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Xue M, Xie Y, Zang X, Zhong Y, Ma X, Sun H, Liu J. Deciphering functional groups of rumen microbiome and their underlying potentially causal relationships in shaping host traits. IMETA 2024; 3:e225. [PMID: 39135684 PMCID: PMC11316931 DOI: 10.1002/imt2.225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 08/15/2024]
Abstract
Over the years, microbiome research has achieved tremendous advancements driven by culture-independent meta-omics approaches. Despite extensive research, our understanding of the functional roles and causal effects of the microbiome on phenotypes remains limited. In this study, we focused on the rumen metaproteome, combining it with metatranscriptome and metabolome data to accurately identify the active functional distributions of rumen microorganisms and specific functional groups that influence feed efficiency. By integrating host genetics data, we established the potentially causal relationships between microbes-proteins/metabolites-phenotype, and identified specific patterns in which functional groups of rumen microorganisms influence host feed efficiency. We found a causal link between Selenomonas bovis and rumen carbohydrate metabolism, potentially mediated by bacterial chemotaxis and a two-component regulatory system, impacting feed utilization efficiency of dairy cows. Our study on the nutrient utilization functional groups in the rumen of high-feed-efficiency dairy cows, along with the identification of key microbiota functional proteins and their potentially causal relationships, will help move from correlation to causation in rumen microbiome research. This will ultimately enable precise regulation of the rumen microbiota for optimized ruminant production.
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Affiliation(s)
- Ming‐Yuan Xue
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
- Xianghu LaboratoryHangzhouChina
| | - Yun‐Yi Xie
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
| | - Xin‐Wei Zang
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
| | - Yi‐Fan Zhong
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
| | - Xiao‐Jiao Ma
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
| | - Hui‐Zeng Sun
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
- Ministry of Education Key Laboratory of Molecular Animal NutritionZhejiang UniversityHangzhouChina
| | - Jian‐Xin Liu
- Institute of Dairy Science, College of Animal SciencesZhejiang UniversityHangzhouChina
- Ministry of Education Key Laboratory of Molecular Animal NutritionZhejiang UniversityHangzhouChina
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2
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Jiang F, Jiang Z, Huang J, Tang P, Cui J, Feng W, Yu C, Fu C, Lu Q. Exploration of potential driving mechanisms of Comamonas testosteroni in polycyclic aromatic hydrocarbons degradation and remodelled bacterial community during co-composting. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:132032. [PMID: 37451101 DOI: 10.1016/j.jhazmat.2023.132032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/14/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a cluster of highly hazardous organic pollutants that are widespread in ecosystems and threaten human health. Composting has been shown to be an effective strategy for PAHs degredation. Here, we used Comamonas testosteroni as an inoculant in composting and investigated the potential mechanisms of PAHs degradation by co-occurrence network and structural equation modelling analysis. The results showed that more than 60% of PAHs were removed and the bacterial community responded to the negative effects of PAHs by upgrading the network. Inoculation with C. testosteroni altered bacterial community succession, intensified bacterial response to PAHs, improved metabolic activity, and promoted the degradation of PAHs during co-composting. The increased in the positive cohesion index of the community suggested that agents increased the cooperative behaviour between bacteria and led to changes in keystones of the bacterial network. However, the topological values of C. testosteroni in the network were not elevated, which confirmed that C. testosteroni altered communities by affecting other bacterial growth rather than its own colonisation. This study strengthens our comprehension of the potential mechanisms for the degradation of PAHs in inoculated composting.
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Affiliation(s)
- Fangzhi Jiang
- College of Life Sciences and Technology, Harbin Normal University, Harbin 150025, China
| | - Ziwei Jiang
- College of Life Sciences and Technology, Harbin Normal University, Harbin 150025, China
| | - Jiayue Huang
- College of Life Sciences and Technology, Harbin Normal University, Harbin 150025, China
| | - Pengfei Tang
- Heilongjiang Provincial Ecological Environment Monitoring Center, Harbin 150056, China
| | - Jizhe Cui
- College of Life Sciences and Technology, Harbin Normal University, Harbin 150025, China
| | - Wenxuan Feng
- College of Life Sciences and Technology, Harbin Normal University, Harbin 150025, China
| | - Chunjing Yu
- College of Life Sciences and Technology, Harbin Normal University, Harbin 150025, China
| | - Chang Fu
- College of Life Sciences and Technology, Harbin Normal University, Harbin 150025, China
| | - Qian Lu
- College of Life Sciences and Technology, Harbin Normal University, Harbin 150025, China.
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Dong Y, Xu D, Zhang J, Wang Q, Pang S, Zhang G, Campos LC, Lv L, Liu X, Gao W, Sun L, Ren Z, Wang P. Enhanced antibiotic wastewater degradation by intimately coupled B-Bi 3O 4Cl photocatalysis and biodegradation reactor: Elucidating degradation principle systematically. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130364. [PMID: 36463742 DOI: 10.1016/j.jhazmat.2022.130364] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
Intimately coupled photocatalysis and biodegradation (ICPB) is an emerging technology that has potential applications in the degradation of bio-recalcitrant pollutants. However, the interaction principles between photocatalysts and biofilms in ICPB have not been well developed. This article covers a cooperative degradation scheme coupling photocatalysis and biodegradation for efficient degradation and mineralization of ciprofloxacin (CIP) using ICPB with B-doped Bi3O4Cl as the photocatalyst. In consequence, a removal rate of ∼95 % is reached after 40 d. The biofilms inside the ICPB carriers can mineralize the photocatalytic products, thus improving the removal rate of total organic carbon (TOC) by more than 20 %. Interior biofilms are not destroyed by CIP or photocatalysis, and they adapt to ICPB of CIP by enriching in Pseudoxanthomonas, Ferruginibacter, Clostridium, Stenotrophomonas and Comamonas and reconstructing their microbial communities using energy produced by the light-excited photoelectrons. Furthermore, this research gives new opinion into the degradation principles of the ICPB system.
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Affiliation(s)
- Yilin Dong
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China; Tianjin Key Laboratory of Clean Energy and Pollutant Control, Tianjin 300401, China
| | - Dongyu Xu
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China; Tianjin Key Laboratory of Clean Energy and Pollutant Control, Tianjin 300401, China
| | - Jie Zhang
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China; Tianjin Key Laboratory of Clean Energy and Pollutant Control, Tianjin 300401, China
| | - Qiuwen Wang
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China; Tianjin Key Laboratory of Clean Energy and Pollutant Control, Tianjin 300401, China
| | - Shaoxuan Pang
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China; Tianjin Key Laboratory of Clean Energy and Pollutant Control, Tianjin 300401, China
| | - Guangming Zhang
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China; Tianjin Key Laboratory of Clean Energy and Pollutant Control, Tianjin 300401, China
| | - Luiza C Campos
- Department of Civil, Environmental and Geomatic Engineering, University College London, London WC1E 6BT, United Kingdom
| | - Longyi Lv
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China; Tianjin Key Laboratory of Clean Energy and Pollutant Control, Tianjin 300401, China
| | - Xiaoyang Liu
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China; Tianjin Key Laboratory of Clean Energy and Pollutant Control, Tianjin 300401, China
| | - Wenfang Gao
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China; Tianjin Key Laboratory of Clean Energy and Pollutant Control, Tianjin 300401, China
| | - Li Sun
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China; Tianjin Key Laboratory of Clean Energy and Pollutant Control, Tianjin 300401, China
| | - Zhijun Ren
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China; Tianjin Key Laboratory of Clean Energy and Pollutant Control, Tianjin 300401, China.
| | - Pengfei Wang
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China; Tianjin Key Laboratory of Clean Energy and Pollutant Control, Tianjin 300401, China.
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Chen HH, Wang YX, Li DF, Liu C, Bi SY, Jiang CY, Liu SJ. Chemoreceptors from the commensal gut Roseburia rectibacter bind to mucin and trigger chemotaxis. Environ Microbiol 2023. [PMID: 36869629 DOI: 10.1111/1462-2920.16365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/02/2023] [Indexed: 03/05/2023]
Abstract
Chemotaxis is crucial for bacterial adherence and colonization of the host gastrointestinal tract. Previous studies have demonstrated that chemotaxis affects the virulence of causative pathogens and the infection in the host. However, the chemotactic abilities of non-pathogenic and commensal gut bacteria have rarely been explored. We observed that Roseburia rectibacter NSJ-69 exhibited flagella-dependent motility and chemotaxis to a variety of molecules, including mucin and propionate. A genome-wide analysis revealed that NSJ-69 has 28 putative chemoreceptors, 15 of which have periplasmic ligand-binding domains (LBDs). These LBD-coding genes were chemically synthesized and expressed heterologously in Escherichia coli. Intensive screening of ligands revealed four chemoreceptors bound to mucin and two bound to propionate. When expressed in Comamonas testosteroni or E. coli, these chemoreceptors elicited chemotaxis toward mucin and propionate. Hybrid chemoreceptors were constructed, and results showed that the chemotactic responses to mucin and propionate were dependent on the LBDs of R. rectibacter chemoreceptors. Our study identified and characterized R. rectibacter chemoreceptors. These results will facilitate further investigations on the involvement of microbial chemotaxis in host colonization.
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Affiliation(s)
- Hong-He Chen
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yu-Xin Wang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, People's Republic of China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Chang Liu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China.,State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, People's Republic of China
| | - Shuang-Yu Bi
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, People's Republic of China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China.,State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, People's Republic of China
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Ortega Á, Matilla MA, Krell T. The Repertoire of Solute-Binding Proteins of Model Bacteria Reveals Large Differences in Number, Type, and Ligand Range. Microbiol Spectr 2022; 10:e0205422. [PMID: 36121253 PMCID: PMC9602780 DOI: 10.1128/spectrum.02054-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/24/2022] [Indexed: 12/31/2022] Open
Abstract
Solute-binding proteins (SBPs) are of central physiological relevance for bacteria. They are located in the extracytosolic space, where they present substrates to transporters but also stimulate different types of transmembrane receptors coordinating compound uptake with signal transduction. SBPs are a superfamily composed of proteins recognized by 45 Pfam profiles. The definition of SBP profiles for bacteria is hampered by the fact that these Pfam profiles recognize sensor domains for different types of signaling proteins or cytosolic proteins with alternative functions. We report here the retrieval of the SBPs from 49 bacterial model strains with different lifestyles and phylogenetic distributions. Proteins were manually curated, and the ligands recognized were predicted bioinformatically. There were very large differences in the number and type of SBPs between strains, ranging from 7 SBPs in Helicobacter pylori 26695 to 189 SBPs in Sinorhizobium meliloti 1021. SBPs were found to represent 0.22 to 5.13% of the total protein-encoding genes. The abundance of SBPs was largely determined by strain phylogeny, and no obvious link with the bacterial lifestyle was noted. Most abundant (36%) were SBPs predicted to recognize amino acids or peptides, followed by those expected to bind different sugars (18%). To the best of our knowledge, this is the first comparative study of bacterial SBP repertoires. Given the importance of SBPs in nutrient uptake and signaling, this study enhances the knowledge of model bacteria and will permit the definition of SBP profiles of other strains. IMPORTANCE SBPs are essential components for many transporters, but multiple pieces of more recent evidence indicate that the SBP-mediated stimulation of different transmembrane receptors is a general and widespread signal transduction mechanism in bacteria. The double function of SBPs in coordinating transport with signal transduction remains to a large degree unexplored and represents a major research need. The definition of the SBP repertoire of the 49 bacterial model strains examined here, along with information on their cognate ligand profiles forms the basis to close this gap in knowledge. Furthermore, this study provides information on the forces that have driven the evolution of transporters with different ligand specificities in bacteria that differ in phylogenetics and lifestyle. This article is also a first step in setting up automatic algorithms that permit the large-scale identification of the SBP repertoire in proteomes.
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Affiliation(s)
- Álvaro Ortega
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence Campus Mare Nostrum, Murcia, Spain
| | - Miguel A. Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Ibrar M, Khan S, Hasan F, Yang X. Biosurfactants and chemotaxis interplay in microbial consortium-based hydrocarbons degradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:24391-24410. [PMID: 35061186 DOI: 10.1007/s11356-022-18492-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
Hydrocarbons are routinely detected at low concentrations, despite the degrading metabolic potential of ubiquitous microorganisms. The potential drivers of hydrocarbons persistence are lower bioavailability and mass transfer limitation. Recently, bioremediation strategies have developed rapidly, but still, the solution is not resilient. Biosurfactants, known to increase bioavailability and augment biodegradation, are tightly linked to bacterial surface motility and chemotaxis, while chemotaxis help bacteria to locate aromatic compounds and increase the mass transfer. Harassing the biosurfactant production and chemotaxis properties of degrading microorganisms could be a possible approach for the complete degradation of hydrocarbons. This review provides an overview of interplay between biosurfactants and chemotaxis in bioremediation. Besides, we discuss the chemical surfactants and biosurfactant-mediated biodegradation by microbial consortium.
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Affiliation(s)
- Muhammad Ibrar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518055, People's Republic of China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, 430074, Hubei, People's Republic of China
| | - Salman Khan
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Fariha Hasan
- Department of Microbiology, Applied, Environmental and Geomicrobiology Laboratory, Quaid-I-Azam University, Islamabad, Pakistan
| | - Xuewei Yang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China.
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518055, People's Republic of China.
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Matilla MA, Velando F, Martín-Mora D, Monteagudo-Cascales E, Krell T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol Rev 2021; 46:6356564. [PMID: 34424339 DOI: 10.1093/femsre/fuab043] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria have evolved many different signal transduction systems that sense signals and generate a variety of responses. Generally, most abundant are transcriptional regulators, sensor histidine kinases and chemoreceptors. Typically, these systems recognize their signal molecules with dedicated ligand-binding domains (LBDs), which, in turn, generate a molecular stimulus that modulates the activity of the output module. There are an enormous number of different LBDs that recognize a similarly diverse set of signals. To give a global perspective of the signals that interact with transcriptional regulators, sensor kinases and chemoreceptors, we manually retrieved information on the protein-ligand interaction from about 1,200 publications and 3D structures. The resulting 811 proteins were classified according to the Pfam family into 127 groups. These data permit a delineation of the signal profiles of individual LBD families as well as distinguishing between families that recognize signals in a promiscuous manner and those that possess a well-defined ligand range. A major bottleneck in the field is the fact that the signal input of many signaling systems is unknown. The signal repertoire reported here will help the scientific community design experimental strategies to identify the signaling molecules for uncharacterised sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
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Li Y, Liang J, Yang S, Yao J, Chen K, Yang L, Zheng W, Tian Y. Finding novel chemoreceptors that specifically sense and trigger chemotaxis toward polycyclic aromatic hydrocarbons in Novosphingobium pentaromativorans US6-1. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:126246. [PMID: 34492992 DOI: 10.1016/j.jhazmat.2021.126246] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 06/13/2023]
Abstract
Bacterial chemotaxis can improve the efficiency of aromatic compound degradation, however, knowledge of how bacteria sense high-molecular-weight polycyclic aromatic hydrocarbons (HMW-PAHs), is limited. Here, the chemotactic responses of Novosphingobium pentaromativorans US6-1 to 9 aromatic compounds were investigated. The results showed that US6-1 chemotactically responded to phenanthrene (PHE), pyrene (PYR), benzo[a]pyrene (BaP) and their six metabolites. Six methyl-accepting chemotaxis proteins (MCPs) were annotated from US6-1 genome, four of which contained putative ligand-binding domains (LBDs). To confirm whether these four MCPs were involved in triggering chemotaxis toward PAHs, the MCP mutants were constructed. Observations showed a loss of the chemotactic responses to benzoate, phthalate, PHE and BaP only in the mutant ∆mcp03030. Surface plasmon resonance (SPR) assays further confirmed that MCP03030LBD specifically bound phthalate, PHE, PYR and BaP, while MCP18870LBD bound only PYR. The mutant ∆mcp03030-∆mcp18870 was then constructed and was shown to have lost the chemotactic response to 5 aromatic compounds. Combined with the effects of outer membrane transporter deletion on chemotaxis and MCP deletion on the PAH degradation, our study demonstrated that the chemoreceptors MCP03030 and MCP18870 can recognize PAHs and their metabolites in the periplasm, triggering metabolism-dependent and metabolism-independent chemotaxis, and be linked with HMW-PAH biodegradation.
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Affiliation(s)
- Yuqian Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiaqing Liang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Shuyue Yang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiebin Yao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Kai Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Luxi Yang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Wei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China
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Ahmad F, Zhu D, Sun J. Bacterial chemotaxis: a way forward to aromatic compounds biodegradation. ENVIRONMENTAL SCIENCES EUROPE 2020; 32:52. [DOI: 10.1186/s12302-020-00329-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/23/2020] [Indexed: 07/23/2024]
Abstract
AbstractWorldwide industrial development has released hazardous polycyclic aromatic compounds into the environment. These pollutants need to be removed to improve the quality of the environment. Chemotaxis mechanism has increased the bioavailability of these hydrophobic compounds to microorganisms. The mechanism, however, is poorly understood at the ligand and chemoreceptor interface. Literature is unable to furnish a compiled review of already published data on up-to-date research on molecular aspects of chemotaxis mechanism, ligand and receptor-binding mechanism, and downstream signaling machinery. Moreover, chemotaxis-linked biodegradation of aromatic compounds is required to understand the chemotaxis role in biodegradation better. To fill this knowledge gap, the current review is an attempt to cover PAHs occurrence, chemical composition, and potential posed risks to humankind. The review will cover the aspects of microbial signaling mechanism, the structural diversity of methyl-accepting chemotaxis proteins at the molecular level, discuss chemotaxis mechanism role in biodegradation of aromatic compounds in model bacterial genera, and finally conclude with the potential of bacterial chemotaxis for aromatics biodegradation.
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Evidence for Pentapeptide-Dependent and Independent CheB Methylesterases. Int J Mol Sci 2020; 21:ijms21228459. [PMID: 33187094 PMCID: PMC7698151 DOI: 10.3390/ijms21228459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 12/22/2022] Open
Abstract
Many bacteria possess multiple chemosensory pathways that are composed of homologous signaling proteins. These pathways appear to be functionally insulated from each other, but little information is available on the corresponding molecular basis. We report here a novel mechanism that contributes to pathway insulation. We show that, of the four CheB paralogs of Pseudomonas aeruginosa PAO1, only CheB2 recognizes a pentapeptide at the C-terminal extension of the McpB (Aer2) chemoreceptor (KD = 93 µM). McpB is the sole chemoreceptor that stimulates the Che2 pathway, and CheB2 is the methylesterase of this pathway. Pectobacterium atrosepticum SCRI1043 has a single CheB, CheB_Pec, and 19 of its 36 chemoreceptors contain a C-terminal pentapeptide. The deletion of cheB_Pec abolished chemotaxis, but, surprisingly, none of the pentapeptides bound to CheB_Pec. To determine the corresponding structural basis, we solved the 3D structure of CheB_Pec. Its structure aligned well with that of the pentapeptide-dependent enzyme from Salmonella enterica. However, no electron density was observed in the CheB_Pec region corresponding to the pentapeptide-binding site in the Escherichia coli CheB. We hypothesize that this structural disorder is associated with the failure to bind pentapeptides. Combined data show that CheB methylesterases can be divided into pentapeptide-dependent and independent enzymes.
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Gavira JA, Matilla MA, Fernández M, Krell T. The structural basis for signal promiscuity in a bacterial chemoreceptor. FEBS J 2020; 288:2294-2310. [PMID: 33021055 DOI: 10.1111/febs.15580] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/10/2020] [Accepted: 09/29/2020] [Indexed: 01/05/2023]
Abstract
Signalling through chemosensory pathways is typically initiated by the binding of signal molecules to the chemoreceptor ligand binding domain (LBD). The PcaY_PP chemoreceptor from Pseudomonas putida KT2440 is characterized by an unusually broad signal range, and minimal requisites for signal binding are the presence of a C6-membered ring and that of a carboxyl group. Previous studies have shown that only some of the multiple signals recognized by this chemoreceptor are of apparent metabolic value. We report here high-resolution structures of PcaY_PP-LBD in the absence and presence of four cognate chemoeffectors and glycerol. The domain formed a four-helix bundle (4HB), and both ligand binding sites of the dimer were occupied with the high-affinity ligands protocatechuate and quinate, whereas the lower-affinity ligands benzoate and salicylate were present in only one site. Ligand binding was verified by microcalorimetric titration of site-directed mutants revealing important roles of an arginine and number of polar residues that establish an extensive hydrogen bonding network with bound ligands. The comparison of the apo and holo structures did not provide evidence for this receptor employing a transmembrane signalling mechanism that involves piston-like shifts of the final helix. Instead, ligand binding caused rigid-body scissoring movements of both monomers of the dimer. Comparisons with the 4HB domains of the Tar and Tsr chemoreceptors revealed significant structural differences. Importantly, the ligand binding site in PcaY_PP-LBD is approximately 8 Å removed from that of the Tar and Tsr receptors. Data indicate a significant amount of structural and functional diversity among 4HB domains. DATABASES: The coordinates and structure factors have been deposited in the protein data band with the following IDs: 6S1A (apo form), 6S18 (bound glycerol), 6S33 (bound protocatechuate), 6S38 (bound quinate), 6S3B (bound benzoate) and 6S37 (bound salicylate).
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Affiliation(s)
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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12
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Matilla MA, Martín-Mora D, Krell T. The use of isothermal titration calorimetry to unravel chemotactic signalling mechanisms. Environ Microbiol 2020; 22:3005-3019. [PMID: 32329116 DOI: 10.1111/1462-2920.15035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022]
Abstract
Chemotaxis is based on the action of chemosensory pathways and is typically initiated by the recognition of chemoeffectors at chemoreceptor ligand-binding domains (LBD). Chemosensory signalling is highly complex; aspect that is not only reflected in the intricate interaction between many signalling proteins but also in the fact that bacteria frequently possess multiple chemosensory pathways and often a large number of chemoreceptors, which are mostly of unknown function. We review here the usefulness of isothermal titration calorimetry (ITC) to study this complexity. ITC is the gold standard for studying binding processes due to its precision and sensitivity, as well as its capability to determine simultaneously the association equilibrium constant, enthalpy change and stoichiometry of binding. There is now evidence that members of all major LBD families can be produced as individual recombinant proteins that maintain their ligand-binding properties. High-throughput screening of these proteins using thermal shift assays offer interesting initial information on chemoreceptor ligands, providing the basis for microcalorimetric analyses and microbiological experimentation. ITC has permitted the identification and characterization of many chemoreceptors with novel specificities. This ITC-based approach can also be used to identify signal molecules that stimulate members of other families of sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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13
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Wang YH, Chen HH, Huang Z, Li XJ, Zhou N, Liu C, Jiang CY, Li DF, Liu SJ. PapA, a peptidoglycan-associated protein, interacts with OmpC and maintains cell envelope integrity. Environ Microbiol 2020; 23:600-612. [PMID: 32329167 DOI: 10.1111/1462-2920.15038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/21/2020] [Indexed: 01/26/2023]
Abstract
The bacterial cell envelope is critical to support and maintain cellular life. In Gram-negative bacterial cells, the outer membrane and the peptidoglycan layer are two important parts of the cell envelope and they harbour abundant proteins. Here, we report the identification and characterization of a previously unknown peptidoglycan-associated protein, PapA, from the Gram-negative Comamonas testosteroni. PapA bound peptidoglycan with its C-terminal domain and interacted with the outer-membrane porin OmpC. The PapA-OmpC complex riveted the outer membrane and the peptidoglycan layer, and played a role in maintaining cell envelope integrity. When papA was disrupted, the mutant CNB-1ΔpapA apparently had an outer membrane partly separated from the peptidoglycan layer. Phenotypically, the mutant CNB-1ΔpapA lost chemotactic responses and had longer lag-phase of growth, less flagellation and higher sensitivity to harsh environments. Totally, 1093 functionally unknown PapA homologues were identified from the public NR protein database and they were mainly distributed in Burkholderiales of Betaproteobacteria. Our finding provides a clue that the PapA homologous proteins might function as a rivet to maintain cell envelope integrity in those Gram-negative bacteria.
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Affiliation(s)
- Yun-Hao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Hong-He Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Zhou Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiao-Jing Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Chang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
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14
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Zhang L, Wei Y, Tao Y, Zhao S, Wei X, Yin X, Liu S, Niu Q. Molecular mechanism of the smart attack of pathogenic bacteria on nematodes. Microb Biotechnol 2020; 13:683-705. [PMID: 31730281 PMCID: PMC7111092 DOI: 10.1111/1751-7915.13508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/16/2019] [Accepted: 10/20/2019] [Indexed: 11/28/2022] Open
Abstract
Nematode-bacterial associations are far-reaching subjects in view of their impact on ecosystems, economies, agriculture and human health. There is still no conclusion regarding which pathogenic bacteria sense nematodes. Here, we found that the pathogenic bacterium Bacillus nematocida B16 was sensitive to C. elegans and could launch smart attacks to kill the nematodes. Further analysis revealed that the spores of B. nematocida B16 are essential virulence factors. Once gaseous molecules (morpholine) produced from C. elegans were sensed, the sporulation of B16 was greatly accelerated. Then, B16 showed maximum attraction to C. elegans during the spore-forming process but had no attraction until all the spores were formed. The disruption of either the spore formation gene spo0A or the germination gene gerD impaired colonization and attenuated infection in B16. In contrast, complementation with the intact genes restored most of the above-mentioned deficient phenotypes, which indicated that the spo0A gene was a key factor in the smart attack of B16 on C. elegans. Further, transcriptome, molecular simulations and quantitative PCR analysis showed that morpholine from C. elegans could promote sporulation and initiate infection by increasing the transcription of the spo0A gene by decreasing the transcription of the rapA and spo0E genes. The overexpression of rapA or spo0E decreased the induced sporulation effect, and morpholine directly reduced the level of phosphorylation of purified recombinant RapA and Spo0E compared to that of Spo0A. Collectively, these findings further support a 'Trojan horse-like' infection model. The significance of our paper is that we showed that the soil-dwelling bacterium B. nematocida B16 has the ability to actively detect, attract and attack their host C. elegans. These studies are the first report on the behaviours, signalling molecules and mechanism of the smart attack of B16 on nematodes and also reveal new insights into microbe-host interactions.
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Affiliation(s)
- Lin Zhang
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
- State Key Laboratory of Cotton BiologyHenan Key Laboratory of Plant Stress BiologySchool of Life SciencesHenan UniversityKaifengHenan475001China
| | - Yuping Wei
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Ye Tao
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Suya Zhao
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Xuyang Wei
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Xiaoyan Yin
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Suyao Liu
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
| | - Qiuhong Niu
- Department of Life Science and BiotechnologyNanyang Normal UniversityNanyang473000China
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15
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O'Banion BS, O'Neal L, Alexandre G, Lebeis SL. Bridging the Gap Between Single-Strain and Community-Level Plant-Microbe Chemical Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:124-134. [PMID: 31687914 DOI: 10.1094/mpmi-04-19-0115-cr] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Although the influence of microbiomes on the health of plant hosts is evident, specific mechanisms shaping the structure and dynamics of microbial communities in the phyllosphere and rhizosphere are only beginning to become clear. Traditionally, plant-microbe interactions have been studied using cultured microbial isolates and plant hosts but the rising use of 'omics tools provides novel snapshots of the total complex community in situ. Here, we discuss the recent advances in tools and techniques used to monitor plant-microbe interactions and the chemical signals that influence these relationships in above- and belowground tissues. Particularly, we highlight advances in integrated microscopy that allow observation of the chemical exchange between individual plant and microbial cells, as well as high-throughput, culture-independent approaches to investigate the total genetic and metabolic contribution of the community. The chemicals discussed have been identified as relevant signals across experimental spectrums. However, mechanistic insight into the specific interactions mediated by many of these chemicals requires further testing. Experimental designs that attempt to bridge the gap in biotic complexity between single strains and whole communities will advance our understanding of the chemical signals governing plant-microbe associations in the rhizosphere and phyllosphere.
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Affiliation(s)
- Bridget S O'Banion
- Department of Microbiology, University of Tennessee, Knoxville, TN, U.S.A
| | - Lindsey O'Neal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee
| | - Gladys Alexandre
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee
| | - Sarah L Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, TN, U.S.A
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16
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Hong Y, Huang Z, Guo L, Ni B, Jiang CY, Li XJ, Hou YJ, Yang WS, Wang DC, Zhulin IB, Liu SJ, Li DF. The ligand-binding domain of a chemoreceptor from Comamonas testosteroni has a previously unknown homotrimeric structure. Mol Microbiol 2019; 112:906-917. [PMID: 31177588 PMCID: PMC6736725 DOI: 10.1111/mmi.14326] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2019] [Indexed: 01/01/2023]
Abstract
Transmembrane chemoreceptors are widely present in Bacteria and Archaea. They play a critical role in sensing various signals outside and transmitting to the cell interior. Here, we report the structure of the periplasmic ligand-binding domain (LBD) of the transmembrane chemoreceptor MCP2201, which governs chemotaxis to citrate and other organic compounds in Comamonas testosteroni. The apo-form LBD crystal revealed a typical four-helix bundle homodimer, similar to previously well-studied chemoreceptors such as Tar and Tsr of Escherichia coli. However, the citrate-bound LBD revealed a four-helix bundle homotrimer that had not been observed in bacterial chemoreceptor LBDs. This homotrimer was further confirmed with size-exclusion chromatography, analytical ultracentrifugation and cross-linking experiments. The physiological importance of the homotrimer for chemotaxis was demonstrated with site-directed mutations of key amino acid residues in C. testosteroni mutants.
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Affiliation(s)
- Yuan Hong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhou Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Bin Ni
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Xiao-Jing Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Yan-Jie Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Si Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Da-Cheng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Igor B. Zhulin
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China,For correspondence. (D.-F.L.); (S.-J.L.); Tel. (+86) 10 64807423; Fax (+86) 10 64807421
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China,For correspondence. (D.-F.L.); (S.-J.L.); Tel. (+86) 10 64807423; Fax (+86) 10 64807421
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17
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Chemotaxis Towards Aromatic Compounds: Insights from Comamonas testosteroni. Int J Mol Sci 2019; 20:ijms20112701. [PMID: 31159416 PMCID: PMC6600141 DOI: 10.3390/ijms20112701] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 02/07/2023] Open
Abstract
Chemotaxis is an important physiological adaptation that allows many motile bacteria to orientate themselves for better niche adaptation. Chemotaxis is best understood in Escherichia coli. Other representative bacteria, such as Rhodobacter sphaeroides, Pseudomonas species, Helicobacter pylori, and Bacillus subtilis, also have been deeply studied and systemically summarized. These bacteria belong to α-, γ-, ε-Proteobacteria, or Firmicutes. However, β-Proteobacteria, of which many members have been identified as holding chemotactic pathways, lack a summary of chemotaxis. Comamonas testosteroni, belonging to β-Proteobacteria, grows with and chemotactically responds to a range of aromatic compounds. This paper summarizes the latest research on chemotaxis towards aromatic compounds, mainly from investigations of C. testosteroni and other Comamonas species.
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18
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Sun Y, Xie Z, Sui F, Liu X, Cheng W. Identification of Cbp1, a c-di-GMP Binding Chemoreceptor in Azorhizobium caulinodans ORS571 Involved in Chemotaxis and Nodulation of the Host Plant. Front Microbiol 2019; 10:638. [PMID: 31001223 PMCID: PMC6454048 DOI: 10.3389/fmicb.2019.00638] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/13/2019] [Indexed: 01/10/2023] Open
Abstract
Cbp1, a chemoreceptor containing a PilZ domain was identified in Azorhizobium caulinodans ORS571, a nitrogen-fixing free-living soil bacterium that induces nodule formation in both the roots and stems of the host legume Sesbania rostrata. Chemoreceptors are responsible for sensing signals in the chemotaxis pathway, which guides motile bacteria to beneficial niches and plays an important role in the establishment of rhizobia-legume symbiosis. PilZ domain proteins are known to bind the second messenger c-di-GMP, an important regulator of motility, biofilm formation and virulence. Cbp1 was shown to bind c-di-GMP through the conserved RxxxR motif of its PilZ domain. A mutant strain carrying a cbp1 deletion was impaired in chemotaxis, a feature that could be restored by genetic complementation. Compared with the wild type strain, the Δcbp1 mutant displayed enhanced aggregation and biofilm formation. The Δcbp1 mutant induced functional nodules when inoculated individually. However, the Δcbp1 mutant was less competitive than the wild type in competitive root colonization and nodulation. These data are in agreement with the hypothesis that the c-di-GMP binding chemoreceptor Cbp1 in A. caulinodans is involved in chemotaxis and nodulation.
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Affiliation(s)
- Yu Sun
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhihong Xie
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Fu Sui
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Wuzeng Cheng
- Shandong Huibang Bohai Agriculture Development Limited Company, Dongying, China
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19
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Chen D, Liu SJ, Du W. Chemotactic screening of imidazolinone-degrading bacteria by microfluidic SlipChip. JOURNAL OF HAZARDOUS MATERIALS 2019; 366:512-519. [PMID: 30562663 DOI: 10.1016/j.jhazmat.2018.12.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/19/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
The group of imidazolinone herbicides, widely used for weed control, is hazardous to some sensitive rotational crops. Thus, rapid elimination of imidazolinones from contaminated soil is significant for the environment. Biodegradation studies have demonstrated the ability of chemotaxis to enhance the biodegradation of pollutants. In this study, we used our newly developed SlipChip device for chemotactic sorting and a microfluidic streak plate device for bacterial cultivation as a new pipeline for screening imidazolinone degraders. The degradation efficiencies of an enrichment consortium and a chemotaxis consortium were determined by HPLC-MS/MS. Both consortia degraded all tested imidazolinones, with the highest efficiency (71.8%) for imazethapyr, and the chemotaxis consortium degraded these compounds approximately 10% more efficiently than the enrichment consortium. Moreover, the community diversities of the enrichment consortium and the chemotaxis consortium were analyzed by 16S rRNA gene amplicon sequencing. The results indicated that members of genus Ochrobactrum primarily contribute to the degradation of imidazolinones. This work proved that chemotaxis toward biodegradable pollutants increases their bioavailability and enhances the biodegradation rate. It also provided a new way to screen effective pollutant degraders and can be applied for the selective isolation of other chemotactic species from environmental samples.
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Affiliation(s)
- Dongwei Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 100049, China.
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20
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Chi H, Wang X, Shao Y, Qin Y, Deng Z, Wang L, Chen S. Engineering and modification of microbial chassis for systems and synthetic biology. Synth Syst Biotechnol 2019; 4:25-33. [PMID: 30560208 PMCID: PMC6290258 DOI: 10.1016/j.synbio.2018.12.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/14/2018] [Accepted: 12/05/2018] [Indexed: 12/14/2022] Open
Abstract
Engineering and modifying synthetic microbial chassis is one of the best ways not only to unravel the fundamental principles of life but also to enhance applications in the health, medicine, agricultural, veterinary, and food industries. The two primary strategies for constructing a microbial chassis are the top-down approach (genome reduction) and the bottom-up approach (genome synthesis). Research programs on this topic have been funded in several countries. The 'Minimum genome factory' (MGF) project was launched in 2001 in Japan with the goal of constructing microorganisms with smaller genomes for industrial use. One of the best examples of the results of this project is E. coli MGF-01, which has a reduced-genome size and exhibits better growth and higher threonine production characteristics than the parental strain [1]. The 'cell factory' project was carried out from 1998 to 2002 in the Fifth Framework Program of the EU (European Union), which tried to comprehensively understand microorganisms used in the application field. One of the outstanding results of this project was the elucidation of proteins secreted by Bacillus subtilis, which was summarized as the 'secretome' [2]. The GTL (Genomes to Life) program began in 2002 in the United States. In this program, researchers aimed to create artificial cells both in silico and in vitro, such as the successful design and synthesis of a minimal bacterial genome by John Craig Venter's group [3]. This review provides an update on recent advances in engineering, modification and application of synthetic microbial chassis, with particular emphasis on the value of learning about chassis as a way to better understand life and improve applications.
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Affiliation(s)
- Haotian Chi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
- Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Xiaoli Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Yue Shao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Ying Qin
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
- Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
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21
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Abstract
Complex chemosensory systems control multiple biological functions in bacteria, such as chemotaxis, gene regulation, and cell cycle progression. Many species contain more than one chemosensory system per genome, but little is known about their potential interplay. In this study, we reveal cross talk between two chemosensory pathways that modulate chemotaxis and biofilm formation in Comamonas testosteroni We demonstrate that some chemoreceptors that govern chemotaxis also contribute to biofilm formation and these chemoreceptors can physically interact with components of both pathways. Finally, we show that the chemotaxis histidine kinase CheA can phosphorylate not only its cognate response regulator CheY2 but also one of the response regulators from the pathway mediating biofilm formation, FlmD. The phosphoryl group transfer from CheA to CheY2 is much faster than that from CheA to FlmD, which is consistent with chemotaxis being a fast response and biofilm formation being a much slower developmental process. We propose that cross talk between chemosensory pathways may play a role in coordination of complex behaviors in bacteria.IMPORTANCE In many bacteria, two or more homologous chemosensory pathways control several cellular functions, such as motility and gene regulation, in response to changes in the cell's microenvironment. Cross talk between signal transduction systems is poorly understood; while generally it is considered to be undesired, in some instances it might be beneficial for coregulation of complex behaviors. We demonstrate that several receptors from the pathway controlling motility can physically interact with downstream components of the pathway controlling biofilm formation. We further show that a kinase from the pathway controlling motility can also phosphorylate a response regulator from the pathway controlling biofilm formation. We propose that cross talk between two chemosensory pathways might be involved in coordination of two types of cell behavior-chemotaxis and biofilm formation.
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22
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Tang Q, Lu T, Liu SJ. Developing a Synthetic Biology Toolkit for Comamonas testosteroni, an Emerging Cellular Chassis for Bioremediation. ACS Synth Biol 2018; 7:1753-1762. [PMID: 29860823 DOI: 10.1021/acssynbio.7b00430] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Synthetic biology is rapidly evolving into a new phase that emphasizes real-world applications such as environmental remediation. Recently, Comamonas testosteroni has become a promising chassis for bioremediation due to its natural pollutant-degrading capacity; however, its application is hindered by the lack of fundamental gene expression tools. Here, we present a synthetic biology toolkit that enables rapid creation of functional gene circuits in C. testosteroni. We first built a shuttle system that allows efficient circuit construction in E. coli and necessary phenotypic testing in C. testosteroni. Then, we tested a set of wildtype inducible promoters, and further used a hybrid strategy to create engineered promoters to expand expression strength and dynamics. Additionally, we tested the T7 RNA Polymerase-PT7 promoter system and reduced its leaky expression through promoter mutation for gene expression. By coupling random library construction with FACS screening, we further developed a synthetic T7 promoter library to confer a wider range of expression strength and dynamic characteristics. This study provides a set of valuable tools to engineer gene circuits in C. testosteroni, facilitating the establishment of the organism as a useful microbial chassis for bioremediation purposes.
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Affiliation(s)
- Qiang Tang
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Environmental Microbiology Research Center, Chinese Academy of Sciences, Beijing 100101, China
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23
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Tang Q, Lu T, Liu SJ. Engineering the bacterium Comamonas testosteroni CNB-1: Plasmid curing and genetic manipulation. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.01.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Bi S, Sourjik V. Stimulus sensing and signal processing in bacterial chemotaxis. Curr Opin Microbiol 2018; 45:22-29. [PMID: 29459288 DOI: 10.1016/j.mib.2018.02.002] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 11/25/2022]
Abstract
Motile bacteria use chemotaxis to migrate towards environments that are favorable for growth and survival. The signaling pathway that mediates this behavior is largely conserved among prokaryotes, with Escherichia coli chemotaxis system being one of the simplest and the best studied. At the core of this pathway are the arrays of clustered chemoreceptors that detect, amplify and integrate various stimuli. Recent work provided deeper understanding of spatial organization and signal processing by these clusters and uncovered the variety of sensory mechanisms used to detect environmental stimuli. Moreover, studies of bacteria with different lifestyles have led to new insights into the diversity and evolutionary conservation of the chemotaxis pathway, as well as the physiological relevance of chemotactic behavior in different environments.
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Affiliation(s)
- Shuangyu Bi
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany.
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25
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Abstract
Chemoreceptors in bacteria detect a variety of signals and feed this information into chemosensory pathways that represent a major mode of signal transduction. The five chemoreceptors from Escherichia coli have served as traditional models in the study of this protein family. Genome analyses revealed that many bacteria contain much larger numbers of chemoreceptors with broader sensory capabilities. Chemoreceptors differ in topology, sensing mode, cellular location, and, above all, the type of ligand binding domain (LBD). Here, we highlight LBD diversity using well-established and emerging model organisms as well as genomic surveys. Nearly a hundred different types of protein domains that are found in chemoreceptor sequences are known or predicted LBDs, but only a few of them are ubiquitous. LBDs of the same class recognize different ligands, and conversely, the same ligand can be recognized by structurally different LBDs; however, recent studies began to reveal common characteristics in signal-LBD relationships. Although signals can stimulate chemoreceptors in a variety of different ways, diverse LBDs appear to employ a universal transmembrane signaling mechanism. Current and future studies aim to establish relationships between LBD types, the nature of signals that they recognize, and the mechanisms of signal recognition and transduction.
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26
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Stack TMM, Johnson WH, Whitman CP. Synthesis and enzymatic ketonization of the 5-(halo)-2-hydroxymuconates and 5-(halo)-2-hydroxy-2,4-pentadienoates. Beilstein J Org Chem 2017; 13:1022-1031. [PMID: 28684981 PMCID: PMC5480330 DOI: 10.3762/bjoc.13.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 05/11/2017] [Indexed: 02/03/2023] Open
Abstract
5-Halo-2-hydroxymuconates and 5-halo-2-hydroxy-2,4-pentadienoates are stable dienols that are proposed intermediates in bacterial meta-fission pathways for the degradation of halogenated aromatic compounds. The presence of the halogen raises questions about how the bulk and/or electronegativity of these substrates would affect enzyme catalysis or whether some pathway enzymes have evolved to accommodate it. To address these questions, 5-halo-2-hydroxymuconates and 5-halo-2-hydroxy-2,4-pentadienoates (5-halo = Cl, Br, F) were synthesized and a preliminary analysis of their enzymatic properties carried out. In aqueous buffer, 5-halo-2-hydroxy-2,4-pentadienoates rapidly equilibrate with the β,γ-unsaturated ketones. For the 5-chloro and 5-bromo derivatives, a slower conversion to the α,β-isomers follows. There is no detectable formation of the α,β-isomer for the 5-fluoro derivative. Kinetic parameters were also obtained for both sets of compounds in the presence of 4-oxalocrotonate tautomerase (4-OT) from Pseudomonas putida mt-2 and Leptothrix cholodnii SP-6. For 5-halo-2-hydroxymuconates, there are no major differences in the kinetic parameters for the two enzymes (following the formation of the β,γ-unsaturated ketones). In contrast, the L. cholodnii SP-6 4-OT is ≈10-fold less efficient than the P. putida mt-2 4-OT in the formation of the β,γ-unsaturated ketones and the α,β-isomers from the 5-halo-2-hydroxy-2,4-pentadienoates. The implications of these findings are discussed. The availability of these compounds will facilitate future studies of the haloaromatic catabolic pathways.
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Affiliation(s)
- Tyler M M Stack
- Department of Molecular Biosciences, College of Natural Sciences, 1 University Station, University of Texas, Austin, TX 78712, USA
| | - William H Johnson
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, 1 University Station, University of Texas, Austin, TX 78712, USA
| | - Christian P Whitman
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, 1 University Station, University of Texas, Austin, TX 78712, USA
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27
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Fernández M, Matilla MA, Ortega Á, Krell T. Metabolic Value Chemoattractants Are Preferentially Recognized at Broad Ligand Range Chemoreceptor of Pseudomonas putida KT2440. Front Microbiol 2017; 8:990. [PMID: 28620365 PMCID: PMC5449446 DOI: 10.3389/fmicb.2017.00990] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/17/2017] [Indexed: 12/18/2022] Open
Abstract
Bacteria have evolved a wide range of chemoreceptors with different ligand specificities. Typically, chemoreceptors bind ligands with elevated specificity and ligands serve as growth substrates. However, there is a chemoreceptor family that has a broad ligand specificity including many compounds that are not of metabolic value. To advance the understanding of this family, we have used the PcaY_PP (PP2643) chemoreceptor of Pseudomonas putida KT2440 as a model. Using Isothermal Titration Calorimetry we showed here that the recombinant ligand binding domain (LBD) of PcaY_PP recognizes 17 different C6-ring containing carboxylic acids with KD values between 3.7 and 138 μM and chemoeffector affinity correlated with the magnitude of the chemotactic response. Mutation of the pcaY_PP gene abolished chemotaxis to these compounds; phenotype that was restored following gene complementation. Growth experiments using PcaY_PP ligands as sole C-sources revealed functional relationships between their metabolic potential and affinity for the chemoreceptor. Thus, only 7 PcaY_PP ligands supported growth and their KD values correlated with the length of the bacterial lag phase. Furthermore, PcaY_PP ligands that did not support growth had significantly higher KD values than those that did. The receptor has thus binds preferentially compounds that serve as C-sources and amongst them those that rapidly promote growth. Tightest binding compounds were quinate, shikimate, 3-dehydroshikimate and protocatechuate, which are at the interception of the biosynthetic shikimate and catabolic quinate pathways. Analytical ultracentrifugation studies showed that ligand free PcaY_PP-LBD is present in a monomer-dimer equilibrium (KD = 57.5 μM). Ligand binding caused a complete shift to the dimeric state, which appears to be a general feature of four-helix bundle LBDs. This study indicates that the metabolic potential of compounds is an important parameter in the molecular recognition by broad ligand range chemoreceptors.
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Affiliation(s)
- Matilde Fernández
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas,Granada, Spain
| | - Miguel A Matilla
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas,Granada, Spain
| | - Álvaro Ortega
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas,Granada, Spain
| | - Tino Krell
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas,Granada, Spain
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28
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Matilla MA, Krell T. Chemoreceptor-based signal sensing. Curr Opin Biotechnol 2017; 45:8-14. [PMID: 28088095 DOI: 10.1016/j.copbio.2016.11.021] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/03/2016] [Accepted: 11/10/2016] [Indexed: 01/02/2023]
Abstract
Chemoreceptors are at the beginning of chemosensory signaling cascades that correspond to a major signal transduction mechanism. Chemoreceptors show a significant structural diversity of their ligand binding domains which present either a mono-modular or bi-modular arrangement. Although the majority of chemoreceptors are of unknown function, significant progress has been made in recent years in their functional annotation, which is reviewed here. In vitro ligand binding studies to recombinant ligand binding domains proved to be an efficient strategy to identify chemoreceptor functions. Obtained information is consistent with the view that a major driving force for the evolution of chemotaxis is to access carbon and nitrogen sources. The use of the newly generated information for the construction of biosensors is discussed.
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Affiliation(s)
- Miguel A Matilla
- 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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29
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Brewster JL, McKellar JLO, Finn TJ, Newman J, Peat TS, Gerth ML. Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae. Sci Rep 2016; 6:35198. [PMID: 27734909 PMCID: PMC5062169 DOI: 10.1038/srep35198] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/26/2016] [Indexed: 01/26/2023] Open
Abstract
Chemoreceptors enable bacteria to detect chemical signals in the environment and navigate towards niches that are favourable for survival. The sensor domains of chemoreceptors function as the input modules for chemotaxis systems, and provide sensory specificity by binding specific ligands. Cache-like domains are the most common extracellular sensor module in prokaryotes, however only a handful have been functionally or structurally characterised. Here, we have characterised a chemoreceptor Cache-like sensor domain (PscD-SD) from the plant pathogen Pseudomonas syringae pv. actinidiae (Psa). High-throughput fluorescence thermal shift assays, combined with isothermal thermal titration calorimetry, revealed that PscD-SD binds specifically to C2 (glycolate and acetate) and C3 (propionate and pyruvate) carboxylates. We solved the structure of PscD-SD in complex with propionate using X-ray crystallography. The structure reveals the key residues that comprise the ligand binding pocket and dictate the specificity of this sensor domain for C2 and C3 carboxylates. We also demonstrate that all four carboxylate ligands are chemoattractants for Psa, but only two of these (acetate and pyruvate) are utilisable carbon sources. This result suggests that in addition to guiding the bacteria towards nutrients, another possible role for carboxylate sensing is in locating potential sites of entry into the host plant.
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Affiliation(s)
- Jodi L Brewster
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - James L O McKellar
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Thomas J Finn
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Janet Newman
- Biomedical Manufacturing Program, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, Victoria, 3052, Australia
| | - Thomas S Peat
- Biomedical Manufacturing Program, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, Victoria, 3052, Australia
| | - Monica L Gerth
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
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