Origins of the Xylella fastidiosa Prophage-Like Regions and Their Impact in Genome Differentiation

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.

Natural Competence Rates Are Variable Among Xylella fastidiosa Strains and Homologous Recombination Occurs In Vitro Between Subspecies fastidiosa and multiplex

“…X. fastidiosa genomes contain high levels of phage and phage-like regions (de Mello Varani et al 2008;Nunes et al 2003;Van Sluys et al 2003), and natural competence could be a mechanism to help cells eliminate new integration of these regions by recombining the homologous DNA without phage sequences, as suggested by a recent study (Croucher et al 2016). Other studies have reported restriction-modification (R-M) systems limiting transformation frequency (Niza et al 2016).…”

Genomic and Biological Analysis of Phage Xfas53 and Related Prophages of Xylella fastidiosa

“…One conclusion from these analyses is that phage may have played a significant role in the evolution of X. fastidiosa (19,44,53). Phage-related sequences make up between 9% and 15% of the Xylella genomes, and 47 phage elements were identified in four genomes (18). Many strain-specific differences are located in prophage (18).…”

“…Phage-related sequences make up between 9% and 15% of the Xylella genomes, and 47 phage elements were identified in four genomes (18). Many strain-specific differences are located in prophage (18). Most of the prophage elements appeared to be the result of independent insertion events, implying that active phages are frequently encountered.…”

“…Most of the prophage elements appeared to be the result of independent insertion events, implying that active phages are frequently encountered. However, most insertions occur in a common 900-kb region and were associated with large genomic rearrangements (18). Whether the prophages are directly responsible for rearrangements or whether sites prone to recombination are also prone to phage integration is not known.…”

“…Presumptive podophage particles were observed by electron microscopy in ultrathin sections of strain Temecula (13). The majority of prophage sequences were reported to be structural genes for siphophage assembly, and putative siphophage were also observed in an unidentified strain (18). Like many bacteria, the polylysogenic status of X. fastidiosa implies that each strain may produce more than one type of phage.…”