Comparative and evolutionary analysis of genes encoding small GTPases and their activating proteins in eukaryotic genomes

RasGAPs: a crucial regulator of extracellular stimuli for homeostasis of cellular functions

Ras and its GTPase activating proteins (GAPs) are among the crucial regulators of extracelluar ligands. Information about these regulators has been elucidated during the course of studies in signal transduction over the last two decades. RasGAPs such as p120GAP and neurofibromin have been studied extensively for their roles as either "negative" regulators or effectors of Ras. Accumulating evidence suggests that these molecules are crucial regulators of extracellular stimuli that serve to maintain the homeostasis of cellular functions. This compendium highlights cellular functions of RasGAPs and their signaling characteristics from the viewpoint of homeostasis, including our recent finding of the phenotype of R-RasGAP mutant mice whose GAP activity is down-regulated.

Comparative transcriptional profiling and evolutionary analysis of the GRAM domain family in eukaryotes

The GRAM domain was found in glucosyltransferases, myotubularins and other membrane-associated proteins. So far, functions for majority of these proteins are yet to be uncovered. In order to address the evolutionary and functional significance of this family members, we have performed a comprehensive investigation on their genome-wide identification, phylogenetic relationship and expression divergence in five different organisms representing monocot/dicot plants, vertebrate/invertebrate animals and yeast, namely, Oryza sativa, Arabidopsis thaliana, Mus musculus, Drosophila melanogaster and Saccharomyces cerevisiae, respectively. We have identified 65 members of GRAM domain family from these organisms. Our data revealed that this family was an ancient group and various organisms had evolved into different family sizes. Large-scale genome duplication and divergence in both expression patterns and functions were significantly contributed to the expansion and retention of this family. Mouse and Drosophila members showed higher divergences in their proteins as indicated by higher Ka/Ks ratios and possessed multiple domains in various combinations. However, in plants, their protein functions were possibly retained with a relatively low divergence as signified by lower Ka/Ks ratios and only one additional domain was combined during evolution. On the other hand, this family in all five organisms exhibited high divergence in their expression patterns both at tissue level and under various biotic and abiotic stresses. These highly divergent expression patterns unraveled the complexity of functions of GRAM domain family. Each member may play specialized roles in a specific tissue or stress condition and may function as regulators of environmental and hormonal signaling.

Multiple domain insertions and losses in the evolution of the Rab prenylation complex

BACKGROUND

Rab proteins are regulators of vesicular trafficking, requiring a lipid modification for proper function, prenylation of C-terminal cysteines. This is catalysed by a complex of a catalytic heterodimer (Rab Geranylgeranyl Transferase - RabGGTase) and an accessory protein (Rab Escort Protein. REP). Components of this complex display domain insertions relative to paralogous proteins. The function of these inserted domains is unclear.

RESULTS

We profiled the domain architecture of the components of the Rab prenylation complex in evolution. We identified the orthologues of the components of the Rab prenylation machinery in 43 organisms, representing the crown eukaryotic groups. We characterize in detail the domain structure of all these components and the phylogenetic relationships between the individual domains.

CONCLUSION

We found different domain insertions in different taxa, in alpha-subunits of RGGTase and REP. Our results suggest that there were multiple insertions, expansions and contractions in the evolution of this prenylation complex.

Perinuclear and nuclear envelope localizations of Arabidopsis Ran proteins

Using phragmoplastin-interacting protein 1 (PhrIP1) as bait, we isolated an Arabidopsis cDNA encoding Ran2, a small Ras-like GTP-binding protein. The interaction between PhrIP1 and Ran2 was confirmed by an in vitro protein-protein interaction assay with purified Ran2 and PhrIP1. The plant Ran2 shares high sequence homology, 78 and 86% at the amino acid level, with human Ran/TC4 and C. elegans Ran, respectively. Our results obtained from enzyme assays and Western blot analysis show that Ran2 has intrinsic GTPase activity and is present in the soluble fraction of Arabidopsis seedling extract. Fluorescent microscopy using anti-Ran2 antibody revealed that the Ran protein is localized in the perinuclear region with the highest concentration at the nuclear envelope. In contrast to its animal counterparts that are present in the nucleoplasm, the Ran protein is absent inside the nucleus. These results suggest that plant Ran proteins may be involved in mediation of nucleocytoplasmic transport and assembly of the nuclear envelope after karyokinesis in plant cells.

Ras-like small GTPases form a large family of proteins in the marine sponge Suberites domuncula

Sponges (Porifera) are the simplest and the most ancient metazoan animals, which branched off first from the common ancestor of all multicellular animals. We have inspected approximately 13,000 partial cDNA sequences (ESTs) from the marine sponge Suberites domuncula and have identified full or partial cDNA sequences coding for approximately 50 different Ras-like small GTPases. Forty-four sponge proteins from the Ras family are described here: 6 proteins from the Ras subfamily, 5 from Rho, 6 from Arf, 1 Ran, and 26 Rabs or Rab-like proteins. No isoforms of these proteins were detected; the closest related proteins are two Rho proteins with 74% identity. Small GTPases from sponge display a higher degree of sequence conservation with orthologues from vertebrates (53%-93% identity) than with those from either Caenorhabditis elegans or Drosophila melanogaster. The real number of small GTPases in this sponge is certainly much higher than 50, because the actual S. domuncula database of approximately 13,000 ESTs contains at most 3000 nonredundant cDNA sequences. The number of genes for Ras-like small GTPases in yeast, C. elegans, D. melanogaster, and humans is 30, 56, 90, and 174, respectively. Both model invertebrates have only 29 Rabs or Rab-like proteins, compared with 26 already found in sponge, and are missing at least 1 Rab (Rab24) present in S. domuncula and mammals. Our results indicate that duplications and diversifications of genes encoding Ras-like small GTPases, especially the Rab subfamily of small GTPases, happened very early in the evolution of Metazoa.

Ras oncogenes and their downstream targets

RAS proteins are small GTPases, which serve as master regulators of a myriad of signaling cascades involved in highly diverse cellular processes. RAS oncogenes have been originally discovered as retroviral oncogenes, and ever since constitutively activating RAS mutations have been identified in human tumors, they are in the focus of intense research. In this review, we summarize the biochemical properties of RAS proteins, trace down the evolution of RAS signaling and present an overview of the spatio-temporal activation of major RAS isoforms. We further discuss RAS effector pathways, their role in normal and transformed cell physiology and summarize ongoing attempts to interfere with aberrant RAS signaling. Finally, we comment on the role of micro RNAs in modulating RAS expression, contribution of RAS to stem cell function and on high-throughput analyses of RAS signaling networks.

Molecular characterization and expression analysis of the Rop GTPase family in Vitis vinifera

Rop/Rac GTPases are plant-specific signalling proteins with multiple roles, some of which have implications in plant development and in hormone signal transduction. Using expressed sequence tag (EST) and gene database analyses, members of the Rop family were characterized for the first time in a perennial species (Vitis vinifera). The grapevine genome was found to contain seven expressed VvRops. The phylogenetic analyses indicated that VvRops could be distributed into four groups, as described in the literature for model plants. Genetic mapping was successfully performed for five VvRops, which were localized on independent linkage groups. Conserved and divergent regions were identified on the protein sequences. The results of VvRop expression obtained by real-time quantitative reverse transcription-PCR analyses indicated that all the organs investigated displayed VvRop expression, however with different patterns. Whereas no total organ specificity for VvRop expression could be evidenced, VvRop9 displayed high expression in developing berries only. During berry development, the transcript profile was generally similar for all the VvRops, i.e. displaying a peak early in the herbaceous phase followed by a decline towards veraison and thereafter. Western blotting gave a similar expression profile for VvRop proteins. Response to growth regulators was generally specific to each VvRop. The potential involvement of specific VvRops in grapevine development is discussed.

Rho GTPases and actin dynamics in membrane protrusions and vesicle trafficking

Rho GTPases are well known to regulate actin dynamics. They activate two types of actin nucleators, WASP/WAVE proteins and Diaphanous-related formins (DRFs), which induce different types of actin organization. Their ability to interact with membranes allows them to target actin polymerization to discrete sites on the plasma membrane and to intracellular membrane compartments and thereby induce membrane protrusions or regulate vesicle movement. Most studies have concentrated on just three of the 22 mammalian Rho proteins, RhoA, Rac1 and Cdc42. However, recent research indicates that several other members of the Rho family, including Rif, RhoD, TC10 and Wrch1, and also related Rho-of-plants proteins (ROPs) in plants, stimulate actin polymerization and affect plasma membrane protrusion and/or vesicular traffic.