DOCSLIB.ORG

Downloaded from NCBI, and Get Sequences in The

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Downloaded from NCBI, and Get Sequences in The bioRxiv preprint doi: https://doi.org/10.1101/461707; this version posted January 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Sulfur reduction coupling with anaerobic ammonium oxidation drives proto-anabolic 2 networks 3 Peng Bao1, 2, *, Guo-Xiang Li1, 2, 3, Hu Li1 4 5 1Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese 6 Academy of Sciences, Xiamen 361021, P. R. China 7 2Ningbo Urban Environment Observation and Station, Chinese Academy of Sciences, 8 Ningbo 315800, P. R. China 9 3University of Chinese Academy of Sciences, Beijing 100049, P. R. China 10 11 Address correspondence to: 12 Dr. Peng Bao 13 Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, P. R. 14 China 15 E-mail: [email protected]; [email protected] 16 17 18 bioRxiv preprint doi: https://doi.org/10.1101/461707; this version posted January 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 19 Abstract 20 The geochemical energy that drives the transition from non-life to life is as yet 21 unknown. Here we show that thiosulfate/sulfate reduction coupling with anaerobic 22 ammonium oxidation (Sammox), could provide the primordial redox equivalents and 23 energy for prebiotic proto-anabolic networks, the reductive acetyl-CoA pathway 24 combined with incomplete reductive tricarboxylic acid (rTCA) cycle, reductive 25 amination and pyrrole synthesis. Fe-S mineral catalysis and thiols/thioesters as energy 26 couplers enhance the efficiency of prebiotic proto-anabolic networks in 27 thiosulfate-fueled Sammox reaction systems under hydrothermal conditions. Results 28 implied that thiosulfate-fueled Sammox should be the primordial reaction driving the 29 construction of proto-anabolic networks rather than sulfate-fueled Sammox, as it 30 could be catalyzed, and also sulfate would have been severely limiting in ancient 31 oceans. To confirm our findings, we isolated and identified a mixtrophic Sammox 32 bacterium, Ralstonia thioammoniphilus GX3-BWBA, which prefer thiosulfate to 33 sulfate. Genomic analysis of R. thioammoniphilus GX3-BWBA implied that this 34 ancient metabolism in modern microbes should contain two stages according to 35 ammonium transformation, —oxidation of ammonium to nitrite and denitrification. 36 The incomplete rTCA cycle and reductive acetyl-CoA pathway were all identified in 37 R. thioammoniphilus GX3-BWBA metabolic networks, which were responsible for 38 chemolithotrophic metabolism. We inferred that Sammox drove the coupling of the 39 biochemical transformation of C, H, O, N, S, and/or Fe simultaneously in Hadean 40 alkaline hydrothermal systems, thereby permitting the emergence of life. The results bioRxiv preprint doi: https://doi.org/10.1101/461707; this version posted January 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 41 bridged the gap in the transition from geochemistry to biochemistry. 42 43 bioRxiv preprint doi: https://doi.org/10.1101/461707; this version posted January 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 44 The transition from non-life to life occurred in the context of geochemical energy 45 derived from element-coupled transformation1-3. The chemistry of life is based on 46 redox reactions, that is, successive transfers of electrons and protons from the six 1,4 47 major elements, i.e., C, H, O, N, S, and P . The H2/CO2 redox couple, which can 48 occur in submarine hydrothermal vents, has been proposed to drive the reductive 49 acetyl-CoA pathway, an ancient metabolic route3,5-7. Nevertheless, the primordial 50 energy source of the H2/CO2 redox couple suffers from the difficulty that the 8 51 exergonic reaction competes with the endergonic reaction for available H2 . The 52 subsequent surface metabolism and thioester world theories still could not answer the 53 question, how the required reduced carbon compounds have been synthesized9,10. 54 Despite this limitation, these theories have emphasized the important roles of 55 thioesters and Fe-S mineral catalysis for driving the primordial rTCA cycle, a central 56 anabolic biochemical pathway whose origins are proposed to trace back to 57 geochemistry9,11,12. 58 Native iron/metals were recently shown to promote the reductive acetyl-CoA 59 pathway and rTCA cycle and strongly support the feasibility of these two primordial 60 synthetic pathways13,14, although they were generally considered to be rare near the 61 Earth’s surface13 and cannot support the long elemental transition from geochemistry 62 to biochemistry. Proto-anabolic networks consisting of the reductive acetyl-CoA 63 pathway together with the complete/incomplete rTCA cycle as primordial synthetic 64 pathways are therefore more logical3,15-18. However, the initial driving force for the 65 rise of proto-anabolic networks is still unclear. Moreover, the roles of N and S bioRxiv preprint doi: https://doi.org/10.1101/461707; this version posted January 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 66 geochemical transformation in the origin of life have been largely ignored because 67 computational analysis has implied that N and S are essential for thermodynamically 68 feasible phosphate-independent metabolism before the rise of last universal common 69 ancestor (LUCA)19. The proto-anabolic networks might be driven by C, H, O, N, S, 70 and/or Fe coupling transformation at their earliest stage of the transition from 71 geochemistry to biochemistry. The co-evolution of the metabolism of those elements 72 may provide strong explanatory power for the origin of life and explain why the 73 structure of metabolic networks is as it is. We therefore speculate that 74 thermodynamically feasible sulfurous species reduction coupling with anaerobic 75 ammonium oxidation reaction20,21,22,23,24 (Eqs. 1, 2; pH=8.0), with/without the 76 catalysis of Fe-S minerals and thioesters, may have been the primordial power force 77 for the rise of proto-anabolic networks. 78 8NH+2-- +2SO +2HCO→ 4N +2HS - +CH COO - +12H O+5H +∆G = -20.0 kJ mol-1 44 3 2 3 2 r (1) 79 4NH+2-- +S O +2HCO→ 2N +2HS- +2HCOO - +5H O+4H +∆G = -13.4 kJ mol-1 (2) 423 3 2 2 r 80 On early Earth, elemental sulfur, sulfite, and thiosulfate were produced 81 abundantly from volcanic and hydrothermal SO2 or from H2S oxidation by iron oxides 82 in sulfide-rich hydrothermal fluid2,15,25. In simulated hydrothermal systems with 26 83 conditions of 300 °C and high pressure, nitrite was readily converted to NH3 , and 84 Ni-Fe metals and alloys were also effective catalysts of N2 reduction to NH3 in 27 85 Hadean hydrothermal systems . There would have been much higher CO2 86 concentrations in the oceans on early Earth because there was perhaps up to 1000 28 87 times more CO2 in the atmosphere than that today . bioRxiv preprint doi: https://doi.org/10.1101/461707; this version posted January 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 88 Hence, when sulfurous species and NH3 in Hadean hydrothermal systems made 89 contact with CO2, there were spontaneous electron and proton transfers for energy 90 generation and organic molecule synthesis via sulfurous species reduction coupling 91 with ammonium oxidation. As sulfate would have been severely limiting in ancient 92 oceans2,29, we termed this process Sammox, and a Sammox microbe is more likely 93 use thiosulfate, elemental sulfur and sulfite as electron acceptor besides sulfate, 94 distinguishing it from previous studies of the coupling elemental biogeochemical 95 cycles1,30. A prebiotic reaction should occur with the ability to branch out into S and 96 N biochemistry, which could contribute to the autocatalysis and evolution of 97 primordial metabolic networks. Thus, Sammox may facilitate the synthesis of 98 thioesters and amino acids, which are essential for the self-amplification of 99 phosphate-independent metabolic networks before the rise of LUCA. We expect that 100 prebiotic chemical evidence of Sammox-powered CO2 fixation, thioesters, amino acid 101 and co-factors synthesis, combined with genetic analysis of a representative Sammox 102 microbe, will provide profound insights into the earliest origins of life and fill in the 103 missing link of the emergence of biochemistry from geochemistry. 104 105 Results and discussion 106 Sammox drives the combination of abiotic reductive acetyl-CoA pathway and 107 incomplete rTCA cycle 108 First, we aimed to verify the feasibility of Sammox-driven abiotic reductive 109 acetyl-CoA pathway, rTCA cycle, and off-cycle reactions (reductive amination and bioRxiv preprint doi: https://doi.org/10.1101/461707; this version posted January 30, 2019.
Load more

Recommended publications
  • INOCULUM DYNAMICS of Ralstonia Spp.: POTENTIAL SOURCES, PERSISTENCE in a LOCAL POPULATION and SELECTION of PHAGES to REDUCE BACTERIA SURVIVAL
    JAQUELINE KIYOMI YAMADA INOCULUM DYNAMICS OF Ralstonia spp.: POTENTIAL SOURCES, PERSISTENCE IN A LOCAL POPULATION AND SELECTION OF PHAGES TO REDUCE BACTERIA SURVIVAL Thesis presented to the Plant Pathology Program of the Universidade Federal de Viçosa in partial fulfillment of the requirements for the degree of Doctor Scientiae. VIÇOSA MINAS GERAIS – BRASIL 2018 ) AGRADECIMENTOS Agradeço a Deus, pela vida, por estar presente em todos os momentos. Agradeço aos meus pais, Jorge e Helena, exemplos de honestidade e humildade, todas as minhas conquistas são fruto do sacrifício deles. À minha irmã, Michelle, por todo apoio. Obrigada Mi! Agradeço ao Filipe Constantino Borel, pelo companheirismo e carinho, fundamental para a conclusão dessa etapa da minha vida. Agradeço à Nina e Júlio Borel, pais de Filipe, por todo apoio. Agradeço à Universidade Federal de Viçosa, ao Departamento de Fitopatologia e à FAPEMIG pela oportunidade e pelo financiamento desse trabalho. Agradeço ao Professor Eduardo Seite Gomide Mizubuti pela oportunidade, paciência e conselhos. Agradeço ao Doutor Carlos Alberto Lopes, pela contribuição para o presente trabalho e pela amizade. Agradeço ao Professor José Rogério e ao Professor Francisco Murilo Zerbini por terem disponibilizados os laboratórios para realização desse trabalho. Agradeço ao Professor Sérgio Oliveira de Paula, em especial ao Roberto de Sousa Dias e ao Vinicius Duarte pela colaboração e pela amizade. Agradeço à Thaís Ribeiro Santiago e à Camila Geovanna Ferro, pelas sugestões e pela amizade. Agradeço a todos que colaboraram com as amostras de solo e água para este trabalho: Paulo E. F. de Macedo, Amanda Guedes, Carla Santin, Leandro H. Yamada, Filipe C.
    [Show full text]
  • Bacterial Diseases of Bananas and Enset: Current State of Knowledge and Integrated Approaches Toward Sustainable Management G
    Bacterial Diseases of Bananas and Enset: Current State of Knowledge and Integrated Approaches Toward Sustainable Management G. Blomme, M. Dita, K. S. Jacobsen, L. P. Vicente, A. Molina, W. Ocimati, Stéphane Poussier, Philippe Prior To cite this version: G. Blomme, M. Dita, K. S. Jacobsen, L. P. Vicente, A. Molina, et al.. Bacterial Diseases of Bananas and Enset: Current State of Knowledge and Integrated Approaches Toward Sustainable Management. Frontiers in Plant Science, Frontiers, 2017, 8, pp.1-25. 10.3389/fpls.2017.01290. hal-01608050 HAL Id: hal-01608050 https://hal.archives-ouvertes.fr/hal-01608050 Submitted on 28 Aug 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License fpls-08-01290 July 22, 2017 Time: 11:6 # 1 REVIEW published: 20 July 2017 doi: 10.3389/fpls.2017.01290 Bacterial Diseases of Bananas and Enset: Current State of Knowledge and Integrated Approaches Toward Sustainable Management Guy Blomme1*, Miguel Dita2, Kim Sarah Jacobsen3, Luis Pérez Vicente4, Agustin
    [Show full text]
  • Whole Genome Characterization of Strains Belonging to the Ralstonia
    Eur J Plant Pathol https://doi.org/10.1007/s10658-020-02190-8 Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex Viola Kurm & Ilse Houwers & Claudia E. Coipan & Peter Bonants & Cees Waalwijk & Theo van der Lee & Balázs Brankovics & Jan van der Wolf Accepted: 17 December 2020 # The Author(s) 2021 Abstract Identification and classification of members of that the increasing availability of whole genome sequences the Ralstonia solanacearum species complex (RSSC) is is not only useful for classification of strains, but also shows challenging due to the heterogeneity of this complex. Whole potential for selection and evaluation of clade specific genome sequence data of 225 strains were used to classify nucleic acid-based amplification methods within the RSSC. strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI Keywords MLSA . ANI . in-silico analysis . Ralstonia score (>95%), 191 out of 192(99.5%) RSSC strains could solanacearum species complex . Phylogenetic be grouped into the three species R. solanacearum, R. classification pseudosolanacearum,andR. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups Introduction (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accor- Bacteria belonging to the Ralstonia solanacearum spe- dance with MLSA. The IIB subgroups found by ANI and cies complex (RSSC) are the causative agents of dis- MLSA also differed in the number of SNPs in the primer eases in plants of many different botanical families.
    [Show full text]
  • Pangenomic Type III Effector Database of the Plant Pathogenic [I]Ralstonia Spp.[I]
    A peer-reviewed version of this preprint was published in PeerJ on 6 August 2019. View the peer-reviewed version (peerj.com/articles/7346), which is the preferred citable publication unless you specifically need to cite this preprint. Sabbagh CRR, Carrere S, Lonjon F, Vailleau F, Macho AP, Genin S, Peeters N. 2019. Pangenomic type III effector database of the plant pathogenic Ralstonia spp. PeerJ 7:e7346 https://doi.org/10.7717/peerj.7346 Pangenomic type III effector database of the plant pathogenic Ralstonia spp. Cyrus Raja Rubenstein Sabbagh Equal first author, 1 , Sébastien Carrère Equal first author, 1 , Fabien Lonjon 2 , Fabienne Vailleau 1 , Alberto P Macho 3 , Stephane Genin 1 , Nemo Peeters Corresp. 1 1 LIPM, Université de Toulouse, INRA, CNRS, Castanet-tolosan, France 2 Department of Cell & Systems Biology, University of Toronto, Toronto, Canada 3 Shanghai center for plant stress biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China Corresponding Author: Nemo Peeters Email address: [email protected] Background. The bacterial plant pathogenic Ralstonia species belong to the beta- proteobacteria order and are soil-borne pathogens causing the vascular bacterial wilt disease, affecting a wide range of plant hosts. These bacteria form a heterogeneous group considered as a “species complex”,” gathering three newly defined species. Like many other Gram negative plant pathogens, Ralstonia pathogenicity relies on a type III secretion system, enabling bacteria to secrete/inject a large repertoire of type III effectors into their plant host cells. T3Es are thought to participate in generating a favorable environment for the pathogen (countering plant immunity and modifying the host metabolism and physiology).
    [Show full text]
  • A Genome-Wide Scan for Genes Under Balancing Selection in the Plant Pathogen Ralstonia Solanacearum José A
    Castillo and Agathos BMC Evolutionary Biology (2019) 19:123 https://doi.org/10.1186/s12862-019-1456-6 RESEARCHARTICLE Open Access A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum José A. Castillo1* and Spiros N. Agathos2 Abstract Background: Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen’s gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common bacterial phytopathogen. We performed a genome-wide scan of Ralstonia solanacearum species complex, an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called ‘bacterial wilt’. Results: Using a sliding window approach, we analyzed 57 genomes from three phylotypes of the R. solanacearum species complex to detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima’sD,θw and Fu & Li’s D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes with known function that map in any of the two main replicons (1.7% of total number of genes). The candidate genes under balancing selection are related to primary metabolism and other basal activities (51.3%) or directly associated to virulence (48.7%), the latter being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process.
    [Show full text]
  • Cas Systems in the Ralstonia Solanacearum Species Complex
    bs_bs_banner MOLECULAR PLANT PATHOLOGY (2019) 20(2), 223–239 DOI: 10.1111/mpp.12750 Characterization of CRISPR-Cas systems in the Ralstonia solanacearum species complex ANDRÉ DA SILVA XAVIER1, JULIANA CRISTINA FRALEON DE ALMEIDA1, ALESSANDRA GONÇALVES DE MELO2, GENEVIÈVE M. ROUSSEAU2,3, DENISE M. TREMBLAY2,3, RAFAEL REIS DE REZENDE1, SYLVAIN MOINEAU2,3 AND POLIANE ALFENAS-ZERBINI1* 1 Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil 2 Département de Biochimie, de Microbiologie, et de Bioinformatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC GIV0A6, Canada 3 Félix d’Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, QC GIV0A6, Canada SUMMARY INTRODUCTION Clustered regularly interspaced short palindromic repeats The Gram-negative plant-pathogenic bacteria Ralstonia spp. be- (CRISPRs) are composed of an array of short DNA repeat se- long to a species complex, the Ralstonia solanacearum species quences separated by unique spacer sequences that are complex (RSSC), which is recognized as a group of considerable flanked by associated (Cas) genes. CRISPR-Cas systems are genetic diversity encompassing phenotypically diverse strains found in the genomes of several microbes and can act as an that can be subdivided into four phylotypes (Allen et al., 2005; adaptive immune mechanism against invading foreign nucleic Prior and Fegan, 2005). Phylotypes I, II and III contain strains acids, such as phage genomes. Here, we studied the CRISPR- predominantly from Asia, America and Africa and surrounding is- Cas systems in plant-pathogenic bacteria of the Ralstonia sola- lands, respectively, whereas phylotype IV is comprised of strains nacearum species complex (RSSC).
    [Show full text]
  • And Genomic Islands in the Ralstonia Solanacearum Species Complex Osiel Silva Gonçalves, Marisa Vieira De Queiroz & Mateus Ferreira Santana*
    www.nature.com/scientificreports OPEN Potential evolutionary impact of integrative and conjugative elements (ICEs) and genomic islands in the Ralstonia solanacearum species complex Osiel Silva Gonçalves, Marisa Vieira de Queiroz & Mateus Ferreira Santana* Ralstonia solanacearum, a soil-borne plant pathogen, encompasses a large number of strains known as R. solanacearum species complex (RSSC). Although it has been suggested that mobile genetic elements (MGEs) may play an important role in the RSSC genome, the evolutionary impact of these elements remains unknown. Here, we identifed and analysed Integrative and Conjugative Elements (ICEs) and Genomic Islands (GIs) in the 121 genomes published for Ralstonia spp., including RSSC strains and three other non-plant pathogenic Ralstonia spp. Our results provided a dataset of 12 ICEs and 31 GIs distributed throughout Ralstonia spp. Four novel ICEs in RSSC were found. Some of these elements cover 5% of the host genome and carry accessory genes with a potential impact on the ftness and pathogenicity of RSSC. In addition, phylogenetic analysis revealed that these MGEs clustered to the same species, but there is evidence of strains from diferent countries that host the same element. Our results provide novel insight into the RSSC adaptation, opening new paths to a better understanding of how these elements afect this soil-borne plant pathogen. Te soil-borne bacterium Ralstonia solanacearum is one of the most devastating phytopathogens worldwide, responsible for bacterial wilt disease in more than 250 plant species 1,2. Strains of R. solanacearum form a het- erogeneous group of species that are divided into four phylotypes corresponding to their geographic origin.
    [Show full text]
  • Overview of Biotic Stresses in Pepper (Capsicum Spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics
    International Journal of Molecular Sciences Review Overview of Biotic Stresses in Pepper (Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics Mario Parisi 1 , Daniela Alioto 2 and Pasquale Tripodi 1,* 1 CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, Italy; [email protected] 2 Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055 Portici, Naples, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-089-386-217 Received: 18 March 2020; Accepted: 5 April 2020; Published: 8 April 2020 Abstract: Pepper (Capsicum spp.) is one of the major vegetable crops grown worldwide largely appreciated for its economic importance and nutritional value. This crop belongs to the large Solanaceae family, which, among more than 90 genera and 2500 species of flowering plants, includes commercially important vegetables such as tomato and eggplant. The genus includes over 30 species, five of which (C. annuum, C. frutescens, C. chinense, C. baccatum, and C. pubescens) are domesticated and mainly grown for consumption as food and for non-food purposes (e.g., cosmetics). The main challenges for vegetable crop improvement are linked to the sustainable development of agriculture, food security, the growing consumers’ demand for food. Furthermore, demographic trends and changes to climate require more efficient use of plant genetic resources in breeding programs. Increases in pepper consumption have been observed in the past 20 years, and for maintaining this trend, the development of new resistant and high yielding varieties is demanded. The range of pathogens afflicting peppers is very broad and includes fungi, viruses, bacteria, and insects.
    [Show full text]
  • Comparative Genomic Analysis of Ralstonia Solanacearum
    Ailloud et al. BMC Genomics (2015) 16:270 DOI 10.1186/s12864-015-1474-8 RESEARCH ARTICLE Open Access Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity Florent Ailloud1,3, Tiffany Lowe2, Gilles Cellier3, David Roche4, Caitilyn Allen2 and Philippe Prior1,5* Abstract Background: Ralstonia solanacearum is a vascular soil-borne plant pathogen with an unusually broad host range. This economically destructive and globally distributed bacterium has thousands of distinct lineages within a heterogeneous and taxonomically disputed species complex. Some lineages include highly host-adapted strains (ecotypes), such as the banana Moko disease-causing strains, the cold-tolerant potato brown rot strains (also known as R3bv2) and the recently emerged Not Pathogenic to Banana (NPB) strains. Results: These distinct ecotypes offer a robust model to study host adaptation and the emergence of ecotypes because the polyphyletic Moko strains include lineages that are phylogenetically close to the monophyletic brown rot and NPB strains. Draft genomes of eight new strains belonging to these three model ecotypes were produced to complement the eleven publicly available R. solanacearum genomes. Using a suite of bioinformatics methods, we searched for genetic and evolutionary features that distinguish ecotypes and propose specific hypotheses concerning mechanisms of host adaptation in the R. solanacearum species complex. Genome-wide, few differences were identified, but gene loss events, non-synonymous polymorphisms, and horizontal gene transfer were identified among type III effectors and were associated with host range differences. Conclusions: This extensive comparative genomics analysis uncovered relatively few divergent features among closely related strains with contrasting biological characteristics; however, several virulence factors were associated with the emergence of Moko, NPB and brown rot and could explain host adaptation.
    [Show full text]
  • Ralstonia Solanacearum, a Widespread Bacterial Plant Pathogen in the Post-Genomic Era
    CORE Metadata, citation and similar papers at core.ac.uk Provided by Diposit Digital de la Universitat de Barcelona Ralstonia solanacearum, a widespread bacterial plant pathogen in the post-genomic era Journal: Molecular Plant Pathology Manuscript ID: MPP-PP-13-026.R1 Manuscript Type: Pathogen Profile Date Submitted by the Author: n/a Complete List of Authors: Peeters, Nemo; INRA UMR441 Laboratoire des Interactions Plantes Micro- organismes (LIPM), 24 chemin de borde rouge, Auzeville CS52627; CNRS UMR2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), 24 cheminProof de borde rouge, Auzeville CS52627 Guidot, Alice; INRA UMR441 Laboratoire des Interactions Plantes Micro- organismes (LIPM), 24 chemin de borde rouge, Auzeville CS52627; CNRS UMR2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), 24 chemin de borde rouge, Auzeville CS52627 Vailleau, Fabienne; INRA UMR441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), 24 chemin de borde rouge, Auzeville CS52627; CNRS UMR2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), 24 chemin de borde rouge, Auzeville CS52627; Université de Toulouse ; INP ; ENSAT, 18 chemin de Borde Rouge Valls, Marc; Department of Genetics, University of Barcelona and Centre for Research in Agricultural Genomics (CRAG)., Edifici CRAG, Campus UAB Keywords: Ralstonia solanacearum Page 1 of 26 1 2 3 4 1 5 6 7 1 Ralstonia solanacearum , a widespread bacterial plant pathogen in the post-genomic era 8 2 Nemo Peeters 1,2* , Alice Guidot 1,2 , Fabienne Vailleau 1,2, 3
    [Show full text]
  • Asian R. Solanacearum Strains Form a Single Genomic Species Despite Divergent Lifestyles
    Ralstonia syzygii, the Blood Disease Bacterium and Some Asian R. solanacearum Strains Form a Single Genomic Species Despite Divergent Lifestyles Benoıˆt Remenant1.¤, Jean-Charles de Cambiaire2., Gilles Cellier2,3, Jonathan M. Jacobs4, Sophie Mangenot6, Vale´rie Barbe6, Aure´lie Lajus5,6, David Vallenet5,6, Claudine Medigue5,6, Mark Fegan7, Caitilyn Allen4, Philippe Prior1* 1 Peuplements Ve´ge´taux et Bioagresseurs en Milieu Tropical (UMR PVBMT), INRA-CIRAD, Saint Pierre, La Re´union, France, 2 Peuplements Ve´ge´taux et Bioagresseurs en Milieu Tropical (UMR PVBMT), CIRAD, Saint Pierre, La Re´union, France, 3 Unite´ Ravageurs et Agents Pathoge`nes Tropicaux, Agence Nationale de Se´curite´ Sanitaire, Laboratoire de la Sante´ des Ve´ge´taux, Saint Pierre, La Re´union, France, 4 Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America, 5 Laboratoire d’Analyse Bioinformatique en Ge´nomique et Me´tabolisme, CNRS-UMR 8030, Evry, France, 6 Institut de Ge´nomique, Genoscope, Commissariat a` l’Energie Atomique (CEA) Direction des Sciences du Vivant, Evry, France, 7 Department of Primary Industries, Biosciences Research Division, Attwood, Victoria, Australia Abstract The Ralstonia solanacearum species complex includes R. solanacearum, R. syzygii, and the Blood Disease Bacterium (BDB). All colonize plant xylem vessels and cause wilt diseases, but with significant biological differences. R. solanacearum is a soilborne bacterium that infects the roots of a broad range of plants. R. syzygii causes Sumatra disease of clove trees and is actively transmitted by cercopoid insects. BDB is also pathogenic to a single host, banana, and is transmitted by pollinating insects. Sequencing and DNA-DNA hybridization studies indicated that despite their phenotypic differences, these three plant pathogens are actually very closely related, falling into the Phylotype IV subgroup of the R.
    [Show full text]
  • 1 Host Adaptation and Microbial Competition Drive Ralstonia Solanacearum Phylotype I
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.10.196865; this version posted July 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Host adaptation and microbial competition drive Ralstonia solanacearum phylotype I 2 evolution in South Korea 3 Maxim Prokchorchik1, Ankita Pandey1, Hayoung Moon1, Wanhui Kim2,3, Hyelim Jeon2,3, 4 Stephen Poole4, Cécile Segonzac 2,3,*, Kee Hoon Sohn1,5,* and Honour C. McCann6,7,* 5 6 1 Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, 7 Republic of Korea. 8 2 Department of Plant Science, Plant Genomics and Breeding Institute and Research Institute 9 of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of 10 Korea. 11 3 Plant Immunity Research Center, Seoul National University, Seoul 08826, Republic of 12 Korea. 13 4 Department of Molecular, Cellular and Developmental Biology, University of California 14 Santa Barbara, Santa Barbara, United States of America. 15 5 School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science 16 and Technology, Pohang 37673, Republic of Korea. 17 6 New Zealand Institute for Advanced Study, Massey University Albany, New Zealand. 18 7 Max Planck Institute for Developmental Biology, Tübingen, Germany. 19 * Corresponding authors. Email: [email protected], [email protected] and 20 [email protected]. 21 22 Keywords: Ralstonia solanacearum, population genomics, plant-microbe interactions, 23 pathogen evolution, microbial competition 24 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.10.196865; this version posted July 10, 2020.
    [Show full text]