcellular structures such as membrane-bound organelles and cytoskeletal transport systems. However, subcellular organization is also important in prokaryotic cells, including rod-shaped bacteria such as E. coli, most of which lack such well-developed systems of organelles and motor proteins for transporting cellular cargoes. In fact, it has remained somewhat mysterious how bacteria are able to organize and spatially segregate their interiors. The E. coli chemotaxis network, a system important for the bacterial response to environmental cues, is one of the best-understood biological signal transduction pathways and serves as a useful model for studying bacterial spatial organization because its components display a nonrandom, periodic distribution in mature cells. Chemotaxis receptors aggregate and cluster into large sensory complexes that localize to the poles of bacteria. To understand how these clusters form and what controls their size and density, we use ultrahigh-resolution light microscopy, called photoactivated localization microscopy (PALM), to visualize individual chemoreceptors in single E. coli cells. From these high-resolution images, we determined that receptors are not actively distributed or attached to specific locations in cells. Instead, we show that random receptor diffusion and receptor–receptor interactions are sufficient to generate the observed complex, ordered pattern. This simple mechanism, termed stochastic self-assembly, may prove to be widespread in both prokaryotic and eukaryotic cells.
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Reilly TJ, Chance DL, Calcutt MJ, Tanner JJ, Felts RL, Waller SC, Henzl MT, Mawhinney TP, Ganjam IK, Fales WH. Characterization of a unique class C acid phosphatase from Clostridium perfringens. Appl Environ Microbiol 2009; 75:3745-54. [PMID: 19363079 PMCID: PMC2687270 DOI: 10.1128/aem.01599-08] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Accepted: 03/29/2009] [Indexed: 11/20/2022] Open
Abstract
Clostridium perfringens is a gram-positive anaerobe and a pathogen of medical importance. The detection of acid phosphatase activity is a powerful diagnostic indicator of the presence of C. perfringens among anaerobic isolates; however, characterization of the enzyme has not previously been reported. Provided here are details of the characterization of a soluble recombinant form of this cell-associated enzyme. The denatured enzyme was approximately 31 kDa and a homodimer in solution. It catalyzed the hydrolysis of several substrates, including para-nitrophenyl phosphate, 4-methylumbelliferyl phosphate, and 3' and 5' nucleoside monophosphates at pH 6. Calculated K(m)s ranged from 0.2 to 0.6 mM with maximum velocity ranging from 0.8 to 1.6 micromol of P(i)/s/mg. Activity was enhanced in the presence of some divalent cations but diminished in the presence of others. Wild-type enzyme was detected in all clinical C. perfringens isolates tested and found to be cell associated. The described enzyme belongs to nonspecific acid phosphatase class C but is devoid of lipid modification commonly attributed to this class.
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Affiliation(s)
- Thomas J Reilly
- Department of Veterinary Pathobiology, University of Missouri, Columbia, 65211, USA.
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38
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Endres RG. Polar chemoreceptor clustering by coupled trimers of dimers. Biophys J 2009; 96:453-63. [PMID: 19167296 DOI: 10.1016/j.bpj.2008.10.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 10/08/2008] [Indexed: 10/21/2022] Open
Abstract
Receptors of bacterial chemotaxis form clusters at the cell poles, where clusters act as "antennas" to amplify small changes in ligand concentration. It is worthy of note that chemoreceptors cluster at multiple length scales. At the smallest scale, receptors form dimers, which assemble into stable timers of dimers. At a large scale, trimers form large polar clusters composed of thousands of receptors. Although much is known about the signaling properties emerging from receptor clusters, it is unknown how receptors localize at the cell poles and what the determining factors are for cluster size. Here, we present a model of polar receptor clustering based on coupled trimers of dimers, where cluster size is determined as a minimum of the cluster-membrane free energy. This energy has contributions from the cluster-membrane elastic energy, penalizing large clusters due to their high intrinsic curvature, and receptor-receptor coupling that favors large clusters. We find that the reduced cluster-membrane curvature mismatch at the curved cell poles leads to large and robust polar clusters, in line with experimental observation, whereas lateral clusters are efficiently suppressed.
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Affiliation(s)
- Robert G Endres
- Division of Molecular Biosciences and Centre for Integrated Systems Biology at Imperial College, Imperial College London, London, United Kingdom.
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Riepl H, Maurer T, Kalbitzer HR, Meier VM, Haslbeck M, Schmitt R, Scharf B. Interaction of CheY2 and CheY2-P with the cognate CheA kinase in the chemosensory-signalling chain of Sinorhizobium meliloti. Mol Microbiol 2008; 69:1373-84. [PMID: 18573176 DOI: 10.1111/j.1365-2958.2008.06342.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
SUMMARY An unusual regulatory mechanism involving two response regulators, CheY1 and CheY2, but no CheZ phosphatase, operates in the chemotactic signalling chain of Sinorhizobium meliloti. Active CheY2-P, phosphorylated by the cognate histidine kinase, CheA, is responsible for flagellar motor control. In the absence of any CheZ phosphatase activity, the level of CheY2-P is quickly reset by a phospho-transfer from CheY2-P first back to CheA, and then to CheY1, which acts as a phosphate sink. In studying the mechanism of this phosphate shuttle, we have used GFP fusions to show that CheY2, but not CheY1, associates with CheA at a cell pole. Cross-linking experiments with the purified proteins revealed that both CheY2 and CheY2-P bind to an isolated P2 ligand-binding domain of CheA, but CheY1 does not. The dissociation constants of CheA-CheY2 and CheA-CheY2-P indicated that both ligands bind with similar affinity to CheA. Based on the NMR structures of CheY2 and CheY2-P, their interactions with the purified P2 domain were analysed. The interacting surface of CheY2 comprises its C-terminal beta4-alpha4-beta5-alpha5 structural elements, whereas the interacting surface of CheY2-P is shifted towards the loop connecting beta5 and alpha5. We propose that the distinct CheY2 and CheY2-P surfaces interact with two overlapping sites in the P2 domain that selectively bind either CheY2 or CheY2-P, depending on whether CheA is active or inactive.
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Affiliation(s)
- Hubert Riepl
- Lehrstuhl für Genetik, Universität Regensburg, Regensburg, Germany
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40
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A sense of self-worth: energy taxis provides insight into how Helicobacter pylori navigates through its environment. J Bacteriol 2008; 190:3095-7. [PMID: 18310332 DOI: 10.1128/jb.00253-08] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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41
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Fujinami S, Sato T, Trimmer JS, Spiller BW, Clapham DE, Krulwich TA, Kawagishi I, Ito M. The voltage-gated Na+ channel NaVBP co-localizes with methyl-accepting chemotaxis protein at cell poles of alkaliphilic Bacillus pseudofirmus OF4. MICROBIOLOGY-SGM 2008; 153:4027-4038. [PMID: 18048917 DOI: 10.1099/mic.0.2007/012070-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Na(V)BP, found in alkaliphilic Bacillus pseudofirmus OF4, is a member of the bacterial voltage-gated Na(+) channel superfamily. The alkaliphile requires Na(V)BP for normal chemotaxis responses and for optimal pH homeostasis during a shift to alkaline conditions at suboptimally low Na(+) concentrations. We hypothesized that interaction of Na(V)BP with one or more other proteins in vivo, specifically methyl-accepting chemotaxis proteins (MCPs), is involved in activation of the channel under the pH conditions that exist in the extremophile and could underpin its role in chemotaxis; MCPs transduce chemotactic signals and generally localize to cell poles of rod-shaped cells. Here, immunofluorescence microscopy and fluorescent protein fusion studies showed that an alkaliphile protein (designated McpX) that cross-reacts with antibodies raised against Bacillus subtilis McpB co-localizes with Na(V)BP at the cell poles of B. pseudofirmus OF4. In a mutant in which Na(V)BP-encoding ncbA is deleted, the content of McpX was close to the wild-type level but McpX was significantly delocalized. A mutant of B. pseudofirmus OF4 was constructed in which cheAW expression was disrupted to assess whether this mutation impaired polar localization of McpX, as expected from studies in Escherichia coli and Salmonella, and, if so, whether Na(V)BP would be similarly affected. Polar localization of both McpX and Na(V)BP was decreased in the cheAW mutant. The results suggest interactions between McpX and Na(V)BP that affect their co-localization. The inverse chemotaxis phenotype of ncbA mutants may result in part from MCP delocalization.
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Affiliation(s)
- Shun Fujinami
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma 374-0193, Japan
| | - Takako Sato
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka 237-0061, Japan
| | - James S Trimmer
- Department of Pharmacology, School of Medicine, University of California, Davis, CA 95616, USA
| | - Benjamin W Spiller
- Howard Hughes Medical Institute, Department of Cardiovascular Research, Children's Hospital and Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - David E Clapham
- Howard Hughes Medical Institute, Department of Cardiovascular Research, Children's Hospital and Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Terry A Krulwich
- Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, NY 10029, USA
| | - Ikuro Kawagishi
- Department of Frontier Bioscience, Faculty of Engineering, Hosei University 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Oura-gun, Gunma 374-0193, Japan
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42
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Borrok MJ, Kolonko EM, Kiessling LL. Chemical probes of bacterial signal transduction reveal that repellents stabilize and attractants destabilize the chemoreceptor array. ACS Chem Biol 2008; 3:101-9. [PMID: 18278851 DOI: 10.1021/cb700211s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The signal transduction cascade responsible for bacterial chemotaxis serves as a model for understanding how cells perceive and respond to their environments. Bacteria react to chemotactic signals by migrating toward attractants and away from repellents. Recent data suggest that the amplification of attractant stimuli depends on receptor collaboration: occupied and unoccupied chemoreceptors act together to relay attractant signals. Attractant signal transmission, therefore, depends on the organization of the chemoreceptors into a lattice of signaling proteins. The importance of this lattice for transducing repellent signals was unexplored. Here, we investigate the role of inter-receptor communication on repellent responses in Escherichia coli. Previously, we found that multivalent displays of attractants are more potent than their monovalent counterparts. To examine the importance of the chemoreceptor lattice in repellent signaling, we synthesized ligands displaying multiple copies of the repellent leucine. Monomeric leucine and low-valency leucine-displaying polymers were sensed as repellents. In contrast, multivalent displays of leucine capable of binding multiple chemoreceptors function not as potent repellents but as attractants. Intriguingly, chemical cross-linking studies indicate that these multivalent ligands, like monovalent attractants, disrupt the cellular chemoreceptor lattice. Thus, repellents stabilize the intrinsic chemoreceptor lattice, and attractants destabilize it. These results indicate that signals can be transmitted with high sensitivity via the disruption of protein-protein interactions. Moreover, our data demonstrate that repellents can be transformed into attractants merely by their multivalent display. These results have implications for designing agonists and antagonists for other signaling systems.
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Affiliation(s)
- M. Jack Borrok
- Department of Biochemistry
- Department of Chemistry
- University of Wisconsin, Madison, Wisconsin 53706
| | - Erin M. Kolonko
- Department of Biochemistry
- Department of Chemistry
- University of Wisconsin, Madison, Wisconsin 53706
| | - Laura L. Kiessling
- Department of Biochemistry
- Department of Chemistry
- University of Wisconsin, Madison, Wisconsin 53706
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43
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Hazelbauer GL, Falke JJ, Parkinson JS. Bacterial chemoreceptors: high-performance signaling in networked arrays. Trends Biochem Sci 2007; 33:9-19. [PMID: 18165013 DOI: 10.1016/j.tibs.2007.09.014] [Citation(s) in RCA: 488] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Revised: 09/10/2007] [Accepted: 09/23/2007] [Indexed: 11/27/2022]
Abstract
Chemoreceptors are crucial components in the bacterial sensory systems that mediate chemotaxis. Chemotactic responses exhibit exquisite sensitivity, extensive dynamic range and precise adaptation. The mechanisms that mediate these high-performance functions involve not only actions of individual proteins but also interactions among clusters of components, localized in extensive patches of thousands of molecules. Recently, these patches have been imaged in native cells, important features of chemoreceptor structure and on-off switching have been identified, and new insights have been gained into the structural basis and functional consequences of higher order interactions among sensory components. These new data suggest multiple levels of molecular interactions, each of which contribute specific functional features and together create a sophisticated signaling device.
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Affiliation(s)
- Gerald L Hazelbauer
- Department of Biochemistry, University of Missouri Columbia, Columbia, MO 65211, USA.
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44
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Endres RG, Falke JJ, Wingreen NS. Chemotaxis receptor complexes: from signaling to assembly. PLoS Comput Biol 2007; 3:e150. [PMID: 17676982 PMCID: PMC1933480 DOI: 10.1371/journal.pcbi.0030150] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Accepted: 06/15/2007] [Indexed: 11/18/2022] Open
Abstract
Complexes of chemoreceptors in the bacterial cytoplasmic membrane allow for the sensing of ligands with remarkable sensitivity. Despite the excellent characterization of the chemotaxis signaling network, very little is known about what controls receptor complex size. Here we use in vitro signaling data to model the distribution of complex sizes. In particular, we model Tar receptors in membranes as an ensemble of different sized oligomer complexes, i.e., receptor dimers, dimers of dimers, and trimers of dimers, where the relative free energies, including receptor modification, ligand binding, and interaction with the kinase CheA determine the size distribution. Our model compares favorably with a variety of signaling data, including dose-response curves of receptor activity and the dependence of activity on receptor density in the membrane. We propose that the kinetics of complex assembly can be measured in vitro from the temporal response to a perturbation of the complex free energies, e.g., by addition of ligand.
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Affiliation(s)
- Robert G Endres
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America.
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45
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Studdert CA, Parkinson JS. In vivo crosslinking methods for analyzing the assembly and architecture of chemoreceptor arrays. Methods Enzymol 2007; 423:414-31. [PMID: 17609143 DOI: 10.1016/s0076-6879(07)23019-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The chemoreceptor molecules that mediate chemotactic responses in bacteria and archaea are physically clustered and operate as highly cooperative arrays. Few experimental approaches are able to investigate the structure-function organization of these chemoreceptor networks in living cells. This chapter describes chemical crosslinking methods that can be applied under normal physiological conditions to explore physical interactions between chemoreceptors and their underlying genetic and structural basis. Most of these crosslinking approaches are based on available atomic structures for chemoreceptor homodimers, the fundamental building block for higher-order networks. However, the general logic of our in vivo crosslinking approaches is readily applicable to other protein-protein interactions and other organisms, even when high-resolution structural information is not available.
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Affiliation(s)
- Claudia A Studdert
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
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46
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Kentner D, Sourjik V. Spatial organization of the bacterial chemotaxis system. Curr Opin Microbiol 2006; 9:619-24. [PMID: 17064953 DOI: 10.1016/j.mib.2006.10.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2006] [Accepted: 10/13/2006] [Indexed: 11/23/2022]
Abstract
Sensory complexes in bacterial chemotaxis are organized in large clusters, building complex signal-processing machinery. Interactions among chemoreceptors are the main determinant of cluster formation and create an allosteric network that is able to integrate and amplify stimuli, before transmitting the signal to downstream proteins. Association of the other proteins with the receptor cluster creates a signalling scaffold, which enhances the efficiency and specificity of the pathway. Clusters localize to specific locations inside the cell, perhaps to ensure their proper distribution during cell division. Clustering is conserved among all studied prokaryotic chemotaxis systems and exemplifies a growing number of bacterial pathways with a reported sub-cellular spatial organization. Moreover, because allostery provides a simple mechanism to achieve very high response sensitivity, it is probable that clustering-based signal amplification is not limited to bacterial chemotaxis but also exists in other prokaryotic and eukaryotic pathways.
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Affiliation(s)
- David Kentner
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
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47
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Abstract
Why do bacteria have shape? Is morphology valuable or just a trivial secondary characteristic? Why should bacteria have one shape instead of another? Three broad considerations suggest that bacterial shapes are not accidental but are biologically important: cells adopt uniform morphologies from among a wide variety of possibilities, some cells modify their shape as conditions demand, and morphology can be tracked through evolutionary lineages. All of these imply that shape is a selectable feature that aids survival. The aim of this review is to spell out the physical, environmental, and biological forces that favor different bacterial morphologies and which, therefore, contribute to natural selection. Specifically, cell shape is driven by eight general considerations: nutrient access, cell division and segregation, attachment to surfaces, passive dispersal, active motility, polar differentiation, the need to escape predators, and the advantages of cellular differentiation. Bacteria respond to these forces by performing a type of calculus, integrating over a number of environmental and behavioral factors to produce a size and shape that are optimal for the circumstances in which they live. Just as we are beginning to answer how bacteria create their shapes, it seems reasonable and essential that we expand our efforts to understand why they do so.
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Affiliation(s)
- Kevin D Young
- Department of Microbiology and Immunology, University of North Dakota School of Medicine, Grand Forks, ND 58202-9037, USA.
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48
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Thompson SR, Wadhams GH, Armitage JP. The positioning of cytoplasmic protein clusters in bacteria. Proc Natl Acad Sci U S A 2006; 103:8209-14. [PMID: 16702547 PMCID: PMC1472454 DOI: 10.1073/pnas.0600919103] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cell division is a carefully orchestrated procedure. Bacterial cells have intricate mechanisms to ensure that genetic material is copied, proofread, and accurately partitioned into daughter cells. Partitioning now appears to also occur for some cytoplasmic proteins. Previously, using chromosomal fluorescent protein fusions, we demonstrated that a subset of Rhodobacter sphaeroides chemotaxis proteins colocalize to a discrete region within the bacterial cytoplasm. Using TlpT-yellow fluorescent protein as a marker for the position of the cytoplasmic protein clusters, we show most cells contain either one cluster localized at mid-cell or two clusters at the one-fourth and three-fourths positions of cell length. The number and positioning of these protein clusters depend on a previously unrecognized bacterial protein positioning factor, PpfA, which has homology to bacterial type I DNA partitioning factors. These data suggest that there is a mechanism involved in partitioning some cytoplasmic proteins upon cell division that is analogous to a mechanism seen for plasmid and chromosomal DNA.
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Affiliation(s)
- Stephen R. Thompson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - George H. Wadhams
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Judith P. Armitage
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
- To whom correspondence should be addressed. E-mail:
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49
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Kiessling LL, Gestwicki JE, Strong LE. Synthetische multivalente Liganden als Sonden für die Signaltransduktion. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502794] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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50
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Kiessling LL, Gestwicki JE, Strong LE. Synthetic multivalent ligands as probes of signal transduction. Angew Chem Int Ed Engl 2006; 45:2348-68. [PMID: 16557636 PMCID: PMC2842921 DOI: 10.1002/anie.200502794] [Citation(s) in RCA: 687] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cell-surface receptors acquire information from the extracellular environment and coordinate intracellular responses. Many receptors do not operate as individual entities, but rather as part of dimeric or oligomeric complexes. Coupling the functions of multiple receptors may endow signaling pathways with the sensitivity and malleability required to govern cellular responses. Moreover, multireceptor signaling complexes may provide a means of spatially segregating otherwise degenerate signaling cascades. Understanding the mechanisms, extent, and consequences of receptor co-localization and interreceptor communication is critical; chemical synthesis can provide compounds to address the role of receptor assembly in signal transduction. Multivalent ligands can be generated that possess a variety of sizes, shapes, valencies, orientations, and densities of binding elements. This Review focuses on the use of synthetic multivalent ligands to characterize receptor function.
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Affiliation(s)
- Laura L Kiessling
- Department of Chemistry, University of Wisconsin--Madison, 1101 University Ave., Madison, WI 53706, USA.
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