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Agbekudzi A, Scharf BE. Chemoreceptors in Sinorhizobium meliloti require minimal pentapeptide tethers to provide adaptational assistance. Mol Microbiol 2024. [PMID: 38798055 DOI: 10.1111/mmi.15282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Sensory adaptation in bacterial chemotaxis is mediated by posttranslational modifications of methyl-accepting chemotaxis proteins (MCPs). In Escherichia coli, the adaptation proteins CheR and CheB tether to a conserved C-terminal receptor pentapeptide. Here,we investigated the function of the pentapeptide motif (N/D)WE(E/N)F in Sinorhizobium meliloti chemotaxis. Isothermal titration calorimetry revealed stronger affinity of the pentapeptides to CheR and activated CheB relative to unmodified CheB. Strains with mutations of the conserved tryptophan in one or all four MCP pentapeptides resulted in a significant decrease or loss of chemotaxis to glycine betaine, lysine, and acetate, chemoattractants sensed by pentapeptide-bearing McpX and pentapeptide-lacking McpU and McpV, respectively. Importantly, we discovered that the pentapeptide mediates chemotaxis when fused to the C-terminus of pentapeptide-lacking chemoreceptors via a flexible linker. We propose that adaptational assistance and a threshold number of available sites enable the efficient docking of adaptation proteins to the chemosensory array. Altogether, these results demonstrate that S. meliloti effectively utilizes a pentapeptide-dependent adaptation system with a minimal number of tethering units to assist pentapeptide-lacking chemoreceptors and hypothesize that the higher abundance of CheR and CheB in S. meliloti compared to E. coli allows for ample recruitment of adaptation proteins to the chemosensory array.
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Affiliation(s)
- Alfred Agbekudzi
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, Virginia, USA
| | - Birgit E Scharf
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, Virginia, USA
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2
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Shumilina J, Soboleva A, Abakumov E, Shtark OY, Zhukov VA, Frolov A. Signaling in Legume-Rhizobia Symbiosis. Int J Mol Sci 2023; 24:17397. [PMID: 38139226 PMCID: PMC10743482 DOI: 10.3390/ijms242417397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/19/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
Legumes represent an important source of food protein for human nutrition and animal feed. Therefore, sustainable production of legume crops is an issue of global importance. It is well-known that legume-rhizobia symbiosis allows an increase in the productivity and resilience of legume crops. The efficiency of this mutualistic association strongly depends on precise regulation of the complex interactions between plant and rhizobia. Their molecular dialogue represents a complex multi-staged process, each step of which is critically important for the overall success of the symbiosis. In particular, understanding the details of the molecular mechanisms behind the nodule formation and functioning might give access to new legume cultivars with improved crop productivity. Therefore, here we provide a comprehensive literature overview on the dynamics of the signaling network underlying the development of the legume-rhizobia symbiosis. Thereby, we pay special attention to the new findings in the field, as well as the principal directions of the current and prospective research. For this, here we comprehensively address the principal signaling events involved in the nodule inception, development, functioning, and senescence.
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Affiliation(s)
- Julia Shumilina
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.S.)
| | - Alena Soboleva
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.S.)
- Biological Faculty, Saint Petersburg State University, 199034 St. Petersburg, Russia;
| | - Evgeny Abakumov
- Biological Faculty, Saint Petersburg State University, 199034 St. Petersburg, Russia;
| | - Oksana Y. Shtark
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (O.Y.S.); (V.A.Z.)
| | - Vladimir A. Zhukov
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (O.Y.S.); (V.A.Z.)
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.S.)
- Biological Faculty, Saint Petersburg State University, 199034 St. Petersburg, Russia;
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3
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Cerna‐Vargas JP, Sánchez‐Romera B, Matilla MA, Ortega Á, Krell T. Sensing preferences for prokaryotic solute binding protein families. Microb Biotechnol 2023; 16:1823-1833. [PMID: 37547952 PMCID: PMC10443332 DOI: 10.1111/1751-7915.14292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/25/2023] [Indexed: 08/08/2023] Open
Abstract
Solute binding proteins (SBPs) are of central physiological relevance for prokaryotes. These proteins present substrates to transporters, but they also stimulate different signal transduction receptors. SBPs form a superfamily of at least 33 protein Pfam families. To assess possible links between SBP sequence and the ligand recognized, we have inspected manually all SBP three-dimensional structures deposited in the protein data bank and retrieved 748 prokaryotic structures that have been solved in complex with bound ligand. These structures were classified into 26 SBP Pfam families. The analysis of the ligands recognized revealed that most families possess a preference for a compound class. There were three families each that bind preferentially saccharides and amino acids. In addition, we identified families that bind preferentially purines, quaternary amines, iron and iron-chelating compounds, oxoanions, bivalent metal ions or phosphates. Phylogenetic analyses suggest convergent evolutionary events that lead to families that bind the same ligand. The functional link between chemotaxis and compound uptake is reflected in similarities in the ligands recognized by SBPs and chemoreceptors. Associating Pfam families with ligand profiles will be of help to design experimental strategies aimed at the identification of ligands for uncharacterized SBPs.
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Affiliation(s)
- Jean Paul Cerna‐Vargas
- Department of Biotechnology and Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
- Centro de Biotecnología y Genómica de Plantas CBGPUniversidad Politécnica de Madrid‐Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Parque Científico y Tecnológico de la UPMMadridSpain
| | - Beatriz Sánchez‐Romera
- Scientific Instrumentation ServiceEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
| | - Miguel A. Matilla
- Department of Biotechnology and Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of ChemistryUniversity of MurciaMurciaSpain
| | - Tino Krell
- Department of Biotechnology and Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
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4
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Han L, Zhang H, Bai X, Jiang B. The peanut root exudate increases the transport and metabolism of nutrients and enhances the plant growth-promoting effects of burkholderia pyrrocinia strain P10. BMC Microbiol 2023; 23:85. [PMID: 36991332 PMCID: PMC10061817 DOI: 10.1186/s12866-023-02818-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/10/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Burkholderia pyrrocinia strain P10 is a plant growth-promoting rhizobacterium (PGPR) that can substantially increase peanut growth. However, the mechanisms and pathways involved in the interaction between B. pyrrocinia P10 and peanut remain unclear. To clarify complex plant-PGPR interactions and the growth-promoting effects of PGPR strains, the B. pyrrocinia P10 transcriptome changes in response to the peanut root exudate (RE) were elucidated and the effects of RE components on biofilm formation and indole-3-acetic acid (IAA) secretion were analyzed. RESULTS During the early interaction phase, the peanut RE enhanced the transport and metabolism of nutrients, including carbohydrates, amino acids, nitrogen, and sulfur. Although the expression of flagellar assembly-related genes was down-regulated, the expression levels of other genes involved in biofilm formation, quorum sensing, and Type II, III, and VI secretion systems were up-regulated, thereby enabling strain P10 to outcompete other microbes to colonize the peanut rhizosphere. The peanut RE also improved the plant growth-promoting effects of strain P10 by activating the expression of genes associated with siderophore biosynthesis, IAA production, and phosphorus solubilization. Additionally, organic acids and amino acids were identified as the dominant components in the peanut RE. Furthermore, strain P10 biofilm formation was induced by malic acid, oxalic acid, and citric acid, whereas IAA secretion was promoted by the alanine, glycine, and proline in the peanut RE. CONCLUSION The peanut RE positively affects B. pyrrocinia P10 growth, while also enhancing colonization and growth-promoting effects during the early interaction period. These findings may help to elucidate the mechanisms underlying complex plant-PGPR interactions, with potential implications for improving the applicability of PGPR strains.
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Affiliation(s)
- Lizhen Han
- College of Life Sciences, Guizhou University, 550025, Guiyang, Guizhou, China.
| | - Hong Zhang
- College of Life Sciences, Guizhou University, 550025, Guiyang, Guizhou, China
| | - Xue Bai
- College of Life Sciences, Guizhou University, 550025, Guiyang, Guizhou, China
| | - Biao Jiang
- College of Life Sciences, Guizhou University, 550025, Guiyang, Guizhou, China
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5
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Velando F, Matilla MA, Zhulin IB, Krell T. Three unrelated chemoreceptors provide Pectobacterium atrosepticum with a broad-spectrum amino acid sensing capability. Microb Biotechnol 2023. [PMID: 36965186 DOI: 10.1111/1751-7915.14255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/27/2023] Open
Abstract
Amino acids are important nutrients and also serve as signals for diverse signal transduction pathways. Bacteria use chemoreceptors to recognize amino acid attractants and to navigate their gradients. In Escherichia coli two likely paralogous chemoreceptors Tsr and Tar detect 9 amino acids, whereas in Pseudomonas aeruginosa the paralogous chemoreceptors PctA, PctB and PctC detect 18 amino acids. Here, we show that the phytobacterium Pectobacterium atrosepticum uses the three non-homologous chemoreceptors PacA, PacB and PacC to detect 19 proteinogenic and several non-proteinogenic amino acids. PacB recognizes 18 proteinogenic amino acids as well as 8 non-proteinogenic amino acids. PacB has a ligand preference for the three branched chain amino acids L-leucine, L-valine and L-isoleucine. PacA detects L-proline next to several quaternary amines. The third chemoreceptor, PacC, is an ortholog of E. coli Tsr and the only one of the 36 P. atrosepticum chemoreceptors that is encoded in the cluster of chemosensory pathway genes. Surprisingly, in contrast to Tsr, which primarily senses serine, PacC recognizes aspartate as the major chemoeffector but not serine. Our results demonstrate that bacteria use various strategies to sense a wide range of amino acids and that it takes more than one chemoreceptor to achieve this goal.
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Affiliation(s)
- Félix Velando
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Miguel A Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Igor B Zhulin
- Department of Microbiology and Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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6
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Matilla MA, Monteagudo-Cascales E, Cerna-Vargas JP, Gumerov VM, Zhulin IB, Krell T. Is it possible to predict signal molecules that are recognized by bacterial receptors? Environ Microbiol 2023; 25:11-16. [PMID: 36054735 PMCID: PMC9851934 DOI: 10.1111/1462-2920.16143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 01/22/2023]
Affiliation(s)
- Miguel A. Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Jean Paul Cerna-Vargas
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Vadim M. Gumerov
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
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7
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Taha, Elgamoudi BA, Andrianova EP, Haselhorst T, Day CJ, Hartley-Tassell LE, King RM, Najnin T, Zhulin IB, Korolik V. Diverse Sensory Repertoire of Paralogous Chemoreceptors Tlp2, Tlp3, and Tlp4 in Campylobacter jejuni. Microbiol Spectr 2022; 10:e0364622. [PMID: 36374080 PMCID: PMC9769880 DOI: 10.1128/spectrum.03646-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Campylobacter jejuni responds to extracellular stimuli via transducer-like chemoreceptors (Tlps). Here, we describe receptor-ligand interactions of a unique paralogue family of dCache_1 (double Calcium channels and chemotaxis) chemoreceptors: Tlp2, Tlp3, and Tlp4. Phylogenetic analysis revealed that Tlp2, Tlp3, and Tlp4 receptors may have arisen through domain duplications, followed by a divergent evolutionary drift, with Tlp3 emerging more recently, and unexpectedly, responded to glycans, as well as multiple organic and amino acids with overlapping specificities. All three Tlps interacted with five monosaccharides and complex glycans, including Lewis's antigens, P antigens, and fucosyl GM1 ganglioside, indicating a potential role in host-pathogen interactions. Analysis of chemotactic motility of single, double, and triple mutants indicated that these chemoreceptors are likely to work together to balance responses to attractants and repellents to modulate chemotaxis in C. jejuni. Molecular docking experiments, in combination with saturation transfer difference nuclear magnetic resonance spectroscopy and competition surface plasmon resonance analysis, illustrated that the ligand-binding domain of Tlp3 possess one major binding pocket with two overlapping, but distinct binding sites able to interact with multiple ligands. A diverse sensory repertoire could provide C. jejuni with the ability to modulate responses to attractant and repellent signals and allow for adaptation in host-pathogen interactions. IMPORTANCE Campylobacter jejuni responds to extracellular stimuli via transducer-like chemoreceptors (Tlps). This remarkable sensory perception mechanism allows bacteria to sense environmental changes and avoid unfavorable conditions or to maneuver toward nutrient sources and host cells. Here, we describe receptor-ligand interactions of a unique paralogue family of chemoreceptors, Tlp2, Tlp3, and Tlp4, that may have arisen through domain duplications, followed by a divergent evolutionary drift, with Tlp3 emerging more recently. Unlike previous reports of ligands interacting with sensory proteins, Tlp2, Tlp3, and Tlp4 responded to many types of chemical compounds, including simple and complex sugars such as those present on human blood group antigens and gangliosides, indicating a potential role in host-pathogen interactions. Diverse sensory repertoire could provide C. jejuni with the ability to modulate responses to attractant and repellent signals and allow for adaptation in host-pathogen interactions.
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Affiliation(s)
- Taha
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Bassam A. Elgamoudi
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Ekaterina P. Andrianova
- Department of Microbiology and Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Christopher J. Day
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | | | - Rebecca M. King
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Tahria Najnin
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Igor B. Zhulin
- Department of Microbiology and Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Victoria Korolik
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
- School of Pharmacy and Medical Science, Griffith University, Gold Coast, Queensland, Australia
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8
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Matilla MA, Velando F, Martín-Mora D, Monteagudo-Cascales E, Krell T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol Rev 2021; 46:6356564. [PMID: 34424339 DOI: 10.1093/femsre/fuab043] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria have evolved many different signal transduction systems that sense signals and generate a variety of responses. Generally, most abundant are transcriptional regulators, sensor histidine kinases and chemoreceptors. Typically, these systems recognize their signal molecules with dedicated ligand-binding domains (LBDs), which, in turn, generate a molecular stimulus that modulates the activity of the output module. There are an enormous number of different LBDs that recognize a similarly diverse set of signals. To give a global perspective of the signals that interact with transcriptional regulators, sensor kinases and chemoreceptors, we manually retrieved information on the protein-ligand interaction from about 1,200 publications and 3D structures. The resulting 811 proteins were classified according to the Pfam family into 127 groups. These data permit a delineation of the signal profiles of individual LBD families as well as distinguishing between families that recognize signals in a promiscuous manner and those that possess a well-defined ligand range. A major bottleneck in the field is the fact that the signal input of many signaling systems is unknown. The signal repertoire reported here will help the scientific community design experimental strategies to identify the signaling molecules for uncharacterised sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
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9
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Noman M, Ahmed T, Ijaz U, Shahid M, Azizullah, Li D, Manzoor I, Song F. Plant-Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants. Int J Mol Sci 2021; 22:6852. [PMID: 34202205 PMCID: PMC8269294 DOI: 10.3390/ijms22136852] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023] Open
Abstract
Plants host diverse but taxonomically structured communities of microorganisms, called microbiome, which colonize various parts of host plants. Plant-associated microbial communities have been shown to confer multiple beneficial advantages to their host plants, such as nutrient acquisition, growth promotion, pathogen resistance, and environmental stress tolerance. Systematic studies have provided new insights into the economically and ecologically important microbial communities as hubs of core microbiota and revealed their beneficial impacts on the host plants. Microbiome engineering, which can improve the functional capabilities of native microbial species under challenging agricultural ambiance, is an emerging biotechnological strategy to improve crop yield and resilience against variety of environmental constraints of both biotic and abiotic nature. This review highlights the importance of indigenous microbial communities in improving plant health under pathogen-induced stress. Moreover, the potential solutions leading towards commercialization of proficient bioformulations for sustainable and improved crop production are also described.
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Affiliation(s)
- Muhammad Noman
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.N.); (T.A.); (U.I.); (A.); (D.L.)
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.N.); (T.A.); (U.I.); (A.); (D.L.)
| | - Usman Ijaz
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.N.); (T.A.); (U.I.); (A.); (D.L.)
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan;
| | - Azizullah
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.N.); (T.A.); (U.I.); (A.); (D.L.)
| | - Dayong Li
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.N.); (T.A.); (U.I.); (A.); (D.L.)
| | - Irfan Manzoor
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; or
| | - Fengming Song
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (M.N.); (T.A.); (U.I.); (A.); (D.L.)
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10
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Compton KK, Scharf BE. Rhizobial Chemoattractants, the Taste and Preferences of Legume Symbionts. FRONTIERS IN PLANT SCIENCE 2021; 12:686465. [PMID: 34017351 PMCID: PMC8129513 DOI: 10.3389/fpls.2021.686465] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 05/21/2023]
Abstract
The development of host-microbe interactions between legumes and their cognate rhizobia requires localization of the bacteria to productive sites of initiation on the plant roots. This end is achieved by the motility apparatus that propels the bacterium and the chemotaxis system that guides it. Motility and chemotaxis aid rhizobia in their competitiveness for space, resources, and nodulation opportunities. Here, we examine studies on chemotaxis of three major model rhizobia, namely Sinorhizobium meliloti, Rhizobium leguminosarum, and Bradyrhizobium japonicum, cataloging their range of attractant molecules and correlating this in the context of root and seed exudate compositions. Current research areas will be summarized, gaps in knowledge discussed, and future directions described.
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Affiliation(s)
| | - Birgit E. Scharf
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, United States
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11
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A Medicago truncatula Metabolite Atlas Enables the Visualization of Differential Accumulation of Metabolites in Root Tissues. Metabolites 2021; 11:metabo11040238. [PMID: 33924579 PMCID: PMC8068785 DOI: 10.3390/metabo11040238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022] Open
Abstract
Plant roots are composed of many differentiated tissue types, with each tissue exhibiting differential quantitative and qualitative accumulation of metabolites. The large-scale nontargeted metabolite profiles of these differentiated tissues are complex, which complicates the interpretation and development of hypotheses relative to the biological roles of differentially localized metabolites. Thus, we created a data visualization tool to aid in the visualization and understanding of differential metabolite accumulations in Medicago truncatula roots. This was achieved through the development of the Medicago truncatula Metabolite Atlas based upon an adaptation of the Arabidopsis Electronic Fluorescent Pictograph (eFP) Browser. Medicago truncatula roots were dissected into border cells, root cap, elongation zone, mature root, and root secretions. Each tissue was then analyzed by UHPLC-QTOF-MS and GC-Q-MS. Data were uploaded into a MySQL database and displayed in the Medicago truncatula Metabolite Atlas. The data revealed unique differential spatial localization of many metabolites, some of which are discussed here. Ultimately, the Medicago truncatula Metabolite Atlas compiles metabolite data into a singular, useful, and publicly available web-based tool that enables the visualization and understanding of differential metabolite accumulation and spatial localization.
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12
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Kraut-Cohen J, Shapiro OH, Dror B, Cytryn E. Pectin Induced Colony Expansion of Soil-Derived Flavobacterium Strains. Front Microbiol 2021; 12:651891. [PMID: 33889143 PMCID: PMC8056085 DOI: 10.3389/fmicb.2021.651891] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/22/2021] [Indexed: 11/20/2022] Open
Abstract
The genus Flavobacterium is characterized by the capacity to metabolize complex organic compounds and a unique gliding motility mechanism. Flavobacteria are often abundant in root microbiomes of various plants, but the factors contributing to this high abundance are currently unknown. In this study, we evaluated the effect of various plant-associated poly- and mono-saccharides on colony expansion of two Flavobacterium strains. Both strains were able to spread on pectin and other polysaccharides such as microcrystalline cellulose. However, only pectin (but not pectin monomers), a component of plant cell walls, enhanced colony expansion on solid surfaces in a dose- and substrate-dependent manner. On pectin, flavobacteria exhibited bi-phasic motility, with an initial phase of rapid expansion, followed by growth within the colonized area. Proteomic and gene expression analyses revealed significant induction of carbohydrate metabolism related proteins when flavobacteria were grown on pectin, including selected SusC/D, TonB-dependent glycan transport operons. Our results show a positive correlation between colony expansion and the upregulation of proteins involved in sugar uptake, suggesting an unknown linkage between specific operons encoding for glycan uptake and metabolism and flavobacterial expansion. Furthermore, within the context of flavobacterial-plant interactions, they suggest that pectin may facilitate flavobacterial expansion on plant surfaces in addition to serving as an essential carbon source.
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Affiliation(s)
- Judith Kraut-Cohen
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Orr H Shapiro
- Institute of Postharvest and Food Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Barak Dror
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel.,Department of Plant Pathology and Microbiology, The R.H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
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Fagorzi C, Bacci G, Huang R, Cangioli L, Checcucci A, Fini M, Perrin E, Natali C, diCenzo GC, Mengoni A. Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis. mSystems 2021. [PMID: 33436514 DOI: 10.1101/2020.06.15.152710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
Rhizobia are ecologically important, facultative plant-symbiotic microbes. In nature, there is a large variability in the association of rhizobial strains and host plants of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of a host plant. RNA sequencing of the model rhizobium Sinorhizobium meliloti exposed to root exudates or luteolin (an inducer of nod genes, involved in the early steps of symbiotic interaction) was performed on a combination of three S. meliloti strains and three alfalfa varieties as host plants. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, 35% were influenced by the strain genotype, 16% were influenced by the plant genotype, and 29% were influenced by strain-by-host plant genotype interactions. We also examined the response of a hybrid S. meliloti strain in which the symbiotic megaplasmid (∼20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes were upregulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes are influenced by the genotypes of both symbiotic partners and their interaction, suggesting a wide spectrum of genetic determinants involved in the phenotypic variation of plant-rhizobium symbiosis.IMPORTANCE A sustainable way for meeting the need of an increased global food demand should be based on a holobiont perspective, viewing crop plants as intimately associated with their microbiome, which helps improve plant nutrition, tolerance to pests, and adverse climate conditions. However, the genetic repertoire needed for efficient association with plants by the microbial symbionts is still poorly understood. The rhizobia are an exemplary model of facultative plant symbiotic microbes. Here, we evaluated whether genotype-by-genotype interactions could be identified in the initial transcriptional response of rhizobium perception of a host plant. We performed an RNA sequencing study to analyze the transcriptomes of different rhizobial strains elicited by root exudates of three alfalfa varieties as a proxy of an early step of the symbiotic interaction. The results indicated strain- and plant variety-dependent variability in the observed transcriptional changes, providing fundamentally novel insights into the genetic basis of rhizobium-plant interactions. Our results provide genetic insights and perspective to aid in the exploitation of natural rhizobium variation for improvement of legume growth in agricultural ecosystems.
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Affiliation(s)
- Camilla Fagorzi
- Department of Biology, University of Florence, Florence, Italy
| | - Giovanni Bacci
- Department of Biology, University of Florence, Florence, Italy
| | - Rui Huang
- Department of Biology, Queen's University, Kingston, Ontario, Canada
| | - Lisa Cangioli
- Department of Biology, University of Florence, Florence, Italy
| | - Alice Checcucci
- Department of Biology, University of Florence, Florence, Italy
| | - Margherita Fini
- Department of Biology, University of Florence, Florence, Italy
| | - Elena Perrin
- Department of Biology, University of Florence, Florence, Italy
| | - Chiara Natali
- Department of Biology, University of Florence, Florence, Italy
| | | | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
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Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis. mSystems 2021; 6:6/1/e00974-20. [PMID: 33436514 PMCID: PMC7901481 DOI: 10.1128/msystems.00974-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Rhizobia are ecologically important, facultative plant-symbiotic microbes. In nature, there is a large variability in the association of rhizobial strains and host plants of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of a host plant. RNA sequencing of the model rhizobium Sinorhizobium meliloti exposed to root exudates or luteolin (an inducer of nod genes, involved in the early steps of symbiotic interaction) was performed on a combination of three S. meliloti strains and three alfalfa varieties as host plants. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, 35% were influenced by the strain genotype, 16% were influenced by the plant genotype, and 29% were influenced by strain-by-host plant genotype interactions. We also examined the response of a hybrid S. meliloti strain in which the symbiotic megaplasmid (∼20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes were upregulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes are influenced by the genotypes of both symbiotic partners and their interaction, suggesting a wide spectrum of genetic determinants involved in the phenotypic variation of plant-rhizobium symbiosis.IMPORTANCE A sustainable way for meeting the need of an increased global food demand should be based on a holobiont perspective, viewing crop plants as intimately associated with their microbiome, which helps improve plant nutrition, tolerance to pests, and adverse climate conditions. However, the genetic repertoire needed for efficient association with plants by the microbial symbionts is still poorly understood. The rhizobia are an exemplary model of facultative plant symbiotic microbes. Here, we evaluated whether genotype-by-genotype interactions could be identified in the initial transcriptional response of rhizobium perception of a host plant. We performed an RNA sequencing study to analyze the transcriptomes of different rhizobial strains elicited by root exudates of three alfalfa varieties as a proxy of an early step of the symbiotic interaction. The results indicated strain- and plant variety-dependent variability in the observed transcriptional changes, providing fundamentally novel insights into the genetic basis of rhizobium-plant interactions. Our results provide genetic insights and perspective to aid in the exploitation of natural rhizobium variation for improvement of legume growth in agricultural ecosystems.
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15
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Aroney STN, Poole PS, Sánchez-Cañizares C. Rhizobial Chemotaxis and Motility Systems at Work in the Soil. FRONTIERS IN PLANT SCIENCE 2021; 12:725338. [PMID: 34512702 PMCID: PMC8429497 DOI: 10.3389/fpls.2021.725338] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/06/2021] [Indexed: 05/17/2023]
Abstract
Bacteria navigate their way often as individual cells through their chemical and biological environment in aqueous medium or across solid surfaces. They swim when starved or in response to physical and chemical stimuli. Flagella-driven chemotaxis in bacteria has emerged as a paradigm for both signal transduction and cellular decision-making. By altering motility, bacteria swim toward nutrient-rich environments, movement modulated by their chemotaxis systems with the addition of pili for surface movement. The numbers and types of chemoreceptors reflect the bacterial niche and lifestyle, with those adapted to complex environments having diverse metabolic capabilities, encoding far more chemoreceptors in their genomes. The Alpha-proteobacteria typify the latter case, with soil bacteria such as rhizobia, endosymbionts of legume plants, where motility and chemotaxis are essential for competitive symbiosis initiation, among other processes. This review describes the current knowledge of motility and chemotaxis in six model soil bacteria: Sinorhizobium meliloti, Agrobacterium fabacearum, Rhizobium leguminosarum, Azorhizobium caulinodans, Azospirillum brasilense, and Bradyrhizobium diazoefficiens. Although motility and chemotaxis systems have a conserved core, rhizobia possess several modifications that optimize their movements in soil and root surface environments. The soil provides a unique challenge for microbial mobility, since water pathways through particles are not always continuous, especially in drier conditions. The effectiveness of symbiont inoculants in a field context relies on their mobility and dispersal through the soil, often assisted by water percolation or macroorganism movement or networks. Thus, this review summarizes the factors that make it essential to consider and test rhizobial motility and chemotaxis for any potential inoculant.
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Compton KK, Hildreth SB, Helm RF, Scharf BE. An Updated Perspective on Sinorhizobium meliloti Chemotaxis to Alfalfa Flavonoids. Front Microbiol 2020; 11:581482. [PMID: 33193213 PMCID: PMC7644916 DOI: 10.3389/fmicb.2020.581482] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/30/2020] [Indexed: 12/25/2022] Open
Abstract
The symbiotic interaction between leguminous plants and their cognate rhizobia allows for the fixation of gaseous dinitrogen into bioavailable ammonia. The perception of host-derived flavonoids is a key initial step for the signaling events that must occur preceding the formation of the nitrogen-fixing organ. Past work investigating chemotaxis – the directed movement of bacteria through chemical gradients – of Bradyrhizobium japonicum, Rhizobium leguminosarum, and Rhizobium meliloti discovered chemotaxis to various organic compounds, but focused on chemotaxis to flavonoids because of their relevance to the symbiosis biochemistry. The current work sought to replicate and further examine Sinorhizobium (Ensifer) meliloti chemotaxis to the flavonoids previously thought to act as the principal attractant molecules prior to the initial signaling stage. Exudate from germinating alfalfa seedlings was analyzed for composition and quantities of different flavonoid compounds using mass spectrometry. The abundance of four prevalent flavonoids in germinating alfalfa seed exudates (SEs) was at a ratio of 200:5:5:1 for hyperoside, luteolin, luteolin-7-glucoside, and chrysoeriol. Using quantitative chemotaxis capillary assays, we did not detect chemotaxis of motile S. meliloti cells to these, and two other flavonoids identified in seed exudates. In support of these findings, the flavonoid fraction of seed exudates was found to be an insignificant attractant relative to the more hydrophilic fraction. Additionally, we observed that cosolvents commonly used to dissolve flavonoids confound the results. We propose that the role flavonoids play in S. meliloti chemotaxis is insignificant relative to other components released by alfalfa seeds.
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Affiliation(s)
- K Karl Compton
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, United States
| | - Sherry B Hildreth
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, United States
| | - Richard F Helm
- Department of Biochemistry, Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, United States
| | - Birgit E Scharf
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, United States
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Programmed Proteolysis of Chemotaxis Proteins in Sinorhizobium meliloti: Features in the C-Terminal Region Control McpU Degradation. J Bacteriol 2020; 202:JB.00124-20. [PMID: 32571966 DOI: 10.1128/jb.00124-20] [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: 03/09/2020] [Accepted: 06/12/2020] [Indexed: 11/20/2022] Open
Abstract
Chemotaxis and motility are important traits that support bacterial survival in various ecological niches and in pathogenic and symbiotic host interaction. Chemotactic stimuli are sensed by chemoreceptors or methyl-accepting chemotaxis proteins (MCPs), which direct the swimming behavior of the bacterial cell. In this study, we present evidence that the cellular abundance of chemoreceptors in the plant symbiont Sinorhizobium meliloti can be altered by the addition of several to as few as one amino acid residues and by including common epitope tags such as 3×FLAG and 6×His at their C termini. To further dissect this phenomenon and its underlying molecular mechanism, we focused on a detailed analysis of the amino acid sensor McpU. Controlled proteolysis is important for the maintenance of an appropriate stoichiometry of chemoreceptors and between chemoreceptors and chemotactic signaling proteins, which is essential for an optimal chemotactic response. We hypothesized that enhanced stability is due to interference with protease binding, thus affecting proteolytic efficacy. Location of the protease recognition site was defined through McpU stability measurements in a series of deletion and amino acid substitution mutants. Deletions in the putative protease recognition site had similar effects on McpU abundance, as did extensions at the C terminus. Our results provide evidence that the programmed proteolysis of chemotaxis proteins in S. meliloti is cell cycle regulated. This posttranslational control, together with regulatory pathways on the transcriptional level, limits the chemotaxis machinery to the early exponential growth phase. Our study identified parallels to cell cycle-dependent processes during asymmetric cell division in Caulobacter crescentus IMPORTANCE The symbiotic bacterium Sinorhizobium meliloti contributes greatly to growth of the agriculturally valuable host plant alfalfa by fixing atmospheric nitrogen. Chemotaxis of S. meliloti cells toward alfalfa roots mediates this symbiosis. The present study establishes programmed proteolysis as a factor in the maintenance of the S. meliloti chemotaxis system. Knowledge about cell cycle-dependent, targeted, and selective proteolysis in S. meliloti is important to understand the molecular mechanisms of maintaining a suitable chemotaxis response. While the role of regulated protein turnover in the cell cycle progression of Caulobacter crescentus is well understood, these pathways are just beginning to be characterized in S. meliloti In addition, our study should alert about the cautionary use of epitope tags for protein quantification.
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Tsai AYL, Oota M, Sawa S. Chemotactic Host-Finding Strategies of Plant Endoparasites and Endophytes. FRONTIERS IN PLANT SCIENCE 2020; 11:1167. [PMID: 32849722 PMCID: PMC7411241 DOI: 10.3389/fpls.2020.01167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/20/2020] [Indexed: 05/04/2023]
Abstract
Plants interact with microorganisms in the environment during all stages of their development and in most of their organs. These interactions can be either beneficial or detrimental for the plant and may be transient or long-term. In extreme cases, microorganisms become endoparastic or endophytic and permanently reside within a plant, while the host plant undergoes developmental reprogramming and produces new tissues or organs as a response to the invasion. Events at the cellular and molecular level following infection have been extensively described, however the mechanisms of how these microorganisms locate their plant hosts via chemotaxis remain largely unknown. In this review, we summarize recent findings concerning the signalling molecules that regulate chemotaxis of endoparasitic/endophytic bacteria, fungi, and nematodes. In particular, we will focus on the molecules secreted by plants that are most likely to act as guidance cues for microorganisms. These compounds are found in a wide range of plant species and show a variety of secondary effects. Interestingly, these compounds show different attraction potencies depending on the species of the invading organism, suggesting that cues perceived in the soil may be more complex than anticipated. However, what the cognate receptors are for these attractants, as well as the mechanism of how these attractants influence these organisms, remain important outstanding questions. Host-targeting marks the first step of plant-microorganism interactions, therefore understanding the signalling molecules involved in this step plays a key role in understanding these interactions as a whole.
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Arapov TD, Saldaña RC, Sebastian AL, Ray WK, Helm RF, Scharf BE. Cellular Stoichiometry of Chemotaxis Proteins in Sinorhizobium meliloti. J Bacteriol 2020; 202:e00141-20. [PMID: 32393521 PMCID: PMC7317046 DOI: 10.1128/jb.00141-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/05/2020] [Indexed: 11/20/2022] Open
Abstract
Chemotaxis systems enable microbes to sense their immediate environment, moving toward beneficial stimuli and away from those that are harmful. In an effort to better understand the chemotaxis system of Sinorhizobium meliloti, a symbiont of the legume alfalfa, the cellular stoichiometries of all ten chemotaxis proteins in S. meliloti were determined. A combination of quantitative immunoblot and mass spectrometry revealed that the protein stoichiometries in S. meliloti varied greatly from those in Escherichia coli and Bacillus subtilis To compare protein ratios to other systems, values were normalized to the central kinase CheA. All S. meliloti chemotaxis proteins exhibited increased ratios to various degrees. The 10-fold higher molar ratio of adaptor proteins CheW1 and CheW2 to CheA might result in the formation of rings in the chemotaxis array that consist of only CheW instead of CheA and CheW in a 1:1 ratio. We hypothesize that the higher ratio of CheA to the main response regulator CheY2 is a consequence of the speed-variable motor in S. meliloti, instead of a switch-type motor. Similarly, proteins involved in signal termination are far more abundant in S. meliloti, which utilizes a phosphate sink mechanism based on CheA retrophosphorylation to inactivate the motor response regulator versus CheZ-catalyzed dephosphorylation as in E. coli and B. subtilis Finally, the abundance of CheB and CheR, which regulate chemoreceptor methylation, was increased compared to CheA, indicative of variations in the adaptation system of S. meliloti Collectively, these results mark significant differences in the composition of bacterial chemotaxis systems.IMPORTANCE The symbiotic soil bacterium Sinorhizobium meliloti contributes greatly to host-plant growth by fixing atmospheric nitrogen. The provision of nitrogen as ammonium by S. meliloti leads to increased biomass production of its legume host alfalfa and diminishes the use of environmentally harmful chemical fertilizers. To better understand the role of chemotaxis in host-microbe interaction, a comprehensive catalogue of the bacterial chemotaxis system is vital, including its composition, function, and regulation. The stoichiometry of chemotaxis proteins in S. meliloti has very few similarities to the systems in Escherichia coli and Bacillus subtilis In addition, total amounts of proteins are significantly lower. S. meliloti exhibits a chemotaxis system distinct from known models by incorporating new proteins as exemplified by the phosphate sink mechanism.
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Affiliation(s)
- Timofey D Arapov
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Amanda L Sebastian
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - W Keith Ray
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Birgit E Scharf
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
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20
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Hida A, Oku S, Miura M, Matsuda H, Tajima T, Kato J. Characterization of methyl-accepting chemotaxis proteins (MCPs) for amino acids in plant-growth-promoting rhizobacterium Pseudomonas protegens CHA0 and enhancement of amino acid chemotaxis by MCP genes overexpression. Biosci Biotechnol Biochem 2020; 84:1948-1957. [PMID: 32538292 DOI: 10.1080/09168451.2020.1780112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Pseudomonas protegens CHA0, known as plant-growth-promoting rhizobacterium, showed positive chemotactic responses toward proteinaceous L-amino acids. Genomic analysis revealed that P. protegens CHA0 possesses four putative chemoreceptors for amino acids (designated CtaA, CtaB, CtaC, and CtaD, respectively). Pseudomonas aeruginosa PCT2, a mutant defective in chemotaxis to amino acids, harboring a plasmid containing each of ctaA, ctaB, ctaC, and ctaD showed chemotactic responses to 20, 4, 4, and 11 types of amino acids, respectively. To enhance chemotaxis toward amino acids, we introduced the plasmids containing ctaA, ctaB, ctaC, or ctaD into P. protegens CHA0. By overexpression of the genes, we succeeded in enhancing chemotaxis toward more than half of the tested ligands. However, unexpectedly, the P. protegens CHA0 transformants showed unchanged or decreased responses to some amino acids when compared to wild-type CHA0. We speculate that alternation of expression of a chemoreceptor may affect the abundance of other chemoreceptors. ABBREVIATIONS cDNA: complementary DNA; LBD: ligand-binding domain; MCP: methyl-accepting chemotaxis protein; PDC: PhoQ/DcuS/CitA; PGPR: plant-growth-promoting rhizobacteria; qRT-PCR: quantitative reverse transcription PCR.
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Affiliation(s)
- Akiko Hida
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University , Hiroshima, Japan
| | - Shota Oku
- Global Career Design Center, Hiroshima University , Higashi-Hiroshima, Japan
| | - Manami Miura
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University , Hiroshima, Japan
| | - Hiroki Matsuda
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University , Hiroshima, Japan
| | - Takahisa Tajima
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University , Hiroshima, Japan
| | - Junichi Kato
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University , Hiroshima, Japan
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Matilla MA, Martín-Mora D, Krell T. The use of isothermal titration calorimetry to unravel chemotactic signalling mechanisms. Environ Microbiol 2020; 22:3005-3019. [PMID: 32329116 DOI: 10.1111/1462-2920.15035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022]
Abstract
Chemotaxis is based on the action of chemosensory pathways and is typically initiated by the recognition of chemoeffectors at chemoreceptor ligand-binding domains (LBD). Chemosensory signalling is highly complex; aspect that is not only reflected in the intricate interaction between many signalling proteins but also in the fact that bacteria frequently possess multiple chemosensory pathways and often a large number of chemoreceptors, which are mostly of unknown function. We review here the usefulness of isothermal titration calorimetry (ITC) to study this complexity. ITC is the gold standard for studying binding processes due to its precision and sensitivity, as well as its capability to determine simultaneously the association equilibrium constant, enthalpy change and stoichiometry of binding. There is now evidence that members of all major LBD families can be produced as individual recombinant proteins that maintain their ligand-binding properties. High-throughput screening of these proteins using thermal shift assays offer interesting initial information on chemoreceptor ligands, providing the basis for microcalorimetric analyses and microbiological experimentation. ITC has permitted the identification and characterization of many chemoreceptors with novel specificities. This ITC-based approach can also be used to identify signal molecules that stimulate members of other families of sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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22
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Ud-Din AIMS, Khan MF, Roujeinikova A. Broad Specificity of Amino Acid Chemoreceptor CtaA of Pseudomonas fluorescens Is Afforded by Plasticity of Its Amphipathic Ligand-Binding Pocket. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:612-623. [PMID: 31909676 DOI: 10.1094/mpmi-10-19-0277-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Motile bacteria follow gradients of nutrients or other environmental cues. Many bacterial chemoreceptors that sense exogenous amino acids contain a double Cache (dCache; calcium channels and chemotaxis receptors) ligand-binding domain (LBD). A growing number of studies suggest that broad-specificity dCache-type receptors that sense more than one amino acid are common. Here, we present an investigation into the mechanism by which the dCache LBD of the chemoreceptor CtaA from a plant growth-promoting rhizobacterium, Pseudomonas fluorescens, recognizes several chemically distinct amino acids. We established that amino acids that signal by directly binding to the CtaA LBD include ones with aliphatic (l-alanine, l-proline, l-leucine, l-isoleucine, l-valine), small polar (l-serine), and large charged (l-arginine) side chains. We determined the structure of CtaA LBD in complex with different amino acids, revealing that its ability to recognize a range of structurally and chemically distinct amino acids is afforded by its easily accessible plastic pocket, which can expand or contract according to the size of the ligand side chain. The amphipathic character of the pocket enables promiscuous interactions with both polar and nonpolar amino acids. The results not only clarify the means by which various amino acids are recognized by CtaA but also reveal that a conserved mobile lid over the ligand-binding pocket adopts the same conformation in all complexes, consistent with this being an important and invariant part of the signaling mechanism.
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Affiliation(s)
- Abu I M S Ud-Din
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Australia, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Mohammad F Khan
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Australia, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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23
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Liu R, Li L, Li Z, Wang W. Impact of Hydrogen on the Transcriptome of Sinorhizobium meliloti 1021 Using RNA-sequencing Technology. Pol J Microbiol 2020; 69:1-10. [PMID: 32067442 PMCID: PMC7256871 DOI: 10.33073/pjm-2020-006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/11/2020] [Accepted: 01/12/2020] [Indexed: 11/05/2022] Open
Abstract
Hydrogen formed during nitrogen fixation in legumes can enter the surrounding soil and confer multiple benefits to crops. Here, we used Sinorhizobium meliloti 1021, whose genome was sequenced in 2001, as a model bacterium to study the relationship between the bacterium and legume. We investigated the effects of hydrogen on the gene expression in S. meliloti using RNA-sequencing technology. We identified 43 genes whose expression was altered by hydrogen treatment; among these, 39 were downregulated, and 4 were upregulated. These genes accounted for 1.5% of the total 2941 annotated genes of the S. meliloti genome. Gene ontology and pathway analyses revealed that the hydrogen-regulated genes were associated with catalytic activity and binding. Further, these genes were primarily involved in arginine, proline, and β-alanine metabolism. Real-time PCR revealed that the transcription levels of SMc02983, cyoB, cyoC, and cyoD were reduced after hydrogen treatment. These results provide a theoretical framework for exploring new metabolic pathways of S. meliloti.
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Affiliation(s)
- Ruirui Liu
- The College of Life Sciences , Northwest University , Xi'an, P.R. China Key Laboratory of Resource Biology and Biotechnology in Western China , Northwest University , Xi'an , P.R. China
| | - Lulu Li
- The College of Life Sciences , Northwest University , Xi'an, P.R. China Key Laboratory of Resource Biology and Biotechnology in Western China , Northwest University , Xi'an , P.R. China
| | - Zhiying Li
- The College of Life Sciences , Northwest University , Xi'an, P.R. China Key Laboratory of Resource Biology and Biotechnology in Western China , Northwest University , Xi'an , P.R. China
| | - Weiwei Wang
- The College of Life Sciences , Northwest University , Xi'an, P.R. China Key Laboratory of Resource Biology and Biotechnology in Western China , Northwest University , Xi'an , P.R. China
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Abstract
Many bacteria possess a large number of chemoreceptors that recognize a variety of different compounds. More than 60% of the genomes analyzed in this study contain paralogous chemoreceptors, suggesting that they emerge with high frequency. We provide first insight on how paralogous receptors have evolved and show that two chemoreceptors with a narrow ligand range have evolved from an ancestral protein with a broad chemoeffector spectrum. Protein structures show that multiple changes in the ligand-binding site account for the differences in the ligand spectrum. This work lays the ground for further studies aimed at establishing whether the principles of ligand-binding evolution reported here can be generalized for a wider spectrum of sensory proteins in bacteria. Chemoreceptor-based signaling pathways are among the major modes of bacterial signal transduction, and Pseudomonas aeruginosa PAO1 is an important model to study their function. Of the 26 chemoreceptors of this strain, PctA has a broad ligand range and responds to most of the proteinogenic amino acids, whereas PctB and PctC have a much narrower range and show strong ligand preference for l-glutamine and γ-aminobutyrate, respectively. Using several comparative genomics approaches, we show that these receptors are paralogs: pctA gene duplication in the common ancestor of the genus Pseudomonas led to pctC, whereas pctB originated through another, independent pctA duplication in the common ancestor of P. aeruginosa. Thus, the broad-range amino acid chemoreceptor was evolutionarily older, and chemoreceptors that complemented “missing” amino acid sensing abilities arose later in specific Pseudomonas lineages. Using comparative sequence analysis, newly solved crystal structures of PctA, PctB, and PctC ligand-binding domains, and their molecular dynamics simulations, we identified a conserved amino acid recognition motif and changes in the ligand-binding pocket that led to novel ligand specificities. In addition, we determined major forces driving the evolution of this group of chemoreceptors.
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Chemoperception of Specific Amino Acids Controls Phytopathogenicity in Pseudomonas syringae pv. tomato. mBio 2019; 10:mBio.01868-19. [PMID: 31575767 PMCID: PMC6775455 DOI: 10.1128/mbio.01868-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
There is substantive evidence that chemotaxis is a key requisite for efficient pathogenesis in plant pathogens. However, information regarding particular bacterial chemoreceptors and the specific plant signal that they sense is scarce. Our work shows that the phytopathogenic bacterium Pseudomonas syringae pv. tomato mediates not only chemotaxis but also the control of pathogenicity through the perception of the plant abundant amino acids Asp and Glu. We describe the specificity of the perception of l- and d-Asp and l-Glu by the PsPto-PscA chemoreceptor and the involvement of this perception in the regulation of pathogenicity-related traits. Moreover, a saturating concentration of d-Asp reduces bacterial virulence, and we therefore propose that ligand-mediated interference of key chemoreceptors may be an alternative strategy to control virulence. Chemotaxis has been associated with the pathogenicity of bacteria in plants and was found to facilitate bacterial entry through stomata and wounds. However, knowledge regarding the plant signals involved in this process is scarce. We have addressed this issue using Pseudomonas syringae pv. tomato, which is a foliar pathogen that causes bacterial speck in tomato. We show that the chemoreceptor P. syringae pv. tomato PscA (PsPto-PscA) recognizes specifically and with high affinity l-Asp, l-Glu, and d-Asp. The mutation of the chemoreceptor gene largely reduced chemotaxis to these ligands but also altered cyclic di-GMP (c-di-GMP) levels, biofilm formation, and motility, pointing to cross talk between different chemosensory pathways. Furthermore, the PsPto-PscA mutant strain showed reduced virulence in tomato. Asp and Glu are the most abundant amino acids in plants and in particular in tomato apoplasts, and we hypothesize that this receptor may have evolved to specifically recognize these compounds to facilitate bacterial entry into the plant. Infection assays with the wild-type strain showed that the presence of saturating concentrations of d-Asp also reduced bacterial virulence.
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Liu X, Xie Z, Wang Y, Sun Y, Dang X, Sun H. A Dual Role of Amino Acids from Sesbania rostrata Seed Exudates in the Chemotaxis Response of Azorhizobium caulinodans ORS571. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1134-1147. [PMID: 30920344 DOI: 10.1094/mpmi-03-19-0059-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Azorhizobium caulinodans ORS571 can induce nodule formation on the roots and the stems of its host legume, Sesbania rostrata. Plant exudates are essential in the dialogue between microbes and their host plant and, in particular, amino acids can play an important role in the chemotactic response of bacteria. Histidine, arginine, and aspartate, which are the three most abundant amino acids present in S. rostrata seed exudates, behave as chemoattractants toward A. caulinodans. A position-specific-iterated BLAST analysis of the methyl-accepting chemotaxis proteins (MCPs) (chemoreceptors) in the genome of A. caulinodans was performed. Among the 43 MCP homologs, two MCPs harboring a dCache domain were selected as possible cognate amino acid MCPs. After analysis of relative gene expression levels and construction of a gene-deleted mutant strain, one of them, AZC_0821 designed as TlpH, was confirmed to be responsible for the chemotactic response to the three amino acids. In addition, it was found that these three amino acids can also influence chemotaxis of A. caulinodans independently of the chemosensory receptors, by being involved in the increase of the expression level of several che and fla genes involved in the chemotaxis pathway and flagella synthesis. Thus, the contribution of amino acids present in seed exudates is directly related to the role as chemoattractants and indirectly related to the role in the regulation of expression of key genes involved in chemotaxis and motility. This "dual role" is likely to influence the formation of biofilms by A. caulinodans and the host root colonization properties of this bacterium.
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Affiliation(s)
- Xiaolin Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhihong Xie
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, People's Republic of China
| | - Yixuan Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yu Sun
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xiaoxiao Dang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Haishuan Sun
- Shandong Huibang Bohai Agriculture Development Limited Company, Dongying, People's Republic of China
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Feng H, Zhang N, Fu R, Liu Y, Krell T, Du W, Shao J, Shen Q, Zhang R. Recognition of dominant attractants by key chemoreceptors mediates recruitment of plant growth-promoting rhizobacteria. Environ Microbiol 2019; 21:402-415. [PMID: 30421582 DOI: 10.1111/1462-2920.14472] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 10/09/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022]
Abstract
Chemotaxis to plant root exudates is supposed to be a prerequisite for efficient root colonization by rhizobacteria. This is a highly multifactorial process since root exudates are complex compound mixtures of which components are recognized by different chemoreceptors. Little information is available as to the key components in root exudates and their receptors that drive colonization related chemotaxis. We present here the first global assessment of this issue using the plant growth-promoting rhizobacterium (PGPR) Bacillus velezensis SQR9 (formerly B. amyloliquefaciens). This strain efficiently colonizes cucumber roots, and here, we show that chemotaxis to cucumber root exudates was essential in this process. We conducted chemotaxis assays using cucumber root exudates at different concentrations, individual exudate components as well as recomposed exudates, taking into account their concentrations detected in root exudates. Results indicated that two key chemoreceptors, McpA and McpC, were essential for root exudate chemotaxis and root colonization. Both receptors possess a broad ligand range and recognize most of the exudate key components identified (malic, fumaric, gluconic and glyceric acids, Lys, Ser, Ala and mannose). The remaining six chemoreceptors did not contribute to exudate chemotaxis. This study provides novel insight into the evolution of the chemotaxis system in rhizobacteria.
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Affiliation(s)
- Haichao Feng
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China.,Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruixin Fu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008, Granada, Spain
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiahui Shao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China.,Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Structure of the sensory domain of McpX from Sinorhizobium meliloti, the first known bacterial chemotactic sensor for quaternary ammonium compounds. Biochem J 2018; 475:3949-3962. [PMID: 30442721 DOI: 10.1042/bcj20180769] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/07/2018] [Accepted: 11/14/2018] [Indexed: 02/01/2023]
Abstract
The α-proteobacterium Sinorhizobium meliloti can live freely in the soil or engage in a symbiosis with its legume host. S. meliloti facilitates nitrogen fixation in root nodules, thus providing pivotal, utilizable nitrogen to the host. The organism has eight chemoreceptors, namely McpT to McpZ and IcpA that facilitate chemotaxis. McpX is the first known bacterial sensor of quaternary ammonium compounds (QACs) such as choline and betaines. Because QACs are exuded at chemotaxis-relevant concentrations by germinating alfalfa seeds, McpX has been proposed to contribute to host-specific chemotaxis. We have determined the crystal structure of the McpX periplasmic region (McpXPR) in complex with the proline betaine at 2.7 Å resolution. In the crystal, the protein forms a symmetric dimer with one proline betaine molecule bound to each monomer of McpXPR within membrane-distal CACHE module. The ligand is bound through cation-πinteractions with four aromatic amino acid residues. Mutational analysis in conjunction with binding studies revealed that a conserved aspartate residue is pivotal for ligand binding. We discovered that, in a striking example of convergent evolution, the ligand-binding site of McpXPR resembles that of a group of structurally unrelated betaine-binding proteins including ProX and OpuAC. Through this comparison and docking studies, we rationalized the specificity of McpXPR for this specific group of ligands. Collectively, our structural, biochemical, and molecular docking data have revealed the molecular determinants in McpX that are crucial for its rare ligand specificity for QACs.
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Martín-Mora D, Fernández M, Velando F, Ortega Á, Gavira JA, Matilla MA, Krell T. Functional Annotation of Bacterial Signal Transduction Systems: Progress and Challenges. Int J Mol Sci 2018; 19:ijms19123755. [PMID: 30486299 PMCID: PMC6321045 DOI: 10.3390/ijms19123755] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/22/2018] [Accepted: 11/22/2018] [Indexed: 01/15/2023] Open
Abstract
Bacteria possess a large number of signal transduction systems that sense and respond to different environmental cues. Most frequently these are transcriptional regulators, two-component systems and chemosensory pathways. A major bottleneck in the field of signal transduction is the lack of information on signal molecules that modulate the activity of the large majority of these systems. We review here the progress made in the functional annotation of sensor proteins using high-throughput ligand screening approaches of purified sensor proteins or individual ligand binding domains. In these assays, the alteration in protein thermal stability following ligand binding is monitored using Differential Scanning Fluorimetry. We illustrate on several examples how the identification of the sensor protein ligand has facilitated the elucidation of the molecular mechanism of the regulatory process. We will also discuss the use of virtual ligand screening approaches to identify sensor protein ligands. Both approaches have been successfully applied to functionally annotate a significant number of bacterial sensor proteins but can also be used to study proteins from other kingdoms. The major challenge consists in the study of sensor proteins that do not recognize signal molecules directly, but that are activated by signal molecule-loaded binding proteins.
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Affiliation(s)
- David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology 'B' and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", 30100 Murcia, Spain.
| | - José A Gavira
- Laboratorio de Estudios Cristalográficos, IACT, (CSIC-UGR), Avenida las Palmeras 4, 18100 Armilla, Spain.
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
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Sinorhizobium meliloti Chemoreceptor McpV Senses Short-Chain Carboxylates via Direct Binding. J Bacteriol 2018; 200:JB.00519-18. [PMID: 30201781 DOI: 10.1128/jb.00519-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 11/20/2022] Open
Abstract
Sinorhizobium meliloti is a soil-dwelling endosymbiont of alfalfa that has eight chemoreceptors to sense environmental stimuli during its free-living state. The functions of two receptors have been characterized, with McpU and McpX serving as general amino acid and quaternary ammonium compound sensors, respectively. Both receptors use a dual Cache (calcium channels and chemotaxis receptors) domain for ligand binding. We identified that the ligand-binding periplasmic region (PR) of McpV contains a single Cache domain. Homology modeling revealed that McpVPR is structurally similar to a sensor domain of a chemoreceptor with unknown function from Anaeromyxobacter dehalogenans, which crystallized with acetate in its binding pocket. We therefore assayed McpV for carboxylate binding and S. meliloti for carboxylate sensing. Differential scanning fluorimetry identified 10 potential ligands for McpVPR Nine of these are monocarboxylates with chain lengths between two and four carbons. We selected seven compounds for capillary assay analysis, which established positive chemotaxis of the S. meliloti wild type, with concentrations of peak attraction at 1 mM for acetate, propionate, pyruvate, and glycolate, and at 100 mM for formate and acetoacetate. Deletion of mcpV or mutation of residues essential for ligand coordination abolished positive chemotaxis to carboxylates. Using microcalorimetry, we determined that dissociation constants of the seven ligands with McpVPR were in the micromolar range. An McpVPR variant with a mutation in the ligand coordination site displayed no binding to isobutyrate or propionate. Of all the carboxylates tested as attractants, only glycolate was detected in alfalfa seed exudates. This work examines the relevance of carboxylates and their sensor to the rhizobium-legume interaction.IMPORTANCE Legumes share a unique association with certain soil-dwelling bacteria known broadly as rhizobia. Through concerted interorganismal communication, a legume allows intracellular infection by its cognate rhizobial species. The plant then forms an organ, the root nodule, dedicated to housing and supplying fixed carbon and nutrients to the bacteria. In return, the engulfed rhizobia, differentiated into bacteroids, fix atmospheric N2 into ammonium for the plant host. This interplay is of great benefit to the cultivation of legumes, such as alfalfa and soybeans, and is initiated by chemotaxis to the host plant. This study on carboxylate chemotaxis contributes to the understanding of rhizobial survival and competition in the rhizosphere and aids the development of commercial inoculants.
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Cellular Stoichiometry of Methyl-Accepting Chemotaxis Proteins in Sinorhizobium meliloti. J Bacteriol 2018; 200:JB.00614-17. [PMID: 29263102 DOI: 10.1128/jb.00614-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/15/2017] [Indexed: 12/29/2022] Open
Abstract
The chemosensory system in Sinorhizobium meliloti has several important deviations from the widely studied enterobacterial paradigm. To better understand the differences between the two systems and how they are optimally tuned, we determined the cellular stoichiometry of the methyl-accepting chemotaxis proteins (MCPs) and the histidine kinase CheA in S. meliloti Quantitative immunoblotting was used to determine the total amount of MCPs and CheA per cell in S. meliloti The MCPs are present in the cell in high abundance (McpV), low abundance (IcpA, McpU, McpX, and McpW), and very low abundance (McpY and McpZ), whereas McpT was below the detection limit. The approximate cellular ratio of these three receptor groups is 300:30:1. The chemoreceptor-to-CheA ratio is 23.5:1, highly similar to that seen in Bacillus subtilis (23:1) and about 10 times higher than that in Escherichia coli (3.4:1). Different from E. coli, the high-abundance receptors in S. meliloti are lacking the carboxy-terminal NWETF pentapeptide that binds the CheR methyltransferase and CheB methylesterase. Using transcriptional lacZ fusions, we showed that chemoreceptors are positively controlled by the master regulators of motility, VisNR and Rem. In addition, FlbT, a class IIA transcriptional regulator of flagellins, also positively regulates the expression of most chemoreceptors except for McpT and McpY, identifying chemoreceptors as class III genes. Taken together, these results demonstrate that the chemosensory complex and the adaptation system in S. meliloti deviates significantly from the established enterobacterial paradigm but shares some similarities with B. subtilisIMPORTANCE The symbiotic soil bacterium Sinorhizobium meliloti is of great agricultural importance because of its nitrogen-fixing properties, which enhances growth of its plant symbiont, alfalfa. Chemotaxis provides a competitive advantage for bacteria to sense their environment and interact with their eukaryotic hosts. For a better understanding of the role of chemotaxis in these processes, detailed knowledge on the regulation and composition of the chemosensory machinery is essential. Here, we show that chemoreceptor gene expression in S. meliloti is controlled through the main transcriptional regulators of motility. Chemoreceptor abundance is much lower in S. meliloti than in Escherichia coli and Bacillus subtilis Moreover, the chemoreceptor-to-kinase CheA ratio is different from that of E. coli but similar to that of B. subtilis.
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Sánchez-Cañizares C, Jorrín B, Durán D, Nadendla S, Albareda M, Rubio-Sanz L, Lanza M, González-Guerrero M, Prieto RI, Brito B, Giglio MG, Rey L, Ruiz-Argüeso T, Palacios JM, Imperial J. Genomic Diversity in the Endosymbiotic Bacterium Rhizobium leguminosarum. Genes (Basel) 2018; 9:E60. [PMID: 29364862 PMCID: PMC5852556 DOI: 10.3390/genes9020060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/16/2018] [Accepted: 01/22/2018] [Indexed: 12/22/2022] Open
Abstract
Rhizobium leguminosarum bv. viciae is a soil α-proteobacterium that establishes a diazotrophic symbiosis with different legumes of the Fabeae tribe. The number of genome sequences from rhizobial strains available in public databases is constantly increasing, although complete, fully annotated genome structures from rhizobial genomes are scarce. In this work, we report and analyse the complete genome of R. leguminosarum bv. viciae UPM791. Whole genome sequencing can provide new insights into the genetic features contributing to symbiotically relevant processes such as bacterial adaptation to the rhizosphere, mechanisms for efficient competition with other bacteria, and the ability to establish a complex signalling dialogue with legumes, to enter the root without triggering plant defenses, and, ultimately, to fix nitrogen within the host. Comparison of the complete genome sequences of two strains of R. leguminosarum bv. viciae, 3841 and UPM791, highlights the existence of different symbiotic plasmids and a common core chromosome. Specific genomic traits, such as plasmid content or a distinctive regulation, define differential physiological capabilities of these endosymbionts. Among them, strain UPM791 presents unique adaptations for recycling the hydrogen generated in the nitrogen fixation process.
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Affiliation(s)
- Carmen Sánchez-Cañizares
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
| | - Beatriz Jorrín
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
| | - David Durán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid (UAM), Ciudad Universitaria de Cantoblanco, Calle Francisco Tomás y Valiente 7, 28049 Madrid, Spain
| | - Suvarna Nadendla
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.N.); (M.G.G.)
| | - Marta Albareda
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Laura Rubio-Sanz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Mónica Lanza
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Rosa Isabel Prieto
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Belén Brito
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Michelle G. Giglio
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.N.); (M.G.G.)
| | - Luis Rey
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Tomás Ruiz-Argüeso
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - José M. Palacios
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Juan Imperial
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223 Madrid, Spain; (C.S.-C.); (B.J.); (D.D.); (M.A.); (L.R.-S.); (M.L.); (M.G.-G.); (R.I.P.); (B.B.); (L.R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 115 bis, 28006 Madrid, Spain
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