Fire blight, caused by the enterobacterium Erwinia amylovora, is a devastating disease of rosaceous plants that has global economic importance for apple and pear production and trade. The complete genome of E. amylovora CFBP 1430 was sequenced, annotated, and compared with the genomes of other Erwinia spp. Several singleton and shared features of the E. amylovora CFBP 1430 genome were identified that offer a first view into evolutionary aspects within the genus Erwinia. Comparative genomics identified or clarified virulence and fitness determinants and secretion systems. Novel insights revealed in the genome of E. amylovora CFBP 1430 hold potential for exploitation to improve the design of more effective fire blight control strategies.
BackgroundThe Type VI secretion apparatus is assembled by a conserved set of proteins encoded within a distinct locus. The putative effector proteins Hcp and VgrG are also encoded within these loci. We have identified numerous distinct Type VI secretion system (T6SS) loci in the genomes of several ecologically diverse Pantoea and Erwinia species and detected the presence of putative effector islands associated with the hcp and vgrG genes.ResultsBetween two and four T6SS loci occur among the Pantoea and Erwinia species. While two of the loci (T6SS-1 and T6SS-2) are well conserved among the various strains, the third (T6SS-3) locus is not universally distributed. Additional orthologous loci are present in Pantoea sp. aB-valens and Erwinia billingiae Eb661. Comparative analysis of the T6SS-1 and T6SS-3 loci showed non-conserved islands associated with the vgrG and hcp, and vgrG genes, respectively. These regions had a G+C content far lower than the conserved portions of the loci. Many of the proteins encoded within the hcp and vgrG islands carry conserved domains, which suggests they may serve as effector proteins for the T6SS. A number of the proteins also show homology to the C-terminal extensions of evolved VgrG proteins.ConclusionsExtensive diversity was observed in the number and content of the T6SS loci among the Pantoea and Erwinia species. Genomic islands could be observed within some of T6SS loci, which are associated with the hcp and vgrG proteins and carry putative effector domain proteins. We propose new hypotheses concerning a role for these islands in the acquisition of T6SS effectors and the development of novel evolved VgrG and Hcp proteins.
BackgroundErwinia pyrifoliae is a newly described necrotrophic pathogen, which causes fire blight on Asian (Nashi) pear and is geographically restricted to Eastern Asia. Relatively little is known about its genetics compared to the closely related main fire blight pathogen E. amylovora.ResultsThe genome of the type strain of E. pyrifoliae strain DSM 12163T, was sequenced using both 454 and Solexa pyrosequencing and annotated. The genome contains a circular chromosome of 4.026 Mb and four small plasmids. Based on their respective role in virulence in E. amylovora or related organisms, we identified several putative virulence factors, including type III and type VI secretion systems and their effectors, flagellar genes, sorbitol metabolism, iron uptake determinants, and quorum-sensing components. A deletion in the rpoS gene covering the most conserved region of the protein was identified which may contribute to the difference in virulence/host-range compared to E. amylovora. Comparative genomics with the pome fruit epiphyte Erwinia tasmaniensis Et1/99 showed that both species are overall highly similar, although specific differences were identified, for example the presence of some phage gene-containing regions and a high number of putative genomic islands containing transposases in the E. pyrifoliae DSM 12163T genome.ConclusionsThe E. pyrifoliae genome is an important addition to the published genome of E. tasmaniensis and the unfinished genome of E. amylovora providing a foundation for re-sequencing additional strains that may shed light on the evolution of the host-range and virulence/pathogenicity of this important group of plant-associated bacteria.
Pantoea vagans is a Gram-negative enterobacterial plant epiphyte of a broad range of plants. Here we report the 4.89-Mb genome sequence of P. vagans strain C9-1 (formerly Pantoea agglomerans), which is commercially registered for biological control of fire blight, a disease of pear and apple trees caused by Erwinia amylovora.Pantoea vagans (syn. Pantoea agglomerans, Erwinia herbicola) (10), is a common plant epiphyte. Strain C9-1, isolated from apple (Malus ϫ domestica 'Jonathan') (Michigan) (5), is registered as BlightBan C9-1 (Nufarms America Inc., Burr Ridge, IL) for biocontrol of fire blight caused by the related enterobacterium Erwinia amylovora. Applied during bloom, C9-1 provides effective disease control, similar to oxytetracycline and slightly less disease control than streptomycin treatment provides (6). As for most biocontrol agents, growth and efficacy vary among locations and years (6). We sequenced the complete genome of P. vagans C9-1 as a step toward elucidating genetic factors that modulate performance reliability.Genomic DNA, isolated using the Wizard genomic DNA purification kit (Promega, Madison, WI) was whole-genome shot-gun sequenced by 454 Life Sciences (Branford, CT) with four runs on a GS-20 sequencer. This resulted in 1,224,924 high-quality filtered reads with an average read length of 97 bp and coverage equivalent to 25 times. Quality filtered sequences were assembled in silico using the 454 Newbler assembler giving 207 contigs, 43 contigs larger than 500 bp. Gap closure and repetitive element sequencing were achieved by PCR walking using the Sanger method on a 3130XL sequencer (Applied Biosystems, Rotkreuz, Switzerland). Final assembly and sequence manipulations were done using the Lasergene package v8.1 (DNASTAR, Madison, WI).The P. vagans C9-1 genome has a 4,025-Mb circular chromosome and three circular plasmids (pPag1 [167,983 bp], pPag2 [165,692 bp], and pPag3 [529,676 bp]). A total of 4,619 coding sequences were predicted (8) using GLIMMER (11) and CRITICA (1). Putative functions of protein-encoding genes were automatically assigned using the GenDB annotation pipeline (9) and manually optimized. The chromosome harbors 7 rRNA operons and 78 tRNAs over the chromosome.The P. vagans C9-1 genome has four large regions containing phage-related genes. Bordering regions could not be identified explicitly (e.g., one phage region is flanked by a tRNA Met[AttL] and an AttR region, while others were on the other side of AttR). Transposon-related genes were largely absent, but small genomic islands were observed. Only plasmid pPag2 contains remnants of transposases and recombinases, including an inactivated ISEhe3 and ISEhe4, related to those on pPATH pag in P. agglomerans pv. gypsophilae 824-1 (4).The P. vagans C9-1 genome contains a repertoire of carbohydrate metabolic pathways identified using the KEGG databases (7). Important biosynthetic genes for antibacterial metabolites (i.e., pantocin A and dapdiamide E) and epiphytic fitness genes (e.g., autoinducer 1 [AI-1] quorum-sensing genes, in...
Xanthomonas arboricola pv. pruni is a quarantine bacterial pathogen that threatens peach production by causing necrotic spots on leaves and fruits, thus with the potential of severely reducing yields. The current understanding of the host plant defense responses to the pathogen is very limited. Using whole transcriptome sequencing, differential gene expression was analyzed at two time points, 2 h and 12 h post inoculation (hpi), by comparing the inoculated samples to their respective controls. On the total of 19,781 known peach genes that were expressed in all time points and conditions, 34 and 263 were differentially expressed at 2 and 12 hpi, respectively. Of those, 82% and 40% were up-regulated, respectively; and 18% and 60% were down-regulated, respectively. The functional annotation based on gene ontology (GO) analysis highlighted that genes involved in metabolic process and response to stress were particularly represented at 2 hpi whereas at 12 hpi cellular and metabolic processes were the categories with the highest number of genes differentially expressed. Of particular interest among the differentially expressed genes identified were several pathogen-associated molecular pattern (PAMP) receptors, disease resistance genes including several RPM1-like and pathogenesis related thaumatin encoding genes. Other genes involved in photosynthesis, in cell wall reorganization, in hormone signaling pathways or encoding cytochrome were also differentially expressed. In addition, novel transcripts were identified, providing another basis for further characterization of plant defense-related genes. Overall, this study gives a first insight of the peach defense mechanisms during the very early stages of infection with a bacterial disease in the case of a compatible interaction.
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