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| Author(s): |
Fernando Domingues Kümmel Tria
Total Authors: 1
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| Document type: | Master's Dissertation |
| Press: | São Paulo. |
| Institution: | Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI) |
| Defense date: | 2013-06-24 |
| Examining board members: |
Aline Maria da Silva;
Jose Miguel Ortega;
João Carlos Setubal
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| Advisor: | Aline Maria da Silva |
| Abstract | |
Xylella fastidiosa is a gram-negative, non-flagellated bacterium responsible for causing economically important diseases such as Pierce\'s disease in grapevines and Citrus Variegated Clorosis (CVC) in sweet orange trees. In the present work we performed in silico analysis on promoter sequences of protein-coding genes from this phytopathogen, including those involved in virulence and pathogenic mechanisms, in an attempt to better understand the underlying transcriptional regulatory dynamics. Two strategies for cis-regulatory elements prediction were applied on promoter sequences from 9a5c strain genome, a proven causal agent of CVC. The first one, known as phylogenetic footprinting, involved the prediction of regulatory motifs conserved on promoter sequences of orthologous transcription units from X. fastidiosa and a set of 7 comparatives species. The criteria to identify orthologous transcription units, i. e., those from different species and whose promoter sequences share at least one common regulatory motif, was studied based on regulatory information available for model organisms: Pseudomonas aeruginosa, Bacillus subtilis and Escherichia coli. The results obtained with the phylogenetic footprinting analysis permitted us to access the underlying transcriptional regulatory network from the species in a comprehensive manner (genome-wide), with a total of 2990 regulatory interactions corresponding to 80 predicted motifs distributed on promoter sequences of 56.8% of all transcription units. In the second strategy regulatory information from E. coli was recovered and used to expand the knowledge of ten regulons in X. fastidiosa, through a scanning process, of which some regulatory interactions were previously described by independent studies. We emphasize some genes related to host invasion and colonization present in the Fur and CRP regulons, two global transcription regulators. Lastly, comparative analysis on corresponding regulatory regions among strains were performed and differences possibly associated to phenotypic variation were identified between 9a5c and J1a12, a non-virulent strain isolated from orange trees, and between 9a5c and Temecula1, a strain associated to Pierce\'s disease on grapevines. (AU) | |
| FAPESP's process: | 10/03382-3 - In silico analysis on promoter sequences of protein-coding genes from Xylella fastidiosa |
| Grantee: | Fernando Domingues Kummel Tria |
| Support Opportunities: | Scholarships in Brazil - Master |