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 compositi...
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2008
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oai:doaj.org-article:bb03036d41854751920db6e1cd36347f2021-11-25T06:17:55ZOrigins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation.1932-620310.1371/journal.pone.0004059https://doaj.org/article/bb03036d41854751920db6e1cd36347f2008-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19116666/?tool=EBIhttps://doaj.org/toc/1932-6203Xylella 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.Alessandro de Mello VaraniRangel Celso SouzaHelder I NakayaWanessa Cristina de LimaLuiz Gonzaga Paula de AlmeidaElliot Watanabe KitajimaJianchi ChenEdwin CiveroloAna Tereza Ribeiro VasconcelosMarie-Anne Van SluysPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 3, Iss 12, p e4059 (2008) |
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Medicine R Science Q Alessandro de Mello Varani Rangel Celso Souza Helder I Nakaya Wanessa Cristina de Lima Luiz Gonzaga Paula de Almeida Elliot Watanabe Kitajima Jianchi Chen Edwin Civerolo Ana Tereza Ribeiro Vasconcelos Marie-Anne Van Sluys Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. |
| description |
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. |
| format |
article |
| author |
Alessandro de Mello Varani Rangel Celso Souza Helder I Nakaya Wanessa Cristina de Lima Luiz Gonzaga Paula de Almeida Elliot Watanabe Kitajima Jianchi Chen Edwin Civerolo Ana Tereza Ribeiro Vasconcelos Marie-Anne Van Sluys |
| author_facet |
Alessandro de Mello Varani Rangel Celso Souza Helder I Nakaya Wanessa Cristina de Lima Luiz Gonzaga Paula de Almeida Elliot Watanabe Kitajima Jianchi Chen Edwin Civerolo Ana Tereza Ribeiro Vasconcelos Marie-Anne Van Sluys |
| author_sort |
Alessandro de Mello Varani |
| title |
Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. |
| title_short |
Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. |
| title_full |
Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. |
| title_fullStr |
Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. |
| title_full_unstemmed |
Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. |
| title_sort |
origins of the xylella fastidiosa prophage-like regions and their impact in genome differentiation. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2008 |
| url |
https://doaj.org/article/bb03036d41854751920db6e1cd36347f |
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