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Damas MSF, Ferreira RL, Campanini EB, Soares GG, Campos LC, Laprega PM, Soares da Costa A, Freire CCDM, Pitondo-Silva A, Cerdeira LT, da Cunha AF, Pranchevicius MCDS. Whole genome sequencing of the multidrug-resistant Chryseobacterium indologenes isolated from a patient in Brazil. Front Med (Lausanne) 2022; 9:931379. [PMID: 35966843 PMCID: PMC9366087 DOI: 10.3389/fmed.2022.931379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 06/30/2022] [Indexed: 12/03/2022] Open
Abstract
Chryseobacterium indologenes is a non-glucose-fermenting Gram-negative bacillus. This emerging multidrug resistant opportunistic nosocomial pathogen can cause severe infections in neonates and immunocompromised patients. This study aimed to present the first detailed draft genome sequence of a multidrug-resistant C. indologenes strain isolated from the cerebrospinal fluid of an infant hospitalized at the Neonatal Intensive Care Unit of Brazilian Tertiary Hospital. We first analyzed the susceptibility of C. indologenes strain to different antibiotics using the VITEK 2 system. The strain demonstrated an outstanding resistance to all the antibiotic classes tested, including β-lactams, aminoglycosides, glycylcycline, and polymyxin. Next, C. indologenes was whole-genome-sequenced, annotated using Prokka and Rapid Annotation using Subsystems Technology (RAST), and screened for orthologous groups (EggNOG), gene ontology (GO), resistance genes, virulence genes, and mobile genetic elements using different software tools. The draft genome contained one circular chromosome of 4,836,765 bp with 37.32% GC content. The genomic features of the chromosome present numerous genes related to cellular processes that are essential to bacteria. The MDR C. indologenes revealed the presence of genes that corresponded to the resistance phenotypes, including genes to β-lactamases (blaIND–13, blaCIA–3, blaTEM–116, blaOXA–209, blaVEB–15), quinolone (mcbG), tigecycline (tet(X6)), and genes encoding efflux pumps which confer resistance to aminoglycosides (RanA/RanB), and colistin (HlyD/TolC). Amino acid substitutions related to quinolone resistance were observed in GyrA (S83Y) and GyrB (L425I and K473R). A mutation that may play a role in the development of colistin resistance was detected in lpxA (G68D). Chryseobacterium indologenes isolate harbored 19 virulence factors, most of which were involved in infection pathways. We identified 13 Genomic Islands (GIs) and some elements associated with one integrative and conjugative element (ICEs). Other elements linked to mobile genetic elements (MGEs), such as insertion sequence (ISEIsp1), transposon (Tn5393), and integron (In31), were also present in the C. indologenes genome. Although plasmids were not detected, a ColRNAI replicon type and the most resistance genes detected in singletons were identified in unaligned scaffolds. We provided a wide range of information toward the understanding of the genomic diversity of C. indologenes, which can contribute to controlling the evolution and dissemination of this pathogen in healthcare settings.
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Affiliation(s)
| | - Roumayne Lopes Ferreira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Emeline Boni Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | | | - Pedro Mendes Laprega
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Andrea Soares da Costa
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | - André Pitondo-Silva
- Programa de Pós-graduação em Odontologia e Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | | | - Maria-Cristina da Silva Pranchevicius
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
- Centro de Ciências Biológicas e da Saúde, Biodiversidade Tropical - BIOTROP, Universidade Federal de São Carlos, São Carlos, Brazil
- *Correspondence: Maria-Cristina da Silva Pranchevicius,
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A Phosphonate Natural Product Made by Pantoea ananatis is Necessary and Sufficient for the Hallmark Lesions of Onion Center Rot. mBio 2021; 12:mBio.03402-20. [PMID: 33531390 PMCID: PMC7858074 DOI: 10.1128/mbio.03402-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Pantoea ananatis is the primary cause of onion center rot. Genetic data suggest that a phosphonic acid natural product is required for pathogenesis; however, the nature of the molecule is unknown. Here, we show that P. ananatis produces at least three phosphonates, two of which were purified and structurally characterized. The first, designated pantaphos, was shown to be 2-(hydroxy[phosphono]methyl)maleate; the second, a probable biosynthetic precursor, was shown to be 2-(phosphonomethyl)maleate. Purified pantaphos is both necessary and sufficient for the hallmark lesions of onion center rot. Moreover, when tested against mustard seedlings, the phytotoxic activity of pantaphos was comparable to the widely used herbicides glyphosate and phosphinothricin. Pantaphos was also active against a variety of human cell lines but was significantly more toxic to glioblastoma cells. Pantaphos showed little activity when tested against a variety of bacteria and fungi.IMPORTANCE Pantoea ananatis is a significant plant pathogen that targets a number of important crops, a problem that is compounded by the absence of effective treatments to prevent its spread. Our identification of pantaphos as the key virulence factor in onion center rot suggests a variety of approaches that could be employed to address this significant plant disease. Moreover, the general phytotoxicity of the molecule suggests that it could be developed into an effective herbicide to counter the alarming rise in herbicide-resistant weeds.
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Gonçalves OS, de Queiroz MV, Santana MF. Potential evolutionary impact of integrative and conjugative elements (ICEs) and genomic islands in the Ralstonia solanacearum species complex. Sci Rep 2020; 10:12498. [PMID: 32719415 PMCID: PMC7385641 DOI: 10.1038/s41598-020-69490-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/13/2020] [Indexed: 11/09/2022] Open
Abstract
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 identified 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 fitness and pathogenicity of RSSC. In addition, phylogenetic analysis revealed that these MGEs clustered to the same species, but there is evidence of strains from different 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 affect this soil-borne plant pathogen.
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Affiliation(s)
- Osiel Silva Gonçalves
- Departamento de Microbiologia, Instituto de Bsiotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Marisa Vieira de Queiroz
- Departamento de Microbiologia, Instituto de Bsiotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Mateus Ferreira Santana
- Departamento de Microbiologia, Instituto de Bsiotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil.
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Barizzone F, Correia S, Herman L. Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 11: suitability of taxonomic units notified to EFSA until September 2019. EFSA J 2020; 18:e05965. [PMID: 32874211 PMCID: PMC7448003 DOI: 10.2903/j.efsa.2020.5965] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance are assessed. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA was updated with 54 biological agents, received between April and September 2019; 23 already had QPS status, 14 were excluded from the QPS exercise (7 filamentous fungi, 6 Escherichia coli, Sphingomonas paucimobilis which was already evaluated). Seventeen, corresponding to 16 TUs, were evaluated for possible QPS status, fourteen of these for the first time, and Protaminobacter rubrum, evaluated previously, was excluded because it is not a valid species. Eight TUs are recommended for QPS status. Lactobacillus parafarraginis and Zygosaccharomyces rouxii are recommended to be included in the QPS list. Parageobacillus thermoglucosidasius and Paenibacillus illinoisensis can be recommended for the QPS list with the qualification 'for production purposes only' and absence of toxigenic potential. Bacillus velezensis can be recommended for the QPS list with the qualification 'absence of toxigenic potential and the absence of aminoglycoside production ability'. Cupriavidus necator, Aurantiochytrium limacinum and Tetraselmis chuii can be recommended for the QPS list with the qualification 'production purposes only'. Pantoea ananatis is not recommended for the QPS list due to lack of body of knowledge in relation to its pathogenicity potential for plants. Corynebacterium stationis, Hamamotoa singularis, Rhodococcus aetherivorans and Rhodococcus ruber cannot be recommended for the QPS list due to lack of body of knowledge. Kodamaea ohmeri cannot be recommended for the QPS list due to safety concerns.
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Seoane P, Tapia-Paniagua ST, Bautista R, Alcaide E, Esteve C, Martínez-Manzanares E, Balebona MC, Claros MG, Moriñigo MA. TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11. PeerJ 2019; 7:e6526. [PMID: 30842906 PMCID: PMC6397758 DOI: 10.7717/peerj.6526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/26/2019] [Indexed: 11/20/2022] Open
Abstract
Probiotic microorganisms are of great interest in clinical, livestock and aquaculture. Knowledge of the genomic basis of probiotic characteristics can be a useful tool to understand why some strains can be pathogenic while others are probiotic in the same species. An automatized workflow called TarSynFlow (Targeted Synteny Workflow) has been then developed to compare finished or draft bacterial genomes based on a set of proteins. When used to analyze the finished genome of the probiotic strain Pdp11 of Shewanella putrefaciens and genome drafts from seven known non-probiotic strains of the same species obtained in this work, 15 genes were found exclusive of Pdp11. Their presence was confirmed by PCR using Pdp11-specific primers. Functional inspection of the 15 genes allowed us to hypothesize that Pdp11 underwent genome rearrangements spurred by plasmids and mobile elements. As a result, Pdp11 presents specific proteins for gut colonization, bile salt resistance and gut pathogen adhesion inhibition, which can explain some probiotic features of Pdp11.
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Affiliation(s)
- Pedro Seoane
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, Spain
| | | | - Rocío Bautista
- Andalusian Platform for Bioinformatics, Universidad de Málaga, Málaga, Spain
| | - Elena Alcaide
- Department of Microbiology and Ecology, Universidad de Valencia, Valencia, Spain
| | - Consuelo Esteve
- Department of Microbiology and Ecology, Universidad de Valencia, Valencia, Spain
| | | | | | - M. Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, Spain
- Andalusian Platform for Bioinformatics, Universidad de Málaga, Málaga, Spain
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Complete Genome Sequence of Enterobacter xiangfangensis Pb204, a South African Strain Capable of Synthesizing Gold Nanoparticles. Microbiol Resour Announc 2018; 7:MRA01406-18. [PMID: 30533853 PMCID: PMC6284085 DOI: 10.1128/mra.01406-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 10/28/2018] [Indexed: 12/02/2022] Open
Abstract
Enterobacter xiangfangensis Pb204, isolated from acid mine decant from a uranium mine, produces a wide variety of gold nanoparticles (AuNPs), ranging from large triangular plates to small spherical AuNPs. The complete genome sequence of this isolate incorporates an integrative and conjugative element which may be pivotal to AuNP synthesis. Enterobacter xiangfangensis Pb204, isolated from acid mine decant from a uranium mine, produces a wide variety of gold nanoparticles (AuNPs), ranging from large triangular plates to small spherical AuNPs. The complete genome sequence of this isolate incorporates an integrative and conjugative element which may be pivotal to AuNP synthesis.
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Matteoli FP, Passarelli-Araujo H, Reis RJA, da Rocha LO, de Souza EM, Aravind L, Olivares FL, Venancio TM. Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost. BMC Genomics 2018; 19:750. [PMID: 30326830 PMCID: PMC6192313 DOI: 10.1186/s12864-018-5130-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/27/2018] [Indexed: 01/11/2023] Open
Abstract
Background Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range of environments, including soil. Results Here we describe the genome sequencing and assessment of plant growth-promoting abilities of S. marcescens UENF-22GI, a strain isolated from mature cattle manure vermicompost. In vitro, S. marcescens UENF-22GI is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with this strain remarkably increased seedling growth and biomass under greenhouse conditions. The S. marcescens UENF-22GI genome has 5 Mb, assembled in 17 scaffolds comprising 4662 genes (4528 are protein-coding). No plasmids were identified. S. marcescens UENF-22GI is phylogenetically placed within a clade comprised almost exclusively of non-clinical strains. We identified genes and operons that are likely responsible for the interesting plant-growth promoting features that were experimentally described. The S. marcescens UENF-22GI genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to its competitiveness against other bacteria. Conclusions Collectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for agriculture. Electronic supplementary material The online version of this article (10.1186/s12864-018-5130-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Filipe P Matteoli
- Laboratório de Química e Função de Proteínas e Peptídeos, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil
| | - Hemanoel Passarelli-Araujo
- Laboratório de Química e Função de Proteínas e Peptídeos, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil
| | - Régis Josué A Reis
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil
| | - Letícia O da Rocha
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil
| | - Emanuel M de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Fabio L Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil.
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil.
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da Silva RA, Pereira LDM, Silveira MC, Jardim R, de Miranda AB. Mining of potential drug targets through the identification of essential and analogous enzymes in the genomes of pathogens of Glycine max, Zea mays and Solanum lycopersicum. PLoS One 2018; 13:e0197511. [PMID: 29799863 PMCID: PMC5969768 DOI: 10.1371/journal.pone.0197511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 05/03/2018] [Indexed: 01/19/2023] Open
Abstract
Pesticides are one of the most widely used pest and disease control measures in plant crops and their indiscriminate use poses a direct risk to the health of populations and environment around the world. As a result, there is a great need for the development of new, less toxic molecules to be employed against plant pathogens. In this work, we employed an in silico approach to study the genes coding for enzymes of the genomes of three commercially important plants, soybean (Glycine max), tomato (Solanum lycopersicum) and corn (Zea mays), as well as 15 plant pathogens (4 bacteria and 11 fungi), focusing on revealing a set of essential and non-homologous isofunctional enzymes (NISEs) that could be prioritized as drug targets. By combining sequence and structural data, we obtained an initial set of 568 cases of analogy, of which 97 were validated and further refined, revealing a subset of 29 essential enzymatic activities with a total of 119 different structural forms, most belonging to central metabolic routes, including the carbohydrate metabolism, the metabolism of amino acids, among others. Further, another subset of 26 enzymatic activities possess a tertiary structure specific for the pathogen, not present in plants, men and Apis mellifera, which may be of importance for the development of specific enzymatic inhibitors against plant diseases that are less harmful to humans and the environment.
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Affiliation(s)
| | | | | | - Rodrigo Jardim
- Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
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Weller‐Stuart T, De Maayer P, Coutinho T. Pantoea ananatis: genomic insights into a versatile pathogen. MOLECULAR PLANT PATHOLOGY 2017; 18:1191-1198. [PMID: 27880983 PMCID: PMC6638271 DOI: 10.1111/mpp.12517] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Pantoea ananatis, a bacterium that is well known for its phytopathogenic characteristics, has been isolated from a myriad of ecological niches and hosts. Infection of agronomic crops, such as maize and rice, can result in substantial economic losses. In the last few years, much of the research performed on P. ananatis has been based on the sequencing and analysis of the genomes of strains isolated from different environments and with different lifestyles. In this review, we summarize the advances made in terms of pathogenicity determinants of phytopathogenic strains of P. ananatis and how this bacterium is able to adapt and survive in such a wide variety of habitats. The diversity and adaptability of P. ananatis can largely be attributed to the plasticity of its genome and the integration of mobile genetic elements on both the chromosome and plasmid. Furthermore, we discuss the recent interest in this species in various biotechnological applications. TAXONOMY Domain Bacteria; Class Gammaproteobacteria; Family Enterobacteriaceae; genus Pantoea; species ananatis. DISEASE SYMPTOMS Pantoea ananatis causes disease on a wide range of plants, and symptoms can range from dieback and stunted growth in Eucalyptus seedlings to chlorosis and bulb rotting in onions. DISEASE CONTROL Currently, the only methods of control of P. ananatis on most plant hosts are the use of resistant clones and cultivars or the eradication of infected plant material. The use of lytic bacteriophages on certain host plants, such as rice, has also achieved a measure of success.
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Affiliation(s)
- Tania Weller‐Stuart
- Forestry and Agricultural Biotechnology Institute (FABI), Department of MicrobiologyUniversity of PretoriaPretoria0002South Africa
| | - Pieter De Maayer
- School of Molecular and Cell BiologyUniversity of the WitwatersrandJohannesburg2050South Africa
| | - Teresa Coutinho
- Forestry and Agricultural Biotechnology Institute (FABI), Department of MicrobiologyUniversity of PretoriaPretoria0002South Africa
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De Maayer P, Aliyu H, Vikram S, Blom J, Duffy B, Cowan DA, Smits THM, Venter SN, Coutinho TA. Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii. Front Microbiol 2017; 8:1755. [PMID: 28959245 PMCID: PMC5603701 DOI: 10.3389/fmicb.2017.01755] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/29/2017] [Indexed: 12/12/2022] Open
Abstract
Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart's wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.
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Affiliation(s)
- Pieter De Maayer
- School of Molecular and Cell Biology, University of the WitwatersrandJohannesburg, South Africa
| | - Habibu Aliyu
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Jochen Blom
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University GiessenGiessen, Germany
| | - Brion Duffy
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied SciencesWinterthur, Switzerland
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Theo H. M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied SciencesWinterthur, Switzerland
| | - Stephanus N. Venter
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Teresa A. Coutinho
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
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Beyond the canonical strategies of horizontal gene transfer in prokaryotes. Curr Opin Microbiol 2017; 38:95-105. [PMID: 28600959 DOI: 10.1016/j.mib.2017.04.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 01/16/2023]
Abstract
Efforts to identify and characterize strategies for horizontal gene transfer (HGT) in prokaryotes could have overlooked some mechanisms that do not entirely fit in with the canonical ones most often described (conjugation of plasmids, phage transduction and transformation). The difficulty in distinguishing the different HGT strategies could have contributed to underestimate their real extent. Here we review non classical HGT strategies: some that require mobile genetic elements (MGEs) and others independent of MGE. Among those strategies that require MGEs, there is a range of newly reported, hybrid and intermediate MGEs mobilizing only their own DNA, others that mobilize preferentially bacterial DNA, or both. Considering HGT strategies independent of MGE, a few are even not restricted to DNA transfer, but can also mobilize other molecules. This review considers those HGT strategies that are less commonly dealt with in the literature. The real impact of these elements could, in some conditions, be more relevant than previously thought.
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Abstract
The large diversity of marine microorganisms harboured by oceans plays an important role in planet sustainability by driving globally important biogeochemical cycles; all primary and most secondary production in the oceans is performed by microorganisms. The largest part of the planet is covered by cold environments; consequently, cold-adapted microorganisms have crucial functional roles in globally important environmental processes and biogeochemical cycles cold-adapted extremophiles are a remarkable model to shed light on the molecular basis of survival at low temperature. The indigenous populations of Antarctic and Arctic microorganisms are endowed with genetic and physiological traits that allow them to live and effectively compete at the temperatures prevailing in polar regions. Some genes, e.g. glycosyltransferases and glycosylsynthetases involved in the architecture of the cell wall, may have been acquired/retained during evolution of polar strains or lost in tropical strains. This present work focusses on temperature and its role in shaping microbial adaptations; however, in assessing the impacts of climate changes on microbial diversity and biogeochemical cycles in polar oceans, it should not be forgotten that physiological studies need to include the interaction of temperature with other abiotic and biotic factors.
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