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Bustamante JA, Ceron JS, Gao IT, Ramirez HA, Aviles MV, Bet Adam D, Brice JR, Cuellar RA, Dockery E, Jabagat MK, Karp DG, Lau JKO, Li S, Lopez-Magaña R, Moore RR, Morin BKR, Nzongo J, Rezaeihaghighi Y, Sapienza-Martinez J, Tran TTK, Huang Z, Duthoy AJ, Barnett MJ, Long SR, Chen JC. A protease and a lipoprotein jointly modulate the conserved ExoR-ExoS-ChvI signaling pathway critical in Sinorhizobium meliloti for symbiosis with legume hosts. PLoS Genet 2023; 19:e1010776. [PMID: 37871041 PMCID: PMC10659215 DOI: 10.1371/journal.pgen.1010776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/20/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
Sinorhizobium meliloti is a model alpha-proteobacterium for investigating microbe-host interactions, in particular nitrogen-fixing rhizobium-legume symbioses. Successful infection requires complex coordination between compatible host and endosymbiont, including bacterial production of succinoglycan, also known as exopolysaccharide-I (EPS-I). In S. meliloti EPS-I production is controlled by the conserved ExoS-ChvI two-component system. Periplasmic ExoR associates with the ExoS histidine kinase and negatively regulates ChvI-dependent expression of exo genes, necessary for EPS-I synthesis. We show that two extracytoplasmic proteins, LppA (a lipoprotein) and JspA (a lipoprotein and a metalloprotease), jointly influence EPS-I synthesis by modulating the ExoR-ExoS-ChvI pathway and expression of genes in the ChvI regulon. Deletions of jspA and lppA led to lower EPS-I production and competitive disadvantage during host colonization, for both S. meliloti with Medicago sativa and S. medicae with M. truncatula. Overexpression of jspA reduced steady-state levels of ExoR, suggesting that the JspA protease participates in ExoR degradation. This reduction in ExoR levels is dependent on LppA and can be replicated with ExoR, JspA, and LppA expressed exogenously in Caulobacter crescentus and Escherichia coli. Akin to signaling pathways that sense extracytoplasmic stress in other bacteria, JspA and LppA may monitor periplasmic conditions during interaction with the plant host to adjust accordingly expression of genes that contribute to efficient symbiosis. The molecular mechanisms underlying host colonization in our model system may have parallels in related alpha-proteobacteria.
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Affiliation(s)
- Julian A. Bustamante
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Josue S. Ceron
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Ivan Thomas Gao
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Hector A. Ramirez
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Milo V. Aviles
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Demsin Bet Adam
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Jason R. Brice
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Rodrigo A. Cuellar
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Eva Dockery
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Miguel Karlo Jabagat
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Donna Grace Karp
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Joseph Kin-On Lau
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Suling Li
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Raymondo Lopez-Magaña
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Rebecca R. Moore
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Bethany Kristi R. Morin
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Juliana Nzongo
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Yasha Rezaeihaghighi
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Joseph Sapienza-Martinez
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Tuyet Thi Kim Tran
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Zhenzhong Huang
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Aaron J. Duthoy
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Melanie J. Barnett
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Sharon R. Long
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Joseph C. Chen
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
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2
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Soto MJ, Pérez J, Muñoz-Dorado J, Contreras-Moreno FJ, Moraleda-Muñoz A. Transcriptomic response of Sinorhizobium meliloti to the predatory attack of Myxococcus xanthus. Front Microbiol 2023; 14:1213659. [PMID: 37405170 PMCID: PMC10315480 DOI: 10.3389/fmicb.2023.1213659] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/01/2023] [Indexed: 07/06/2023] Open
Abstract
Bacterial predation impacts microbial community structures, which can have both positive and negative effects on plant and animal health and on environmental sustainability. Myxococcus xanthus is an epibiotic soil predator with a broad range of prey, including Sinorhizobium meliloti, which establishes nitrogen-fixing symbiosis with legumes. During the M. xanthus-S. meliloti interaction, the predator must adapt its transcriptome to kill and lyse the target (predatosome), and the prey must orchestrate a transcriptional response (defensome) to protect itself against the biotic stress caused by the predatory attack. Here, we describe the transcriptional changes taking place in S. meliloti in response to myxobacterial predation. The results indicate that the predator induces massive changes in the prey transcriptome with up-regulation of protein synthesis and secretion, energy generation, and fatty acid (FA) synthesis, while down-regulating genes required for FA degradation and carbohydrate transport and metabolism. The reconstruction of up-regulated pathways suggests that S. meliloti modifies the cell envelop by increasing the production of different surface polysaccharides (SPSs) and membrane lipids. Besides the barrier role of SPSs, additional mechanisms involving the activity of efflux pumps and the peptide uptake transporter BacA, together with the production of H2O2 and formaldehyde have been unveiled. Also, the induction of the iron-uptake machinery in both predator and prey reflects a strong competition for this metal. With this research we complete the characterization of the complex transcriptional changes that occur during the M. xanthus-S. meliloti interaction, which can impact the establishment of beneficial symbiosis with legumes.
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Affiliation(s)
- María José Soto
- Departamento de Biotecnología y Protección Ambiental, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juana Pérez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - José Muñoz-Dorado
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | | | - Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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Brito-Santana P, Duque-Pedraza JJ, Bernabéu-Roda LM, Carvia-Hermoso C, Cuéllar V, Fuentes-Romero F, Acosta-Jurado S, Vinardell JM, Soto MJ. Sinorhizobium meliloti DnaJ Is Required for Surface Motility, Stress Tolerance, and for Efficient Nodulation and Symbiotic Nitrogen Fixation. Int J Mol Sci 2023; 24:ijms24065848. [PMID: 36982921 PMCID: PMC10055731 DOI: 10.3390/ijms24065848] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Bacterial surface motility is a complex microbial trait that contributes to host colonization. However, the knowledge about regulatory mechanisms that control surface translocation in rhizobia and their role in the establishment of symbiosis with legumes is still limited. Recently, 2-tridecanone (2-TDC) was identified as an infochemical in bacteria that hampers microbial colonization of plants. In the alfalfa symbiont Sinorhizobium meliloti, 2-TDC promotes a mode of surface motility that is mostly independent of flagella. To understand the mechanism of action of 2-TDC in S. meliloti and unveil genes putatively involved in plant colonization, Tn5 transposants derived from a flagellaless strain that were impaired in 2-TDC-induced surface spreading were isolated and genetically characterized. In one of the mutants, the gene coding for the chaperone DnaJ was inactivated. Characterization of this transposant and newly obtained flagella-minus and flagella-plus dnaJ deletion mutants revealed that DnaJ is essential for surface translocation, while it plays a minor role in swimming motility. DnaJ loss-of-function reduces salt and oxidative stress tolerance in S. meliloti and hinders the establishment of efficient symbiosis by affecting nodule formation efficiency, cellular infection, and nitrogen fixation. Intriguingly, the lack of DnaJ causes more severe defects in a flagellaless background. This work highlights the role of DnaJ in the free-living and symbiotic lifestyles of S. meliloti.
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Affiliation(s)
- Paula Brito-Santana
- Estación Experimental del Zaidín, CSIC, Department of Biotechnology and Environmental Protection, 18008 Granada, Spain
| | - Julián J Duque-Pedraza
- Estación Experimental del Zaidín, CSIC, Department of Biotechnology and Environmental Protection, 18008 Granada, Spain
| | - Lydia M Bernabéu-Roda
- Estación Experimental del Zaidín, CSIC, Department of Biotechnology and Environmental Protection, 18008 Granada, Spain
| | - Cristina Carvia-Hermoso
- Estación Experimental del Zaidín, CSIC, Department of Biotechnology and Environmental Protection, 18008 Granada, Spain
| | - Virginia Cuéllar
- Estación Experimental del Zaidín, CSIC, Department of Biotechnology and Environmental Protection, 18008 Granada, Spain
| | - Francisco Fuentes-Romero
- Facultad de Biología, Departamento de Microbiología, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Sebastián Acosta-Jurado
- Centro Andaluz de Biología del Desarrollo, CSIC, Junta de Andalucía, Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, 41013 Seville, Spain
| | - José-María Vinardell
- Facultad de Biología, Departamento de Microbiología, Universidad de Sevilla, 41012 Sevilla, Spain
| | - María J Soto
- Estación Experimental del Zaidín, CSIC, Department of Biotechnology and Environmental Protection, 18008 Granada, Spain
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Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes. mBio 2022; 13:e0182322. [PMID: 36286519 PMCID: PMC9765617 DOI: 10.1128/mbio.01823-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here, we use naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti paired with two genotypes of the host Medicago truncatula in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype-partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, (i) loci whose identities depend on the environment, (ii) those that depend on the host genotype with which rhizobia interact, and (iii) universal loci that are likely important in all or most environments. IMPORTANCE Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.
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Acosta-Jurado S, Fuentes-Romero F, Ruiz-Sainz JE, Janczarek M, Vinardell JM. Rhizobial Exopolysaccharides: Genetic Regulation of Their Synthesis and Relevance in Symbiosis with Legumes. Int J Mol Sci 2021; 22:6233. [PMID: 34207734 PMCID: PMC8227245 DOI: 10.3390/ijms22126233] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/03/2021] [Accepted: 06/06/2021] [Indexed: 12/11/2022] Open
Abstract
Rhizobia are soil proteobacteria able to engage in a nitrogen-fixing symbiotic interaction with legumes that involves the rhizobial infection of roots and the bacterial invasion of new organs formed by the plant in response to the presence of appropriate bacterial partners. This interaction relies on a complex molecular dialogue between both symbionts. Bacterial N-acetyl-glucosamine oligomers called Nod factors are indispensable in most cases for early steps of the symbiotic interaction. In addition, different rhizobial surface polysaccharides, such as exopolysaccharides (EPS), may also be symbiotically relevant. EPS are acidic polysaccharides located out of the cell with little or no cell association that carry out important roles both in free-life and in symbiosis. EPS production is very complexly modulated and, frequently, co-regulated with Nod factors, but the type of co-regulation varies depending on the rhizobial strain. Many studies point out a signalling role for EPS-derived oligosaccharides in root infection and nodule invasion but, in certain symbiotic couples, EPS can be dispensable for a successful interaction. In summary, the complex regulation of the production of rhizobial EPS varies in different rhizobia, and the relevance of this polysaccharide in symbiosis with legumes depends on the specific interacting couple.
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Affiliation(s)
- Sebastián Acosta-Jurado
- Department of Microbiology, University of Sevilla, Avda. Reina Mercedes 6, 41012 Seville, Spain; (S.A.-J.); (F.F.-R.); (J.-E.R.-S.)
| | - Francisco Fuentes-Romero
- Department of Microbiology, University of Sevilla, Avda. Reina Mercedes 6, 41012 Seville, Spain; (S.A.-J.); (F.F.-R.); (J.-E.R.-S.)
| | - Jose-Enrique Ruiz-Sainz
- Department of Microbiology, University of Sevilla, Avda. Reina Mercedes 6, 41012 Seville, Spain; (S.A.-J.); (F.F.-R.); (J.-E.R.-S.)
| | - Monika Janczarek
- Department of Industrial and Environmental Microbiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - José-María Vinardell
- Department of Microbiology, University of Sevilla, Avda. Reina Mercedes 6, 41012 Seville, Spain; (S.A.-J.); (F.F.-R.); (J.-E.R.-S.)
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El Alaoui A, Raklami A, Bechtaoui N, El Gharmali A, Ouhammou A, Imziln B, Achouak W, Pajuelo E, Oufdou K. Use of native plants and their associated bacteria rhizobiomes to remediate-restore Draa Sfar and Kettara mining sites, Morocco. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:232. [PMID: 33772660 DOI: 10.1007/s10661-021-08977-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Soil and mine tailings are unreceptive to plant growth representing an imminent threat to the environment and resource sustainability. Using indigenous plants and their associated rhizobacteria to restore mining sites would be an eco-friendly solution to mitigate soil-metal toxicity. Soil prospection from Draa Sfar and Kettara mining sites in Morocco was carried out during different seasons for native plant sampling and rhizobacteria screening. The sites have been colonized by fifteen tolerant plant species having different capacities to accumulate Cu, Zn, and P in their shoots/root systems. In Draa Sfar mine, Suaeda vera J.F. Gmel., Sarcocornia fruticosa (L.) A.J. Scott., and Frankenia corymbosa Desf. accumulated mainly Cu (more than 90 mg kg-1), Atriplex halimus L. accumulated Zn (mg kg-1), and Frankenia corymbosa Desf. accumulated Pb (14 mg kg-1). As for Kettara mine, Aizoon canariense L. mainly accumulated Zn (270 mg kg-1), whereas Forsskalea tenacissima L. was the best shoot Cu accumulator with up to 50 mg kg-1, whereas Cu accumulation in roots was 21 mg kg-1. The bacterial screening revealed the strains' abilities to tolerate heavy metals up to 50 mg kg-1 Cu, 250 mg kg-1 Pb, and 150 mg kg-1 Zn. Isolated strains belonged mainly to Bacillaceae (73.33%) and Pseudomonadaceae (10%) and expressed different plant growth-promoting traits, alongside their antifungal activity. Results from this study will provide an insight into the ability of native plants and their associated rhizobacteria to serve as a basis for remediation-restoration strategies.
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Affiliation(s)
- Abdelkhalek El Alaoui
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
- LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, Aix-Marseille University, CEA, CNRS, UMR7265, F-13108, Saint Paul Lez Durance, France
| | - Anas Raklami
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco.
| | - Noura Bechtaoui
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Abdelhay El Gharmali
- Laboratory of Water, Biodiversity and Global Change, Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Ahmed Ouhammou
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Boujamaa Imziln
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
| | - Wafa Achouak
- LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, Aix-Marseille University, CEA, CNRS, UMR7265, F-13108, Saint Paul Lez Durance, France
| | - Eloisa Pajuelo
- Department of Microbiology and Parasitology, University of Seville, PO Box 1095, 41080, Seville, Spain
| | - Khalid Oufdou
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, PO Box 2390, Marrakech, Morocco
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Wong JEMM, Gysel K, Birkefeldt TG, Vinther M, Muszyński A, Azadi P, Laursen NS, Sullivan JT, Ronson CW, Stougaard J, Andersen KR. Structural signatures in EPR3 define a unique class of plant carbohydrate receptors. Nat Commun 2020; 11:3797. [PMID: 32732998 PMCID: PMC7392887 DOI: 10.1038/s41467-020-17568-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/05/2020] [Indexed: 11/21/2022] Open
Abstract
Receptor-mediated perception of surface-exposed carbohydrates like lipo- and exo-polysaccharides (EPS) is important for non-self recognition and responses to microbial associated molecular patterns in mammals and plants. In legumes, EPS are monitored and can either block or promote symbiosis with rhizobia depending on their molecular composition. To establish a deeper understanding of receptors involved in EPS recognition, we determined the structure of the Lotus japonicus (Lotus) exopolysaccharide receptor 3 (EPR3) ectodomain. EPR3 forms a compact structure built of three putative carbohydrate-binding modules (M1, M2 and LysM3). M1 and M2 have unique βαββ and βαβ folds that have not previously been observed in carbohydrate binding proteins, while LysM3 has a canonical βααβ fold. We demonstrate that this configuration is a structural signature for a ubiquitous class of receptors in the plant kingdom. We show that EPR3 is promiscuous, suggesting that plants can monitor complex microbial communities though this class of receptors. Exopolysaccharides (EPS) are perceived by legumes and regulate symbiosis with rhizobia. Here the authors describe the structure of the Lotus EPS receptor, EPR3 and show that it has atypical βαββ and βαβ folds that represent a structural signature for a unique class of EPS receptors in the plant kingdom.
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Affiliation(s)
- Jaslyn E M M Wong
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark.,MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Kira Gysel
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Thea G Birkefeldt
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Maria Vinther
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Nick S Laursen
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark
| | - Kasper R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark.
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Wu Y, Li YH, Shang JY, Wang ET, Chen L, Huo B, Sui XH, Tian CF, Chen WF, Chen WX. Multiple Genes of Symbiotic Plasmid and Chromosome in Type II Peanut Bradyrhizobium Strains Corresponding to the Incompatible Symbiosis With Vigna radiata. Front Microbiol 2020; 11:1175. [PMID: 32655513 PMCID: PMC7324677 DOI: 10.3389/fmicb.2020.01175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/07/2020] [Indexed: 11/19/2022] Open
Abstract
Rhizobia are capable of establishing compatible symbiosis with their hosts of origin and plants in the cross-nodulation group that the hosts of origin belonged to. However, different from the normal peanut Bradyrhizobium (Type I strains), the Type II strains showed incompatible symbiosis with Vigna radiata. Here, we employed transposon mutagenesis to identify the genetic loci related to this incompatibility in Type II strain CCBAU 53363. As results, seven Tn5 transposon insertion mutants resulted in an increase in nodule number on V. radiata. By sequencing analysis of the sequence flanking Tn5 insertion, six mutants were located in the chromosome of CCBAU 53363, respectively encoding acyltransferase (L265) and hypothetical protein (L615)—unique to CCBAU 53363, two hypothetical proteins (L4 and L82), tripartite tricarboxylate transporter substrate binding protein (L373), and sulfur oxidation c-type cytochrome SoxA (L646), while one mutant was in symbiotic plasmid encoding alanine dehydrogenase (L147). Significant differences were observed in L147 gene sequences and the deduced protein 3D structures between the Type II (in symbiotic plasmid) and Type I strains (in chromosome). Conversely, strains in both types shared high homologies in the chromosome genes L373 and L646 and in their protein 3D structures. These data indicated that the symbiotic plasmid gene in Type II strains might have directly affected their symbiosis incompatibility, whereas the chromosome genes might be indirectly involved in this process by regulating the plasmid symbiosis genes. The seven genes may initially explain the complication associated with symbiotic incompatibility.
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Affiliation(s)
- Yue Wu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yong Hua Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiao Ying Shang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - En Tao Wang
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Mexico City, Mexico
| | - La Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Bin Huo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xin Hua Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chang Fu Tian
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen Feng Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen Xin Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
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Gosai J, Anandhan S, Bhattacharjee A, Archana G. Elucidation of quorum sensing components and their role in regulation of symbiotically important traits in Ensifer nodulating pigeon pea. Microbiol Res 2020; 231:126354. [DOI: 10.1016/j.micres.2019.126354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/12/2019] [Accepted: 10/13/2019] [Indexed: 11/15/2022]
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Xiong YW, Ju XY, Li XW, Gong Y, Xu MJ, Zhang CM, Yuan B, Lv ZP, Qin S. Fermentation conditions optimization, purification, and antioxidant activity of exopolysaccharides obtained from the plant growth-promoting endophytic actinobacterium Glutamicibacter halophytocola KLBMP 5180. Int J Biol Macromol 2019; 153:1176-1185. [PMID: 31756484 DOI: 10.1016/j.ijbiomac.2019.10.247] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/26/2019] [Accepted: 10/26/2019] [Indexed: 01/05/2023]
Abstract
In this study, an endophytic actinobacterium Glutamicibacter halophytocola KLBMP 5180, was investigated for the production and antioxidant activity of exopolysaccharides (EPSs). First, the suitable fermentation time, temperature, inoculation volume, pH value, and the carbon and nitrogen sources for EPSs production were obtained using the one variable at a time method (OVAT). Then, a central composition design was used for fermentation conditions optimization to obtain the maximum EPS yield. The optimal medium and condition were as follows: 100 mL broth in 250 mL Erlenmeyer flasks, including 3.65 g/L maltose, 9.88 g/L malt extract, 3.40 g/L yeast extract, 1.41 g/L MnCl2, pH 7.5, culture temperature 28 °C, and 200 rpm for 7 days, which increased the yield of EPSs to 2.89 g/L. Two purified EPSs, 5180EPS-1 (MW 58.9 kDa) and 5180EPS-2 (10.5 kDa), comprising rhamnose, galacturonic acid, glucose, glucuronic acid, xylose, and arabinose, were obtained for chemical analysis and antioxidant evaluation. The scavenging ability and reducing power of the superoxide anion and hydroxyl radicals demonstrated the moderate in vitro antioxidant activities of the two EPSs, thus indicating their potential to be a new source of natural antioxidants. However, further structure elucidation and functional studies need to be continued.
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Affiliation(s)
- You-Wei Xiong
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province (KLBMP), School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Xiu-Yun Ju
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province (KLBMP), School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Xue-Wei Li
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province (KLBMP), School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Yuan Gong
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province (KLBMP), School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Ming-Jie Xu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province (KLBMP), School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Chun-Mei Zhang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province (KLBMP), School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Bo Yuan
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province (KLBMP), School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Zuo-Peng Lv
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province (KLBMP), School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Sheng Qin
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province (KLBMP), School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China.
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11
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Liu X, Xie Z. Inactivation of the Phosphatase CheZ Alters Cell-Surface Properties of Azorhizobium caulinodans ORS571 and Symbiotic Association with Sesbania rostrata. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1547-1556. [PMID: 31287368 DOI: 10.1094/mpmi-05-19-0143-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Azorhizobium caulinodans can form root and stem nodules with the host plant Sesbania rostrata. The role of the CheZ phosphatase in the A. caulinodans chemotaxis pathway was previously explored using the nonchemotactic cheZ mutant strain (AC601). This mutant displayed stronger attachment to the root surface, enhancing early colonization; however, this did not result in increased nodulation efficiency. In this study, we further investigated the role of CheZ in the interaction between strain ORS571 and the roots of its host plant. By tracking long-term colonization dynamic of cheZ mutant marked with LacZ, we found a decrease of colonization of the cheZ mutant during this process. Furthermore, the cheZ mutant could not spread on the root surface freely and was gradually outcompeted by the wild type in original colonization sites. Quantitative reverse-transcription PCR analyses showed that exp genes encoding exopolysaccharides synthesis, including oac3, were highly expressed in the cheZ mutant. Construction of a strain carrying a deletion of both cheZ and oac3 resulted in a mutant strain defective in the colonization process to the same extent as found with the oac3 single-mutant strain. This result suggested that the enhanced colonization of the cheZ mutant may be achieved through regulating the formation of exopolysaccharides. This shows the importance of the chemotactic proteins in the interaction between rhizobia and host plants, and expands our understanding of the symbiosis interaction between rhizobium and host plant.
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Affiliation(s)
- Xiaolin Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
- Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, People's Republic of China
| | - Zhihong Xie
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, People's Republic of China
- Center for Ocean Mag-Science, Chinese Academy of Sciences, Qingdao, People's Republic of China
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12
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Ratib NR, Sabio EY, Mendoza C, Barnett MJ, Clover SB, Ortega JA, Dela Cruz FM, Balderas D, White H, Long SR, Chen EJ. Genome-wide identification of genes directly regulated by ChvI and a consensus sequence for ChvI binding in Sinorhizobium meliloti. Mol Microbiol 2018; 110:596-615. [PMID: 30192418 DOI: 10.1111/mmi.14119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/16/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022]
Abstract
ExoS/ChvI two-component signaling in the nitrogen-fixing α-proteobacterium Sinorhizobium meliloti is required for symbiosis and regulates exopolysaccharide production, motility, cell envelope integrity and nutrient utilization in free-living bacteria. However, identification of many ExoS/ChvI direct transcriptional target genes has remained elusive. Here, we performed chromatin immunoprecipitation followed by microarray analysis (chIP-chip) to globally identify DNA regions bound by ChvI protein in S. meliloti. We then performed qRT-PCR with chvI mutant strains to test ChvI-dependent expression of genes downstream of the ChvI-bound DNA regions. We identified 64 direct target genes of ChvI, including exoY, rem and chvI itself. We also identified ChvI direct target candidates, like exoR, that are likely controlled by additional regulators. Analysis of upstream sequences from the 64 ChvI direct target genes identified a 15 bp-long consensus sequence. Using electrophoretic mobility shift assays and transcriptional fusions with exoY, SMb21440, SMc00084, SMc01580, chvI, and ropB1, we demonstrated this consensus sequence is important for ChvI binding to DNA and transcription of ChvI direct target genes. Thus, we have comprehensively identified ChvI regulon genes and a 'ChvI box' bound by ChvI. Many ChvI direct target genes may influence the cell envelope, consistent with the critical role of ExoS/ChvI in growth and microbe-host interactions.
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Affiliation(s)
- Nicole R Ratib
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Erich Y Sabio
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Carolina Mendoza
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | | | - Sarah B Clover
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Jesus A Ortega
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Francesca M Dela Cruz
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - David Balderas
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Holly White
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Sharon R Long
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Esther J Chen
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
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Abstract
Fixed (reduced) soil nitrogen plays a critical role in soil fertility and successful food growth. Much soil fertility relies on symbiotic nitrogen fixation: the bacterial partner infects the host plant roots and reduces atmospheric dinitrogen in exchange for host metabolic fuel, a process that involves complex interactions between the partners mediated by changes in gene expression in each partner. Here we test the roles of a family of 11 extracytoplasmic function (ECF) gene regulatory proteins (sigma factors [σs]) that interact with RNA polymerase to determine if they play a significant role in establishing a nitrogen-fixing symbiosis or in responding to various stresses, including cell envelope stress. We discovered that symbiotic nitrogen fixation occurs even when all 11 of these regulatory genes are deleted, that most ECF sigma factors control accessory functions, and that none of the ECF sigma factors are required to survive envelope stress. Bacteria must sense alterations in their environment and respond with changes in function and/or structure in order to cope. Extracytoplasmic function sigma factors (ECF σs) modulate transcription in response to cellular and environmental signals. The symbiotic nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti carries genes for 11 ECF-like σs (RpoE1 to -E10 and FecI). We hypothesized that some of these play a role in mediating the interaction between the bacterium and its plant symbiotic partner. The bacterium senses changes in its immediate environment as it establishes contact with the plant root, initiates invasion of the plant as the root nodule is formed, traverses several root cell layers, and enters plant cortical cells via endocytosis. We used genetics, transcriptomics, and functionality to characterize the entire S. meliloti cohort of ECF σs. We discovered new targets for individual σs, confirmed others by overexpressing individual ECF σs, and identified or confirmed putative promoter motifs for nine of them. We constructed precise deletions of each ECF σ gene and its demonstrated or putative anti-σ gene and also a strain in which all 11 ECF σ and anti-σ genes were deleted. This all-ECF σ deletion strain showed no major defects in free-living growth, in Biolog Phenotype MicroArray assays, or in response to multiple stresses. None of the ECF σs were required for symbiosis on the host plants Medicago sativa and Medicago truncatula: the strain deleted for all ECF σ and anti-σ genes was symbiotically normal. IMPORTANCE Fixed (reduced) soil nitrogen plays a critical role in soil fertility and successful food growth. Much soil fertility relies on symbiotic nitrogen fixation: the bacterial partner infects the host plant roots and reduces atmospheric dinitrogen in exchange for host metabolic fuel, a process that involves complex interactions between the partners mediated by changes in gene expression in each partner. Here we test the roles of a family of 11 extracytoplasmic function (ECF) gene regulatory proteins (sigma factors [σs]) that interact with RNA polymerase to determine if they play a significant role in establishing a nitrogen-fixing symbiosis or in responding to various stresses, including cell envelope stress. We discovered that symbiotic nitrogen fixation occurs even when all 11 of these regulatory genes are deleted, that most ECF sigma factors control accessory functions, and that none of the ECF sigma factors are required to survive envelope stress.
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