Abstract
Xylella fastidiosa is a Gram negative plant pathogen causing many economically important diseases, and analyses of completely sequenced X. fastidiosa genome strains allowed the identification of many prophage-like elements and possibly phage remnants, accounting for up to 15% of the genome composition. To better evaluate the recent evolution of the X. fastidiosa chromosome backbone among distinct pathovars, the number and location of prophage-like regions on two finished genomes (9a5c and Temecula1), and in two candidate molecules (Ann1 and Dixon) were assessed. Based on comparative best bidirectional hit analyses, the majority (51%) of the predicted genes in the X. fastidiosa prophage-like regions are related to structural phage genes belonging to the Siphoviridae family. Electron micrograph reveals the existence of putative viral particles with similar morphology to lambda phages in the bacterial cell in planta. Moreover, analysis of microarray data indicates that 9a5c strain cultivated under stress conditions presents enhanced expression of phage anti-repressor genes, suggesting switches from lysogenic to lytic cycle of phages under stress-induced situations. Furthermore, virulence-associated proteins and toxins are found within these prophage-like elements, thus suggesting an important role in host adaptation. Finally, clustering analyses of phage integrase genes based on multiple alignment patterns reveal they group in five lineages, all possessing a tyrosine recombinase catalytic domain, and phylogenetically close to other integrases found in phages that are genetic mosaics and able to perform generalized and specialized transduction. Integration sites and tRNA association is also evidenced. In summary, we present comparative and experimental evidence supporting the association and contribution of phage activity on the differentiation of Xylella genomes.
Highlights
Xylella fastidiosa is a gram-negative gamma-proteobacterium known to cause several economically important diseases in cultivated crops and many other plant species
A specific strategy to resolve the assembly of phage-related regions was developed which generated candidate molecules for each strain, making possible the identification of prophage-like elements and phage remnants In the same way, identification of all predicted integrase genes and prophage-like regions were carried in Xf-CVC 9a5c and Xf-PD Temecula strain genomes
All four X. fastidiosa genomes were scanned for the presence of predicted integrases associated to clusters of genes related to phages
Summary
Xylella fastidiosa is a gram-negative gamma-proteobacterium known to cause several economically important diseases in cultivated crops and many other plant species. The strain 9a5c (Xf-CVC) was the first plant pathogen whose genome was completely sequenced [1]. Previous studies demonstrated that 98% of the Xf-PD genes are shared with Xf-CVC, with an average amino acid identity (considering only the coding regions) of 95.7%, and the main differences are from bacteriophage-derived regions. These bacteriophage-derived regions are responsible for chromosomal rearrangements and deletions in X. fastidiosa strains, playing a decisive role on the genome evolution of this plant pathogen [1,3]
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