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Natural Recombination among Type I Restriction-Modification Systems Creates Diverse Genomic Methylation Patterns among Xylella fastidiosa Strains. Appl Environ Microbiol 2023; 89:e0187322. [PMID: 36598481 PMCID: PMC9888226 DOI: 10.1128/aem.01873-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Xylella fastidiosa is an important bacterial plant pathogen causing high-consequence diseases in agricultural crops around the world. Although as a species X. fastidiosa can infect many host plants, there is significant variability between strains regarding virulence on specific host plant species and other traits. Natural competence and horizontal gene transfer are believed to occur frequently in X. fastidiosa and likely influence the evolution of this pathogen. However, some X. fastidiosa strains are difficult to manipulate genetically using standard transformation techniques. Several type I restriction-modification (R-M) systems are encoded in the X. fastidiosa genome, which may influence horizontal gene transfer and recombination. Type I R-M systems themselves may undergo recombination, exchanging target recognition domains (TRDs) between specificity subunits (hsdS) to generate novel alleles with new target specificities. In this study, several conserved type I R-M systems were compared across 129 X. fastidiosa genome assemblies representing all known subspecies and 32 sequence types. Forty-four unique TRDs were identified among 50 hsdS alleles, which are arrayed in 31 allele profiles that are generally conserved within a monophyletic cluster of strains. Inactivating mutations were identified in type I R-M systems of specific strains, showing heterogeneity in the complements of functional type I R-M systems across X. fastidiosa. Genomic DNA methylation patterns were characterized in 20 X. fastidiosa strains and associated with type I R-M system allele profiles. Overall, these data suggest hsdS genes recombine among Xylella strains and/or unknown donors, and the resulting TRD reassortment establishes differential epigenetic modifications across Xylella lineages. IMPORTANCE Economic impacts on agricultural production due to X. fastidiosa have been severe in the Americas, Europe, and parts of Asia. Despite a long history of research on this pathogen, certain fundamental questions regarding the biology, pathogenicity, and evolution of X. fastidiosa have still not been answered. Wide-scale whole-genome sequencing has begun to provide more insight into X. fastidiosa genetic diversity and horizontal gene transfer, but the mechanics of genomic recombination in natural settings and the extent to which this directly influences bacterial phenotypes such as plant host range are not well understood. Genome methylation is an important factor in horizontal gene transfer and bacterial recombination that has not been comprehensively studied in X. fastidiosa. This study characterizes methylation associated with type I restriction-modification systems across a wide range of X. fastidiosa strains and lays the groundwork for a better understanding of X. fastidiosa biology and evolution through epigenetics.
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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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Comparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems. Microorganisms 2022; 10:microorganisms10050914. [PMID: 35630358 PMCID: PMC9148166 DOI: 10.3390/microorganisms10050914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 02/06/2023] Open
Abstract
Xylella fastidiosa causes diseases in many plant species. Originally confined to the Americas, infecting mainly grapevine, citrus, and coffee, X. fastidiosa has spread to several plant species in Europe causing devastating diseases. Many pathogenicity and virulence factors have been identified, which enable the various X. fastidiosa strains to successfully colonize the xylem tissue and cause disease in specific plant hosts, but the mechanisms by which this happens have not been fully elucidated. Here we present thorough comparative analyses of 94 whole-genome sequences of X. fastidiosa strains from diverse plant hosts and geographic regions. Core-genome phylogeny revealed clades with members sharing mostly a geographic region rather than a host plant of origin. Phylogenetic trees for 1605 orthologous CDSs were explored for potential candidates related to host specificity using a score of mapping metrics. However, no candidate host-specificity determinants were strongly supported using this approach. We also show that X. fastidiosa accessory genome is represented by an abundant and heterogeneous mobilome, including a diversity of prophage regions. Our findings provide a better understanding of the diversity of phylogenetically close genomes and expand the knowledge of X. fastidiosa mobile genetic elements and immunity systems.
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Novel Virulent Bacteriophages Infecting Mediterranean Isolates of the Plant Pest Xylella fastidiosa and Xanthomonas albilineans. Viruses 2021; 13:v13050725. [PMID: 33919362 PMCID: PMC8143317 DOI: 10.3390/v13050725] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/12/2021] [Accepted: 04/17/2021] [Indexed: 12/21/2022] Open
Abstract
Xylella fastidiosa (Xf) is a plant pathogen causing significant losses in agriculture worldwide. Originating from America, this bacterium caused recent epidemics in southern Europe and is thus considered an emerging pathogen. As the European regulations do not authorize antibiotic treatment in plants, alternative treatments are urgently needed to control the spread of the pathogen and eventually to cure infected crops. One such alternative is the use of phage therapy, developed more than 100 years ago to cure human dysentery and nowadays adapted to agriculture. The first step towards phage therapy is the isolation of the appropriate bacteriophages. With this goal, we searched for phages able to infect Xf strains that are endemic in the Mediterranean area. However, as Xf is truly a fastidious organism, we chose the phylogenetically closest and relatively fast-growing organism X. albineans as a surrogate host for the isolation step. Our results showed the isolation from various sources and preliminary characterization of several phages active on different Xf strains, namely, from the fastidiosa (Xff), multiplex (Xfm), and pauca (Xfp) subspecies, as well as on X. albilineans. We sequenced their genomes, described their genomic features, and provided a phylogeny analysis that allowed us to propose new taxonomic elements. Among the 14 genomes sequenced, we could identify two new phage species, belonging to two new genera of the Caudoviricetes order, namely, Usmevirus (Podoviridae family) and Subavirus (Siphoviridae family). Interestingly, no specific phages could be isolated from infected plant samples, whereas one was isolated from vector insects captured in a contaminated area, and several from surface and sewage waters from the Marseille area.
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From Nucleotides to Satellite Imagery: Approaches to Identify and Manage the Invasive Pathogen Xylella fastidiosa and Its Insect Vectors in Europe. SUSTAINABILITY 2020. [DOI: 10.3390/su12114508] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biological invasions represent some of the most severe threats to local communities and ecosystems. Among invasive species, the vector-borne pathogen Xylella fastidiosa is responsible for a wide variety of plant diseases and has profound environmental, social and economic impacts. Once restricted to the Americas, it has recently invaded Europe, where multiple dramatic outbreaks have highlighted critical challenges for its management. Here, we review the most recent advances on the identification, distribution and management of X. fastidiosa and its insect vectors in Europe through genetic and spatial ecology methodologies. We underline the most important theoretical and technological gaps that remain to be bridged. Challenges and future research directions are discussed in the light of improving our understanding of this invasive species, its vectors and host–pathogen interactions. We highlight the need of including different, complimentary outlooks in integrated frameworks to substantially improve our knowledge on invasive processes and optimize resources allocation. We provide an overview of genetic, spatial ecology and integrated approaches that will aid successful and sustainable management of one of the most dangerous threats to European agriculture and ecosystems.
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Perez-Quintero AL, Ortiz-Castro M, Lang JM, Rieux A, Wu G, Liu S, Chapman TA, Chang C, Ziegle J, Peng Z, White FF, Plazas MC, Leach JE, Broders K. Genomic Acquisitions in Emerging Populations of Xanthomonas vasicola pv. vasculorum Infecting Corn in the United States and Argentina. PHYTOPATHOLOGY 2020; 110:1161-1173. [PMID: 32040377 DOI: 10.1094/phyto-03-19-0077-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonas vasicola pv. vasculorum is an emerging bacterial plant pathogen that causes bacterial leaf streak on corn. First described in South Africa in 1949, reports of this pathogen have greatly increased in the past years in South America and in the United States. The rapid spread of this disease in North and South America may be due to more favorable environmental conditions, susceptible hosts and/or genomic changes that favored the spread. To understand whether genetic mechanisms exist behind the recent spread of X. vasicola pv. vasculorum, we used comparative genomics to identify gene acquisitions in X. vasicola pv. vasculorum genomes from the United States and Argentina. We sequenced 41 genomes of X. vasicola pv. vasculorum and the related sorghum-infecting X. vasicola pv. holcicola and performed comparative analyses against all available X. vasicola genomes. Time-measured phylogenetic analyses showed that X. vasicola pv. vasculorum strains from the United States and Argentina are closely related and arose from two introductions to North and South America. Gene content comparisons identified clusters of genes enriched in corn X. vasicola pv. vasculorum that showed evidence of horizontal transfer including one cluster corresponding to a prophage found in all X. vasicola pv. vasculorum strains from the United States and Argentina as well as in X. vasicola pv. holcicola strains. In this work, we explore the genomes of an emerging phytopathogen population as a first step toward identifying genetic changes associated with the emergence. The acquisitions identified may contain virulence determinants or other factors associated with the spread of X. vasicola pv. vasculorum in North and South America and will be the subject of future work.
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Affiliation(s)
- Alvaro L Perez-Quintero
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
| | - Mary Ortiz-Castro
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
| | - Jillian M Lang
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
| | | | - Guangxi Wu
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, U.S.A
| | - Toni A Chapman
- Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | | | | | - Zhao Peng
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Maria Cristina Plazas
- Laboratorio de Fitopatología y Microbiología, Universidad Católica de Córdoba, Ob. Trejo 323, Córdoba, Argentina
| | - Jan E Leach
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
| | - Kirk Broders
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panamá
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Liu X, Tang K, Zhang D, Li Y, Liu Z, Yao J, Wood TK, Wang X. Symbiosis of a P2‐family phage and deep‐sea
Shewanella putrefaciens. Environ Microbiol 2019; 21:4212-4232. [DOI: 10.1111/1462-2920.14781] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/12/2019] [Accepted: 08/13/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaoxiao Liu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Dali Zhang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Yangmei Li
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhe Liu
- Guangdong Provincial Center for Disease Control and Prevention Guangdong Provincial Institute of Public Health Guangzhou 511430 China
| | - Jianyun Yao
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
| | - Thomas K. Wood
- Department of Chemical Engineering Pennsylvania State University University Park PA 16802‐4400 USA
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences Beijing 100049 China
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Sicard A, Zeilinger AR, Vanhove M, Schartel TE, Beal DJ, Daugherty MP, Almeida RPP. Xylella fastidiosa: Insights into an Emerging Plant Pathogen. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:181-202. [PMID: 29889627 DOI: 10.1146/annurev-phyto-080417-045849] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The bacterium Xylella fastidiosa re-emerged as a plant pathogen of global importance in 2013 when it was first associated with an olive tree disease epidemic in Italy. The current threat to Europe and the Mediterranean basin, as well as other world regions, has increased as multiple X. fastidiosa genotypes have now been detected in Italy, France, and Spain. Although X. fastidiosa has been studied in the Americas for more than a century, there are no therapeutic solutions to suppress disease development in infected plants. Furthermore, because X. fastidiosa is an obligatory plant and insect vector colonizer, the epidemiology and dynamics of each pathosystem are distinct. They depend on the ecological interplay of plant, pathogen, and vector and on how interactions are affected by biotic and abiotic factors, including anthropogenic activities and policy decisions. Our goal with this review is to stimulate discussion and novel research by contextualizing available knowledge on X. fastidiosa and how it may be applicable to emerging diseases.
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Affiliation(s)
- Anne Sicard
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA;
- Biologie et Génétique des Interactions Plant-Parasite, UMR 0385, Centre de Coopération Internationale en Recherche Agronomique pour le Développement-Institut National de la Recherche Agronomique-Montpellier SupAgro, Campus International de Baillarguet, 34398 Montpellier CEDEX 05, France
| | - Adam R Zeilinger
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA;
| | - Mathieu Vanhove
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA;
| | - Tyler E Schartel
- Department of Entomology, University of California, Riverside, California 92521, USA
| | - Dylan J Beal
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA;
| | - Matthew P Daugherty
- Department of Entomology, University of California, Riverside, California 92521, USA
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA;
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9
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Koskella B, Taylor TB. Multifaceted Impacts of Bacteriophages in the Plant Microbiome. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:361-380. [PMID: 29958076 DOI: 10.1146/annurev-phyto-080417-045858] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Plant-associated bacteria face multiple selection pressures within their environments and have evolved countless adaptations that both depend on and shape bacterial phenotype and their interaction with plant hosts. Explaining bacterial adaptation and evolution therefore requires considering each of these forces independently as well as their interactions. In this review, we examine how bacteriophage viruses (phages) can alter the ecology and evolution of plant-associated bacterial populations and communities. This includes influencing a bacterial population's response to both abiotic and biotic selection pressures and altering ecological interactions within the microbiome and between the bacteria and host plant. We outline specific ways in which phages can alter bacterial phenotype and discuss when and how this might impact plant-microbe interactions, including for plant pathogens. Finally, we highlight key open questions in phage-bacteria-plant research and offer suggestions for future study.
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Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California 94720, USA;
| | - Tiffany B Taylor
- The Milner Centre for Evolution and Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom;
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Tirumalai MR, Stepanov VG, Wünsche A, Montazari S, Gonzalez RO, Venkateswaran K, Fox GE. Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates. BMC Microbiol 2018; 18:57. [PMID: 29884123 PMCID: PMC5994023 DOI: 10.1186/s12866-018-1191-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022] Open
Abstract
Background Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis. Results The FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results. Conclusions It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. pumilus likely belong to the B. safensis group. Electronic supplementary material The online version of this article (10.1186/s12866-018-1191-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Madhan R Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Andrea Wünsche
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Saied Montazari
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Racquel O Gonzalez
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Kasturi Venkateswaran
- Biotechnology & Planetary Protection Group, NASA Jet Propulsion Laboratories, California Institute of Technology, Pasadena, CA, 91109, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA.
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11
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Ding F, Allen V, Luo W, Zhang S, Duan Y. Molecular mechanisms underlying heat or tetracycline treatments for citrus HLB control. HORTICULTURE RESEARCH 2018; 5:30. [PMID: 29872535 PMCID: PMC5981314 DOI: 10.1038/s41438-018-0038-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/06/2018] [Accepted: 03/27/2018] [Indexed: 05/05/2023]
Abstract
Huanglongbing (HLB), a destructive plant bacterial disease, severely impedes worldwide citrus production. In our previous reports, we revealed the molecular mechanisms of host plant responses that underlie thermotherapy against HLB. In this study, we investigated the molecular mechanism underlying heat or tetracycline treatments on the HLB bacterium, 'Candidatus Liberibacter asiaticus' (Las) by focusing on Las prophage/phage conversion under stress conditions. By comparing the prophage FP1 and FP2 copy number to the copy number of 16S rDNA in HLB-affected plants, we found that the relative copy number of both FP1 and FP2 increased significantly, ranging from 3.4- to 6.7-fold change when Las-infected samples underwent a temperature shift from 23 to 37, 42 or 45 °C. When treated with tetracycline at 50-150 and 200-250 µg/ml, respectively, the relative copy number of both FP1 and FP2 increased by 3.4- to 6.0-fold. In addition, analyses of Las prophage structural gene and antirepressor gene copy numbers showed similar trends for all treatments. Furthermore, transmission electron microscopy provided direct evidence of lysogenic to lytic conversion upon temperature increase. These results not only provide new insight into the molecular mechanisms underlying heat or tetracycline treatment but also suggest a novel HLB control strategy by enhancing the endogenous conversion from Las prophages to phages.
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Affiliation(s)
- Fang Ding
- Hubei Key Laboratory of PLant Pathology, Huazhong Agricultural University, 430070 Wuhan, Hubei P.R. China
- USDA-ARS-USHRL, Fort Pierce, FL 34945 USA
| | | | - Weiqi Luo
- USDA-ARS-USHRL, Fort Pierce, FL 34945 USA
- Center for Integrated Pest Management, North Carolina State University, Raleigh, NC 27606 USA
| | - Shouan Zhang
- IFAS-TREC, University of Florida, Homestead, FL 33031 USA
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Kandel PP, Almeida RPP, Cobine PA, De La Fuente L. Natural Competence Rates Are Variable Among Xylella fastidiosa Strains and Homologous Recombination Occurs In Vitro Between Subspecies fastidiosa and multiplex. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:589-600. [PMID: 28459171 DOI: 10.1094/mpmi-02-17-0053-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Xylella fastidiosa, an etiological agent of emerging crop diseases around the world, is naturally competent for the uptake of DNA from the environment that is incorporated into its genome by homologous recombination. Homologous recombination between subspecies of X. fastidiosa was inferred by in silico studies and was hypothesized to cause disease emergence. However, no experimental data are available on the degree to which X. fastidiosa strains are capable of competence and whether recombination can be experimentally demonstrated between subspecies. Here, using X. fastidiosa strains from different subspecies, natural competence in 11 of 13 strains was confirmed with plasmids containing antibiotic markers flanked by homologous regions and, in three of five strains, with dead bacterial cells used as source of donor DNA. Recombination frequency differed among strains and was correlated to growth rate and twitching motility. Moreover, intersubspecific recombination occurred readily between strains of subsp. fastidiosa and multiplex, as demonstrated by movement of antibiotic resistance and green fluorescent protein from donor to recipient cells and confirmed by DNA sequencing of the flanking arms of recombinant strains. Results demonstrate that natural competence is widespread among X. fastidiosa strains and could have an impact in pathogen adaptation and disease development.
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Affiliation(s)
- Prem P Kandel
- 1 Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, U.S.A
| | - Rodrigo P P Almeida
- 2 Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, U.S.A.; and
| | - Paul A Cobine
- 3 Department of Biological Sciences, Auburn University
| | - Leonardo De La Fuente
- 1 Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, U.S.A
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Alencar VC, Jabes DL, Menegidio FB, Sassaki GL, de Souza LR, Puzer L, Meneghetti MCZ, Lima MA, Tersariol ILDS, de Oliveira RC, Nunes LR. Functional and Evolutionary Characterization of a UDP-Xylose Synthase Gene from the Plant Pathogen Xylella fastidiosa, Involved in the Synthesis of Bacterial Lipopolysaccharide. Biochemistry 2017; 56:779-792. [PMID: 28125217 DOI: 10.1021/acs.biochem.6b00886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Xylella fastidiosa is a plant-infecting bacillus, responsible for many important crop diseases, such as Pierce's disease of vineyards, citrus variegated chlorosis, and coffee leaf scorch (CLS), among others. Recent genomic comparisons involving two CLS-related strains, belonging to X. fastidiosa subsp. pauca, revealed that one of them carries a frameshift mutation that inactivates a gene encoding an oxidoreductase of the short-chain dehydrogenase/reductase (SDR) superfamily, which may play important roles in determining structural variations in bacterial glycans and glycoconjugates. However, the exact nature of this SDR has been a matter of controversy, as different annotations of X. fastidiosa genomes have implicated it in distinct reactions. To confirm the nature of this mutated SDR, a comparative analysis was initially performed, suggesting that it belongs to a subgroup of SDR decarboxylases, representing a UDP-xylose synthase (Uxs). Functional assays, using a recombinant derivative of this enzyme, confirmed its nature as XfUxs, and carbohydrate composition analyses, performed with lipopolysaccharide (LPS) molecules obtained from different strains, indicate that inactivation of the X. fastidiosa uxs gene affects the LPS structure among CLS-related X. fastidiosa strains. Finally, a comparative sequence analysis suggests that this mutation is likely to result in a morphological and evolutionary hallmark that differentiates two subgroups of CLS-related strains, which may influence interactions between these bacteria and their plant and/or insect hosts.
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Affiliation(s)
- Valquíria Campos Alencar
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC) , Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes, SP CEP 08780-911, Brazil
| | - Daniela Leite Jabes
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC) , Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes, SP CEP 08780-911, Brazil
| | - Fabiano Bezerra Menegidio
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC) , Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes, SP CEP 08780-911, Brazil
| | - Guilherme Lanzi Sassaki
- Setor de Ciências Biológicas-Departamento de Bioquímica e Biologia Molecular Laboratório de Química de Carboidratos, Universidade Federal do Paraná (UFPR) , Rua Cel. Francisco H. dos Santos, 100, Curitiba, Paraná CEP 81531-980, Brazil
| | - Lucas Rodrigo de Souza
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC) , Rua Santa Adélia, 166, Santo André, SP CEP 09210-170, Brazil
| | - Luciano Puzer
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC) , Rua Santa Adélia, 166, Santo André, SP CEP 09210-170, Brazil
| | - Maria Cecília Zorél Meneghetti
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP) , Rua Três de Maio, Vila Clementino, São Paulo CEP 04044-020, Brazil
| | - Marcelo Andrade Lima
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP) , Rua Três de Maio, Vila Clementino, São Paulo CEP 04044-020, Brazil
| | - Ivarne Luis Dos Santos Tersariol
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP) , Rua Três de Maio, Vila Clementino, São Paulo CEP 04044-020, Brazil
| | - Regina Costa de Oliveira
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes (UMC) , Av. Dr. Cândido Xavier de Almeida Souza, 200, Mogi das Cruzes, SP CEP 08780-911, Brazil
| | - Luiz R Nunes
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC) , Rua Santa Adélia, 166, Santo André, SP CEP 09210-170, Brazil
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Mendes JS, Santiago AS, Toledo MAS, Horta MAC, de Souza AA, Tasic L, de Souza AP. In vitro Determination of Extracellular Proteins from Xylella fastidiosa. Front Microbiol 2016; 7:2090. [PMID: 28082960 PMCID: PMC5183587 DOI: 10.3389/fmicb.2016.02090] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/09/2016] [Indexed: 12/20/2022] Open
Abstract
The phytopathogen Xylella fastidiosa causes economic losses in important agricultural crops. Xylem vessel occlusion caused by biofilm formation is the major mechanism underlying the pathogenicity of distinct strains of X. fastidiosa. Here, we provide a detailed in vitro characterization of the extracellular proteins of X. fastidiosa. Based on the results, we performed a comparison with a strain J1a12, which cannot induce citrus variegated chlorosis symptoms when inoculated into citrus plants. We then extend this approach to analyze the extracellular proteins of X. fastidiosa in media supplemented with calcium. We verified increases in extracellular proteins concomitant with the days of growth and, consequently, biofilm development (3-30 days). Outer membrane vesicles carrying toxins were identified beginning at 10 days of growth in the 9a5c strain. In addition, a decrease in extracellular proteins in media supplemented with calcium was observed in both strains. Using mass spectrometry, 71 different proteins were identified during 30 days of X. fastidiosa biofilm development, including proteases, quorum-sensing proteins, biofilm formation proteins, hypothetical proteins, phage-related proteins, chaperones, toxins, antitoxins, and extracellular vesicle membrane components.
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Affiliation(s)
- Juliano S. Mendes
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de CampinasCampinas, Brazil
| | - André S. Santiago
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de CampinasCampinas, Brazil
| | - Marcelo A. S. Toledo
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de CampinasCampinas, Brazil
| | - Maria A. C. Horta
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de CampinasCampinas, Brazil
| | | | - Ljubica Tasic
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual de CampinasCampinas, Brazil
| | - Anete P. de Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de CampinasCampinas, Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de CampinasCampinas, Brazil
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15
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Marcelletti S, Scortichini M. Xylella fastidiosa CoDiRO strain associated with the olive quick decline syndrome in southern Italy belongs to a clonal complex of the subspecies pauca that evolved in Central America. Microbiology (Reading) 2016; 162:2087-2098. [DOI: 10.1099/mic.0.000388] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Simone Marcelletti
- Council for Agricultural Research and Analysis of Agricultural Economics (CREA), Research Centre for Fruit Trees, Via di Fioranello 52, I-00134 Roma, Italy
| | - Marco Scortichini
- Council for Agricultural Research and Analysis of Agricultural Economics (CREA), Research Centre for Fruit Trees, Via Torrino 3, I-81100 Caserta, Italy
- Council for Agricultural Research and Analysis of Agricultural Economics (CREA), Research Centre for Fruit Trees, Via di Fioranello 52, I-00134 Roma, Italy
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16
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Nwugo CC, Doud MS, Duan YP, Lin H. Proteomics analysis reveals novel host molecular mechanisms associated with thermotherapy of 'Ca. Liberibacter asiaticus'-infected citrus plants. BMC PLANT BIOLOGY 2016; 16:253. [PMID: 27842496 PMCID: PMC5109811 DOI: 10.1186/s12870-016-0942-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/02/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Citrus Huanglongbing (HLB), which is linked to the bacterial pathogen 'Ca. Liberibacter asiaticus' (Las), is the most devastating disease of citrus plants, and longer-term control measures via breeding or genetic engineering have been unwieldy because all cultivated citrus species are susceptible to the disease. However, the degree of susceptibility varies among citrus species, which has prompted efforts to identify potential Las resistance/tolerance-related genes in citrus plants for application in breeding or genetic engineering programs. Plant exposure to one form of stress has been shown to serendipitously induce innate resistance to other forms of stress and a recent study showed that continuous heat treatment (40 to 42 °C) reduced Las titer and HLB-associated symptoms in citrus seedlings. The goal of the present study was to apply comparative proteomics analysis via 2-DE and mass spectrometry to elucidate the molecular processes associated with heat-induced mitigation of HLB in citrus plants. Healthy or Las-infected citrus grapefruit plants were exposed to room temperature or to continuous heat treatment of 40 °C for 6 days. RESULTS An exhaustive total protein extraction process facilitated the identification of 107 differentially-expressed proteins in response to Las and/or heat treatment, which included a strong up-regulation of chaperones including small (23.6, 18.5 and 17.9 kDa) heat shock proteins, a HSP70-like protein and a ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO)-binding 60 kDa chaperonin, particularly in response to heat treatment. Other proteins that were generally down-regulated due to Las infection but up-regulated in response to heat treatment include RuBisCO activase, chlorophyll a/b binding protein, glucosidase II beta subunit-like protein, a putative lipoxygenase protein, a ferritin-like protein, and a glutathione S-transferase. CONCLUSIONS The differentially-expressed proteins identified in this study highlights a premier characterization of the molecular mechanisms potentially involved in the reversal of Las-induced pathogenicity processes in citrus plants and are hence proposed targets for application towards the development of cisgenic Las-resistant/tolerant citrus plants.
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Affiliation(s)
- Chika C. Nwugo
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, 93648 CA USA
| | - Melissa S. Doud
- USDA, Agricultural Research Service, U.S. Horticultural Research Laboratory, Fort Pierce, 34945 FL USA
| | - Yong-ping Duan
- USDA, Agricultural Research Service, U.S. Horticultural Research Laboratory, Fort Pierce, 34945 FL USA
| | - Hong Lin
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, 93648 CA USA
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17
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Burbank LP, Stenger DC. Plasmid Vectors for Xylella fastidiosa Utilizing a Toxin-Antitoxin System for Stability in the Absence of Antibiotic Selection. PHYTOPATHOLOGY 2016; 106:928-936. [PMID: 27088393 DOI: 10.1094/phyto-02-16-0097-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The phytopathogen Xylella fastidiosa causes disease in a variety of important crop and landscape plants. Functional genetic studies have led to a broader understanding of virulence mechanisms used by this pathogen in the grapevine host. Plasmid shuttle vectors are important tools in studies of bacterial genetics but there are only a limited number of plasmid vectors available that replicate in X. fastidiosa, and even fewer that are retained without antibiotic selection. Two plasmids are described here that show stable replication in X. fastidiosa and are effective for gene complementation both in vitro and in planta. Plasmid maintenance is facilitated by incorporation of the PemI/PemK plasmid addiction system, consisting of PemK, an endoribonuclease toxin, and its cognate antitoxin, PemI. Vector pXf20pemIK utilizes a native X. fastidiosa replication origin as well as a high-copy-number pUC origin for propagation in Escherichia coli cloning strains. Broad-host-range vector pBBR5pemIK is a medium- to low-copy-number plasmid based on the pBBR1 backbone. Both plasmids are maintained for extended periods of time in the absence of antibiotic selection, as well as up to 14 weeks in grapevine, without affecting bacterial fitness. These plasmids present an alternative to traditional complementation and expression vectors which rely on antibiotic selection for plasmid retention.
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Affiliation(s)
- Lindsey P Burbank
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Ave., Parlier, CA 93648-9757
| | - Drake C Stenger
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Ave., Parlier, CA 93648-9757
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18
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Marcelletti S, Scortichini M. Genome-wide comparison and taxonomic relatedness of multiple Xylella fastidiosa strains reveal the occurrence of three subspecies and a new Xylella species. Arch Microbiol 2016; 198:803-12. [PMID: 27209415 DOI: 10.1007/s00203-016-1245-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/13/2016] [Accepted: 05/16/2016] [Indexed: 11/30/2022]
Abstract
A total of 21 Xylella fastidiosa strains were assessed by comparing their genomes to infer their taxonomic relationships. The whole-genome-based average nucleotide identity and tetranucleotide frequency correlation coefficient analyses were performed. In addition, a consensus tree based on comparisons of 956 core gene families, and a genome-wide phylogenetic tree and a Neighbor-net network were constructed with 820,088 nucleotides (i.e., approximately 30-33 % of the entire X. fastidiosa genome). All approaches revealed the occurrence of three well-demarcated genetic clusters that represent X. fastidiosa subspecies fastidiosa, multiplex and pauca, with the latter appeared to diverge. We suggest that the proposed but never formally described subspecies 'sandyi' and 'morus' are instead members of the subspecies fastidiosa. These analyses support the view that the Xylella strain isolated from Pyrus pyrifolia in Taiwan is likely to be a new species. A widely used multilocus sequence typing analysis yielded conflicting results.
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Affiliation(s)
- Simone Marcelletti
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca per le Colture Arboree, Via di Fioranello, 52, 00134, Rome, Italy
| | - Marco Scortichini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca per le Colture Arboree, Via di Fioranello, 52, 00134, Rome, Italy. .,Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca per le Colture Arboree, Via Torrino, 3, 81100, Caserta, Italy.
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A λ Cro-Like Repressor Is Essential for the Induction of Conjugative Transfer of SXT/R391 Elements in Response to DNA Damage. J Bacteriol 2015; 197:3822-33. [PMID: 26438816 DOI: 10.1128/jb.00638-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/26/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Integrative and conjugative elements (ICEs) of the SXT/R391 family are the main contributors to acquired multidrug resistance in the seventh pandemic lineage of Vibrio cholerae, the etiological agent of the diarrheal disease cholera. Conjugative transfer of SXT/R391 ICEs is triggered by antibiotics and agents promoting DNA damage through RecA-dependent autoproteolysis of SetR, an ICE-encoded λ CI-like repressor. Here, we describe the role of CroS, a distant λ Cro homolog, as a key component contributing to the regulation of expression of the activator SetCD that orchestrates the expression of the conjugative transfer genes. We show that deletion of croS abolishes the SOS response-dependent induction of SXT despite the presence of a functional setR gene. Using quantitative reverse transcription-PCR and lacZ reporter assays, we also show that CroS represses setR and setCD expression by binding to operator sites shared with SetR. Furthermore, we provide evidence of an additional operator site bound by SetR and CroS. Finally, we show that SetCD expression generates a positive feedback loop due to SXT excision and replication in a fraction of the cell population. Together, these results refine our understanding of the genetic regulation governing the propagation of major vectors of multidrug resistance. IMPORTANCE Healthcare systems worldwide are challenged by an alarming drug resistance crisis caused by the massive and rapid propagation of antibiotic resistance genes and the associated emergence of multidrug-resistant pathogenic bacteria. SXT/R391 ICEs contribute to this phenomenon not only in clinical and environmental vibrios but also in several members of the family Enterobacteriaceae. We have identified and characterized here the regulator CroS as a key factor in the stimulation of conjugative transfer of these ICEs in response to DNA-damaging agents. We have also untangled conflicting evidence regarding autoactivation of transfer by the master activator of SXT/R391 ICEs, SetCD. Discovery of CroS provides a clearer and more complete understanding of the regulatory network that governs the dissemination of SXT/R391 ICEs in bacterial populations.
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20
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Askora A, Yamada T. Two different evolutionary lines of filamentous phages in Ralstonia solanacearum: their effects on bacterial virulence. Front Genet 2015; 6:217. [PMID: 26150828 PMCID: PMC4471427 DOI: 10.3389/fgene.2015.00217] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/03/2015] [Indexed: 12/18/2022] Open
Abstract
The integration and excision of various filamentous phage genomes into and out of their host chromosomes occurs by site-specific recombination. The mechanisms proposed for these events include reactions mediated by phage-encoded recombinases and host recombination systems. Site-specific integration of filamentous phages plays a vital role in a variety of biological functions of the host, such as phase variation of certain pathogenic bacterial virulence factors. The importance of these filamentous phages in bacterial evolution is rapidly increasing with the discovery of new phages that are involved in pathogenicity. Studies of the diversity of two different filamentous phages infecting the phytopathogen Ralstonia solanacearum provide us with novel insights into the dynamics of phage genomes, biological roles of prophages, and the regulation and importance of phage-host interactions.
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Affiliation(s)
- Ahmed Askora
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, Zagazig Egypt
| | - Takashi Yamada
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima Japan
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21
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Comparative genomic analysis of coffee-infecting Xylella fastidiosa strains isolated from Brazil. Microbiology (Reading) 2015; 161:1018-1033. [DOI: 10.1099/mic.0.000068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/28/2015] [Indexed: 12/28/2022] Open
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23
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Scientific Opinion on the risks to plant health posed byXylella fastidiosain the EU territory, with the identification and evaluation of risk reduction options. EFSA J 2015. [DOI: 10.2903/j.efsa.2015.3989] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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24
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Ahmad AA, Askora A, Kawasaki T, Fujie M, Yamada T. The filamentous phage XacF1 causes loss of virulence in Xanthomonas axonopodis pv. citri, the causative agent of citrus canker disease. Front Microbiol 2014; 5:321. [PMID: 25071734 PMCID: PMC4076744 DOI: 10.3389/fmicb.2014.00321] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/11/2014] [Indexed: 12/15/2022] Open
Abstract
In this study, filamentous phage XacF1, which can infect Xanthomonas axonopodis pv. citri (Xac) strains, was isolated and characterized. Electron microscopy showed that XacF1 is a member of the family Inoviridae and is about 600 nm long. The genome of XacF1 is 7325 nucleotides in size, containing 13 predicted open reading frames (ORFs), some of which showed significant homology to Ff-like phage proteins such as ORF1 (pII), ORF2 (pV), ORF6 (pIII), and ORF8 (pVI). XacF1 showed a relatively wide host range, infecting seven out of 11 strains tested in this study. Frequently, XacF1 was found to be integrated into the genome of Xac strains. This integration occurred at the host dif site (attB) and was mediated by the host XerC/D recombination system. The attP sequence was identical to that of Xanthomonas phage Cf1c. Interestingly, infection by XacF1 phage caused several physiological changes to the bacterial host cells, including lower levels of extracellular polysaccharide production, reduced motility, slower growth rate, and a dramatic reduction in virulence. In particular, the reduction in virulence suggested possible utilization of XacF1 as a biological control agent against citrus canker disease.
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Affiliation(s)
- Abdelmonim Ali Ahmad
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
| | - Ahmed Askora
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
- Department of Microbiology, Faculty of Science, Zagazig UniversityZagazig, Sharkia, Egypt
| | - Takeru Kawasaki
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
| | - Makoto Fujie
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
| | - Takashi Yamada
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima UniversityHigashi-Hiroshima, Japan
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Zhou L, Powell CA, Li W, Irey M, Duan Y. Prophage-mediated dynamics of 'Candidatus Liberibacter asiaticus' populations, the destructive bacterial pathogens of citrus huanglongbing. PLoS One 2013; 8:e82248. [PMID: 24349235 PMCID: PMC3862640 DOI: 10.1371/journal.pone.0082248] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/22/2013] [Indexed: 01/21/2023] Open
Abstract
Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. There are at least two prophages in the chromosomes of Candidatus Liberibacter asiaticus' (Las) Floridian isolates. Las is both unculturable and the most prevalent species of Liberibacter pathogens that cause huanglongbing (HLB), a worldwide destructive disease of citrus. In this study, seven new prophage variants resulting from two hyper-variable regions were identified by screening clone libraries of infected citrus, periwinkle and psyllids. Among them, Types A and B share highly conserved sequences and localize within the two prophages, FP1 and FP2, respectively. Although Types B and C were abundant in all three libraries, Type A was much more abundant in the libraries from the Las-infected psyllids than from the Las-infected plants, and Type D was only identified in libraries from the infected host plants but not from the infected psyllids. Sequence analysis of these variants revealed that the variations may result from recombination and rearrangement events. Conventional PCR results using type-specific molecular markers indicated that A, B, C and D are the four most abundant types in Las-infected citrus and periwinkle. However, only three types, A, B and C are abundant in Las-infected psyllids. Typing results for Las-infected citrus field samples indicated that mixed populations of Las bacteria present in Floridian isolates, but only the Type D population was correlated with the blotchy mottle symptom. Extended cloning and sequencing of the Type D region revealed a third prophage/phage in the Las genome, which may derive from the recombination of FP1 and FP2. Dramatic variations in these prophage regions were also found among the global Las isolates. These results are the first to demonstrate the prophage/phage-mediated dynamics of Las populations in plant and insect hosts, and their correlation with insect transmission and disease development.
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Affiliation(s)
- Lijuan Zhou
- Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida, United States of America
- Indian River Research and Education Center, University of Florida, Fort Pierce, Florida, United States of America
| | - Charles A. Powell
- Indian River Research and Education Center, University of Florida, Fort Pierce, Florida, United States of America
| | - Wenbin Li
- Center for Plant Health, Science and Technology, Animal and Plant health Inspection Service, US Department of Agriculture, Beltsville, Maryland, United States of America
| | - Mike Irey
- Southern Garden Citrus, U. S. Sugar Corp., Clewiston, Florida, United States of America
| | - Yongping Duan
- Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida, United States of America
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26
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Varani AM, Monteiro-Vitorello CB, Nakaya HI, Van Sluys MA. The role of prophage in plant-pathogenic bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:429-451. [PMID: 23725471 DOI: 10.1146/annurev-phyto-081211-173010] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A diverse set of phage lineages is associated with the bacterial plant-pathogen genomes sequenced to date. Analysis of 37 genomes revealed 5,169 potential genes (approximately 4.3 Mbp) of phage origin, and at least 50% had no function assigned or are nonessential to phage biology. Some phytopathogens have transcriptionally active prophage genes under conditions that mimic plant infection, suggesting an association between plant disease and prophage transcriptional modulation. The role of prophages within genomes for cell biology varies. For pathogens such as Pectobacterium, Pseudomonas, Ralstonia, and Streptomyces, involvement of prophage in disease symptoms has been demonstrated. In Xylella and Xanthomonas, prophage activity is associated with genome rearrangements and strain differentiation. For other pathogens, prophage roles are yet to be established. This review integrates available information in a unique interface ( http://propnav.esalq.usp.br ) that may be assessed to improve research in prophage biology and its association with genome evolution and pathogenicity.
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Affiliation(s)
- Alessandro M Varani
- Departamento de Genética (LGN), Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13418-900 Piracicaba/SP, Brazil
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Hoffman MT, Doud MS, Williams L, Zhang MQ, Ding F, Stover E, Hall D, Zhang S, Jones L, Gooch M, Fleites L, Dixon W, Gabriel D, Duan YP. Heat treatment eliminates 'Candidatus Liberibacter asiaticus' from infected citrus trees under controlled conditions. PHYTOPATHOLOGY 2013; 103:15-22. [PMID: 23035631 DOI: 10.1094/phyto-06-12-0138-r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Huanglongbing (HLB) is one of the most destructive diseases of citrus worldwide. The three known causal agents of HLB are species of α-proteobacteria: 'Candidatus Liberibacter asiaticus', 'Ca. L. africanus', and 'Ca. L. americanus'. Previous studies have found distinct variations in temperature sensitivity and tolerance among these species. Here, we describe the use of controlled heat treatments to cure HLB caused by 'Ca. L. asiaticus', the most prevalent and heat-tolerant species. Using temperature-controlled growth chambers, we evaluated the time duration and temperature required to suppress or eliminate the 'Ca. L. asiaticus' bacterium in citrus, using various temperature treatments for time periods ranging from 2 days to 4 months. Results of quantitative polymerase chain reaction (qPCR) after treatment illustrate significant decreases in the 'Ca. L. asiaticus' bacterial titer, combined with healthy vigorous growth by all surviving trees. Repeated qPCR testing confirmed that previously infected, heat-treated plants showed no detectable levels of 'Ca. L. asiaticus', while untreated control plants remained highly infected. Continuous thermal exposure to 40 to 42°C for a minimum of 48 h was sufficient to significantly reduce titer or eliminate 'Ca. L. asiaticus' bacteria entirely in HLB-affected citrus seedlings. This method may be useful for the control of 'Ca. Liberibacter'-infected plants in nursery and greenhouse settings.
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Affiliation(s)
- Michele T Hoffman
- United States Department of Agriculture, Agriculture Reserch Service, United States Horticultural Research Laboratory, Fort Pierce, FL 34945, USA
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Abstract
The history of advances in research on Xylella fastidiosa provides excellent examples of how paradigms both advance and limit our scientific understanding of plant pathogens and the plant diseases they cause. I describe this from a personal perspective, having been directly involved with many persons who made paradigm-changing discoveries, beginning with the discovery that a bacterium, not a virus, causes Pierce's disease of grape and other plant diseases in numerous plant species, including important crop and forest species.
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Affiliation(s)
- Alexander Purcell
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720-3114, USA.
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Site-specific recombination systems in filamentous phages. Mol Genet Genomics 2012; 287:525-30. [DOI: 10.1007/s00438-012-0700-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 05/21/2012] [Indexed: 12/18/2022]
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Nunney L, Elfekih S, Stouthamer R. The importance of multilocus sequence typing: cautionary tales from the bacterium Xylella fastidiosa. PHYTOPATHOLOGY 2012; 102:456-460. [PMID: 22236051 DOI: 10.1094/phyto-10-11-0298] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Microbial identification methods have evolved rapidly over the last few decades. One such method is multilocus sequence typing (MLST). MLST is a powerful tool for understanding the evolutionary dynamics of pathogens and to gain insight into their genetic diversity. We illustrate the importance of accurate typing by reporting on three problems that have arisen in the study of a single bacterial species, the plant pathogen Xylella fastidiosa. Two of these were particularly serious since they concerned contamination of important research material that has had detrimental consequences for Xylella research: the contamination of DNA used in the sequencing of an X. fastidiosa genome (Ann-1) with DNA from another X. fastidiosa strain, and the unrecognized mislabeling of a strain (Temecula1) distributed from a culture collection (ATCC). We advocate the routine use of MLST to define strains maintained in culture collections and emphasize the importance of confirming the purity of DNA submitted for sequencing. We also present a third example that illustrates the value of MLST in guiding the choice of taxonomic types. Beyond these situations, there is a strong case for MLST whenever an isolate is used experimentally, especially where genotypic differences are suspected to influence the outcome.
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31
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Varani AM, Monteiro-Vitorello CB, de Almeida LGP, Souza RC, Cunha OL, Lima WC, Civerolo E, Van Sluys MA, Vasconcelos ATR. Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains. Genet Mol Biol 2012; 35:149-52. [PMID: 22481888 PMCID: PMC3313504 DOI: 10.1590/s1415-47572012005000019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 12/09/2011] [Indexed: 11/21/2022] Open
Abstract
The Xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of Xylella genomes. Here we describe a database and tools for exploring the biology of this important plant pathogen. The hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. It is available from web site http://www.xylella.lncc.br.
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Affiliation(s)
- Alessandro M Varani
- Genome and Transposable Elements Laboratory, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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32
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Killiny N, Almeida RPP. Gene regulation mediates host specificity of a bacterial pathogen. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:791-7. [PMID: 23761371 DOI: 10.1111/j.1758-2229.2011.00288.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Many bacterial plant pathogens have a gene-for-gene relationship that determines host specificity. However, there are pathogens such as the xylem-limited bacterium Xylella fastidiosa that do not carry genes considered essential for the gene-for-gene model, such as those coding for a type III secretion system and effector molecules. Nevertheless, X. fastidiosa subspecies are host specific. A comparison of symptom development and host colonization after infection of plants with several mutant strains in two hosts, grapevines and almonds, indicated that X. fastidiosa virulence mechanisms are similar in those plants. Thus, we tested if modification of gene regulation patterns, by affecting the production of a cell-cell signalling molecule (DSF), impacted host specificity in X. fastidiosa. Results show that disruption of the rpfF locus, required for DSF synthesis, in a strain incapable of causing disease in grapevines, leads to symptom development in that host. These data are indicative that the core machinery required for the colonization of grapevines is present in that strain, and that changes in gene regulation alone can lead X. fastidiosa to exploit a novel host. The study of the evolution and mechanisms of host specificity mediated by gene regulation at the genome level could lead to important insights on the emergence of new diseases.
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Affiliation(s)
- Nabil Killiny
- Citrus Research and Education Center, Department of Entomology and Nematology, University of Florida, IFAS, 700 Experiment Station Road, Lake Alfred, FL 33850, USA. Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
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33
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Matsumoto A, Igo MM. Species-specific type II restriction-modification system of Xylella fastidiosa temecula1. Appl Environ Microbiol 2010; 76:4092-5. [PMID: 20418439 PMCID: PMC2893502 DOI: 10.1128/aem.03034-09] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 04/19/2010] [Indexed: 11/20/2022] Open
Abstract
The transformation efficiency of Xylella fastidiosa can be increased by interfering with restriction by the strain-specific type II system encoded by the PD1607 and PD1608 genes. Here, we report results for two strategies: in vitro methylation using M.SssI and isolation of DNA from an Escherichia coli strain expressing the methylase PD1607.
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Affiliation(s)
- Ayumi Matsumoto
- Department of Microbiology, University of California, Davis, One Shields Avenue, Davis, California 95616
| | - Michele M. Igo
- Department of Microbiology, University of California, Davis, One Shields Avenue, Davis, California 95616
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Summer EJ, Enderle CJ, Ahern SJ, Gill JJ, Torres CP, Appel DN, Black MC, Young R, Gonzalez CF. Genomic and biological analysis of phage Xfas53 and related prophages of Xylella fastidiosa. J Bacteriol 2010; 192:179-90. [PMID: 19897657 PMCID: PMC2798268 DOI: 10.1128/jb.01174-09] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 10/27/2009] [Indexed: 02/07/2023] Open
Abstract
We report the plaque propagation and genomic analysis of Xfas53, a temperate phage of Xylella fastidiosa. Xfas53 was isolated from supernatants of X. fastidiosa strain 53 and forms plaques on the sequenced strain Temecula. Xfas53 forms short-tailed virions, morphologically similar to podophage P22. The 36.7-kb genome is predicted to encode 45 proteins. The Xfas53 terminase and structural genes are related at a protein and gene order level to P22. The left arm of the Xfas53 genome has over 90% nucleotide identity to multiple prophage elements of the sequenced X. fastidiosa strains. This arm encodes proteins involved in DNA metabolism, integration, and lysogenic control. In contrast to Xfas53, each of these prophages encodes head and DNA packaging proteins related to the siphophage lambda and tail morphogenesis proteins related to those of myophage P2. Therefore, it appears that Xfas53 was formed by recombination between a widespread family of X. fastidiosa P2-related prophage elements and a podophage distantly related to phage P22. The lysis cassette of Xfas53 is predicted to encode a pinholin, a signal anchor and release (SAR) endolysin, and Rz and Rz1 equivalents. The holin gene encodes a pinholin and appears to be subject to an unprecedented degree of negative regulation at both the level of expression, with rho-independent transcriptional termination and RNA structure-dependent translational repression, and the level of holin function, with two upstream translational starts predicted to encode antiholin products. A notable feature of Xfas53 and related prophages is the presence of 220- to 390-nucleotide degenerate tandem direct repeats encoding putative DNA binding proteins. Additionally, each phage encodes at least two BroN domain-containing proteins possibly involved in lysogenic control. Xfas53 exhibits unusually slow adsorption kinetics, possibly an adaptation to the confined niche of its slow-growing host.
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Affiliation(s)
- Elizabeth J. Summer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, Department of Plant Pathology and Microbiology, Texas A&M University, College, Station, Texas 77843-2132, Texas AgriLife Research and Extension Center, Uvalde, Texas 78801-6205
| | - Christopher J. Enderle
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, Department of Plant Pathology and Microbiology, Texas A&M University, College, Station, Texas 77843-2132, Texas AgriLife Research and Extension Center, Uvalde, Texas 78801-6205
| | - Stephen J. Ahern
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, Department of Plant Pathology and Microbiology, Texas A&M University, College, Station, Texas 77843-2132, Texas AgriLife Research and Extension Center, Uvalde, Texas 78801-6205
| | - Jason J. Gill
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, Department of Plant Pathology and Microbiology, Texas A&M University, College, Station, Texas 77843-2132, Texas AgriLife Research and Extension Center, Uvalde, Texas 78801-6205
| | - Cruz P. Torres
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, Department of Plant Pathology and Microbiology, Texas A&M University, College, Station, Texas 77843-2132, Texas AgriLife Research and Extension Center, Uvalde, Texas 78801-6205
| | - David N. Appel
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, Department of Plant Pathology and Microbiology, Texas A&M University, College, Station, Texas 77843-2132, Texas AgriLife Research and Extension Center, Uvalde, Texas 78801-6205
| | - Mark C. Black
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, Department of Plant Pathology and Microbiology, Texas A&M University, College, Station, Texas 77843-2132, Texas AgriLife Research and Extension Center, Uvalde, Texas 78801-6205
| | - Ry Young
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, Department of Plant Pathology and Microbiology, Texas A&M University, College, Station, Texas 77843-2132, Texas AgriLife Research and Extension Center, Uvalde, Texas 78801-6205
| | - Carlos F. Gonzalez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, Department of Plant Pathology and Microbiology, Texas A&M University, College, Station, Texas 77843-2132, Texas AgriLife Research and Extension Center, Uvalde, Texas 78801-6205
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Wang X, Kim Y, Wood TK. Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms. ISME JOURNAL 2009; 3:1164-79. [PMID: 19458652 DOI: 10.1038/ismej.2009.59] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Earlier, we discovered that the global regulator, Hha, is related to cell death in biofilms and regulates cryptic prophage genes. Here, we show that Hha induces excision of prophages, CP4-57 and DLP12, by inducing excision genes and by reducing SsrA synthesis. SsrA is a tmRNA that is important for rescuing stalled ribosomes, contains an attachment site for CP4-57 and is shown here to be required for CP4-57 excision. These prophages impact biofilm development, as the deletion of 35 genes individually of prophages, CP4-57 and DLP12, increase biofilm formation up to 17-fold, and five genes decrease biofilm formation up to sixfold. In addition, CP4-57 excises during early biofilm development but not in planktonic cells, whereas DLP12 excision was detected at all the developmental stages for both biofilm and planktonic cells. CP4-57 excision leads to a chromosome region devoid of prophage and to the formation of a phage circle (which is lost). These results were corroborated by a whole-transcriptome analysis that showed that complete loss of CP4-57 activated the expression of the flg, flh and fli motility operons and repressed expression of key enzymes in the tricarboxylic acid cycle and of enzymes for lactate utilization. Prophage excision also results in the expression of cell lysis genes that reduce cell viability (for example, alpA, intA and intD). Hence, defective prophages are involved in host physiology through Hha and in biofilm formation by generating a diversified population with specialized functions in terms of motility and nutrient metabolism.
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Affiliation(s)
- Xiaoxue Wang
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
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