Master thesis proposal - Paula Duque (ICG) and Ana Margarida Fortes (BioISI)

Submitted by bioisidirector… on Fri, 03/17/2017 - 12:13

Ana Margarida Fortes and her team are applying functional genomics to the study of grape ripening and biotic stress responses in grapevine. They are using transcriptomic, metabolomic and transgenic approaches to understand biotic stress response in wine grape together with the investigation of the promoters of the genes involved in resistance. They are also interested in the identification of regulatory or structural genes controlling grape development and ripening as a way to improve grape quality traits. The main focus is to establish regulatory networks and creating models of fruit ripening and fruit response against pathogens. This topic has been mostly studied in vegetative tissues so the study of the neglected fruits will open an important window of opportunities for innovative applications.

Master thesis proposal

Alternative splicing in grapevine: Genome-wide characterization and expression analyses of SR proteins during development and stress responses

Supervisor: Paula Duque, Instituto Gulbenkian de Ciência, Oeiras; email: duquep@igc.gulbenkian.pt

Co-supervisor: Ana Margarida Fortes, BIOISI, FCUL, Lisboa; email: amfortes@fc.ul.pt

Serine/arginine-rich (SR) proteins are highly conserved RNA-binding proteins that play crucial roles in the execution and regulation of pre-mRNA splicing. In particular, they are established modulators of alternative splicing, a posttranscriptional mechanism that generates transcriptome diversity and functional complexity in higher eukaryotes. In the plant model Arabidopsis thaliana, both the expression and splicing patterns of SR protein genes are controlled in a temporal and spatial manner, with genetics studies revealing in vivo roles during development and stress responses1-3. By contrast, knowledge of SR proteins in grapevine, a major crop worldwide, is extremely limited but recent data indicate differential expression of genes coding for these splicing factors during grape ripening and in response to fungal infection4,5.

In the frame of this Master thesis, the student will conduct an in-depth characterization of grapevine SR proteins, aiming at the identification of all SR protein genes in the fully-sequenced grapevine genome. Using data available in the grapevine databases as well as RT-qPCR, a study of SR gene structure and promoters will be followed by phylogenetic analysis and expression analyses in several tissues, developmental processes and stress conditions. Finally, expression and coexpression data will be combined with phylogenetic/orthology analyses to pinpoint key candidate SR protein genes involved in grape ripening and biotic stress responses. For these genes, alternative splicing patterns will be analyzed using RT-PCR.

This project will contribute to the understanding of how alternative splicing enhances transcriptome complexity in grapevine in particular during development and stress responses.

 

Relevant Publications:

1. Carvalho et al. (2010) Plant Physiol 154, 772-783.

2. Carvalho et al. (2016) Plant Cell 28, 1910-1925.

3. Palusa et al. (2007) Plant J 49, 1091-1107.

4. Agudelo-Romero et al. (2015) J Exp Bot 66, 1769-1785.

5. Fortes et al. (2011) BMC Plant Biol 11, 149.