Dataset Information

Genomic Analysis of Phylotype I Strain EP1 Reveals Substantial Divergence from Other Strains in the Ralstonia solanacearum Species Complex.

ABSTRACT: Ralstonia solanacearum species complex is a devastating group of phytopathogens with an unusually wide host range and broad geographical distribution. R. solanacearum isolates may differ considerably in various properties including host range and pathogenicity, but the underlying genetic bases remain vague. Here, we conducted the genome sequencing of strain EP1 isolated from Guangdong Province of China, which belongs to phylotype I and is highly virulent to a range of solanaceous crops. Its complete genome contains a 3.95-Mb chromosome and a 2.05-Mb mega-plasmid, which is considerably bigger than reported genomes of other R. solanacearum strains. Both the chromosome and the mega-plasmid have essential house-keeping genes and many virulence genes. Comparative analysis of strain EP1 with other 3 phylotype I and 3 phylotype II, III, IV strains unveiled substantial genome rearrangements, insertions and deletions. Genome sequences are relatively conserved among the 4 phylotype I strains, but more divergent among strains of different phylotypes. Moreover, the strains exhibited considerable variations in their key virulence genes, including those encoding secretion systems and type III effectors. Our results provide valuable information for further elucidation of the genetic basis of diversified virulences and host range of R. solanacearum species.

SUBMITTER: Li P

PROVIDER: S-EPMC5080846 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Genomic Analysis of Phylotype I Strain EP1 Reveals Substantial Divergence from Other Strains in the Ralstonia solanacearum Species Complex.

Li Peng P Wang Dechen D Yan Jinli J Zhou Jianuan J Deng Yinyue Y Jiang Zide Z Cao Bihao B He Zifu Z Zhang Lianhui L

Frontiers in microbiology 20161026

Ralstonia solanacearum species complex is a devastating group of phytopathogens with an unusually wide host range and broad geographical distribution. R. solanacearum isolates may differ considerably in various properties including host range and pathogenicity, but the underlying genetic bases remain vague. Here, we conducted the genome sequencing of strain EP1 isolated from Guangdong Province of China, which belongs to phylotype I and is highly virulent to a range of solanaceous c ...[more]

PMID: 27833603

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Project description:Quorum sensing (QS) is a widely conserved bacterial regulatory mechanism that relies on production and perception of autoinducing chemical signals to coordinate diverse cooperative activities, such as virulence, exoenzyme secretion, and biofilm formation. In Ralstonia solanacearum, a phytopathogen causing severe bacterial wilt diseases in many plant species, previous studies identified the PhcBSR QS system, which plays a key role in regulation of its physiology and virulence. In this study, we found that R. solanacearum strain EP1 contains the genes encoding uncharacterized LuxI/LuxR (LuxI/R) QS homologues (RasI/RasR [designated RasI/R here]). To determine the roles of the RasI/R system in strain EP1, we constructed a specific reporter for the signals catalyzed by RasI. Chromatography separation and structural analysis showed that RasI synthesized primarily N-(3-hydroxydodecanoyl)-homoserine lactone (3-OH-C12-HSL). In addition, we showed that the transcriptional expression of rasI is regulated by RasR in response to 3-OH-C12-HSL. Phenotype analysis unveiled that the RasI/R system plays a critical role in modulation of cellulase production, motility, biofilm formation, oxidative stress response, and virulence of R. solanacearum EP1. We then further characterized this system by determining the RasI/R regulon using transcriptome sequencing (RNA-seq) analysis, which showed that this newly identified QS system regulates the transcriptional expression of over 154 genes associated with bacterial physiology and pathogenic properties. Taken together, the findings from this study present an essential new QS system in regulation of R. solanacearum physiology and virulence and provide new insight into the complicated regulatory mechanisms and networks in this important plant pathogen. IMPORTANCE Quorum sensing (QS) is a key regulator of virulence factors in many plant-pathogenic bacteria. Previous studies unveiled two QS systems (i.e., PhcBSR and SolI/R) in several R. solanacearum strains. The PhcBSR QS system is known for its key roles in regulation of bacterial virulence, and the LuxI/LuxR (SolI/R) QS system appears dispensable for pathogenicity in a number of R. solanacearum strains. In this study, a new functional QS system (i.e., RasI/R) was identified and characterized in R. solanacearum strain EP1 isolated from infected eggplants. Phenotype analyses showed that the RasI/R system plays an important role in regulation of a range of biological activities associated with bacterial virulence. This QS system produces and responds to the QS signal 3-OH-C12-HSL and hence regulates critical bacterial abilities in survival and infection. To date, multiple QS signaling circuits in R. solanacearum strains are still not well understood. Our findings from this study provide new insight into the complicated QS regulatory networks that govern the physiology and virulence of R. solanacearum and present a valid target and clues for the control and prevention of bacterial wilt diseases.

Project description:Background. Reliable genotyping that provides an accurate description of diversity in the context of pathogen emergence is required for the establishment of strategies to improve disease management. MultiLocus variable number tandem repeat analysis (MLVA) is a valuable genotyping method. It can be performed at small evolutionary scales where high discriminatory power is needed. Strains of the Ralstonia solanacearum species complex (RSSC) are highly genetically diverse. These destructive pathogens are the causative agent of bacterial wilt on an unusually broad range of host plants worldwide. In this study, we developed an MLVA scheme for genotyping the African RSSC phylotype III. Methods. We selected different publicly available tandem repeat (TR) loci and additional TR loci from the genome of strain CMR15 as markers. Based on these loci, a new phylotype III-MLVA scheme is presented. MLVA and multiLocus sequence typing (MLST) were compared at the global, regional, and local scales. Different populations of epidemiologically related and unrelated RSSC phylotype III strains were used. Results and Discussion. Sixteen polymorphic TR loci, which included seven microsatellites and nine minisatellites, were selected. These TR loci were distributed throughout the genome (chromosome and megaplasmid) and located in both coding and intergenic regions. The newly developed RS3-MLVA16 scheme was more discriminative than MLST. RS3-MLVA16 showed good ability in differentiating strains at global, regional, and local scales, and it especially highlighted epidemiological links between closely related strains at the local scale. RS3-MLVA16 also underlines genetic variability within the same MLST-type and clonal complex, and gives a first overview of population structure. Overall, RS3-MLVA16 is a promising genotyping method for outbreak investigation at a fine scale, and it could be used for outbreak investigation as a first-line, low-cost assay for the routine screening of RSSC phylotype III.

Project description:The Ralstonia solanacearum species complex (RSSC) is a highly diverse cluster of bacterial strains found worldwide, many of which are destructive and cause bacterial wilt (BW) in a wide range of host plants. In 2009, potato production in Madagascar was dramatically affected by several BW epidemics. Controlling this disease is critical for Malagasy potato producers. The first important step toward control is the characterization of strains and their putative origins. The genetic diversity and population structure of the RSSC were investigated in the major potato production areas of the Highlands. A large collection of strains (n = 1224) was assigned to RSSC phylotypes based on multiplex polymerase chain reaction (PCR). Phylotypes I and III have been present in Madagascar for a long time but rarely associated with major potato BW outbreaks. The marked increase of BW prevalence was found associated with phylotype IIB sequevar 1 (IIB-1) strains (n = 879). This is the first report of phylotype IIB-1 strains in Madagascar. In addition to reference strains, epidemic IIB-1 strains (n = 255) were genotyped using the existing MultiLocus Variable-Number Tandem Repeat Analysis (MLVA) scheme RS2-MLVA9, producing 31 haplotypes separated into two related clonal complexes (CCs). One major CC included most of the worldwide haplotypes distributed across wide areas. A regional-scale investigation suggested that phylotype IIB-1 strains were introduced and massively spread via latently infected potato seed tubers. Additionally, the genetic structure of phylotype IIB-1 likely resulted from a bottleneck/founder effect. The population structure of phylotype III, described here for the first time in Madagascar, exhibited a different pattern. Phylotype III strains (n = 217) were genotyped using the highly discriminatory MLVA scheme RS3-MLVA16. High genetic diversity was uncovered, with 117 haplotypes grouped into 11 CCs. Malagasy phylotype III strains were highly differentiated from continental African strains, suggesting no recent migration from the continent. Overall, population structure of phylotype III involves individual small CCs that correlate to restricted geographic areas in Madagascar. The evidence suggests, if at all, that African phylotype III strains are not efficiently transmitted through latently infected potato seed tubers.

Dataset Information

Genomic Analysis of Phylotype I Strain EP1 Reveals Substantial Divergence from Other Strains in the Ralstonia solanacearum Species Complex.

Publications

Genomic Analysis of Phylotype I Strain EP1 Reveals Substantial Divergence from Other Strains in the <i>Ralstonia solanacearum</i> Species Complex.

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