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Habteweld A, Kantor M, Kantor C, Handoo Z. Understanding the dynamic interactions of root-knot nematodes and their host: role of plant growth promoting bacteria and abiotic factors. FRONTIERS IN PLANT SCIENCE 2024; 15:1377453. [PMID: 38745927 PMCID: PMC11091308 DOI: 10.3389/fpls.2024.1377453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024]
Abstract
Root-knot nematodes (Meloidogyne spp., RKN) are among the most destructive endoparasitic nematodes worldwide, often leading to a reduction of crop growth and yield. Insights into the dynamics of host-RKN interactions, especially in varied biotic and abiotic environments, could be pivotal in devising novel RKN mitigation measures. Plant growth-promoting bacteria (PGPB) involves different plant growth-enhancing activities such as biofertilization, pathogen suppression, and induction of systemic resistance. We summarized the up-to-date knowledge on the role of PGPB and abiotic factors such as soil pH, texture, structure, moisture, etc. in modulating RKN-host interactions. RKN are directly or indirectly affected by different PGPB, abiotic factors interplay in the interactions, and host responses to RKN infection. We highlighted the tripartite (host-RKN-PGPB) phenomenon with respect to (i) PGPB direct and indirect effect on RKN-host interactions; (ii) host influence in the selection and enrichment of PGPB in the rhizosphere; (iii) how soil microbes enhance RKN parasitism; (iv) influence of host in RKN-PGPB interactions, and (v) the role of abiotic factors in modulating the tripartite interactions. Furthermore, we discussed how different agricultural practices alter the interactions. Finally, we emphasized the importance of incorporating the knowledge of tripartite interactions in the integrated RKN management strategies.
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Affiliation(s)
- Alemayehu Habteweld
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Northeast Area, Beltsville, MD, United States
| | - Mihail Kantor
- Plant Pathology and Environmental Microbiology Department, Pennsylvania State University, University Park, PA, United States
| | - Camelia Kantor
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, United States
| | - Zafar Handoo
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA, ARS, Northeast Area, Beltsville, MD, United States
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Lin H, Ning X, Wang D, Wang Q, Bai Y, Qu J. Quorum-sensing gene regulates hormetic effects induced by sulfonamides in Comamonadaceae. Appl Environ Microbiol 2023; 89:e0166223. [PMID: 38047646 PMCID: PMC10734536 DOI: 10.1128/aem.01662-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE Antibiotics can induce dose-dependent hormetic effects on bacterial cell proliferation, i.e., low-dose stimulation and high-dose inhibition. However, the underlying molecular basis has yet to be clarified. Here, we showed that sulfonamides play dual roles as a weapon and signal against Comamonas testosteroni that can modulate cell physiology and phenotype. Subsequently, through investigating the hormesis mechanism, we proposed a comprehensive regulatory pathway for the hormetic effects of Comamonas testosteroni low-level sulfonamides and determined the generality of the observed regulatory model in the Comamonadaceae family. Considering the prevalence of Comamonadaceae in human guts and environmental ecosystems, we provide critical insights into the health and ecological effects of antibiotics.
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Affiliation(s)
- Hui Lin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Xue Ning
- MaREI Centre, Environmental Research Institute, School of Engineering, University College Cork, Cork, Ireland
| | - Donglin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qiaojuan Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Science, Beijing, China
| | - Yaohui Bai
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jiuhui Qu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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3
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Zhang S, Kan J, Liu X, Wu Y, Zhang M, Ou J, Wang J, An L, Li D, Wang L, Wang X, Fang R, Jia Y. Phytopathogenic bacteria utilize host glucose as a signal to stimulate virulence through LuxR homologues. MOLECULAR PLANT PATHOLOGY 2023; 24:359-373. [PMID: 36762904 PMCID: PMC10013830 DOI: 10.1111/mpp.13302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/17/2022] [Accepted: 01/14/2023] [Indexed: 06/18/2023]
Abstract
Chemical signal-mediated biological communication is common within bacteria and between bacteria and their hosts. Many plant-associated bacteria respond to unknown plant compounds to regulate bacterial gene expression. However, the nature of the plant compounds that mediate such interkingdom communication and the underlying mechanisms remain poorly characterized. Xanthomonas campestris pv. campestris (Xcc) causes black rot disease on brassica vegetables. Xcc contains an orphan LuxR regulator (XccR) which senses a plant signal that was validated to be glucose by HPLC-MS. The glucose concentration increases in apoplast fluid after Xcc infection, which is caused by the enhanced activity of plant sugar transporters translocating sugar and cell-wall invertases releasing glucose from sucrose. XccR recruits glucose, but not fructose, sucrose, glucose 6-phosphate, and UDP-glucose, to activate pip expression. Deletion of the bacterial glucose transporter gene sglT impaired pathogen virulence and pip expression. Structural prediction showed that the N-terminal domain of XccR forms an alternative pocket neighbouring the AHL-binding pocket for glucose docking. Substitution of three residues affecting structural stability abolished the ability of XccR to bind to the luxXc box in the pip promoter. Several other XccR homologues from plant-associated bacteria can also form stable complexes with glucose, indicating that glucose may function as a common signal molecule for pathogen-plant interactions. The conservation of a glucose/XccR/pip-like system in plant-associated bacteria suggests that some phytopathogens have evolved the ability to utilize host compounds as virulence signals, indicating that LuxRs mediate an interkingdom signalling circuit.
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Affiliation(s)
- Siyuan Zhang
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jinhong Kan
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Present address:
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xin Liu
- State Key Laboratory of Plant Genomics, Collaborative Innovation Center of Genetics and DevelopmentInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Yao Wu
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Mingyang Zhang
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Jinqing Ou
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Juan Wang
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Lin An
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Defeng Li
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Li Wang
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Xiu‐Jie Wang
- State Key Laboratory of Plant Genomics, Collaborative Innovation Center of Genetics and DevelopmentInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Rongxiang Fang
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Yantao Jia
- State Key Laboratory of Plant GenomicsInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
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Cell-Cell Signaling Proteobacterial LuxR Solos: a Treasure Trove of Subgroups Having Different Origins, Ligands, and Ecological Roles. mSystems 2023; 8:e0103922. [PMID: 36802056 PMCID: PMC10134790 DOI: 10.1128/msystems.01039-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Many proteobacteria possess LuxR solos which are quorum sensing LuxR-type regulators that are not paired with a cognate LuxI-type synthase. LuxR solos have been implicated in intraspecies, interspecies, and interkingdom communication by sensing endogenous and exogenous acyl-homoserine lactones (AHLs) as well as non-AHL signals. LuxR solos are likely to play a major role in microbiome formation, shaping, and maintenance through many different cell-cell signaling mechanisms. This review intends to assess the different types and discuss the possible functional roles of the widespread family of LuxR solo regulators. In addition, an analysis of LuxR solo types and variability among the totality of publicly available proteobacterial genomes is presented. This highlights the importance of these proteins and will encourage scientists to mobilize and study them in order to increase our knowledge of novel cell-cell mechanisms that drive bacterial interactions in the context of complex bacterial communities.
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Chávez-Moctezuma MP, Martínez-Cámara R, Hernández-Salmerón J, Moreno-Hagelsieb G, Santoyo G, Valencia-Cantero E. Comparative genomic and functional analysis of Arthrobacter sp. UMCV2 reveals the presence of luxR-related genes inducible by the biocompound N, N-dimethylhexadecilamine. Front Microbiol 2022; 13:1040932. [PMID: 36386619 PMCID: PMC9659744 DOI: 10.3389/fmicb.2022.1040932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/10/2022] [Indexed: 09/29/2023] Open
Abstract
Quorum sensing (QS) is a bacterial cell-cell communication system with genetically regulated mechanisms dependent on cell density. Canonical QS systems in gram-negative bacteria possess an autoinducer synthase (LuxI family) and a transcriptional regulator (LuxR family) that respond to an autoinducer molecule. In Gram-positive bacteria, the LuxR transcriptional regulators "solo" (not associated with a LuxI homolog) may play key roles in intracellular communication. Arthrobacter sp. UMCV2 is an actinobacterium that promotes plant growth by emitting the volatile organic compound N, N-dimethylhexadecylamine (DMHDA). This compound induces iron deficiency, defense responses in plants, and swarming motility in Arthrobacter sp. UMCV2. In this study, the draft genome of this bacterium was assembled and compared with the genomes of type strains of the Arthrobacter genus, finding that it does not belong to any previously described species. Genome explorations also revealed the presence of 16 luxR-related genes, but no luxI homologs were discovered. Eleven of these sequences possess the LuxR characteristic DNA-binding domain with a helix-turn-helix motif and were designated as auto-inducer-related regulators (AirR). Four sequences possessed LuxR analogous domains and were designated as auto-inducer analogous regulators (AiaR). When swarming motility was induced with DMHDA, eight airR genes and two aiaR genes were upregulated. These results indicate that the expression of multiple luxR-related genes is induced in actinobacteria, such as Arthrobacter sp. UMCV2, by the action of the bacterial biocompound DMHDA when QS behavior is produced.
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Affiliation(s)
| | - Ramiro Martínez-Cámara
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
- Tecnológico Nacional de México, Morelia, Michoacán, Mexico
| | | | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
| | - Eduardo Valencia-Cantero
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
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Gupta A, Singh UB, Sahu PK, Paul S, Kumar A, Malviya D, Singh S, Kuppusamy P, Singh P, Paul D, Rai JP, Singh HV, Manna MC, Crusberg TC, Kumar A, Saxena AK. Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19053141. [PMID: 35270832 DOI: 10.3390/ijerph190531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 05/28/2023]
Abstract
Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.
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Affiliation(s)
- Amrita Gupta
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Udai B Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Pramod K Sahu
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Surinder Paul
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Adarsh Kumar
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Deepti Malviya
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Shailendra Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Pandiyan Kuppusamy
- ICAR-Central Institute for Research on Cotton Technology, Ginning Training Centre, Nagpur 440023, India
| | - Prakash Singh
- Department of Plant Breeding and Genetics, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Dumraon 802136, India
| | - Diby Paul
- Pilgram Marpeck School of Science, Technology, Engineering and Mathematics, Truett McConnel University, 100 Alumni Dr., Cleveland, GA 30528, USA
| | - Jai P Rai
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Harsh V Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Madhab C Manna
- Soil Biology Division, ICAR-Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal 462038, India
| | - Theodore C Crusberg
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
| | - Arun Kumar
- Department of Agronomy, Bihar Agricultural University, Sabour, Bhagalpur 813210, India
| | - Anil K Saxena
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
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Gupta A, Singh UB, Sahu PK, Paul S, Kumar A, Malviya D, Singh S, Kuppusamy P, Singh P, Paul D, Rai JP, Singh HV, Manna MC, Crusberg TC, Kumar A, Saxena AK. Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:3141. [PMID: 35270832 PMCID: PMC8910389 DOI: 10.3390/ijerph19053141] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 12/01/2022]
Abstract
Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.
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Affiliation(s)
- Amrita Gupta
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Udai B. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Pramod K. Sahu
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Surinder Paul
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Adarsh Kumar
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Deepti Malviya
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Shailendra Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Pandiyan Kuppusamy
- ICAR-Central Institute for Research on Cotton Technology, Ginning Training Centre, Nagpur 440023, India;
| | - Prakash Singh
- Department of Plant Breeding and Genetics, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Dumraon 802136, India;
| | - Diby Paul
- Pilgram Marpeck School of Science, Technology, Engineering and Mathematics, Truett McConnel University, 100 Alumni Dr., Cleveland, GA 30528, USA;
| | - Jai P. Rai
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Harsh V. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Madhab C. Manna
- Soil Biology Division, ICAR-Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal 462038, India;
| | - Theodore C. Crusberg
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA;
| | - Arun Kumar
- Department of Agronomy, Bihar Agricultural University, Sabour, Bhagalpur 813210, India;
| | - Anil K. Saxena
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
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Liu F, Hu M, Zhang Z, Xue Y, Chen S, Hu A, Zhang LH, Zhou J. Dickeya Manipulates Multiple Quorum Sensing Systems to Control Virulence and Collective Behaviors. FRONTIERS IN PLANT SCIENCE 2022; 13:838125. [PMID: 35211146 PMCID: PMC8860905 DOI: 10.3389/fpls.2022.838125] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/07/2022] [Indexed: 06/12/2023]
Abstract
Soft rot Pectobacteriaceae (SRP), typical of Pectobacterium and Dickeya, are a class of Gram-negative bacterial pathogens that cause devastating diseases on a wide range of crops and ornamental plants worldwide. Quorum sensing (QS) is a cell-cell communication mechanism regulating the expression of specific genes by releasing QS signal molecules associated with cell density, in most cases, involving in the vital process of virulence and infection. In recent years, several types of QS systems have been uncovered in Dickeya pathogens to control diverse biological behaviors, especially bacterial pathogenicity and transkingdom interactions. This review depicts an integral QS regulation network of Dickeya, elaborates in detail the regulation of specific QS system on different biological functions of the pathogens and hosts, aiming at providing a systematic overview of Dickeya pathogenicity and interactions with hosts, and, finally, expects the future prospective of effectively controlling the bacterial soft rot disease caused by Dickeya by quenching the key QS signal.
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Abstract
LuxR solos are related to quorum sensing (QS) LuxR family regulators; however, they lack a cognate LuxI family protein. LuxR solos are widespread and almost exclusively found in proteobacteria. In this study, we investigated the distribution and conservation of LuxR solos in the fluorescent pseudomonads group. Our analysis of more than 600 genomes revealed that the majority of fluorescent Pseudomonas spp. carry one or more LuxR solos, occurring considerably more frequently than complete LuxI/LuxR archetypical QS systems. Based on the adjacent gene context and conservation of the primary structure, nine subgroups of LuxR solos have been identified that are likely to be involved in the establishment of communication networks. Modeling analysis revealed that the majority of subgroups shows some substitutions at the invariant amino acids of the ligand-binding pocket of QS LuxRs, raising the possibility of binding to non-acyl-homoserine lactone (AHL) ligands. Several mutants and gene expression studies on some LuxR solos belonging to different subgroups were performed in order to shed light on their response. The commonality of LuxR solos among fluorescent pseudomonads is an indication of their important role in cell-cell signaling. IMPORTANCE Cell-cell communication in bacteria is being extensively studied in simple settings and uses chemical signals and cognate regulators/receptors. Many Gram-negative proteobacteria use acyl-homoserine lactones (AHLs) synthesized by LuxI family proteins and cognate LuxR-type receptors to regulate their quorum sensing (QS) target loci. AHL-QS circuits are the best studied QS systems; however, many proteobacterial genomes also contain one or more LuxR solos, which are QS-related LuxR proteins which are unpaired to a cognate LuxI. A few LuxR solos have been implicated in intraspecies, interspecies, and interkingdom signaling. Here, we report that LuxR solo homologs occur considerably more frequently than complete LuxI/LuxR QS systems within the Pseudomonas fluorescens group of species and that they are characterized by different genomic organizations and primary structures and can be subdivided into several subgroups. The P. fluorescens group consists of more than 50 species, many of which are found in plant-associated environments. The role of LuxR solos in cell-cell signaling in fluorescent pseudomonads is discussed.
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Pan H, Pierson LS, Pierson EA. PcsR2 Is a LuxR-Type Regulator That Is Upregulated on Wheat Roots and Is Unique to Pseudomonas chlororaphis. Front Microbiol 2020; 11:560124. [PMID: 33244313 PMCID: PMC7683790 DOI: 10.3389/fmicb.2020.560124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/09/2020] [Indexed: 11/13/2022] Open
Abstract
LuxR solos are common in plant-associated bacteria and increasingly recognized for playing important roles in plant-microbe interkingdom signaling. Unlike the LuxR-type transcriptional regulators of prototype LuxR/LuxI quorum sensing systems, luxR solos do not have a LuxI-type autoinducer synthase gene associated with them. LuxR solos in plant-pathogenic bacteria are important for virulence and in plant endosymbionts contribute to symbiosis. In the present study, we characterized an atypical LuxR solo, PcsR2, in the biological control species Pseudomonas chlororaphis 30-84 that is highly conserved among sequenced P. chlororaphis strains. Unlike most LuxR solos in the plant-associated bacteria characterized to date, pcsR2 is not associated with a proline iminopeptidase gene and the protein has an atypical N-terminal binding domain. We created a pcsR2 deletion mutant and used quantitative RT-PCR to show that the expression of pcsR2 and genes in the operon immediately downstream was upregulated ∼10-fold when the wild type strain was grown on wheat roots compared to planktonic culture. PcsR2 was involved in upregulation. Using a GFP transcriptional reporter, we found that expression of pcsR2 responded specifically to root-derived substrates as compared to leaf-derived substrates but not to endogenous AHLs. Compared to the wild type, the mutant was impaired in the ability to utilize root carbon and nitrogen sources in wheat root macerate and to colonize wheat roots. Phenazine production and most biofilm traits previously shown to be correlated with phenazine production also were diminished in the mutant. Gene expression of several of the proteins in the phenazine regulatory network including PhzR, Pip (phenazine inducing protein) and RpeA/RpeB were reduced in the mutant, and overexpression of these genes in trans restored phenazine production in the mutant to wild-type levels, indicating PcsR2 affects the activity of the these regulatory genes upstream of RpeA/RpeB via an undetermined mechanism. Our results indicate PcsR2 upregulates the expression of the adjacent operon in response to unknown wheat root-derived signals and belongs to a novel subfamily of LuxR-type transcriptional regulators found in sequenced P. chlororaphis strains.
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Affiliation(s)
- Huiqiao Pan
- Molecular and Environmental Plant Sciences Program, Texas A&M University, College Station, TX, United States.,Department of Horticulture Sciences, Texas A&M University, College Station, TX, United States
| | - Leland S Pierson
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
| | - Elizabeth A Pierson
- Molecular and Environmental Plant Sciences Program, Texas A&M University, College Station, TX, United States.,Department of Horticulture Sciences, Texas A&M University, College Station, TX, United States.,Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
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11
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Regaiolo A, Dominelli N, Andresen K, Heermann R. The Biocontrol Agent and Insect Pathogen Photorhabdus luminescens Interacts with Plant Roots. Appl Environ Microbiol 2020; 86:e00891-20. [PMID: 32591378 PMCID: PMC7440798 DOI: 10.1128/aem.00891-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/18/2020] [Indexed: 01/27/2023] Open
Abstract
The number of sustainable agriculture techniques to improve pest management and environmental safety is rising, as biological control agents are used to enhance disease resistance and abiotic stress tolerance in crops. Here, we investigated the capacity of the Photorhabdus luminescens secondary variant to react to plant root exudates and their behavior toward microorganisms in the rhizosphere. P. luminescens is known to live in symbiosis with entomopathogenic nematodes (EPNs) and to be highly pathogenic toward insects. The P. luminescens-EPN relationship has been widely studied, and this combination has been used as a biological control agent; however, not much attention has been paid to the putative lifestyle of P. luminescens in the rhizosphere. We performed transcriptome analysis to show how P. luminescens responds to plant root exudates. The analysis highlighted genes involved in chitin degradation, biofilm regulation, formation of flagella, and type VI secretion system. Furthermore, we provide evidence that P. luminescens can inhibit growth of phytopathogenic fungi. Finally, we demonstrated a specific interaction of P. luminescens with plant roots. Understanding the role and the function of this bacterium in the rhizosphere might accelerate the progress in biocontrol manipulation and elucidate the peculiar mechanisms adopted by plant growth-promoting rhizobacteria in plant root interactions.IMPORTANCE Insect-pathogenic Photorhabdus luminescens bacteria are widely used in biocontrol strategies against pests. Very little is known about the life of these bacteria in the rhizosphere. Here, we show that P. luminescens can specifically react to and interact with plant roots. Understanding the adaptation of P. luminescens in the rhizosphere is highly important for the biotechnological application of entomopathogenic bacteria and could improve future sustainable pest management in agriculture.
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Affiliation(s)
- Alice Regaiolo
- Johannes-Gutenberg-University Mainz, Institute of Molecular Physiology (imP), Microbiology and Wine Research, Mainz, Germany
| | - Nazzareno Dominelli
- Johannes-Gutenberg-University Mainz, Institute of Molecular Physiology (imP), Microbiology and Wine Research, Mainz, Germany
| | - Karsten Andresen
- Johannes-Gutenberg-University Mainz, Institute of Molecular Physiology (imP), Microbiology and Wine Research, Mainz, Germany
| | - Ralf Heermann
- Johannes-Gutenberg-University Mainz, Institute of Molecular Physiology (imP), Microbiology and Wine Research, Mainz, Germany
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12
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LuxR Solos in the Plant Endophyte Kosakonia sp. Strain KO348. Appl Environ Microbiol 2020; 86:AEM.00622-20. [PMID: 32332134 PMCID: PMC7301841 DOI: 10.1128/aem.00622-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/10/2020] [Indexed: 12/30/2022] Open
Abstract
Cell-cell signaling in bacteria allows a synchronized and coordinated behavior of a microbial community. LuxR solos represent a subfamily of proteins in proteobacteria which most commonly detect and respond to signals produced exogenously by other microbes or eukaryotic hosts. Here, we report that a plant-beneficial bacterial endophyte belonging to the novel genus of Kosakonia possesses two LuxR solos; one is involved in the detection of exogenous N-acyl homoserine lactone quorum sensing signals and the other in detecting a compound(s) produced by the host plant. These two Kosakonia LuxR solos are therefore most likely involved in interspecies and interkingdom signaling. Endophytes are microorganisms that live inside plants and are often beneficial for the host. Kosakonia is a novel bacterial genus that includes several species that are diazotrophic and plant associated. This study revealed two quorum sensing-related LuxR solos, designated LoxR and PsrR, in the plant endophyte Kosakonia sp. strain KO348. LoxR modeling and biochemical studies demonstrated that LoxR binds N-acyl homoserine lactones (AHLs) in a promiscuous way. PsrR, on the other hand, belongs to the subfamily of plant-associated-bacterium (PAB) LuxR solos that respond to plant compounds. Target promoter studies as well as modeling and phylogenetic comparisons suggest that PAB LuxR solos are likely to respond to different plant compounds. Finally, LoxR is involved in the regulation of T6SS and PsrR plays a role in root endosphere colonization. IMPORTANCE Cell-cell signaling in bacteria allows a synchronized and coordinated behavior of a microbial community. LuxR solos represent a subfamily of proteins in proteobacteria which most commonly detect and respond to signals produced exogenously by other microbes or eukaryotic hosts. Here, we report that a plant-beneficial bacterial endophyte belonging to the novel genus of Kosakonia possesses two LuxR solos; one is involved in the detection of exogenous N-acyl homoserine lactone quorum sensing signals and the other in detecting a compound(s) produced by the host plant. These two Kosakonia LuxR solos are therefore most likely involved in interspecies and interkingdom signaling.
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13
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Tobias NJ, Brehm J, Kresovic D, Brameyer S, Bode HB, Heermann R. New Vocabulary for Bacterial Communication. Chembiochem 2020; 21:759-768. [PMID: 31709676 PMCID: PMC7154725 DOI: 10.1002/cbic.201900580] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Indexed: 12/21/2022]
Abstract
Quorum sensing (QS) is widely accepted as a procedure that bacteria use to converse. However, prevailing thinking places acyl homoserine lactones (AHLs) at the forefront of this communication pathway in Gram-negative bacteria. With the advent of high-throughput genomics and the subsequent influx of bacterial genomes, bioinformatics analysis has determined that the genes encoding AHL biosynthesis, originally discovered to be indispensable for QS (LuxI-like proteins and homologues), are often absent in QS-capable bacteria. Instead, the sensing protein (LuxR-like proteins) is present with an apparent inability to produce any outgoing AHL signal. Recently, several signals for these LuxR solos have been identified. Herein, advances in the field of QS are discussed, with a particular focus on recent research in the field of bacterial cell-cell communication.
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Affiliation(s)
- Nicholas J. Tobias
- Fachbereich BiowissenschaftenMerck-Stiftungsprofessur für Molekulare BiotechnologieGoethe-Universität FrankfurtMax-von-Laue-Strasse 960438Frankfurt am MainGermany
- LOEWE Center for Translational Biodiversity in Genomics (TBG)Frankfurt am MainGermany
| | - Jannis Brehm
- Institut für Molekulare PhysiologieMikrobiologie und WeinforschungJohannes-Gutenberg-Universität MainzJohann-Joachim-Becher-Weg 1355128MainzGermany
| | - Darko Kresovic
- Fachbereich BiowissenschaftenMerck-Stiftungsprofessur für Molekulare BiotechnologieGoethe-Universität FrankfurtMax-von-Laue-Strasse 960438Frankfurt am MainGermany
| | - Sophie Brameyer
- Biozentrum, Bereich MikrobiologieLudwig-Maximilians-Universität MünchenGroßhaderner Strasse 2–482152MartinsriedGermany
| | - Helge B. Bode
- Fachbereich BiowissenschaftenMerck-Stiftungsprofessur für Molekulare BiotechnologieGoethe-Universität FrankfurtMax-von-Laue-Strasse 960438Frankfurt am MainGermany
- LOEWE Center for Translational Biodiversity in Genomics (TBG)Frankfurt am MainGermany
- Buchmann Institute for Molecular Life Sciences (BMLS)Goethe-Universität FrankfurtMax-von-Laue-Strasse 1560438Frankfurt am MainGermany
| | - Ralf Heermann
- Institut für Molekulare PhysiologieMikrobiologie und WeinforschungJohannes-Gutenberg-Universität MainzJohann-Joachim-Becher-Weg 1355128MainzGermany
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14
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Coque JJR, Álvarez-Pérez JM, Cobos R, González-García S, Ibáñez AM, Diez Galán A, Calvo-Peña C. Advances in the control of phytopathogenic fungi that infect crops through their root system. ADVANCES IN APPLIED MICROBIOLOGY 2020; 111:123-170. [PMID: 32446411 DOI: 10.1016/bs.aambs.2020.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Productivity and economic sustainability of many herbaceous and woody crops are seriously threatened by numerous phytopathogenic fungi. While symptoms associated with phytopathogenic fungal infections of aerial parts (leaves, stems and fruits) are easily observable and therefore recognizable, allowing rapid or preventive action to control this type of infection, the effects produced by soil-borne fungi that infect plants through their root system are more difficult to detect. The fact that these fungi initiate infection and damage underground implies that the first symptoms are not as easily noticeable, and therefore both crop yield and plant survival are frequently severely compromised by the time the infection is found. In this paper we will review and discuss recent insights into plant-microbiota interactions in the root system crucial to understanding the beginning of the infectious process. We will also review different methods for diminishing and controlling the infection rate by phytopathogenic fungi penetrating through the root system including both the traditional use of biocontrol agents such as antifungal compounds as well as some new strategies that could be used because of their effective application, such as nanoparticles, virus-based nanopesticides, or inoculation of plant material with selected endophytes. We will also review the possibility of modeling and influencing the composition of the microbial population in the rhizosphere environment as a strategy for nudging the plant-microbiome interactions toward enhanced beneficial outcomes for the plant, such as controlling the infectious process.
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Affiliation(s)
- Juan José R Coque
- Instituto de Investigación de la Viña y el Vino, Universidad de León, León, Spain.
| | | | - Rebeca Cobos
- Instituto de Investigación de la Viña y el Vino, Universidad de León, León, Spain
| | | | - Ana M Ibáñez
- Instituto de Investigación de la Viña y el Vino, Universidad de León, León, Spain
| | - Alba Diez Galán
- Instituto de Investigación de la Viña y el Vino, Universidad de León, León, Spain
| | - Carla Calvo-Peña
- Instituto de Investigación de la Viña y el Vino, Universidad de León, León, Spain
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15
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Han S, Shen D, Wang Y, Chou S, Gomelsky M, Gao Y, Qian G. A YajQ-LysR-like, cyclic di-GMP-dependent system regulating biosynthesis of an antifungal antibiotic in a crop-protecting bacterium, Lysobacter enzymogenes. MOLECULAR PLANT PATHOLOGY 2020; 21:218-229. [PMID: 31747123 PMCID: PMC6988422 DOI: 10.1111/mpp.12890] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
YajQ, a binding protein of the universal bacterial second messenger cyclic di-GMP (c-di-GMP), affects virulence in several bacterial pathogens, including Xanthomonas campestris. In this bacterium, YajQ interacts with the transcription factor LysR. Upon c-di-GMP binding, the whole c-di-GMP-YajQ-LysR complex is found to dissociate from DNA, resulting in virulence gene regulation. Here, we identify a YajQ-LysR-like system in the bacterial biocontrol agent Lysobacter enzymogenes OH11 that secretes an antifungal antibiotic, heat-stable antifungal factor (HSAF) against crop fungal pathogens. We show that the YajQ homologue, CdgL (c-di-GMP receptor interacting with LysR) affects expression of the HSAF biosynthesis operon by interacting with the transcription activator LysR. The CdgL-LysR interaction enhances the apparent affinity of LysR to the promoter region upstream of the HSAF biosynthesis operon, which increases operon expression. Unlike the homologues CdgL (YajQ)-LysR system in X. campestris, we show that c-di-GMP binding to CdgL seems to weaken CdgL-LysR interactions and promote the release of CdgL from the LysR-DNA complex, which leads to decreased expression. Together, this study takes the YajQ-LysR-like system from bacterial pathogens to a crop-protecting bacterium that is able to regulate antifungal HSAF biosynthesis via disassembly of the c-di-GMP receptor-transcription activator complex.
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Affiliation(s)
- Sen Han
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests)Nanjing Agricultural UniversityNanjing210095P.R. China
| | - Danyu Shen
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests)Nanjing Agricultural UniversityNanjing210095P.R. China
| | - Yu‐Chuan Wang
- Institute of Biochemistry, and NCHU Agricultural Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan
| | - Shan‐Ho Chou
- Institute of Biochemistry, and NCHU Agricultural Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan
| | - Mark Gomelsky
- Department of Molecular BiologyUniversity of WyomingLaramieWyoming82071USA
| | - Yong‐Gui Gao
- School of Biological SciencesNanyang Technological University60 Nanyang DriveSingapore637551Singapore
| | - Guoliang Qian
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests)Nanjing Agricultural UniversityNanjing210095P.R. China
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16
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Feng L, Schaefer AL, Hu M, Chen R, Greenberg EP, Zhou J. Virulence Factor Identification in the Banana Pathogen Dickeya zeae MS2. Appl Environ Microbiol 2019; 85:e01611-19. [PMID: 31540986 PMCID: PMC6856320 DOI: 10.1128/aem.01611-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/16/2019] [Indexed: 11/20/2022] Open
Abstract
The phytopathogen Dickeya zeae MS2 is a particularly virulent agent of banana soft rot disease. To begin to understand this banana disease and to understand the role of quorum sensing and quorum-sensing-related regulatory elements in D. zeae MS2, we sequenced its genome and queried the sequence for genes encoding LuxR homologs. We identified a canonical LuxR-LuxI homolog pair similar to those in other members of the genus Dickeya The quorum-sensing signal for this pair was N-3-oxo-hexanoyl-homoserine lactone, and the circuit affected motility, cell clumping, and production of the pigment indigoidine, but it did not affect infections of banana seedlings in our experiments. We also identified a luxR homolog linked to a gene annotated as encoding a proline iminopeptidase. Similar linked pairs have been associated with virulence in other plant pathogens. We show that mutants with deletions in the proline iminopeptidase gene are attenuated for virulence. Surprisingly, a mutant with a deletion in the gene encoding the LuxR homolog shows normal virulence.IMPORTANCEDickeya zeae is an emerging banana soft rot pathogen in China. We used genome sequencing and annotation to create an inventory of potential virulence factors and virulence gene regulators encoded in Dickeya zeae MS2, a particularly virulent strain. We created mutations in several genes and tested these mutants in a banana seedling infection model. A strain with a mutated proline iminopeptidase gene, homologs of which are important for disease in the Xanthomonas species phytopathogens, was attenuated for soft rot symptoms in our model. Understanding how the proline iminopeptidase functions as a virulence factor may lead to insights about how to control the disease, and it is of general importance as homologs of the proline iminopeptidase occur in dozens of plant-associated bacteria.
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Affiliation(s)
- Luwen Feng
- Guangdong Province Sociomicrobiology Basic Science and Frontier Technology Research Team & Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, People's Republic of China
| | - Amy L Schaefer
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Ming Hu
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, People's Republic of China
| | - Ruiyi Chen
- Guangdong Province Sociomicrobiology Basic Science and Frontier Technology Research Team & Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, People's Republic of China
| | - E Peter Greenberg
- Guangdong Province Sociomicrobiology Basic Science and Frontier Technology Research Team & Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, People's Republic of China
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Jianuan Zhou
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, People's Republic of China
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17
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Chua KO, See-Too WS, Ee R, Lim YL, Yin WF, Chan KG. In silico Analysis Reveals Distribution of Quorum Sensing Genes and Consistent Presence of LuxR Solos in the Pandoraea Species. Front Microbiol 2019; 10:1758. [PMID: 31447806 PMCID: PMC6691176 DOI: 10.3389/fmicb.2019.01758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/16/2019] [Indexed: 01/11/2023] Open
Abstract
The most common quorum sensing (QS) system in Gram-negative bacteria consists of signaling molecules called N-acyl-homoserine lactones (AHLs), which are synthesized by an enzyme AHL synthase (LuxI) and detected by a transcriptional regulator (LuxR) that are usually located in close proximity. However, many recent studies have also evidenced the presence of LuxR solos that are LuxR-related proteins in Proteobacteria that are devoid of a cognate LuxI AHL synthase. Pandoraea species are opportunistic pathogens frequently isolated from sputum specimens of cystic fibrosis (CF) patients. We have previously shown that P. pnomenusa strains possess QS activity. In this study, we examined the presence of QS activity in all type strains of Pandoraea species and acquired their complete genome sequences for holistic bioinformatics analyses of QS-related genes. Only four out of nine type strains (P. pnomenusa, P. sputorum, P. oxalativorans, and P. vervacti) showed QS activity, and C8-HSL was the only AHL detected. A total of 10 canonical luxIs with adjacent luxRs were predicted by bioinformatics from the complete genomes of aforementioned species and publicly available Pandoraea genomes. No orphan luxI was identified in any of the genomes. However, genes for two LuxR solos (LuxR2 and LuxR3 solos) were identified in all Pandoraea genomes (except two draft genomes with one LuxR solo gene), and P. thiooxydans was the only species that harbored no QS-related activity and genes. Except the canonical LuxR genes, LuxIs and LuxR solos of Pandoraea species were distantly related to the other well-characterized QS genes based on phylogenetic clustering. LuxR2 and LuxR3 solos might represent two novel evolutionary branches of LuxR system as they were found exclusively only in the genus. As a few luxR solos were located in close proximity with prophage sequence regions in the genomes, we thus postulated that these luxR solos could be transmitted into genus Pandoraea by transduction process mediated by bacteriophage. The bioinformatics approach developed in this study forms the basis for further characterization of closely related species. Overall, our findings improve the current understanding of QS in Pandoraea species, which is a potential pharmacological target in battling Pandoraea infections in CF patients.
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Affiliation(s)
- Kah-Ooi Chua
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yan-Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,International Genome Centre, Jiangsu University, Zhenjiang, China
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18
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Wang N, Wang L, Zhu K, Hou S, Chen L, Mi D, Gui Y, Qi Y, Jiang C, Guo JH. Plant Root Exudates Are Involved in Bacillus cereus AR156 Mediated Biocontrol Against Ralstonia solanacearum. Front Microbiol 2019; 10:98. [PMID: 30766525 PMCID: PMC6365458 DOI: 10.3389/fmicb.2019.00098] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/16/2019] [Indexed: 11/13/2022] Open
Abstract
The biological control process mediated by microbes relies on multiple interactions among plants, pathogens and biocontrol agents (BCAs). One such efficient BCA is Bacillus cereus AR156, a bacterial strain that controls a broad spectrum of plant diseases and potentially works as a microbe elicitor of plant immune reactions. It remains unclear, however, whether the interaction between plants and B. cereus AR156 may facilitate composition changes of plant root exudates and whether these changes directly affect the growth of both plant pathogens and B. cereus AR156 itself. Here, we addressed these questions by analyzing the influences of root exudate changes mediated by B. cereus AR156 during biocontrol against tomato bacterial wilt caused by Ralstonia solanacearum. Indeed, some upregulated metabolites in tomato root exudates induced by B. cereus AR156 (REB), such as lactic acid and hexanoic acid, induced the growth and motile ability of in vitro B. cereus AR156 cells. Exogenously applying hexanoic acid and lactic acid to tomato plants showed positive biocontrol efficacy (46.6 and 39.36%) against tomato bacterial wilt, compared with 51.02% by B. cereus AR156 itself. Furthermore, fructose, lactic acid, sucrose and threonine at specific concentrations stimulated the biofilm formation of B. cereus AR156 in Luria-Bertan- Glycerol- Magnesium medium (LBGM), and we also detected more colonized cells of B. cereus AR156 on the tomato root surface after adding these four compounds to the system. These observations suggest that the ability of B. cereus AR156 to induce some specific components in plant root exudates was probably involved in further biocontrol processes.
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Affiliation(s)
- Ning Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Luyao Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Kai Zhu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Sensen Hou
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Lin Chen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Dandan Mi
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Ying Gui
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Yijun Qi
- Tsinghua-Peking Center for Life Sciences, Beijing, China.,Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Chunhao Jiang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Jian-Hua Guo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Nanjing, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
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19
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Javvadi SG, Cescutti P, Rizzo R, Lonzarich V, Navarini L, Licastro D, Guarnaccia C, Venturi V. The spent culture supernatant of Pseudomonas syringae contains azelaic acid. BMC Microbiol 2018; 18:199. [PMID: 30486794 PMCID: PMC6264629 DOI: 10.1186/s12866-018-1352-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 11/20/2018] [Indexed: 11/12/2022] Open
Abstract
Background Pseudomonas syringae pv. actinidiae (PSA) is an emerging kiwifruit bacterial pathogen which since 2008 has caused considerable losses. No quorum sensing (QS) signaling molecule has yet been reported from PSA and the aim of this study was to identify possible intercellular signals produced by PSA. Results A secreted metabolome analysis resulted in the identification of 83 putative compounds, one of them was the nine carbon saturated dicarboxylic acid called azelaic acid. Azelaic acid, which is a nine-carbon (C9) saturated dicarboxylic acid, has been reported in plants as a mobile signal that primes systemic defenses. In addition, its structure,(which is associated with fatty acid biosynthesis) is similar to other known bacterial QS signals like the Diffusible Signal Facor (DSF). For these reason it could be acting as s signal molecule. Analytical and structural studies by NMR spectroscopy confirmed that in PSA spent supernatants azelaic acid was present. Quantification studies further revealed that 20 μg/L of were present and was also found in the spent supernatants of several other P. syringae pathovars. The RNAseq transcriptome study however did not determine whether azelaic acid could behave as a QS molecule. Conclusions This study reports of the possible natural biosynthesis of azelaic acid by bacteria. The production of azelaic acid by P. syringae pathovars can be associated with plant-bacteria signaling. Electronic supplementary material The online version of this article (10.1186/s12866-018-1352-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Paola Cescutti
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Roberto Rizzo
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | | | | | | | - Corrado Guarnaccia
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.
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20
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A plant-responsive bacterial-signaling system senses an ethanolamine derivative. Proc Natl Acad Sci U S A 2018; 115:9785-9790. [PMID: 30190434 DOI: 10.1073/pnas.1809611115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Certain plant-associated Proteobacteria sense their host environment by detecting an unknown plant signal recognized by a member of a LuxR subfamily of transcription factors. This interkingdom communication is important for both mutualistic and pathogenic interactions. The Populus root endophyte Pseudomonas sp. GM79 possesses such a regulator, named PipR. In a previous study we reported that PipR activates an adjacent gene (pipA) coding for a proline iminopeptidase in response to Populus leaf macerates and peptides and that this activation is dependent on a putative ABC-type transporter [Schaefer AL, et al. (2016) mBio 7:e01101-16]. In this study we identify a chemical derived from ethanolamine that induces PipR activity at picomolar concentrations, and we present evidence that this is the active inducer present in plant leaf macerates. First, a screen of more than 750 compounds indicated ethanolamine was a potent inducer for the PipR-sensing system; however, ethanolamine failed to bind to the periplasmic-binding protein (PBP) required for the signal response. This led us to discover that a specific ethanolamine derivative, N-(2-hydroxyethyl)-2-(2-hydroxyethylamino) acetamide (HEHEAA), binds to the PBP and serves as a potent PipR-dependent inducer. We also show that a compound, which coelutes with HEHEAA in HPLC and induces pipA gene expression in a PipR-dependent manner, can be found in Populus leaf macerates. This work sheds light on how plant-associated bacteria can sense their environment and on the nature of inducers for a family of plant-responsive LuxR-like transcription factors found in plant-associated bacteria.
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Nobori T, Mine A, Tsuda K. Molecular networks in plant-pathogen holobiont. FEBS Lett 2018; 592:1937-1953. [PMID: 29714033 DOI: 10.1002/1873-3468.13071] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/13/2018] [Accepted: 04/23/2018] [Indexed: 12/31/2022]
Abstract
Plant immune receptors enable detection of a multitude of microbes including pathogens. The recognition of microbes activates various plant signaling pathways, such as those mediated by phytohormones. Over the course of coevolution with microbes, plants have expanded their repertoire of immune receptors and signaling components, resulting in highly interconnected plant immune networks. These immune networks enable plants to appropriately respond to different types of microbes and to coordinate immune responses with developmental programs and environmental stress responses. However, the interconnectivity in plant immune networks is exploited by microbial pathogens to promote pathogen fitness in plants. Analogous to plant immune networks, virulence-related pathways in bacterial pathogens are also interconnected. Accumulating evidence implies that some plant-derived compounds target bacterial virulence networks. Thus, the plant immune and bacterial virulence networks intimately interact with each other. Here, we highlight recent insights into the structures of the plant immune and bacterial virulence networks and the interactions between them. We propose that small molecules derived from plants and/or bacterial pathogens connect the two molecular networks, forming supernetworks in the plant-bacterial pathogen holobiont.
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Affiliation(s)
- Tatsuya Nobori
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Akira Mine
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, Kusatsu, Japan.,JST, PRESTO, Kawaguchi-shi, Japan
| | - Kenichi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Heat-Stable Antifungal Factor (HSAF) Biosynthesis in Lysobacter enzymogenes Is Controlled by the Interplay of Two Transcription Factors and a Diffusible Molecule. Appl Environ Microbiol 2018; 84:AEM.01754-17. [PMID: 29101199 DOI: 10.1128/aem.01754-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/01/2017] [Indexed: 01/15/2023] Open
Abstract
Lysobacter enzymogenes is a Gram-negative, environmentally ubiquitous bacterium that produces a secondary metabolite, called heat-stable antifungal factor (HSAF), as an antifungal factor against plant and animal fungal pathogens. 4-Hydroxybenzoic acid (4-HBA) is a newly identified diffusible factor that regulates HSAF synthesis via L. enzymogenes LysR (LysRLe), an LysR-type transcription factor (TF). Here, to identify additional TFs within the 4-HBA regulatory pathway that control HSAF production, we reanalyzed the LenB2-based transcriptomic data, in which LenB2 is the enzyme responsible for 4-HBA production. This survey led to identification of three TFs (Le4806, Le4969, and Le3904). Of them, LarR (Le4806), a member of the MarR family proteins, was identified as a new TF that participated in the 4-HBA-dependent regulation of HSAF production. Our data show the following: (i) that LarR is a downstream component of the 4-HBA regulatory pathway controlling the HSAF level, while LysRLe is the receptor of 4-HBA; (ii) that 4-HBA and LysRLe have opposite regulatory effects on larR transcription whereby larR transcript is negatively modulated by 4-HBA while LysRLe, in contrast, exerts positive transcriptional regulation by directly binding to the larR promoter without being affected by 4-HBA in vitro; (iii) that LarR, similar to LysRLe, can bind to the promoter of the HSAF biosynthetic gene operon, leading to positive regulation of HSAF production; and (iv) that LarR and LysRLe cannot interact and instead control HSAF biosynthesis independently. These results outline a previously uncharacterized mechanism by which biosynthesis of the antibiotic HSAF in L. enzymogenes is modulated by the interplay of 4-HBA, a diffusible molecule, and two different TFs.IMPORTANCE Bacteria use diverse chemical signaling molecules to regulate a wide range of physiological and cellular processes. 4-HBA is an "old" chemical molecule that is produced by diverse bacterial species, but its regulatory function and working mechanism remain largely unknown. We previously found that 4-HBA in L. enzymogenes could serve as a diffusible factor regulating HSAF synthesis via LysRLe Here, we further identified LarR, an MarR family protein, as a second TF that participates in the 4-HBA-dependent regulation of HSAF biosynthesis. Our results dissected how LarR acts as a protein linker to connect 4-HBA and HSAF synthesis, whereby LarR also has cross talk with LysRLe Thus, our findings not only provide fundamental insight regarding how a diffusible molecule (4-HBA) adopts two different types of TFs for coordinating HSAF biosynthesis but also show the use of applied microbiology to increase the yield of the antibiotic HSAF by modification of the 4-HBA regulatory pathway in L. enzymogenes.
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23
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Interkingdom signaling in plant-microbe interactions. SCIENCE CHINA-LIFE SCIENCES 2017; 60:785-796. [PMID: 28755299 DOI: 10.1007/s11427-017-9092-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/04/2017] [Indexed: 12/18/2022]
Abstract
The widespread communications between prokaryotes and eukaryotes via signaling molecules are believed to affect gene expression in both partners. During the communication process, the contacted organisms produce and release small molecules that establish communication channels between two kingdoms-this procedure is known as interkingdom signaling. Interkingdom communications are widespread between pathogenic or beneficial bacteria and their host plants, with diversified outcomes depending on the specific chemical-triggered signaling pathways. Deciphering the signals or language of this interkingdom communication and uncovering the underlying mechanisms are major current challenges in this field. It is evident that diverse signaling molecules can be produced or derived from bacteria and plants, and researchers have sought to identify these signals and explore the mechanisms of the signaling pathways. The results of such studies will lead to the development of strategies to improve plant disease resistance through controlling interkingdom signals, rather than directly killing the pathogenic bacteria. Also, the identification of signals produced by beneficial bacteria will be useful for agricultural applications. In this review, we summarize the recent progress of cross-kingdom interactions between plant and bacteria, and how LuxR-family transcription factors in plant associated bacterial quorum sensing system are involved in the interkingdom signaling.
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Alagarasan G, Aswathy KS, Madhaiyan M. Shoot the Message, Not the Messenger-Combating Pathogenic Virulence in Plants by Inhibiting Quorum Sensing Mediated Signaling Molecules. FRONTIERS IN PLANT SCIENCE 2017; 8:556. [PMID: 28446917 PMCID: PMC5388769 DOI: 10.3389/fpls.2017.00556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/28/2017] [Indexed: 06/07/2023]
Abstract
Immunity, virulence, biofilm formation, and survival in the host environment are regulated by the versatile nature of density dependent microbial cell signaling, also called quorum sensing (QS). The QS molecules can associate with host plant tissues and, at times, cause a change in its gene expression at the downstream level through inter-kingdom cross talking. Progress in controlling QS through fungicide/bactericide in pathogenic microscopic organisms has lead to a rise of antibiotic resistance pathogens. Here, we review the application of selective quorum quenching (QQ) endophytes to control phytopathogens that are shared by most, if not all, terrestrial plant species as well as aquatic plants. Allowing the plants to posses endophytic colonies through biotization will be an additional and a sustainable encompassing methodology resulting in attenuated virulence rather than killing the pathogens. Furthermore, the introduced endophytes could serve as a potential biofertilizer and bioprotection agent, which in turn increases the PAMP- triggered immunity and hormonal systemic acquired resistance (SAR) in plants through SA-JA-ET signaling systems. This paper discusses major challenges imposed by QS and QQ application in biotechnology.
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Affiliation(s)
- Ganesh Alagarasan
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi VishwavidyalayaRaipur, India
| | - Kumar S. Aswathy
- Department of Agricultural Microbiology, Tamilnadu Agricultural UniversityCoimbatore, India
| | - Munusamy Madhaiyan
- Biomaterials and Biocatalyst, Temasek Lifesciences Laboratory, National University of SingaporeSingapore, Singapore
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25
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Su Z, Chen H, Wang P, Tombosa S, Du L, Han Y, Shen Y, Qian G, Liu F. 4-Hydroxybenzoic acid is a diffusible factor that connects metabolic shikimate pathway to the biosynthesis of a unique antifungal metabolite inLysobacter enzymogenes. Mol Microbiol 2017; 104:163-178. [DOI: 10.1111/mmi.13619] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Zhenhe Su
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University; Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education Nanjing; 210095 People's Republic of China
| | - Hongfu Chen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University; Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education Nanjing; 210095 People's Republic of China
| | - Ping Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University; Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education Nanjing; 210095 People's Republic of China
| | - Simon Tombosa
- Department of Chemistry; University of Nebraska-Lincoln; Lincoln NE 68588
| | - Liangcheng Du
- Department of Chemistry; University of Nebraska-Lincoln; Lincoln NE 68588
| | - Yong Han
- Department of Chemistry; University of Nebraska-Lincoln; Lincoln NE 68588
- Department of Natural Products, Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences; Shandong University; Jinan 250100 People's Republic of China
| | - Yuemao Shen
- Department of Natural Products, Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences; Shandong University; Jinan 250100 People's Republic of China
| | - Guoliang Qian
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University; Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education Nanjing; 210095 People's Republic of China
| | - Fengquan Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University; Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education Nanjing; 210095 People's Republic of China
- Department of Plant Pathology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences; Nanjing 210014 People's Republic of China
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26
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Mahoney AK, Yin C, Hulbert SH. Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat ( Triticum aestivum) Cultivars. FRONTIERS IN PLANT SCIENCE 2017; 8:132. [PMID: 28243246 PMCID: PMC5303725 DOI: 10.3389/fpls.2017.00132] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/23/2017] [Indexed: 05/23/2023]
Abstract
Minimal tillage management of extensive crops like wheat can provide significant environmental services but can also lead to adverse interactions between soil borne microbes and the host. Little is known about the ability of the wheat cultivar to alter the microbial community from a long-term recruitment standpoint, and whether this recruitment is consistent across field sites. To address this, nine winter wheat cultivars were grown for two consecutive seasons on the same plots on two different farm sites and assessed for their ability to alter the rhizosphere bacterial communities in a minimal tillage system. Using deep amplicon sequencing of the V1-V3 region of the 16S rDNA, a total of 26,604 operational taxonomic units (OTUs) were found across these two sites. A core bacteriome consisting of 962 OTUs were found to exist in 95% of the wheat rhizosphere samples. Differences in the relative abundances for these wheat cultivars were observed. Of these differences, 24 of the OTUs were found to be significantly different by wheat cultivar and these differences occurred at both locations. Several of the cultivar-associated OTUs were found to correspond with strains that may provide beneficial services to the host plant. Network correlations demonstrated significant co-occurrences for different taxa and their respective OTUs, and in some cases, these interactions were determined by the wheat cultivar. Microbial abundances did not play a role in the number of correlations, and the majority of the co-occurrences were shown to be positively associated. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was used to determine potential functions associated with OTUs by association with rhizosphere members which have sequenced metagenomics data. Potentially beneficial pathways for nitrogen, sulfur, phosphorus, and malate metabolism, as well as antimicrobial compounds, were inferred from this analysis. Differences in these pathways and their associated functions were found to differ by wheat cultivar. In conclusion, our study suggests wheat cultivars are involved in shaping the rhizosphere by differentially altering the bacterial OTUs consistently across different sites, and these altered bacterial communities may provide beneficial services to the host.
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Affiliation(s)
- Aaron K. Mahoney
- Department of Plant Pathology, Washington State University, PullmanWA, USA
- Molecular Plant Sciences, Washington State University, PullmanWA, USA
| | - Chuntao Yin
- Department of Plant Pathology, Washington State University, PullmanWA, USA
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, PullmanWA, USA
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27
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LetR is a TetR family transcription factor from Lysobacter controlling antifungal antibiotic biosynthesis. Appl Microbiol Biotechnol 2017; 101:3273-3282. [PMID: 28108764 DOI: 10.1007/s00253-017-8117-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 12/29/2016] [Accepted: 12/31/2016] [Indexed: 12/23/2022]
Abstract
Heat-stable antifungal factor (HSAF) is a newly identified and broad-spectrum antifungal antibiotic from Lysobacter enzymogenes, a ubiquitous environmental proteobacterium. Yet, the regulatory mechanism for HSAF biosynthesis in L. enzymogenes remains poorly understood. Here, we report the identification of a TetR-family protein Le1552 (LetR) from L. enzymogenes strain OH11 that is involved in transcriptional repression of HSAF production. Bacterial one-hybrid and gel mobility shift assays show that LetR directly binds to PHSAF (the promoter region of the HSAF biosynthesis operon). A DNA truncation assay further reveals a core region in PHSAF that is responsible for LetR binding. In-frame deletion of letR in wild-type OH11 is found to significantly increase HSAF levels and key biosynthetic gene transcription, while overexpression of letR in the wild-type background remarkably reduces HSAF levels as well as related gene expression instead. Together, we have identified not only a new regulator for the HSAF biosynthesis but also constructed a higher HSAF-producing deletion strain (ΔletR) of L. enzymogenes, which shall be of great value in promoting HSAF production for pharmaceutical and biological control purposes.
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28
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A LuxR Homolog in a Cottonwood Tree Endophyte That Activates Gene Expression in Response to a Plant Signal or Specific Peptides. mBio 2016; 7:mBio.01101-16. [PMID: 27486195 PMCID: PMC4981722 DOI: 10.1128/mbio.01101-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED Homologs of the LuxR acyl-homoserine lactone (AHL) quorum-sensing signal receptor are prevalent in Proteobacteria isolated from roots of the Eastern cottonwood tree, Populus deltoides Many of these isolates possess an orphan LuxR homolog, closely related to OryR from the rice pathogen Xanthomonas oryzae OryR does not respond to AHL signals but, instead, responds to an unknown plant compound. We discovered an OryR homolog, PipR, in the cottonwood endophyte Pseudomonas sp. strain GM79. The genes adjacent to pipR encode a predicted ATP-binding cassette (ABC) peptide transporter and peptidases. We purified the putative peptidases, PipA and AapA, and confirmed their predicted activities. A transcriptional pipA-gfp reporter was responsive to PipR in the presence of plant leaf macerates, but it was not influenced by AHLs, similar to findings with OryR. We found that PipR also responded to protein hydrolysates to activate pipA-gfp expression. Among many peptides tested, the tripeptide Ser-His-Ser showed inducer activity but at relatively high concentrations. An ABC peptide transporter mutant failed to respond to leaf macerates, peptone, or Ser-His-Ser, while peptidase mutants expressed higher-than-wild-type levels of pipA-gfp in response to any of these signals. Our studies are consistent with a model where active transport of a peptidelike signal is required for the signal to interact with PipR, which then activates peptidase gene expression. The identification of a peptide ligand for PipR sets the stage to identify plant-derived signals for the OryR family of orphan LuxR proteins. IMPORTANCE We describe the transcription factor PipR from a Pseudomonas strain isolated as a cottonwood tree endophyte. PipR is a member of the LuxR family of transcriptional factors. LuxR family members are generally thought of as quorum-sensing signal receptors, but PipR is one of an emerging subfamily of LuxR family members that respond to compounds produced by plants. We found that PipR responds to a peptidelike compound, and we present a model for Pip system signal transduction. A better understanding of plant-responsive LuxR homologs and the compounds to which they respond is of general importance, as they occur in dozens of bacterial species that are associated with economically important plants and, as we report here, they also occur in members of certain root endophyte communities.
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29
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Wang R, Xu H, Du L, Chou SH, Liu H, Liu Y, Liu F, Qian G. A TonB-dependent receptor regulates antifungal HSAF biosynthesis in Lysobacter. Sci Rep 2016; 6:26881. [PMID: 27241275 PMCID: PMC4886534 DOI: 10.1038/srep26881] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/25/2016] [Indexed: 11/25/2022] Open
Abstract
Lysobacter species are Gram-negative bacteria that are emerging as new sources of antibiotics, including HSAF (Heat Stable Antifungal Factor), which was identified from L. enzymogenes with a new mode of action. LesR, a LuxR solo, was recently shown to regulate the HSAF biosynthesis via an unidentified mechanism in L. enzymogenes OH11. Here, we used a comparative proteomic approach to identify the LesR targets and found that LesR influenced the expression of 33 proteins belonging to 10 functional groups, with 9 proteins belonging to the TBDR (TonB-Dependent Receptor) family. The fundamental role of bacterial TBDR in nutrient uptake motivates us to explore their potential regulation on HSAF biosynthesis which is also modulated by nutrient condition. Six out of 9 TBDR coding genes were individually in-frame deleted. Phenotypic and gene-expression assays showed that TBDR7, whose level was lower in a strain overexpressing lesR, was involved in regulating HSAF yield. TBDR7 was not involved in the growth, but played a vital role in transcribing the key HSAF biosynthetic gene. Taken together, the current lesR-based proteomic study provides the first report that TBDR7 plays a key role in regulating antibiotic (HSAF) biosynthesis, a function which has never been found for TBDRs in bacteria.
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Affiliation(s)
- Ruping Wang
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Huiyong Xu
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Shan-Ho Chou
- Institute of Biochemistry, and NCHU Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Hongxia Liu
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Youzhou Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, P.R. China
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Nanjing 210014, P.R. China
| | - Guoliang Qian
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, P.R. China
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Corral-Lugo A, Daddaoua A, Ortega A, Espinosa-Urgel M, Krell T. So different and still so similar: The plant compound rosmarinic acid mimics bacterial homoserine lactone quorum sensing signals. Commun Integr Biol 2016; 9:e1156832. [PMID: 27195067 PMCID: PMC4857781 DOI: 10.1080/19420889.2016.1156832] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 01/30/2023] Open
Abstract
Apart from inter-bacteria communication quorum sensing (QS) mechanisms also enable inter-domain interactions. To interfere with bacterial QS, plants were found to secrete compounds; most of which of unknown identity. We have identified the plant compound rosmarinic acid (RA) to modulate Pseudomonas aeruginosa QS by binding to the RhlR QS regulator. RA was found to be a homoserine-lactone (HSL) mimic that caused agonistic effects on transcription, resulting ultimately in a stimulation of several RhlR controlled phenotypes like virulence factor synthesis or biofilm formation. Our study was initiated by in silico screening of an RhlR model with compound libraries, demonstrating that this approach is suitable to tackle a major bottleneck in signal transduction research, which is the identification of sensor protein ligands. Previous work has shown that plant compounds interfere with the function of orphan QS regulators. Our study demonstrates that this has not necessarily to be the case since RhlR forms a functional pair with the RhlI synthase. A wide range of structurally dissimilar compounds have been found to mimic HSLs suggesting that this class of QS regulators is characterized by a significant plasticity in the recognition of effector molecules. Further research will show to what extent RA impacts on QS mechanisms of other bacteria.
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Affiliation(s)
- Andrés Corral-Lugo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , C/ Prof. Albareda , Granada, Spain
| | - Abdelali Daddaoua
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , C/ Prof. Albareda , Granada, Spain
| | - Alvaro Ortega
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , C/ Prof. Albareda , Granada, Spain
| | - Manuel Espinosa-Urgel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , C/ Prof. Albareda , Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , C/ Prof. Albareda , Granada, Spain
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Ismail AS, Valastyan JS, Bassler BL. A Host-Produced Autoinducer-2 Mimic Activates Bacterial Quorum Sensing. Cell Host Microbe 2016; 19:470-80. [PMID: 26996306 DOI: 10.1016/j.chom.2016.02.020] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/26/2016] [Accepted: 02/29/2016] [Indexed: 12/31/2022]
Abstract
Host-microbial symbioses are vital to health; nonetheless, little is known about the role crosskingdom signaling plays in these relationships. In a process called quorum sensing, bacteria communicate with one another using extracellular signal molecules called autoinducers. One autoinducer, AI-2, is proposed to promote interspecies bacterial communication, including in the mammalian gut. We show that mammalian epithelia produce an AI-2 mimic activity in response to bacteria or tight-junction disruption. This AI-2 mimic is detected by the bacterial AI-2 receptor, LuxP/LsrB, and can activate quorum-sensing-controlled gene expression, including in the enteric pathogen Salmonella typhimurium. AI-2 mimic activity is induced when epithelia are directly or indirectly exposed to bacteria, suggesting that a secreted bacterial component(s) stimulates its production. Mutagenesis revealed genes required for bacteria to both detect and stimulate production of the AI-2 mimic. These findings uncover a potential role for the mammalian AI-2 mimic in fostering crosskingdom signaling and host-bacterial symbioses.
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Affiliation(s)
- Anisa S Ismail
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Julie S Valastyan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815 USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815 USA.
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32
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Corral-Lugo A, Daddaoua A, Ortega A, Espinosa-Urgel M, Krell T. Rosmarinic acid is a homoserine lactone mimic produced by plants that activates a bacterial quorum-sensing regulator. Sci Signal 2016; 9:ra1. [PMID: 26732761 DOI: 10.1126/scisignal.aaa8271] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Quorum sensing is a bacterial communication mechanism that controls genes, enabling bacteria to live as communities, such as biofilms. Homoserine lactone (HSL) molecules function as quorum-sensing signals for Gram-negative bacteria. Plants also produce previously unidentified compounds that affect quorum sensing. We identified rosmarinic acid as a plant-derived compound that functioned as an HSL mimic. In vitro assays showed that rosmarinic acid bound to the quorum-sensing regulator RhlR of Pseudomonas aeruginosa PAO1 and competed with the bacterial ligand N-butanoyl-homoserine lactone (C4-HSL). Furthermore, rosmarinic acid stimulated a greater increase in RhlR-mediated transcription in vitro than that of C4-HSL. In P. aeruginosa, rosmarinic acid induced quorum sensing-dependent gene expression and increased biofilm formation and the production of the virulence factors pyocyanin and elastase. Because P. aeruginosa PAO1 infection induces rosmarinic acid secretion from plant roots, our results indicate that rosmarinic acid secretion is a plant defense mechanism to stimulate a premature quorum-sensing response. P. aeruginosa is a ubiquitous pathogen that infects plants and animals; therefore, identification of rosmarinic acid as an inducer of premature quorum-sensing responses may be useful in agriculture and inform human therapeutic strategies.
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Affiliation(s)
- Andrés Corral-Lugo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Abdelali Daddaoua
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Alvaro Ortega
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Manuel Espinosa-Urgel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain.
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Gardiner M, Fernandes ND, Nowakowski D, Raftery M, Kjelleberg S, Zhong L, Thomas T, Egan S. VarR controls colonization and virulence in the marine macroalgal pathogen Nautella italica R11. Front Microbiol 2015; 6:1130. [PMID: 26528274 PMCID: PMC4602140 DOI: 10.3389/fmicb.2015.01130] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/28/2015] [Indexed: 01/16/2023] Open
Abstract
There is increasing evidence to suggest that macroalgae (seaweeds) are susceptible to infectious disease. However, to date, little is known about the mechanisms that facilitate the colonization and virulence of microbial seaweed pathogens. One well-described example of a seaweed disease is the bleaching of the red alga Delisea pulchra, which can be caused by the bacterium Nautella italica R11, a member of the Roseobacter clade. This pathogen contains a unique luxR-type gene, varR, which we hypothesize controls its colonization and virulence. We show here that a varR knock-out strain is deficient in its ability to cause disease in D. pulchra and is defective in biofilm formation and attachment to a common algal polysaccharide. Moreover complementation of the varR gene in trans can restore these functions to the wild type levels. Proteomic analysis of bacterial cells in planktonic and biofilm growth highlight the potential importance of nitrogen scavenging, mobilization of energy reserves, and stress resistance in the biofilm lifestyle of N. italica R11. Moreover, we show that VarR regulates the expression of a specific subset of biofilm-associated proteins. Taken together these data suggest that VarR controls colonization and persistence of N. italica R11 on the surface of a macroalgal host and that it is an important regulator of virulence.
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Affiliation(s)
- Melissa Gardiner
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, The University of New South Wales Sydney, NSW, Australia
| | - Neil D Fernandes
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, The University of New South Wales Sydney, NSW, Australia
| | - Dennis Nowakowski
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, The University of New South Wales Sydney, NSW, Australia
| | - Mark Raftery
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, The University of New South Wales Sydney, NSW, Australia
| | - Staffan Kjelleberg
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, The University of New South Wales Sydney, NSW, Australia ; Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore Singapore
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, The University of New South Wales Sydney, NSW, Australia
| | - Torsten Thomas
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, The University of New South Wales Sydney, NSW, Australia
| | - Suhelen Egan
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, The University of New South Wales Sydney, NSW, Australia
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da Silva DP, Patel HK, González JF, Devescovi G, Meng X, Covaceuszach S, Lamba D, Subramoni S, Venturi V. Studies on synthetic LuxR solo hybrids. Front Cell Infect Microbiol 2015; 5:52. [PMID: 26151032 PMCID: PMC4471428 DOI: 10.3389/fcimb.2015.00052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 05/26/2015] [Indexed: 11/13/2022] Open
Abstract
A sub-group of LuxR family of proteins that plays important roles in quorum sensing, a process of cell-cell communication, is widespread in proteobacteria. These proteins have a typical modular structure consisting of N-ter autoinducer binding and C-ter helix-turn-helix (HTH) DNA binding domains. The autoinducer binding domain recognizes signaling molecules which are most often N-acyl homoserine lactones (AHLs) but could also be other novel and yet unidentified molecules. In this study we carried out a series of specific domain swapping and promoter activation experiments as a first step to engineer synthetic signaling modules, taking advantage of the modularity and the versatile/diverse signal specificities of LuxR proteins. In our experiments the N-ter domains from different LuxR homologs were either interchanged or placed in tandem followed by a C-ter domain. The rational design of the hybrid proteins was supported by a structure-based homology modeling studies of three members of the LuxR family (i.e., LasR, RhlR, and OryR being chosen for their unique ligand binding specificities) and of selected chimeras. Our results reveal that these LuxR homologs were able to activate promoter elements that were not their usual targets; we also show that hybrid LuxR proteins retained the ability to recognize the signal specific for their N- ter autoinducer binding domain. However, the activity of hybrid LuxR proteins containing two AHL binding domains in tandem appears to depend on the organization and nature of the introduced domains. This study represents advances in the understanding of the modularity of LuxR proteins and provides additional possibilities to use hybrid proteins in both basic and applied synthetic biology based research.
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Affiliation(s)
- Daniel Passos da Silva
- Bacteriology and Plant Bacteriology, International Centre for Genetic Engineering and Biotechnology Trieste, Italy ; Centro de Ciencias da Saude, Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
| | - Hitendra K Patel
- Bacteriology and Plant Bacteriology, International Centre for Genetic Engineering and Biotechnology Trieste, Italy
| | - Juan F González
- Bacteriology and Plant Bacteriology, International Centre for Genetic Engineering and Biotechnology Trieste, Italy
| | - Giulia Devescovi
- Bacteriology and Plant Bacteriology, International Centre for Genetic Engineering and Biotechnology Trieste, Italy
| | - Xianfa Meng
- Bacteriology and Plant Bacteriology, International Centre for Genetic Engineering and Biotechnology Trieste, Italy
| | - Sonia Covaceuszach
- Istituto di Cristallografia, Unità Organizzativa di Supporto di Basovizza (Trieste), Consiglio Nazionale delle Ricerche Trieste, Italy
| | - Doriano Lamba
- Istituto di Cristallografia, Unità Organizzativa di Supporto di Basovizza (Trieste), Consiglio Nazionale delle Ricerche Trieste, Italy
| | - Sujatha Subramoni
- Bacteriology and Plant Bacteriology, International Centre for Genetic Engineering and Biotechnology Trieste, Italy
| | - Vittorio Venturi
- Bacteriology and Plant Bacteriology, International Centre for Genetic Engineering and Biotechnology Trieste, Italy
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Martínez P, Huedo P, Martinez-Servat S, Planell R, Ferrer-Navarro M, Daura X, Yero D, Gibert I. Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839). Front Cell Infect Microbiol 2015; 5:41. [PMID: 26029670 PMCID: PMC4432800 DOI: 10.3389/fcimb.2015.00041] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/28/2015] [Indexed: 11/22/2022] Open
Abstract
Quorum Sensing (QS) mediated by Acyl Homoserine Lactone (AHL) molecules are probably the most widespread and studied among Gram-negative bacteria. Canonical AHL systems are composed by a synthase (LuxI family) and a regulator element (LuxR family), whose genes are usually adjacent in the genome. However, incomplete AHL-QS machinery lacking the synthase LuxI is frequently observed in Proteobacteria, and the regulator element is then referred as LuxR solo. It has been shown that certain LuxR solos participate in interspecific communication by detecting signals produced by different organisms. In the case of Stenotrophomonas maltophilia, a preliminary genome sequence analysis revealed numerous putative luxR genes, none of them associated to a luxI gene. From these, the hypothetical LuxR solo Smlt1839, here designated SmoR, presents a conserved AHL binding domain and a helix-turn-helix DNA binding motif. Its genomic organization—adjacent to hchA gene—indicate that SmoR belongs to the new family “LuxR regulator chaperone HchA-associated.” AHL-binding assays revealed that SmoR binds to AHLs in-vitro, at least to oxo-C8-homoserine lactone, and it regulates operon transcription, likely by recognizing a conserved palindromic regulatory box in the hchA upstream region. Supplementation with concentrated supernatants from Pseudomonas aeruginosa, which contain significant amounts of AHLs, promoted swarming motility in S. maltophilia. Contrarily, no swarming stimulation was observed when the P. aeruginosa supernatant was treated with the lactonase AiiA from Bacillus subtilis, confirming that AHL contributes to enhance the swarming ability of S. maltophilia. Finally, mutation of smoR resulted in a swarming alteration and an apparent insensitivity to the exogenous AHLs provided by P. aeruginosa. In conclusion, our results demonstrate that S. maltophilia senses AHLs produced by neighboring bacteria through the LuxR solo SmoR, regulating population behaviors such as swarming motility.
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Affiliation(s)
- Paula Martínez
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain ; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Pol Huedo
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain ; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Sònia Martinez-Servat
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain ; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Raquel Planell
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Mario Ferrer-Navarro
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Xavier Daura
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain ; Catalan Institution for Research and Advanced Studies Barcelona, Spain
| | - Daniel Yero
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain ; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Isidre Gibert
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain ; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
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Xu H, Zhao Y, Qian G, Liu F. XocR, a LuxR solo required for virulence in Xanthomonas oryzae pv. oryzicola. Front Cell Infect Microbiol 2015; 5:37. [PMID: 25932456 PMCID: PMC4399327 DOI: 10.3389/fcimb.2015.00037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 03/31/2015] [Indexed: 01/15/2023] Open
Abstract
Xanthomonas oryzae pv. oryzicola (Xoc) causes bacterial leaf streak (BLS) in rice, a serious bacterial disease of rice in Asia and parts of Africa. The virulence mechanisms of Xoc are not entirely clear and control measures for BLS are poorly developed. The solo LuxR proteins are widespread and shown to be involved in virulence in some plant associated bacteria (PAB). Here, we have cloned and characterized a PAB LuxR solo from Xoc, named as XocR. Mutation of xocR almost completely impaired the virulence ability of Xoc on host rice, but did not alter the ability to trigger HR (hypersensitive response, a programmed cell death) on non-host (plant) tobacco, suggesting the diversity of function of xocR in host and non-host plants. We also provide evidence to show that xocR is involved in the regulation of growth-independent cell motility in response to a yet-to-be-identified rice signal, as mutation of xocR impaired cell swimming motility of wild-type Rs105 in the presence but not absence of rice macerate. We further found that xocR regulated the transcription of two characterized virulence-associated genes (recN and trpE) in the presence of rice macerate. The promoter regions of recN and trpE possessed a potential binding motif (an imperfect pip box-like element) of XocR, raising the possibility that XocR might directly bind the promoter regions of these two genes to regulate their transcriptional activity. Our studies add a new member of PAB LuxR solos and also provide new insights into the role of PAB LuxR solo in the virulence of Xanthomonas species.
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Affiliation(s)
- Huiyong Xu
- Institute of Plant Protection, Jiangsu Academy of Agricultural ScienceNanjing, China
- College of Plant Protection, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of EducationNanjing, China
| | - Yancun Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural ScienceNanjing, China
| | - Guoliang Qian
- College of Plant Protection, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of EducationNanjing, China
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural ScienceNanjing, China
- College of Plant Protection, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of EducationNanjing, China
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Subramoni S, Florez Salcedo DV, Suarez-Moreno ZR. A bioinformatic survey of distribution, conservation, and probable functions of LuxR solo regulators in bacteria. Front Cell Infect Microbiol 2015; 5:16. [PMID: 25759807 PMCID: PMC4338825 DOI: 10.3389/fcimb.2015.00016] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 02/02/2015] [Indexed: 12/25/2022] Open
Abstract
LuxR solo transcriptional regulators contain both an autoinducer binding domain (ABD; N-terminal) and a DNA binding Helix-Turn-Helix domain (HTH; C-terminal), but are not associated with a cognate N-acyl homoserine lactone (AHL) synthase coding gene in the same genome. Although a few LuxR solos have been characterized, their distributions as well as their role in bacterial signal perception and other processes are poorly understood. In this study we have carried out a systematic survey of distribution of all ABD containing LuxR transcriptional regulators (QS domain LuxRs) available in the InterPro database (IPR005143), and identified those lacking a cognate AHL synthase. These LuxR solos were then analyzed regarding their taxonomical distribution, predicted functions of neighboring genes and the presence of complete AHL-QS systems in the genomes that carry them. Our analyses reveal the presence of one or multiple predicted LuxR solos in many proteobacterial genomes carrying QS domain LuxRs, some of them harboring genes for one or more AHL-QS circuits. The presence of LuxR solos in bacteria occupying diverse environments suggests potential ecological functions for these proteins beyond AHL and interkingdom signaling. Based on gene context and the conservation levels of invariant amino acids of ABD, we have classified LuxR solos into functionally meaningful groups or putative orthologs. Surprisingly, putative LuxR solos were also found in a few non-proteobacterial genomes which are not known to carry AHL-QS systems. Multiple predicted LuxR solos in the same genome appeared to have different levels of conservation of invariant amino acid residues of ABD questioning their binding to AHLs. In summary, this study provides a detailed overview of distribution of LuxR solos and their probable roles in bacteria with genome sequence information.
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Affiliation(s)
- Sujatha Subramoni
- Grupo de Bioprospección, Facultad de Ingeniería, Universidad de La Sabana, Campus del Puente del Común Chía, Colombia
| | | | - Zulma R Suarez-Moreno
- Grupo de Bioprospección, Facultad de Ingeniería, Universidad de La Sabana, Campus del Puente del Común Chía, Colombia
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Xu J, Zhou L, Venturi V, He YW, Kojima M, Sakakibari H, Höfte M, De Vleesschauwer D. Phytohormone-mediated interkingdom signaling shapes the outcome of rice-Xanthomonas oryzae pv. oryzae interactions. BMC PLANT BIOLOGY 2015; 15:10. [PMID: 25605284 PMCID: PMC4307914 DOI: 10.1186/s12870-014-0411-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 12/30/2014] [Indexed: 05/25/2023]
Abstract
BACKGROUND Small-molecule hormones are well known to play key roles in the plant immune signaling network that is activated upon pathogen perception. In contrast, little is known about whether phytohormones also directly influence microbial virulence, similar to what has been reported in animal systems. RESULTS In this paper, we tested the hypothesis that hormones fulfill dual roles in plant-microbe interactions by orchestrating host immune responses, on the one hand, and modulating microbial virulence traits, on the other. Employing the rice-Xanthomonas oryzae pv. oryzae (Xoo) interaction as a model system, we show that Xoo uses the classic immune hormone salicylic acid (SA) as a trigger to activate its virulence-associated quorum sensing (QS) machinery. Despite repressing swimming motility, sodium salicylate (NaSA) induced production of the Diffusible Signal Factor (DSF) and Diffusible Factor (DF) QS signals, with resultant accumulation of xanthomonadin and extracellular polysaccharides. In contrast, abscisic acid (ABA), which favors infection by Xoo, had little impact on DF- and DSF-mediated QS, but promoted bacterial swimming via the LuxR solo protein OryR. Moreover, we found both DF and DSF to influence SA- and ABA-responsive gene expression in planta. CONCLUSIONS Together our findings indicate that the rice SA and ABA signaling pathways cross-communicate with the Xoo DF and DSF QS systems and underscore the importance of bidirectional interkingdom signaling in molding plant-microbe interactions.
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Affiliation(s)
- Jing Xu
- Lab of Phytopathology, Department of Crop Protection, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Lian Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy.
| | - Ya-Wen He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan.
| | - Hitoshi Sakakibari
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan.
| | - Monica Höfte
- Lab of Phytopathology, Department of Crop Protection, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - David De Vleesschauwer
- Lab of Phytopathology, Department of Crop Protection, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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Gan HM, Gan HY, Ahmad NH, Aziz NA, Hudson AO, Savka MA. Whole genome sequencing and analysis reveal insights into the genetic structure, diversity and evolutionary relatedness of luxI and luxR homologs in bacteria belonging to the Sphingomonadaceae family. Front Cell Infect Microbiol 2015; 4:188. [PMID: 25621282 PMCID: PMC4288048 DOI: 10.3389/fcimb.2014.00188] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/16/2014] [Indexed: 12/18/2022] Open
Abstract
Here we report the draft genomes and annotation of four N-acyl homoserine lactone (AHL)-producing members from the family Sphingomonadaceae. Comparative genomic analyses of 62 Sphingomonadaceae genomes were performed to gain insights into the distribution of the canonical luxI/R-type quorum sensing (QS) network within this family. Forty genomes contained at least one luxR homolog while the genome of Sphingobium yanoikuyae B1 contained seven Open Reading Frames (ORFs) that have significant homology to that of luxR. Thirty-three genomes contained at least one luxI homolog while the genomes of Sphingobium sp. SYK6, Sphingobium japonicum, and Sphingobium lactosutens contained four luxI. Using phylogenetic analysis, the sphingomonad LuxR homologs formed five distinct clades with two minor clades located near the plant associated bacteria (PAB) LuxR solo clade. This work for the first time shows that 13 Sphingobium and one Sphingomonas genome(s) contain three convergently oriented genes composed of two tandem luxR genes proximal to one luxI (luxR-luxR-luxI). Interestingly, luxI solos were identified in two Sphingobium species and may represent species that contribute to AHL-based QS system by contributing AHL molecules but are unable to perceive AHLs as signals. This work provides the most comprehensive description of the luxI/R circuitry and genome-based taxonomical description of the available sphingomonad genomes to date indicating that the presence of luxR solos and luxI solos are not an uncommon feature in members of the Sphingomonadaceae family.
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Affiliation(s)
- Han Ming Gan
- School of Science, Monash University Malaysia Petaling Jaya, Malaysia ; Genomics Facility, Monash University Malaysia Petaling Jaya, Malaysia
| | - Huan You Gan
- School of Science, Monash University Malaysia Petaling Jaya, Malaysia ; Genomics Facility, Monash University Malaysia Petaling Jaya, Malaysia
| | - Nurul H Ahmad
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology Rochester NY, USA
| | - Nazrin A Aziz
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology Rochester NY, USA
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology Rochester NY, USA
| | - Michael A Savka
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology Rochester NY, USA
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Quiza L, St-Arnaud M, Yergeau E. Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering. FRONTIERS IN PLANT SCIENCE 2015; 6:507. [PMID: 26236319 PMCID: PMC4500914 DOI: 10.3389/fpls.2015.00507] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/25/2015] [Indexed: 05/18/2023]
Abstract
The goal of microbiome engineering is to manipulate the microbiome toward a certain type of community that will optimize plant functions of interest. For instance, in crop production the goal is to reduce disease susceptibility, increase nutrient availability increase abiotic stress tolerance and increase crop yields. Various approaches can be devised to engineer the plant-microbiome, but one particularly promising approach is to take advantage of naturally evolved plant-microbiome communication channels. This is, however, very challenging as the understanding of the plant-microbiome communication is still mostly rudimentary and plant-microbiome interactions varies between crops species (and even cultivars), between individual members of the microbiome and with environmental conditions. In each individual case, many aspects of the plant-microorganisms relationship should be thoroughly scrutinized. In this article we summarize some of the existing plant-microbiome engineering studies and point out potential avenues for further research.
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Affiliation(s)
- Liliana Quiza
- Energy, Mining and Environment, National Research Council Canada, MontréalQC, Canada
- Institut de Recherche en Biologie Végétale – Jardin Botanique de Montréal and Université de Montréal, MontréalQC, Canada
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale – Jardin Botanique de Montréal and Université de Montréal, MontréalQC, Canada
| | - Etienne Yergeau
- Energy, Mining and Environment, National Research Council Canada, MontréalQC, Canada
- *Correspondence: Etienne Yergeau, National Research Council Canada, 6100 Royalmount Avenue, Montréal, QC H4P 2R2, Canada,
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Coutinho BG, Licastro D, Mendonça-Previato L, Cámara M, Venturi V. Plant-Influenced Gene Expression in the Rice Endophyte Burkholderia kururiensis M130. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:10-21. [PMID: 25494355 DOI: 10.1094/mpmi-07-14-0225-r] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Burkholderia kururiensis M130 is one of the few rice endophytic diazotrophic bacteria identified thus far which is able to enhance growth of rice. To date, very little is known of how strain M130 and other endophytes enter and colonize plants. Here, we identified genes of strain M130 that are differentially regulated in the presence of rice plant extract. A genetic screening of a promoter probe transposon mutant genome bank and RNAseq analysis were performed. The screening of 10,100 insertions of the genomic transposon reporter library resulted in the isolation of 61 insertions displaying differential expression in response to rice macerate. The RNAseq results validated this screen and indicated that this endophytic bacterium undergoes major changes in the presence of plant extract regulating 27.7% of its open reading frames. A large number of differentially expressed genes encode membrane transporters and secretion systems, indicating that the exchange of molecules is an important aspect of bacterial endophytic growth. Genes related to motility, chemotaxis, and adhesion were also overrepresented, further suggesting plant–bacteria interaction. This work highlights the potential close signaling taking place between plants and bacteria and helps us to begin to understand the adaptation of an endophyte in planta.
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Patel HK, Ferrante P, Covaceuszach S, Lamba D, Scortichini M, Venturi V. The kiwifruit emerging pathogen Pseudomonas syringae pv. actinidiae does not produce AHLs but possesses three luxR solos. PLoS One 2014; 9:e87862. [PMID: 24498215 PMCID: PMC3909224 DOI: 10.1371/journal.pone.0087862] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/30/2013] [Indexed: 12/30/2022] Open
Abstract
Pseudomonas syringae pv. actinidiae (Psa) is an emerging phytopathogen causing bacterial canker disease in kiwifruit plants worldwide. Quorum sensing (QS) gene regulation plays important roles in many different bacterial plant pathogens. In this study we analyzed the presence and possible role of N-acyl homoserine lactone (AHL) quorum sensing in Psa. It was established that Psa does not produce AHLs and that a typical complete LuxI/R QS system is absent in Psa strains. Psa however possesses three putative luxR solos designated here as PsaR1, PsaR2 and PsaR3. PsaR2 belongs to the sub-family of LuxR solos present in many plant associated bacteria (PAB) that binds and responds to yet unknown plant signal molecules. PsaR1 and PsaR3 are highly similar to LuxRs which bind AHLs and are part of the canonical LuxI/R AHL QS systems. Mutation in all the three luxR solos of Psa showed reduction of in planta survival and also showed additive effect if more than one solo was inactivated in double mutants. Gene promoter analysis revealed that the three solos are not auto-regulated and investigated their possible role in several bacterial phenotypes.
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Affiliation(s)
| | - Patrizia Ferrante
- Research Centre for Fruit Crops, Agricultural Research Council, Roma, Italy
| | - Sonia Covaceuszach
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, U.O.S di Trieste, Trieste, Italy
| | - Doriano Lamba
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, U.O.S di Trieste, Trieste, Italy
| | - Marco Scortichini
- Research Centre for Fruit Crops, Agricultural Research Council, Roma, Italy
- Research Unit for Fruit Trees, Agricultural Research Council, Caserta, Italy
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
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Dudnik A, Dudler R. Genomics-Based Exploration of Virulence Determinants and Host-Specific Adaptations of Pseudomonas syringae Strains Isolated from Grasses. Pathogens 2014; 3:121-48. [PMID: 25437611 PMCID: PMC4235733 DOI: 10.3390/pathogens3010121] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 12/14/2022] Open
Abstract
The Pseudomonas syringae species complex has recently been named the number one plant pathogen, due to its economic and environmental impacts, as well as for its role in scientific research. The bacterium has been repeatedly reported to cause outbreaks on bean, cucumber, stone fruit, kiwi and olive tree, as well as on other crop and non-crop plants. It also serves as a model organism for research on the Type III secretion system (T3SS) and plant-pathogen interactions. While most of the current work on this pathogen is either carried out on one of three model strains found on dicot plants with completely sequenced genomes or on isolates obtained from recent outbreaks, not much is known about strains isolated from grasses (Poaceae). Here, we use comparative genomics in order to identify putative virulence-associated genes and other Poaceae-specific adaptations in several newly available genome sequences of strains isolated from grass species. All strains possess only a small number of known Type III effectors, therefore pointing to the importance of non-Type III secreted virulence factors. The implications of this finding are discussed.
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Affiliation(s)
- Alexey Dudnik
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
| | - Robert Dudler
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
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Patel HK, Suárez-Moreno ZR, Degrassi G, Subramoni S, González JF, Venturi V. Bacterial LuxR solos have evolved to respond to different molecules including signals from plants. FRONTIERS IN PLANT SCIENCE 2013; 4:447. [PMID: 24273546 DOI: 10.3389/fpls.2013.00447.03] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 10/19/2013] [Indexed: 05/26/2023]
Abstract
A future challenge will be understanding the extensive communication that most likely takes place in bacterial interspecies and interkingdom signaling between plants and bacteria. A major bacterial inter-cellular signaling system in Gram-negative bacteria is LuxI/R quorum sensing (QS) based on the production (via the LuxI-family proteins) and detection (via the LuxR-family proteins) of N-acyl homoserine lactones (AHLs) signaling molecules. LuxR proteins which have the same modular structure of QS LuxRs but are devoid of a cognate LuxI AHL synthase are called solos. LuxR solos have been shown to be responsible to respond to exogenous AHLs produced by neighboring cells as well endogenously produced AHLs. It is now also evident that some LuxR proteins have evolved from the ability to binding AHLs and respond to other molecules/signals. For example, recent research has shown that a sub-family of LuxR solos responds to small molecules produced by plants. This indicates the presence of a uni-directional interkingdom signaling system occurring from plants to bacteria. In addition LuxR solos have now been also implicated to respond to endogenously produced signals which are not AHLs. In this Mini Review article we will discuss current trends and implications of the role of LuxR solos in bacterial responses to other signals using proteins related to AHL QS systems.
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Affiliation(s)
- Hitendra K Patel
- International Centre for Genetic Engineering and Biotechnology Trieste, Italy
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Covaceuszach S, Degrassi G, Venturi V, Lamba D. Structural insights into a novel interkingdom signaling circuit by cartography of the ligand-binding sites of the homologous quorum sensing LuxR-family. Int J Mol Sci 2013; 14:20578-96. [PMID: 24132148 PMCID: PMC3821632 DOI: 10.3390/ijms141020578] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/13/2013] [Accepted: 10/01/2013] [Indexed: 01/06/2023] Open
Abstract
Recent studies have identified a novel interkingdom signaling circuit, via plant signaling molecules, and a bacterial sub-family of LuxR proteins, bridging eukaryotes and prokaryotes. Indeed pivotal plant-bacteria interactions are regulated by the so called Plant Associated Bacteria (PAB) LuxR solo regulators that, although closely related to the quorum sensing (QS) LuxR family, do not bind or respond to canonical quorum sensing N-acyl homoserine lactones (AHLs), but only to specific host plant signal molecules. The large body of structural data available for several members of the QS LuxR family complexed with different classes of ligands (AHLs and other compounds), has been exploited to dissect the cartography of their regulatory domains through structure-based multiple sequence alignments, structural superimposition and a comparative analysis of the contact residues involved in ligand binding. In the absence of experimentally determined structures of members of the PAB LuxR solos subfamily, an homology model of its prototype OryR is presented, aiming to elucidate the architecture of its ligand-binding site. The obtained model, in combination with the cartography of the regulatory domains of the homologous QS LuxRs, provides novel insights into the 3D structure of its ligand-binding site and unveils the probable molecular determinants responsible for differences in selectivity towards specific host plant signal molecules, rather than to canonical QS compounds.
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Affiliation(s)
- Sonia Covaceuszach
- Institute of Crystallography, National Research Council, Trieste Outstation, Area Science Park-Basovizza, S.S. n° 14 Km 163.5, I-34149 Trieste, Italy; E-Mail:
| | - Giuliano Degrassi
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy; E-Mail:
- IBIOBA-CONICET-ICGEB, International Centre for Genetic Engineering and Biotechnology, Scientific and Technological Center, Godoy Cruz 2390, C1425FQD, Buenos Aires, Argentina
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34149 Trieste, Italy; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (V.V.); (D.L.); Tel.: +39-40-3757319 (V.V.); +39-40-3758514 (D.L.); Fax: +39-40-226555 (V.V.); +39-40-9221126 (D.L.)
| | - Doriano Lamba
- Institute of Crystallography, National Research Council, Trieste Outstation, Area Science Park-Basovizza, S.S. n° 14 Km 163.5, I-34149 Trieste, Italy; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (V.V.); (D.L.); Tel.: +39-40-3757319 (V.V.); +39-40-3758514 (D.L.); Fax: +39-40-226555 (V.V.); +39-40-9221126 (D.L.)
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Mendes R, Garbeva P, Raaijmakers JM. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 2013; 37:634-63. [DOI: 10.1111/1574-6976.12028] [Citation(s) in RCA: 1382] [Impact Index Per Article: 125.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 05/22/2013] [Accepted: 05/27/2013] [Indexed: 12/18/2022] Open
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González JF, Myers MP, Venturi V. The inter-kingdom solo OryR regulator of Xanthomonas oryzae is important for motility. MOLECULAR PLANT PATHOLOGY 2013; 14:211-21. [PMID: 23083431 PMCID: PMC6638885 DOI: 10.1111/j.1364-3703.2012.00843.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The LuxR-type transcriptional regulator OryR of the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo) is a member of a subgroup of regulators found in plant-associated bacteria that are known to respond to plant signals. OryR has been shown previously to positively regulate the neighbouring pip gene and to be important for rice virulence. The role of this inter-kingdom signalling regulator was investigated through a genome-wide transcriptome analysis. OryR was found to positively regulate 220 genes, whereas 110 were down-regulated. A significant over-representation of movement-related genes among the positively regulated ones was found, including 30 flagellar genes, accounting for 14% of the up-regulated genes above the two-fold cut-off value. In Xoo, both swimming and swarming respond to rice macerate and OryR plays a role in the induction of both of these types of motility under these conditions. In this study, we have also shown that the flagellar regulator flhF contains a lux box-like element in its promoter region, similar to the oryR-regulated neighbouring pip gene; via the use of a transcriptional fusion reporter, it was shown that flhF is regulated by OryR. Finally, the role of OryR in motility was also demonstrated by the significant reduction in flagellin content in the oryR Xoo mutant with respect to the wild-type, as observed by in planta proteomics studies.
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Affiliation(s)
- Juan F González
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
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González JF, Venturi V. A novel widespread interkingdom signaling circuit. TRENDS IN PLANT SCIENCE 2013; 18:167-74. [PMID: 23089307 DOI: 10.1016/j.tplants.2012.09.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 09/14/2012] [Accepted: 09/21/2012] [Indexed: 05/08/2023]
Abstract
Extensive communication is believed to occur between eukaryotes and prokaryotes via signaling molecules; this field of research is now called interkingdom signaling. Recently, it has been discovered that many different plant-associated bacteria possess a protein closely related to the quorum-sensing (QS) LuxR-family protein that binds and responds to plant compounds. This LuxR protein does not have a cognate N-acyl homoserine lactone (AHL) signal synthase and therefore is regarded as a 'solo' or 'orphan'. The protein is involved in interkingdom signaling in rhizobia, xanthomonads, and pseudomonads, regulating processes important for plant-bacteria interaction. In this review, we focus on this new interkingdom signaling circuit, which is widespread among pathogenic and beneficial plant-associated bacteria.
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Affiliation(s)
- Juan F González
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
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49
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Patel HK, Suárez-Moreno ZR, Degrassi G, Subramoni S, González JF, Venturi V. Bacterial LuxR solos have evolved to respond to different molecules including signals from plants. FRONTIERS IN PLANT SCIENCE 2013; 4:447. [PMID: 24273546 PMCID: PMC3824090 DOI: 10.3389/fpls.2013.00447] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 10/19/2013] [Indexed: 05/08/2023]
Abstract
A future challenge will be understanding the extensive communication that most likely takes place in bacterial interspecies and interkingdom signaling between plants and bacteria. A major bacterial inter-cellular signaling system in Gram-negative bacteria is LuxI/R quorum sensing (QS) based on the production (via the LuxI-family proteins) and detection (via the LuxR-family proteins) of N-acyl homoserine lactones (AHLs) signaling molecules. LuxR proteins which have the same modular structure of QS LuxRs but are devoid of a cognate LuxI AHL synthase are called solos. LuxR solos have been shown to be responsible to respond to exogenous AHLs produced by neighboring cells as well endogenously produced AHLs. It is now also evident that some LuxR proteins have evolved from the ability to binding AHLs and respond to other molecules/signals. For example, recent research has shown that a sub-family of LuxR solos responds to small molecules produced by plants. This indicates the presence of a uni-directional interkingdom signaling system occurring from plants to bacteria. In addition LuxR solos have now been also implicated to respond to endogenously produced signals which are not AHLs. In this Mini Review article we will discuss current trends and implications of the role of LuxR solos in bacterial responses to other signals using proteins related to AHL QS systems.
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Affiliation(s)
| | | | | | | | | | - Vittorio Venturi
- *Correspondence: Vittorio Venturi, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy e-mail:
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50
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Venturi V, Fuqua C. Chemical signaling between plants and plant-pathogenic bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:17-37. [PMID: 23915131 DOI: 10.1146/annurev-phyto-082712-102239] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Studies of chemical signaling between plants and bacteria in the past have been largely confined to two models: the rhizobial-legume symbiotic association and pathogenesis between agrobacteria and their host plants. Recent studies are beginning to provide evidence that many plant-associated bacteria undergo chemical signaling with the plant host via low-molecular-weight compounds. Plant-produced compounds interact with bacterial regulatory proteins that then affect gene expression. Similarly, bacterial quorum-sensing signals result in a range of functional responses in plants. This review attempts to highlight current knowledge in chemical signaling that takes place between pathogenic bacteria and plants. This chemical communication between plant and bacteria, also referred to as interkingdom signaling, will likely become a major research field in the future, as it allows the design of specific strategies to create plants that are resistant to plant pathogens.
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Affiliation(s)
- Vittorio Venturi
- International Center for Genetic Engineering and Biotechnology, 34149 Trieste, Italy.
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