Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation

Authors: DE MELLO VARANI, ALLESSANDRO - UNIV SAO PAULO, BRAZIL; SOUZA, RANGEL - NATL LAB SCI COMPUT,BRZ; NAKAYA, HELDER - UNIV SAO PAULO, BRAZIL; DE LIMA, WANESSA - UNIV SAO PAULO, BRAZIL; DE ALMEIDA, LUIZ PAULA - NATL LAB SCI COMPUT,BRZ; KITAJIMA, ELILIOT - UNIC SAO PAULO, BRAZIL; Chen, Jianchi; Civerolo, Edwin; VASCONCELOS, ANA - NATL LAB SCI COMPUT,BRZ; VAN SLUYS, MARIE-ANNE - UNIV SAO PAULO, BRAZIL

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/20/2008
Publication Date: 12/31/2008
Citation: De Mello Varani, A., Souza, R., Nakaya, H., De Lima, W., De Almeida, L., Kitajima, E., Chen, J., Civerolo, E.L., Vasconcelos, A., Van Sluys, M. 2008. Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. PLoS One. 3(12):e4059. doi:10.1371/journal.pone.0004059.

Interpretive Summary: Xylella fastidiosa is a plant pathogen that causes many economically important diseases. Analyses of completely sequenced X. fastidiosa genomes showed sequences of phages, or bacterial viruses, account for up to 15 percent of the genome composition. We analyzed the sequences of these phages with respect to their relationships to pathogenicity and host-pathogen interactions. Microarray data indicate that X. fastidiosa cultivated under stress conditions can switch from the lysogenic stage (phage sequence incorporated into bacterial chromosome) to the lytic stage (phage sequence detached from bacterial chromosome). Several genes of virulence-associated proteins and toxins were found within phage elements. Finally, all of the X. fastidiosa phages were grouped into five clusters. We present comparative and experimental evidence supporting the association between phage activity and X. fastidiosa gene expression under stress conditions. The significance of this work is that manipulation of X. fastidiosa phage gene expression is a potential means to mitigate disease development.

Technical 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. Moreover, it is found virulence- associated proteins and toxins 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.