Dicty News Electronic Edition Volume 24, number 3 February 18, 2005 Please submit abstracts of your papers as soon as they have been accepted for publication by sending them to dicty@northwestern.edu or by using the form at http://dictybase.org/db/cgi-bin/dictyBase/abstract_submit. Back issues of Dicty-News, the Dicty Reference database and other useful information is available at dictyBase - http://dictybase.org. ============= Abstracts ============= Loss of the Dictyostelium RasC protein alters vegetative cell size, motility and endocytosis. Chinten James Lim , Karl A. Zawadzkià, Meenal Khosla, David M. Secko, George B. Spiegelman and Gerald Weeks. Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T1Z3 Canada. Exp. Cell Res., in press In addition to its previously established roles in cAMP relay and cAMP chemotaxis, loss of signal transduction through the RasC protein was found to impact a number of vegetative cell functions. Vegetative rasC- cells exhibited reduced random motility, were less polarized and had aberrant F-actin distribution. Cells lacking RasC also contained more protein and were larger in size than wildtype cells. These increases were associated with increased liquid phase endocytosis. Despite the increase in cell size, cytokinesis was relatively normal and there was no change in the rate of cell division. rasC- cells also chemotaxed poorly to folate and exhibited reduced F-actin accumulation, reduced ERK2 phosphorylation and reduced Akt/PKB phosphorylation in response to folate, indicating that RasC was also involved in transducing chemotactic signals in vegetative cells. Submitted by: Gerry Weeks [gerwee@interchange.ubc.ca] ----------------------------------------------------------------------------- Epistasis analysis with global transcriptional phenotypes Nancy Van Driessche, Janez Demsar, Ezgi O. Booth, Paul Hill, Peter Juvan, Blaz Zupan, Adam Kuspa and Gad Shaulsky Baylor College of Medicine, Houston, TX, USA and University of Ljubljana, Ljubljana, Slovenia. Nature Genetics, in press Classical epistasis analysis can determine the order of function of genes in pathways using morphological, biochemical and other such phenotypes. It requires knowledge of the pathwayâs phenotypic output and a variety of experimental expertise, so it is unsuitable for genome-scale analysis. Here we show the utility of microarray profiles of mutants as phenotypes for epistasis analysis. Considering genes that regulate Dictyostelium protein kinase A activity, we determine known and unknown epistatic relationships and reconstruct a genetic network with microarray phenotypes alone. This work demonstrates that microarray data can provide a uniform, quantitative tool for large-scale genetic network analysis. Submitted by: Gad Shaulsky [gadi@bcm.tmc.edu] ----------------------------------------------------------------------------- A comparative sequence analysis reveals a common GBD/FH3-FH1-FH2-DAD architecture in formins from Dictyostelium, fungi and metazoa. Francisco Rivero(1), Tetsuya Muramoto(3), Ann-Kathrin Meyer(1), Hideko Urushihara(3), Taro Q. P. Uyeda(2), Chikako Kitayama(2) 1. Center for Biochemistry and Center for Molecular Medicine, Medical Faculty, University of Cologne. Joseph-Stelzmann-Strasse 52, 50931 Kšln, Germany 2. Gene Function Research Center, Tsukuba Central #4 National Institute of Advanced Industrial Science and Technology (AIST) Higashi 1-1-1 Tsukuba-shi, Ibaraki 305-8562, Japan 3. Institute of Biological Science, University of Tsukuba, Tsukuba-shi, Ibaraki 305-8572, Japan BMC Genomics, in press Background Formins are multidomain proteins defined by a conserved FH2 (formin homology 2) domain with actin nucleation activity preceded by a proline-rich FH1 domain. Formins act as profilin-modulated processive actin nucleators conserved throughout a wide range of eukaryotes. Results We present a detailed sequence analysis of the 10 formins (ForA to J) identified in the genome of the social amoeba Dictyostelium discoideum. With the exception of ForI and ForC all other formins conform to the domain structure GBD/FH3-FH1-FH2-DAD, where DAD is the Diaphanous autoinhibition domain and GBD/FH3 is the Rho GTPase-binding domain/formin homology 3 domain that we propose to represent a single domain. ForC lacks an FH1 domain, ForI lacks recognizable GBD/FH3 and DAD domains and ForA, E and J have additional unique domains. To establish the relationship between formins of Dictyostelium and other organisms we constructed a phylogenetic tree based on the alignment of FH2 domains. Real-time PCR was used to study the expression pattern of formin genes. Expression of forC, D, I and J increased during transition to multi-cellular stages, while the rest of genes displayed less marked developmental variations. During sexual development, expression of forH and forI displayed a significant increase in fusion competent cells. Conclusions Our analysis allows some preliminary insight into the functionality of Dictyostelium formins: all isoforms might display actin nucleation activity and, with the exception of ForI, might also be susceptible to autoinhibition and to regulation by Rho GTPases. The architecture GBD/FH3-FH1-FH2-DAD appears common to almost all Dictyostelium, fungal and metazoan formins, for which we propose the denomination of conventional formins, and implies a common regulatory mechanism. Submitted by: Francisco Rivero [francisco.rivero@uni-koeln.de] ============================================================================== [End Dicty News, volume 24, number 3]