Microarray Analyses of Xylella fastidiosa Provide Evidence of Coordinated Transcription Control of Laterally Transferred Elements

Abstract

Genetically distinct strains of the plant bacterium Xylella fastidiosa (Xf) are responsible for a variety of plant diseases, accounting for severe economic damage throughout the world. Using as a reference the genome of Xf 9a5c strain, associated with citrus variegated chlorosis (CVC), we developed a microarray-based comparison involving 12 Xf isolates, providing a thorough assessment of the variation in genomic composition across the group. Our results demonstrate that Xf displays one of the largest flexible gene pools characterized to date, with several horizontally acquired elements, such as prophages, plasmids, and genomic islands (GIs), which contribute up to 18% of the final genome. Transcriptome analysis of bacteria grown under different conditions shows that most of these elements are transcriptionally active, and their expression can be influenced in a coordinated manner by environmental stimuli. Finally, evaluation of the genetic composition of these laterally transferred elements identified differences that may help to explain the adaptability of Xf strains to infect such a wide range of plant species

Genomic Insights into Xylella fastidiosa Interactions with Plant and Insect Hosts

“…The prevalence of prophages and phage remnants within X. fastidiosa genomes contrasts with the absence of identifiable transposons, which are abundant in Xanthomonas genomes (Monteiro-Vitorello et al 2005). Prophages are also candidates for inducing rearrangements within the X. fastidiosa genome, due to the activity of their integrase genes (Moreira et al 2005;Nunes et al 2003).…”

“…However, as discussed later, the distribution of individual subspecies is more limited, suggesting that geographical isolation has been important in the evolution of this bacterium. Furthermore, as with grapevine isolates in Taiwan, evidence indicates that at least some isolates causing disease in plum in Brazil originated from North America (Nunes et al 2003) and that grapevine isolates in the United States originated from Central America (Nunney et al 2010). Therefore, X. fastidiosa populations appeared to have remained largely isolated due to geographical barriers, but recent human activity has resulted in dispersal over continental distances.…”

“…The availability of novel loci and alleles can result in the emergence of epidemic isolates that have the potential to exploit host plants previously not susceptible to disease as a result of X. fastidiosa infection. Although not conclusively demonstrated, independent studies have suggested that X. fastidiosa diseases can emerge via gene exchange between isolates (Almeida et al 2008;Nunes et al 2003;Nunney et al 2012). Therefore, increases in genetic diversity, driven by the introduction of foreign genotypes, carry risks that go beyond the potential host range of the newly arrived isolate.…”

“…Among subspecies, it is evident that X. fastidiosa's flexible genome is primarily composed of laterally transferred phage-like elements, including prophages (Nunes et al 2003;van Sluys et al 2003;Varani et al 2008).…”

“…These contribute to the gene diversity of X. fastidiosa and provide potential avenues for horizontal gene transfer (HGT) both within and between species. Due to the ability of HGT to confer new phenotypes on Venn diagram for the number of predicted coding sequences that are shared and unique from representative genomes of subspecies multiplex, fastidiosa, and pauca calculated with EDGAR (Blom et al 2009), using a protein-protein BLAST e-value cutoff of 10 -6 and 70 % amino acid identity bacteria and modify their ecological niche, there is intense interest in exploring the contribution of these elements to the distinct virulence traits of different isolates, including the ability to colonize novel host plants (Moreira et al 2005;Nunes et al 2003).…”