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Timilsina S, Kaur A, Sharma A, Ramamoorthy S, Vallad GE, Wang N, White FF, Potnis N, Goss EM, Jones JB. Xanthomonas as a Model System for Studying Pathogen Emergence and Evolution. PHYTOPATHOLOGY 2024; 114:1433-1446. [PMID: 38648116 DOI: 10.1094/phyto-03-24-0084-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
In this review, we highlight studies in which whole-genome sequencing, comparative genomics, and population genomics have provided unprecedented insights into past and ongoing pathogen evolution. These include new understandings of the adaptive evolution of secretion systems and their effectors. We focus on Xanthomonas pathosystems that have seen intensive study and improved our understanding of pathogen emergence and evolution, particularly in the context of host specialization: citrus canker, bacterial blight of rice, and bacterial spot of tomato and pepper. Across pathosystems, pathogens appear to follow a pattern of bursts of evolution and diversification that impact host adaptation. There remains a need for studies on the mechanisms of host range evolution and genetic exchange among closely related but differentially host-specialized species and to start moving beyond the study of specific strain and host cultivar pairwise interactions to thinking about these pathosystems in a community context.
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Affiliation(s)
- Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Amandeep Kaur
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Anuj Sharma
- Department of Horticultural Sciences, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | | | - Gary E Vallad
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | - Nian Wang
- Department of Microbiology and Cell Science, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
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Chapagain P, Ali A, Kidane DT, Farone M, Salem M. Characterisation of sRNAs enriched in outer membrane vesicles of pathogenic Flavobacterium psychrophilum causing Bacterial Cold Water Disease in rainbow trout. JOURNAL OF EXTRACELLULAR BIOLOGY 2024; 3:e161. [PMID: 38947174 PMCID: PMC11212332 DOI: 10.1002/jex2.161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/15/2024] [Accepted: 05/22/2024] [Indexed: 07/02/2024]
Abstract
Flavobacterium psychrophilum (Fp) causes Bacterial Cold Water Disease in salmonids. During host-pathogen interactions, gram-negative bacteria, such as Fp, release external membrane vesicles (OMVs) harbouring cargos, such as DNA, RNA and virulence factors. This study aimed to characterise the potential role of the OMVs' small RNAs (sRNAs) in the Fp-rainbow trout host-pathogen interactions. sRNAs carried within OMVs were isolated from Fp. RNA-Seq datasets from whole-cell Fp and their isolated OMVs indicated substantial enrichment of specific sRNAs in the OMVs compared to the parent cell. Many of the OMV-packaged sRNAs were located in the pathogenicity islands of Fp. Conservation of sRNAs in 65 strains with variable degrees of virulence was reported. Dual RNA-Seq of host and pathogen transcriptomes on day 5 post-infection of Fp -resistant and -susceptible rainbow trout genetic lines revealed correlated expression of OMV-packaged sRNAs and their predicted host's immune gene targets. In vitro, treatment of the rainbow trout epithelial cell line RTgill-W1 with OMVs showed signs of cytotoxicity accompanied by dynamic changes in the expression of host genes when profiled 24 h following treatment. The OMV-treated cells, similar to the Fp -resistant fish, showed downregulated expression of the suppressor of cytokine signalling 1 (SOCS1) gene, suggesting induction of phagosomal maturation. Other signs of modulating the host gene expression following OMV-treatment include favouring elements from the phagocytic, endocytic and antigen presentation pathways in addition to HSP70, HSP90 and cochaperone proteins, which provide evidence for a potential role of OMVs in boosting the host immune response. In conclusion, the study identified novel microbial targets and inherent characteristics of OMVs that could open up new avenues of treatment and prevention of fish infections.
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Affiliation(s)
- Pratima Chapagain
- Department of Medicine, Division of Diabetes, Endocrinology and MetabolismVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Ali Ali
- Department of Animal and Avian SciencesUniversity of MarylandCollege ParkMarylandUSA
| | - Destaalem T. Kidane
- Department of Biology and Molecular Bioscience ProgramMiddle Tennessee State UniversityMurfreesboroTennesseeUSA
| | - Mary Farone
- Department of Biology and Molecular Bioscience ProgramMiddle Tennessee State UniversityMurfreesboroTennesseeUSA
| | - Mohamed Salem
- Department of Animal and Avian SciencesUniversity of MarylandCollege ParkMarylandUSA
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Frantsuzova E, Bogun A, Kopylova O, Vetrova A, Solyanikova I, Streletskii R, Delegan Y. Genomic, Phylogenetic and Physiological Characterization of the PAH-Degrading Strain Gordonia polyisoprenivorans 135. BIOLOGY 2024; 13:339. [PMID: 38785821 PMCID: PMC11117675 DOI: 10.3390/biology13050339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/07/2024] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
Abstract
The strain Gordonia polyisoprenivorans 135 is able to utilize a wide range of aromatic compounds. The aim of this work was to study the features of genetic organization and biotechnological potential of the strain G. polyisoprenivorans 135 as a degrader of aromatic compounds. The study of the genome of the strain 135 and the pangenome of the G. polyisoprenivorans species revealed that some genes, presumably involved in PAH catabolism, are atypical for Gordonia and belong to the pangenome of Actinobacteria. Analyzing the intergenic regions of strain 135 alongside the "panIGRome" of G. polyisoprenivorans showed that some intergenic regions in strain 135 also differ from those located between the same pairs of genes in related strains. The strain G. polyisoprenivorans 135 in our work utilized naphthalene (degradation degree 39.43%) and grew actively on salicylate. At present, this is the only known strain of G. polyisoprenivorans with experimentally confirmed ability to utilize these compounds.
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Affiliation(s)
- Ekaterina Frantsuzova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Olga Kopylova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
- Pushchino Branch of Federal State Budgetary Educational Institution of Higher Education “Russian Biotechnology University (ROSBIOTECH)”, 142290 Pushchino, Moscow Region, Russia
| | - Anna Vetrova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Inna Solyanikova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
- Regional Microbiological Center, Belgorod State University, 308015 Belgorod, Russia
| | - Rostislav Streletskii
- Laboratory of Ecological Soil Science, Faculty of Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
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Roy S, Mittal P, Tayi L, Bondada S, Ray MK, Patel HK, Sonti RV. Xanthomonas oryzae pv. oryzae Exoribonuclease R Is Required for Complete Virulence in Rice, Optimal Motility, and Growth Under Stress. PHYTOPATHOLOGY 2022; 112:501-510. [PMID: 34384245 DOI: 10.1094/phyto-07-21-0310-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Exoribonuclease R (RNase R) is a 3' hydrolytic exoribonuclease that can degrade structured RNA. Mutation in RNase R affects virulence of certain human pathogenic bacteria. The aim of this study was to determine whether RNase R is necessary for virulence of the phytopathogen that causes bacterial blight in rice, Xanthomonas oryzae pv. oryzae (Xoo). In silico analysis has indicated that RNase R is highly conserved among various xanthomonads. Amino acid sequence alignment of Xoo RNase R with RNase R from various taxa indicated that Xoo RNase R clustered with RNase R of order Xanthomonadales. To study its role in virulence, we generated a gene disruption mutant of Xoo RNase R. The Xoo rnr- mutant is moderately virulence deficient, and the complementing strain (rnr-/pHM1::rnr) rescued the virulence deficiency of the mutant. We investigated swimming and swarming motilities in both nutrient-deficient minimal media and nutrient-optimal media. We observed that RNase R mutation has adversely affected the swimming and swarming motilities of Xoo in optimal media. However, in nutrient-deficient media only swimming motility was noticeably affected. Growth curves in optimal media at suboptimal temperature (15°C cold stress) indicate that the Xoo rnr- mutant grows more slowly than the Xoo wild type and complementing strain (rnr-/pHM1::rnr). Given these findings, we report for the first time that RNase R function is necessary for complete virulence of Xoo in rice. It is also important for motility of Xoo in media and for growth of Xoo at suboptimal temperature.
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Affiliation(s)
- Sharmila Roy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Pragya Mittal
- MRC Human Genetics Unit, University of Edinburgh, Crewe Road South, Edinburgh, UK, EH4 2XU
| | - Lavanya Tayi
- Center for Plant Molecular Biology, Osmania University, Tarnaka, Hyderabad, Telangana State, India 500007
| | - Sahitya Bondada
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Malay K Ray
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Hitendra K Patel
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Ramesh V Sonti
- Indian Institute of Science Education and Research, Tirupati, Andhra Pradesh, India 517507
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Secrete or perish: The role of secretion systems in Xanthomonas biology. Comput Struct Biotechnol J 2020; 19:279-302. [PMID: 33425257 PMCID: PMC7777525 DOI: 10.1016/j.csbj.2020.12.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/13/2020] [Accepted: 12/13/2020] [Indexed: 12/22/2022] Open
Abstract
Bacteria of the Xanthomonas genus are mainly phytopathogens of a large variety of crops of economic importance worldwide. Xanthomonas spp. rely on an arsenal of protein effectors, toxins and adhesins to adapt to the environment, compete with other microorganisms and colonize plant hosts, often causing disease. These protein effectors are mainly delivered to their targets by the action of bacterial secretion systems, dedicated multiprotein complexes that translocate proteins to the extracellular environment or directly into eukaryotic and prokaryotic cells. Type I to type VI secretion systems have been identified in Xanthomonas genomes. Recent studies have unravelled the diverse roles played by the distinct types of secretion systems in adaptation and virulence in xanthomonads, unveiling new aspects of their biology. In addition, genome sequence information from a wide range of Xanthomonas species and pathovars have become available recently, uncovering a heterogeneous distribution of the distinct families of secretion systems within the genus. In this review, we describe the architecture and mode of action of bacterial type I to type VI secretion systems and the distribution and functions associated with these important nanoweapons within the Xanthomonas genus.
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Tang D, Chen X, Jia Y, Liang Y, He Y, Lu T, Zhu C, Han B, An S, Tang J. Genome-wide screen and functional analysis in Xanthomonas reveal a large number of mRNA-derived sRNAs, including the novel RsmA-sequester RsmU. MOLECULAR PLANT PATHOLOGY 2020; 21:1573-1590. [PMID: 32969159 PMCID: PMC7694677 DOI: 10.1111/mpp.12997] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/02/2020] [Accepted: 08/26/2020] [Indexed: 05/07/2023]
Abstract
Although bacterial small noncoding RNAs (sRNAs) are known to play a critical role in various cellular processes, including pathogenesis, the identity and action of such sRNAs are still poorly understood in many organisms. Here we have performed a genome-wide screen and functional analysis of the sRNAs in Xanthomonas campestris pv. campestris (Xcc), an important phytopathogen. The 50-500-nt RNA fragments isolated from the wild-type strain grown in a virulence gene-inducing condition were sequenced and a total of 612 sRNA candidates (SRCs) were identified. The majority (82%) of the SRCs were derived from mRNA, rather than specific sRNA genes. A representative panel of 121 SRCs were analysed by northern blotting; 117 SRCs were detected, supporting the contention that the overwhelming majority of the 612 SRCs identified are indeed sRNAs. Phenotypic analysis of strains overexpressing different candidates showed that a particular sRNA, RsmU, acts as a negative regulator of virulence, the hypersensitive response, and cell motility in Xcc. In vitro electrophoretic mobility shift assay and in vivo coimmunoprecipitation analyses indicated that RsmU interacted with the global posttranscriptional regulator RsmA, although sequence analysis displayed that RsmU is not a member of the sRNAs families known to antagonize RsmA. Northern blotting analyses demonstrated that RsmU has two isoforms that are processed from the 3'-untranslated region of the mRNA of XC1332 predicted to encode ComEA, a periplasmic protein required for DNA uptake in bacteria. This work uncovers an unexpected major sRNA biogenesis strategy in bacteria and a hidden layer of sRNA-mediated virulence regulation in Xcc.
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Affiliation(s)
- Dong‐Jie Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Xiao‐Lin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life Science and TechnologyGuangxi UniversityNanningChina
- Present address:
Plant Protection Research InstituteGuangxi Academy of Agricultural Science174 Daxue RoadNanningGuangxi530007China
| | - Yu Jia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Yu‐Wei Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Yuan‐Ping He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Ting‐Ting Lu
- National Center for Gene Research & Institute of Plant Physiology and EcologyShanghai Institutes of Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Chuan‐Rang Zhu
- National Center for Gene Research & Institute of Plant Physiology and EcologyShanghai Institutes of Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Bin Han
- National Center for Gene Research & Institute of Plant Physiology and EcologyShanghai Institutes of Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Shi‐Qi An
- National Biofilms Innovation CentreBiological SciencesUniversity of SouthamptonSouthamptonUK
| | - Ji‐Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesCollege of Life Science and TechnologyGuangxi UniversityNanningChina
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Cenens W, Andrade MO, Llontop E, Alvarez-Martinez CE, Sgro GG, Farah CS. Bactericidal type IV secretion system homeostasis in Xanthomonas citri. PLoS Pathog 2020; 16:e1008561. [PMID: 32453788 PMCID: PMC7286519 DOI: 10.1371/journal.ppat.1008561] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 06/10/2020] [Accepted: 04/18/2020] [Indexed: 11/19/2022] Open
Abstract
Several Xanthomonas species have a type IV secretion system (T4SS) that injects a cocktail of antibacterial proteins into neighbouring Gram-negative bacteria, often leading to rapid lysis upon cell contact. This capability represents an obvious fitness benefit since it can eliminate competition while the liberated contents of the lysed bacteria could provide an increase in the local availability of nutrients. However, the production of this Mega Dalton-sized molecular machine, with over a hundred subunits, also imposes a significant metabolic cost. Here we show that the chromosomal virB operon, which encodes the structural genes of this T4SS in X. citri, is regulated by the conserved global regulator CsrA. Relieving CsrA repression from the virB operon produced a greater number of T4SSs in the cell envelope and an increased efficiency in contact-dependent lysis of target cells. However, this was also accompanied by a physiological cost leading to reduced fitness when in co-culture with wild-type X. citri. We show that T4SS production is constitutive despite being downregulated by CsrA. Cells subjected to a wide range of rich and poor growth conditions maintain a constant density of T4SSs in the cell envelope and concomitant interbacterial competitiveness. These results show that CsrA provides a constant though partial repression on the virB operon, independent of the tested growth conditions, in this way controlling T4SS-related costs while at the same time maintaining X. citri's aggressive posture when confronted by competitors.
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Affiliation(s)
- William Cenens
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), Av. Prof. Lineu Prestes 748, São Paulo, SP, Brazil
| | - Maxuel O. Andrade
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, R. Giuseppe Máximo Scolfaro, Campinas, SP, Brazil
| | - Edgar Llontop
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), Av. Prof. Lineu Prestes 748, São Paulo, SP, Brazil
| | - Cristina E. Alvarez-Martinez
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Rua Monteiro Lobato, Campinas, SP, Brazil
| | - Germán G. Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), Av. Prof. Lineu Prestes 748, São Paulo, SP, Brazil
| | - Chuck S. Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), Av. Prof. Lineu Prestes 748, São Paulo, SP, Brazil
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Timilsina S, Potnis N, Newberry EA, Liyanapathiranage P, Iruegas-Bocardo F, White FF, Goss EM, Jones JB. Xanthomonas diversity, virulence and plant-pathogen interactions. Nat Rev Microbiol 2020; 18:415-427. [PMID: 32346148 DOI: 10.1038/s41579-020-0361-8] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2020] [Indexed: 12/19/2022]
Abstract
Xanthomonas spp. encompass a wide range of plant pathogens that use numerous virulence factors for pathogenicity and fitness in plant hosts. In this Review, we examine recent insights into host-pathogen co-evolution, diversity in Xanthomonas populations and host specificity of Xanthomonas spp. that have substantially improved our fundamental understanding of pathogen biology. We emphasize the virulence factors in xanthomonads, such as type III secreted effectors including transcription activator-like effectors, type II secretion systems, diversity resulting in host specificity, evolution of emerging strains, activation of susceptibility genes and strategies of host evasion. We summarize the genomic diversity in several Xanthomonas spp. and implications for disease outbreaks, management strategies and breeding for disease resistance.
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Affiliation(s)
- Sujan Timilsina
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Neha Potnis
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Eric A Newberry
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | | | | | - Frank F White
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Erica M Goss
- Plant Pathology Department, University of Florida, Gainesville, FL, USA. .,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| | - Jeffrey B Jones
- Plant Pathology Department, University of Florida, Gainesville, FL, USA.
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Liu X, Yan Y, Wu H, Zhou C, Wang X. Biological and transcriptomic studies reveal hfq is required for swimming, biofilm formation and stress response in Xanthomonas axonpodis pv. citri. BMC Microbiol 2019; 19:103. [PMID: 31113370 PMCID: PMC6530196 DOI: 10.1186/s12866-019-1476-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/07/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Hfq is a widely conserved bacterial RNA-binding protein which generally mediates the global regulatory activities involv ed in physiological process and virulence. The goal of this study was to characterize the biological function of hfq gene in Xanthomonas axonpodis pv. citri (Xac), the causal agent of citrus canker disease. RESULTS An hfq mutant in Xac was generated by plasmid integration. The loss of hfq resulted in attenuation of bacterial growth, motility and biofilm formation. In addition, the hfq mutation impaired Xac resistance to H2O2 and both high and low pH environments, but did not affect the virulence to citrus. RNA-Seq analyses indicated that Hfq played roles in regulating the expression of 746 genes. In hfq mutant, gene expression related to chemotaxis, secretion system, two-component system, quorum sensing and flagellar assembly were repressed, whereas expression of ribosomal genes were significantly up-regulated. The down-regulated expression of three bacterial chemotaxis related genes and seven flagella genes, which involved in cell growth and biofilm formation, were further validated by RT-qPCR. CONCLUSIONS The study demonstrated that hfq was involved in multiple biological processes in Xac. The results could serve as initiate points for identifying regulatory sRNAs and genes controlled by Hfq-sRNA interactions in Xac.
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Affiliation(s)
- Xuelu Liu
- National Engineering Research Center for Citrus, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, 400712, People's Republic of China
| | - Yuping Yan
- National Engineering Research Center for Citrus, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, 400712, People's Republic of China.,, Present address: Agriculture commission of Guangan district, Guangan, Sichuan, China
| | - Haodi Wu
- National Engineering Research Center for Citrus, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, 400712, People's Republic of China
| | - Changyong Zhou
- National Engineering Research Center for Citrus, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, 400712, People's Republic of China
| | - Xuefeng Wang
- National Engineering Research Center for Citrus, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, 400712, People's Republic of China.
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Genome sequence of Xanthomonas fuscans subsp. fuscans strain Xff49: a new isolate obtained from common beans in Southern Brazil. Braz J Microbiol 2019; 50:357-367. [PMID: 30850979 DOI: 10.1007/s42770-019-00050-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 01/21/2019] [Indexed: 01/22/2023] Open
Abstract
The genus Xanthomonas comprises Gram-negative bacteria, many of which are phytopathogens. Xanthomonas fuscans subsp. fuscans is one of the most devastating pathogens affecting the bean plant, resulting in the common bacterial blight of bean (CBB). The disease is mainly foliar and affects a wide variety of bean species, thus acting as the yield-limiting factor for the bean crop. Here, we report the whole-genome sequencing of a new strain of X. fuscans subsp. fuscans, named Xff49, isolated from the infected and symptomatic beans from Capão do Leão, Southern Brazil. The genetic analysis demonstrated the presence of single-nucleotide variants (SNVs) in this strain, potentially affecting the mobilome, cell mobility, and inorganic ion metabolism. In addition, the analysis resulted in the identification of a new plasmid similar to the pAX22 derived from Achromobacter denitrificans, which was named plX, along with plA and plC, previously reported in other strains of X. fuscans subsp. fuscans. Xff49 represents the first Brazilian genome of X. fuscans subsp. fuscans and might provide useful information applicable to the studies of phylogenetics, evolution, and pathogenomics, thereby allowing a better understanding of the genomic features present in the Brazilian strains.
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Carvalho Garcia A, Dos Santos VLP, Santos Cavalcanti TC, Collaço LM, Graf H. Bacterial Small RNAs in the Genus Herbaspirillum spp. Int J Mol Sci 2018; 20:ijms20010046. [PMID: 30583511 PMCID: PMC6337395 DOI: 10.3390/ijms20010046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/12/2018] [Accepted: 12/12/2018] [Indexed: 12/26/2022] Open
Abstract
The genus Herbaspirillum includes several strains isolated from different grasses. The identification of non-coding RNAs (ncRNAs) in the genus Herbaspirillum is an important stage studying the interaction of these molecules and the way they modulate physiological responses of different mechanisms, through RNA⁻RNA interaction or RNA⁻protein interaction. This interaction with their target occurs through the perfect pairing of short sequences (cis-encoded ncRNAs) or by the partial pairing of short sequences (trans-encoded ncRNAs). However, the companion Hfq can stabilize interactions in the trans-acting class. In addition, there are Riboswitches, located at the 5' end of mRNA and less often at the 3' end, which respond to environmental signals, high temperatures, or small binder molecules. Recently, CRISPR (clustered regularly interspaced palindromic repeats), in prokaryotes, have been described that consist of serial repeats of base sequences (spacer DNA) resulting from a previous exposure to exogenous plasmids or bacteriophages. We identified 285 ncRNAs in Herbaspirillum seropedicae (H. seropedicae) SmR1, expressed in different experimental conditions of RNA-seq material, classified as cis-encoded ncRNAs or trans-encoded ncRNAs and detected RNA riboswitch domains and CRISPR sequences. The results provide a better understanding of the participation of this type of RNA in the regulation of the metabolism of bacteria of the genus Herbaspirillum spp.
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Affiliation(s)
- Amanda Carvalho Garcia
- Department of Internal Medicine, Federal University of Paraná, Curitiba 80.060-240, Brazil.
| | | | | | - Luiz Martins Collaço
- Department of Pathology, Federal University of Paraná, PR, Curitiba 80.060-240, Brazil.
| | - Hans Graf
- Department of Internal Medicine, Federal University of Paraná, Curitiba 80.060-240, Brazil.
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Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology (Reading) 2017; 163:1117-1144. [DOI: 10.1099/mic.0.000473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jessica Schneider
- Bioinformatics Resource Facility, Centrum für Biotechnologie, Universität Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Frank-Jörg Vorhölter
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
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Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data. J Biotechnol 2017; 253:55-61. [DOI: 10.1016/j.jbiotec.2017.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 11/18/2022]
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Sundin GW, Wang N, Charkowski AO, Castiblanco LF, Jia H, Zhao Y. Perspectives on the Transition From Bacterial Phytopathogen Genomics Studies to Applications Enhancing Disease Management: From Promise to Practice. PHYTOPATHOLOGY 2016; 106:1071-1082. [PMID: 27183301 DOI: 10.1094/phyto-03-16-0117-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The advent of genomics has advanced science into a new era, providing a plethora of "toys" for researchers in many related and disparate fields. Genomics has also spawned many new fields, including proteomics and metabolomics, furthering our ability to gain a more comprehensive view of individual organisms and of interacting organisms. Genomic information of both bacterial pathogens and their hosts has provided the critical starting point in understanding the molecular bases of how pathogens disrupt host cells to cause disease. In addition, knowledge of the complete genome sequence of the pathogen provides a potentially broad slate of targets for the development of novel virulence inhibitors that are desperately needed for disease management. Regarding plant bacterial pathogens and disease management, the potential for utilizing genomics resources in the development of durable resistance is enhanced because of developing technologies that enable targeted modification of the host. Here, we summarize the role of genomics studies in furthering efforts to manage bacterial plant diseases and highlight novel genomics-enabled strategies heading down this path.
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Affiliation(s)
- George W Sundin
- First and fourth authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing; second and fifth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Lake Alfred; third author: Department of Plant Pathology, University of Wisconsin-Madison; sixth author: Department of Crop Sciences, University of Illinois at Urbana-Champaign
| | - Nian Wang
- First and fourth authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing; second and fifth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Lake Alfred; third author: Department of Plant Pathology, University of Wisconsin-Madison; sixth author: Department of Crop Sciences, University of Illinois at Urbana-Champaign
| | - Amy O Charkowski
- First and fourth authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing; second and fifth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Lake Alfred; third author: Department of Plant Pathology, University of Wisconsin-Madison; sixth author: Department of Crop Sciences, University of Illinois at Urbana-Champaign
| | - Luisa F Castiblanco
- First and fourth authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing; second and fifth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Lake Alfred; third author: Department of Plant Pathology, University of Wisconsin-Madison; sixth author: Department of Crop Sciences, University of Illinois at Urbana-Champaign
| | - Hongge Jia
- First and fourth authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing; second and fifth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Lake Alfred; third author: Department of Plant Pathology, University of Wisconsin-Madison; sixth author: Department of Crop Sciences, University of Illinois at Urbana-Champaign
| | - Youfu Zhao
- First and fourth authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing; second and fifth authors: Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Lake Alfred; third author: Department of Plant Pathology, University of Wisconsin-Madison; sixth author: Department of Crop Sciences, University of Illinois at Urbana-Champaign
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Leßmeier L, Alkhateeb RS, Schulte F, Steffens T, Loka TP, Pühler A, Niehaus K, Vorhölter FJ. Applying DNA affinity chromatography to specifically screen for sucrose-related DNA-binding transcriptional regulators of Xanthomonas campestris. J Biotechnol 2016; 232:89-98. [DOI: 10.1016/j.jbiotec.2016.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/22/2016] [Accepted: 04/05/2016] [Indexed: 11/28/2022]
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