title: Transcription profiling of signal transduction-related genes in sugarcane tissues.
abstract: A collection of 237,954 sugarcane ESTs was examined in search of signal transduction genes. Over 3500 components involved in several aspects of signal transduction, transcription, development, cell cycle, stress responses and pathogen interaction were compiled into the Sugarcane Signal Transduction (SUCAST) Catalogue. Sequence comparisons and protein domain analysis revealed 477 receptors, 510 protein kinases, 107 protein phosphatases, 75 small GTPases, 17 G-proteins, 114 calcium and inositol metabolism proteins, and over 600 transcription factors. The elements were distributed into 29 main categories subdivided into 409 sub-categories. Genes with no matches in the public databases and of unknown function were also catalogued. A cDNA microarray was constructed to profile individual variation of plants cultivated in the field and transcript abundance in six plant organs (flowers, roots, leaves, lateral buds, and 1st and 4th internodes). From 1280 distinct elements analyzed, 217 (17%) presented differential expression in two biological samples of at least one of the tissues tested. A total of 153 genes (12%) presented highly similar expression levels in all tissues. A virtual profile matrix was constructed and the expression profiles were validated by real-time PCR. The expression data presented can aid in assigning function for the sugarcane genes and be useful for promoter characterization of this and other economically important grasses.
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748 05508-900, São Paulo, Brasil.
authors.forename: Flávia Stal
authors.initials: FS
authors.lastname: Papini-Terzi
authors.forename: Flávia Riso
authors.initials: FR
authors.lastname: Rocha
authors.forename: Ricardo Zorzetto Nicoliello
authors.initials: RZ
authors.lastname: Vêncio
authors.forename: Kátia Cristina
authors.initials: KC
authors.lastname: Oliveira
authors.forename: Juliana de Maria
authors.initials: Jde M
authors.lastname: Felix
authors.forename: Renato
authors.initials: R
authors.lastname: Vicentini
authors.forename: Cristiane de Souza
authors.initials: Cde S
authors.lastname: Rocha
authors.forename: Ana Carolina Quirino
authors.initials: AC
authors.lastname: Simões
authors.forename: Eugênio César
authors.initials: EC
authors.lastname: Ulian
authors.forename: Sônia Marli Zingaretti
authors.initials: SM
authors.lastname: di Mauro
authors.forename: Aline Maria
authors.initials: AM
authors.lastname: da Silva
authors.forename: Carlos Alberto de Bragança
authors.initials: CA
authors.lastname: Pereira
authors.forename: Marcelo
authors.initials: M
authors.lastname: Menossi
authors.forename: Gláucia Mendes
authors.initials: GM
authors.lastname: Souza
mesh_terms: D019295:Computational Biology; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D046228:Microarray Analysis; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D031786:Saccharum / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics*; D013045:Species Specificity; D014158:Transcription, Genetic