Putative Vitis vinifera Rop- and Rab-GAP-, GEF-, and GDI-interacting proteins uncovered with novel methods for public genomic and EST database analysis.
To understand how grapevine Rop and Rab proteins achieve their functional versatility in signalling, identification of the putative VvRop- and VvRab-interacting proteins was performed using newly designed tools. In this study, sequences encoding eight full-length proteins for VvRop GTPase-activating proteins (GAPs), five for VvRabGAPs, six for VvRop guanine nucleotide exchange factors (GEFs), one for VvRabGEF, five for VvRop GDP dissociation inhibitors (GDIs), and three for VvRabGDIs were identified. These proteins had a CRIB motif or PH domain, a TBC domain, a PRONE domain, a DENN domain, or GDI signatures, respectively. By bootstrap analysis, an unrooted consensus phylogenetic tree was constructed which indicated that VvRopGDIs and VvRopGEFs--but not VvRopGAP--belonged to the same clade, and that VvRabGEF1 protein was more closely related to VvRopGAPs than to the other putative VvRab-interacting proteins. Twenty-two genes out of 28 encoding putative VvRop- and VvRab-interacting proteins could be located on identified grapevine chromosomes. Generally one gene was anchored on one chromosome, but in some cases up to four genes were located on the same chromosome. Expression patterns of the genes encoding putative VvRop- and VvRab-interacting proteins were also examined using a newly developed tool based on public expressed sequence tag (EST) database analysis. Expression patterns were sometimes found to be specific to an organ or a developmental stage. Although some limitations exist, the use of EST database analysis is stressed, in particular in the case of species where expression data are obtained at high costs in terms of time and effort.
Abbal
Philippe
P
UMR 1083, Sciences pour l'OEnologie, INRA, 2 Place Viala, F-34060 Montpellier, France.
Tesniere
Catherine
C
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020690:GTPase-Activating Proteins / Q000737:chemistry / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D020730:Guanine Nucleotide Dissociation Inhibitors / Q000737:chemistry / Q000378:metabolism; D020662:Guanine Nucleotide Exchange Factors / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D027843:Vitis / Q000235:genetics / Q000378:metabolism*; D020691:rab GTP-Binding Proteins / Q000737:chemistry / Q000378:metabolism
D020690:GTPase-Activating Proteins; D020730:Guanine Nucleotide Dissociation Inhibitors; D020662:Guanine Nucleotide Exchange Factors; D010940:Plant Proteins; D020691:rab GTP-Binding Proteins