Sugarcane Promoters

The Project

We aim to identify sugarcane ESTs with tissue/organ specific expression or that are stress-induced for subsequent promoter isolation and characterization. We are using in silico analyses, cDNA microarrays to select candidate ESTs and RT-PCR to confirm expression specificity. The sequences of the validated ESTs will be used to design primers for further promoter identification and cloning using a genome-walking strategy. Future studies will involve the functional characterization of these promoters. This knowledge will allow us to exploit these regulatory sequences in sugarcane biotechnology.

The SUCAST Chips

The Project

cDNA microarrays are used to monitor genome activity and to associate function to new genes. The SUCAST arrays are produced in the CAGE Lab and are currently being used to profile sugarcane tissues, to identify differentially expressed genes in plants treated with phytohormones and submitted to stresses, and to point to molecular markers that may aid in improvement of sugarcane varieties. Differential expression also points to promoters that may aid in the construction of suitable sugarcane expression vectors.

SUCAST - Sugarcane Signal Transduction

Identification of Signal Transduction Components of the Sugarcane Genome

The goal of this project is to identify ESTs for signal transduction components in the sugarcane genome. The analysis will be a a collaboration between Dr. Glaucia Mendes Souza and Dr. Aline Maria da Silva's laboratories, where research in several aspects of signal transduction of growth and development is currently underway. Special attention will be given to conserved modules found to be regulators of developmental processes in other systems (receptors, G-proteins, cyclases, kinases, phosphatases, lipid metabolism components, Ca2+ metabolism components, proteases and peptidases, to mention a few). In particular, the databank will be analysed for the presence of pathways where similarities to confirmed signal transduction elements in the Arabdopsis and rice genomes are found. It has been estimated that 54% of higher plant genes can be assigned some degree of function by comparing them to known genes. On the basis of sequence analysis, it has been inferred that 13% of Arabdopsis genes are involved in transcription or signal transduction. Although annotation alone will not provide ultimate confirmation of the participation of a particular gene in a process it lays the ground where functional genomics can be built on.

Please send any requests or problem reports to the bioinformatics team (This email address is being protected from spambots. You need JavaScript enabled to view it.).

The SUCAST Catalogue

The Project

The SUCAST Catalogue contains over 3500 components, with around 2900 involved in several aspects of cell signalling and transcription. Extensive annotation, sequence comparisons and conserved protein domain analysis were used to cathegorize receptors, protein kinases, protein phosphatases, small GTPases, G-proteins, calcium and inositol metabolism proteins and other signal transductio-related proteins. Over 600 transcription factors were also indexed. Whenever possible the components were linked to putative pathways. The characterization of their expression profile in the different sugarcane tissues and in plants submitted to biotic and abiotic stress is underway.

Please send any requests or problem reports to the bioinformatics team (This email address is being protected from spambots. You need JavaScript enabled to view it.).