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Motoche-Monar C, Andrade D, Pijal WD, Hidrobo F, Armas R, Sánchez-Real E, Rocha-Chauca G, Castillo JA. CRISPRals: A Web Database for Assessing the CRISPR Defense System in the Ralstonia solanacearum Species Complex to Avoid Phage Resistance. PHYTOPATHOLOGY 2024:PHYTO01240010SC. [PMID: 38427684 DOI: 10.1094/phyto-01-24-0010-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) has been widely characterized as a defense system against phages and other invading elements in bacteria and archaea. A low percentage of Ralstonia solanacearum species complex (RSSC) strains possess the CRISPR array and the CRISPR-associated proteins (Cas) that would confer immunity against various phages. To provide a wide-range screen of the CRISPR presence in the RSSC, we analyzed 378 genomes of RSSC strains to find the CRISPR locus. We found that 20.1, 14.3, and 54.5% of the R. solanacearum, R. pseudosolanacearum, and R. syzygii strains, respectively, possess the CRISPR locus. In addition, we performed further analysis to identify the respective phages that are restricted by the CRISPR arrays. We found 252 different phages infecting different strains of the RSSC, by means of the identification of similarities between the protospacers in phages and spacers in bacteria. We compiled this information in a database with web access called CRISPRals (https://crisprals.yachaytech.edu.ec/). Additionally, we made available a number of tools to detect and identify CRISPR array and Cas genes in genomic sequences that could be uploaded by users. Finally, a matching tool to relate bacteria spacer with phage protospacer sequences is available. CRISPRals is a valuable resource for the scientific community that contributes to the study of bacteria-phage interaction and a starting point that will help to design efficient phage therapy strategies.
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Affiliation(s)
- Cristofer Motoche-Monar
- Phage Therapy Group, School of Biological Sciences and Engineering, Yachay Tech University, Hcda San José y Proyecto Yachay, 100115, Imbabura, Ecuador
| | - Diego Andrade
- Phage Therapy Group, School of Mathematical and Computational Sciences, Yachay Tech University, Hcda San José y Proyecto Yachay, 100115, Imbabura, Ecuador
| | - Washington D Pijal
- Phage Therapy Group, School of Mathematical and Computational Sciences, Yachay Tech University, Hcda San José y Proyecto Yachay, 100115, Imbabura, Ecuador
| | - Francisco Hidrobo
- Phage Therapy Group, School of Mathematical and Computational Sciences, Yachay Tech University, Hcda San José y Proyecto Yachay, 100115, Imbabura, Ecuador
| | - Rolando Armas
- Phage Therapy Group, School of Mathematical and Computational Sciences, Yachay Tech University, Hcda San José y Proyecto Yachay, 100115, Imbabura, Ecuador
| | - Emily Sánchez-Real
- Phage Therapy Group, School of Biological Sciences and Engineering, Yachay Tech University, Hcda San José y Proyecto Yachay, 100115, Imbabura, Ecuador
| | - Gabriela Rocha-Chauca
- Phage Therapy Group, School of Biological Sciences and Engineering, Yachay Tech University, Hcda San José y Proyecto Yachay, 100115, Imbabura, Ecuador
| | - José A Castillo
- Phage Therapy Group, School of Biological Sciences and Engineering, Yachay Tech University, Hcda San José y Proyecto Yachay, 100115, Imbabura, Ecuador
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Sasaki T, Takita S, Fujishiro T, Shintani Y, Nojiri S, Yasui R, Yonesaki T, Otsuka Y. Phage single-stranded DNA-binding protein or host DNA damage triggers the activation of the AbpAB phage defense system. mSphere 2023; 8:e0037223. [PMID: 37882551 PMCID: PMC10732053 DOI: 10.1128/msphere.00372-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/06/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Although numerous phage defense systems have recently been discovered in bacteria, how these systems defend against phage propagation or sense phage infections remains unclear. The Escherichia coli AbpAB defense system targets several lytic and lysogenic phages harboring DNA genomes. A phage-encoded single-stranded DNA-binding protein, Gp32, activates this system similar to other phage defense systems such as Retron-Eco8, Hachiman, ShosTA, Nhi, and Hna. DNA replication inhibitors or defects in DNA repair factors activate the AbpAB system, even without phage infection. This is one of the few examples of activating phage defense systems without phage infection or proteins. The AbpAB defense system may be activated by sensing specific DNA-protein complexes.
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Affiliation(s)
- Takaomi Sasaki
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Saya Takita
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Yunosuke Shintani
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Satoki Nojiri
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Ryota Yasui
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Tetsuro Yonesaki
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yuichi Otsuka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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3
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Pacios O, Blasco L, Ortiz Cartagena C, Bleriot I, Fernández-García L, López M, Barrio-Pujante A, Cuenca FF, Aracil B, Oteo-Iglesias J, Tomás M. Molecular studies of phages- Klebsiella pneumoniae in mucoid environment: innovative use of mucolytic agents prior to the administration of lytic phages. Front Microbiol 2023; 14:1286046. [PMID: 37886069 PMCID: PMC10598653 DOI: 10.3389/fmicb.2023.1286046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Mucins are important glycoproteins that form a protective layer throughout the gastrointestinal and respiratory tracts. There is scientific evidence of increase in phage-resistance in the presence of mucin for some bacterial pathogens. Manipulation in mucin composition may ultimately influence the effectiveness of phage therapy. In this work, two clinical strains of K. pneumoniae (K3574 and K3325), were exposed to the lytic bacteriophage vB_KpnS-VAC35 in the presence and absence of mucin on a long-term co-evolution assay, in an attempt to mimic in vitro the exposure to mucins that bacteria and their phages face in vivo. Enumerations of the bacterial and phage counts at regular time intervals were conducted, and extraction of the genomic DNA of co-evolved bacteria to the phage, the mucin and both was performed. We determined the frequency of phage-resistant mutants in the presence and absence of mucin and including a mucolytic agent (N-acetyl L-cysteine, NAC), and sequenced them using Nanopore. We phenotypically demonstrated that the presence of mucin induces the emergence of bacterial resistance against lytic phages, effectively decreased in the presence of NAC. In addition, the genomic analysis revealed some of the genes relevant to the development of phage resistance in long-term co-evolution, with a special focus on the mucoid environment. Genes involved in the metabolism of carbohydrates were mutated in the presence of mucin. In conclusion, the use of mucolytic agents prior to the administration of lytic phages could be an interesting therapeutic option when addressing K. pneumoniae infections in environments where mucin is overproduced.
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Affiliation(s)
- Olga Pacios
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Grupo de Estudio de los Mecanismos de Resistencia Antimicrobiana (GEMARA) formando parte de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Lucía Blasco
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Grupo de Estudio de los Mecanismos de Resistencia Antimicrobiana (GEMARA) formando parte de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Concha Ortiz Cartagena
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Grupo de Estudio de los Mecanismos de Resistencia Antimicrobiana (GEMARA) formando parte de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Inés Bleriot
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Grupo de Estudio de los Mecanismos de Resistencia Antimicrobiana (GEMARA) formando parte de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Laura Fernández-García
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Grupo de Estudio de los Mecanismos de Resistencia Antimicrobiana (GEMARA) formando parte de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - María López
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Grupo de Estudio de los Mecanismos de Resistencia Antimicrobiana (GEMARA) formando parte de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Antonio Barrio-Pujante
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Grupo de Estudio de los Mecanismos de Resistencia Antimicrobiana (GEMARA) formando parte de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
| | - Felipe Fernández Cuenca
- Grupo de Estudio de los Mecanismos de Resistencia Antimicrobiana (GEMARA) formando parte de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
- Unidad Clínica de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario Virgen Macarena, Instituto de Biomedicina de Sevilla (Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla), Sevilla, Spain
- MePRAM, Proyecto de Medicina de Precisión contra las resistencias Antimicrobianas, Madrid, Spain
| | - Belén Aracil
- MePRAM, Proyecto de Medicina de Precisión contra las resistencias Antimicrobianas, Madrid, Spain
- Laboratorio de Referencia e Investigación de Resistencias a Antibióticos e Infecciones Sanitarias, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Grupo de Estudio de los Mecanismos de Resistencia Antimicrobiana (GEMARA) formando parte de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
- MePRAM, Proyecto de Medicina de Precisión contra las resistencias Antimicrobianas, Madrid, Spain
- Laboratorio de Referencia e Investigación de Resistencias a Antibióticos e Infecciones Sanitarias, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - María Tomás
- Grupo de Microbiología Traslacional y Multidisciplinar (MicroTM)-Servicio de Microbiología Instituto de Investigación Biomédica A Coruña (INIBIC), Hospital A Coruña (CHUAC), Universidad de A Coruña (UDC), A Coruña, Spain
- Grupo de Estudio de los Mecanismos de Resistencia Antimicrobiana (GEMARA) formando parte de la Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica (SEIMC), Madrid, Spain
- MePRAM, Proyecto de Medicina de Precisión contra las resistencias Antimicrobianas, Madrid, Spain
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Vailleau F, Genin S. Ralstonia solanacearum: An Arsenal of Virulence Strategies and Prospects for Resistance. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:25-47. [PMID: 37506349 DOI: 10.1146/annurev-phyto-021622-104551] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The group of strains constituting the Ralstonia solanacearum species complex (RSSC) is a prominent model for the study of plant-pathogenic bacteria because of its impact on agriculture, owing to its wide host range, worldwide distribution, and long persistence in the environment. RSSC strains have led to numerous studies aimed at deciphering the molecular bases of virulence, and many biological functions and mechanisms have been described to contribute to host infection and pathogenesis. In this review, we put into perspective recent advances in our understanding of virulence in RSSC strains, both in terms of the inventory of functions that participate in this process and their evolutionary dynamics. We also present the different strategies that have been developed to combat these pathogenic strains through biological control, antimicrobial agents, plant genetics, or microbiota engineering.
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Affiliation(s)
- Fabienne Vailleau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France; ,
| | - Stéphane Genin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France; ,
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5
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Baroukh C, Cottret L, Pires E, Peyraud R, Guidot A, Genin S. Insights into the metabolic specificities of pathogenic strains from the Ralstonia solanacearum species complex. mSystems 2023; 8:e0008323. [PMID: 37341493 PMCID: PMC10470067 DOI: 10.1128/msystems.00083-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/14/2023] [Indexed: 06/22/2023] Open
Abstract
All the strains grouped under the species Ralstonia solanacearum represent a species complex responsible for many diseases on agricultural crops throughout the world. The strains have different lifestyles and host range. Here, we investigated whether specific metabolic pathways contribute to strain diversification. To this end, we carried out systematic comparisons on 11 strains representing the diversity of the species complex. We reconstructed the metabolic network of each strain from its genome sequence and looked for the metabolic pathways differentiating the different reconstructed networks and, by extension, the different strains. Finally, we conducted an experimental validation by determining the metabolic profile of each strain with the Biolog technology. Results revealed that the metabolism is conserved between strains, with a core metabolism composed of 82% of the pan-reactome. The three species composing the species complex could be distinguished according to the presence/absence of some metabolic pathways, in particular, one involving salicylic acid degradation. Phenotypic assays revealed that the trophic preferences on organic acids and several amino acids such as glutamine, glutamate, aspartate, and asparagine are conserved between strains. Finally, we generated mutants lacking the quorum-sensing-dependent regulator PhcA in four diverse strains, and we showed that the phcA-dependent trade-off between growth and production of virulence factors is conserved across the R. solanacearum species complex. IMPORTANCE Ralstonia solanacearum is one of the most important threats to plant health worldwide, causing disease on a very large range of agricultural crops such as tomato or potato. Behind the R. solanacearum name are hundreds of strains with different host range and lifestyle, classified into three species. Studying the differences between strains allows to better apprehend the biology of the pathogens and the specificity of some strains. None of the published genomic comparative studies have focused on the metabolism of the strains so far. We developed a new bioinformatic pipeline to build high-quality metabolic networks and used a combination of metabolic modeling and high-throughput phenotypic Biolog microplates to look for the metabolic differences between 11 strains across the three species. Our study revealed that genes encoding enzymes are overall conserved, with few variations between strains. However, more variations were observed when considering substrate usage. These variations probably result from regulation rather than the presence or absence of enzymes in the genome.
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Affiliation(s)
- Caroline Baroukh
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Ludovic Cottret
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Emma Pires
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Rémi Peyraud
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Alice Guidot
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Stéphane Genin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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6
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Greenrod STE, Stoycheva M, Elphinstone J, Friman VP. Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum species complex. BMC Genomics 2022; 23:689. [PMID: 36199029 PMCID: PMC9535894 DOI: 10.1186/s12864-022-08909-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Background Ralstonia solanacearum species complex (RSSC) strains are destructive plant pathogenic bacteria and the causative agents of bacterial wilt disease, infecting over 200 plant species worldwide. In addition to chromosomal genes, their virulence is mediated by mobile genetic elements including integrated DNA of bacteriophages, i.e., prophages, which may carry fitness-associated auxiliary genes or modulate host gene expression. Although experimental studies have characterised several prophages that shape RSSC virulence, the global diversity, distribution, and wider functional gene content of RSSC prophages are unknown. In this study, prophages were identified in a diverse collection of 192 RSSC draft genome assemblies originating from six continents. Results Prophages were identified bioinformatically and their diversity investigated using genetic distance measures, gene content, GC, and total length. Prophage distributions were characterised using metadata on RSSC strain geographic origin and lineage classification (phylotypes), and their functional gene content was assessed by identifying putative prophage-encoded auxiliary genes. In total, 313 intact prophages were identified, forming ten genetically distinct clusters. These included six prophage clusters with similarity to the Inoviridae, Myoviridae, and Siphoviridae phage families, and four uncharacterised clusters, possibly representing novel, previously undescribed phages. The prophages had broad geographical distributions, being present across multiple continents. However, they were generally host phylogenetic lineage-specific, and overall, prophage diversity was proportional to the genetic diversity of their hosts. The prophages contained many auxiliary genes involved in metabolism and virulence of both phage and bacteria. Conclusions Our results show that while RSSC prophages are highly diverse globally, they make lineage-specific contributions to the RSSC accessory genome, which could have resulted from shared coevolutionary history. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08909-7.
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Affiliation(s)
| | | | - John Elphinstone
- Fera Science Ltd, National Agri-Food Innovation Campus, Sand Hutton, York, UK
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7
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Wei L, Zhang Q, Xie A, Xiao Y, Guo K, Mu S, Xie Y, Li Z, He T. Isolation of Bioactive Compounds, Antibacterial Activity, and Action Mechanism of Spore Powder From Aspergillus niger xj. Front Microbiol 2022; 13:934857. [PMID: 35898902 PMCID: PMC9309528 DOI: 10.3389/fmicb.2022.934857] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Aspergillus fungi can produce a wide range of secondary metabolites, and they have represented a potential resource of novel bioactive compounds. Bacterial plant diseases have a serious impact on the sustainable development of agriculture worldwide, so it is necessary to use natural antibacterial compounds in microorganisms to control plant pathogens. This study was conducted to investigate the bioactive compounds of Aspergillus niger xj, three plant pathogens (Agrobacterium tumefaciens T-37, Erwinia carotovora EC-1, and Ralstonia solanacearum RS-2) were used as indicator bacteria, according to the biological activity tracking, five compounds were isolated from A. niger xj spore powder, and characterization of compounds was done by NMR (1H-NMR and 13C-NMR) and EI-MS and was identified as ergosterol (1), β-sitosterol (2), 5-pentadecylresorcinol (3), 5-hydroxymethyl-2-furancarboxylic acid (4), and succinimide (5). Compounds 3 and 5 were isolated from A. niger xj for the first time. The minimum inhibitory concentration (MIC) of five compounds against three plant pathogens was evaluated, the results showed that compound 4 exhibited the strongest antibacterial activity against tested bacteria, and RS-2 was the most sensitive to compound 4, showing the lowest MIC of 15.56 μg/ml. We concluded that the mechanism of action of the compound 4 against RS-2 might be described as compound 4 acting on bacterial protein synthesis and intracellular metabolism according to the results of the scanning electron microscopy observation, permeability of cell membrane and SDS-PAGE. These results indicated that compound 4 has good potential to be as a biocontrol agent. In conclusion, the results from this study demonstrated that the compounds with antibacterial activity are of great significance of the prevention and control of plant phytopathogenic bacteria, and they may be applicable to exploring alternative approaches to integrated control of phytopathogens.
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Affiliation(s)
- Longfeng Wei
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Guizhou Key Laboratory of Agricultural Biotechnology, Guiyang, China
| | - Qinyu Zhang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Ailin Xie
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Yang Xiao
- Institution of Supervision and Inspection Product Quality of Guizhou Province, Guiyang, China
| | - Kun Guo
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Shuzhen Mu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Yudan Xie
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Zhu Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Guizhou Key Laboratory of Agricultural Biotechnology, Guiyang, China
| | - Tengxia He
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
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Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13. Viruses 2021; 14:v14010006. [PMID: 35062209 PMCID: PMC8778798 DOI: 10.3390/v14010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 12/25/2022] Open
Abstract
Klebsiella pneumoniae is a human pathogen that worsens the prognosis of many immunocompromised patients. Here, we annotated and compared the genomes of two lytic phages that infect clinical strains of K. pneumoniae (vB_KpnM-VAC13 and vB_KpnM-VAC66) and phenotypically characterized vB_KpnM-VAC66 (time of adsorption of 12 min, burst size of 31.49 ± 0.61 PFU/infected cell, and a host range of 20.8% of the tested strains). Transmission electronic microscopy showed that vB_KpnM-VAC66 belongs to the Myoviridae family. The genomic analysis of the phage vB_KpnM-VAC66 revealed that its genome encoded 289 proteins. When compared to the genome of vB_KpnM-VAC13, they showed a nucleotide similarity of 97.56%, with a 93% of query cover, and the phylogenetic study performed with other Tevenvirinae phages showed a close common ancestor. However, there were 21 coding sequences which differed. Interestingly, the main differences were that vB_KpnM-VAC66 encoded 10 more homing endonucleases than vB_KpnM-VAC13, and that the nucleotidic and amino-acid sequences of the L-shaped tail fiber protein were highly dissimilar, leading to different three-dimensional protein predictions. Both phages differed significantly in their host range. These viruses may be useful in the development of alternative therapies to antibiotics or as a co-therapy increasing its antimicrobial potential, especially when addressing multidrug resistant (MDR) pathogens.
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Gonçalves OS, Souza FDO, Bruckner FP, Santana MF, Alfenas-Zerbini P. Widespread distribution of prophages signaling the potential for adaptability and pathogenicity evolution of Ralstonia solanacearum species complex. Genomics 2021; 113:992-1000. [PMID: 33626339 DOI: 10.1016/j.ygeno.2021.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/16/2021] [Accepted: 02/18/2021] [Indexed: 12/27/2022]
Abstract
Integrated bacteriophages (prophages) can impact host cells, affecting their lifestyle, genomic diversity, and fitness. However, many basic aspects of how these organisms affect the host cell remain poorly understood. Ralstonia solanacearum is a gram-negative plant pathogenic bacterium that encompasses a great diversity of ecotypes regarded as a species complex (R. solanacearum Species Complex - RSSC). RSSC genomes have a mosaic structure containing numerous elements, signaling the potential for its evolution through horizontal gene transfer. Here, we analyzed 120 Ralstonia spp. genomes from the public database to identify prophage sequences. In total, 379 prophage-like elements were found in the chromosome and megaplasmid of Ralstonia spp. These elements encode genes related to host fitness, virulence factors, antibiotic resistance, and niche adaptation, which might contribute to RSSC adaptability. Prophage-like elements are widespread into the complex in different species and geographic origins, suggesting that the RSSC phages are ancestrally acquired. Complete prophages belonging to the families Inoviridae, Myoviridae, and Siphoviridae were found, being the members of Inoviridae the most abundant. Analysis of CRISPR-Cas spacer sequences demonstrated the presence of prophages sequences that indicate successive infection events during bacterial evolution. Besides complete prophages, we also demonstrated 14 novel putative prophages integrated into Ralstonia spp. genomes. Altogether, our results provide insights into the diversity of prophages in RSSC genomes and suggest that these elements may deeply affect the virulence and host adaptation and shaping the genomes among the strains of this important pathogen.
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Affiliation(s)
- Osiel Silva Gonçalves
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG CEP 36570-000, Brazil
| | - Flávia de Oliveira Souza
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG CEP 36570-000, Brazil
| | - Fernanda Prieto Bruckner
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG CEP 36570-000, Brazil
| | - Mateus Ferreira Santana
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG CEP 36570-000, Brazil.
| | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG CEP 36570-000, Brazil.
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