Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation.
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.
de Mello Varani
Alessandro
A
Genome and Transposable Elements Laboratory (GaTE Lab), Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
Souza
Rangel Celso
RC
Nakaya
Helder I
HI
de Lima
Wanessa Cristina
WC
Paula de Almeida
Luiz Gonzaga
LG
Kitajima
Elliot Watanabe
EW
Chen
Jianchi
J
Civerolo
Edwin
E
Vasconcelos
Ana Tereza Ribeiro
AT
Van Sluys
Marie-Anne
MA
D019143:Evolution, Molecular; D005798:Genes, Bacterial; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D016679:Genome, Viral / Q000235:genetics*; D019426:Integrases / Q000378:metabolism; D046529:Microscopy, Electron, Transmission; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D039002:Prophages / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism; D044167:Xylella / Q000145:classification / Q000235:genetics* / Q000254:growth & development
D012343:RNA, Transfer; D019426:Integrases