dictyNews Electronic Edition Volume 36, number 7 March 4, 2011 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 dictyNews, the Dicty Reference database and other useful information is available at dictyBase - http://dictybase.org. Follow dictyBase on twitter: http://twitter.com/dictybase ========= Abstracts ========= Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum Richard Sucgang1*, Alan Kuo2*, Xiangjun Tian3*, William Salerno1*, Anup Parikh4, Christa L. Feasley5, Eileen Dalin2, Hank Tu2, Eryong Huang4, Kerrie Barry2, Erika Lindquist2, Harris Shapiro2, David Bruce2, Jeremy Schmutz2, Asaf Salamov2, Petra Fey6, Pascale Gaudet6, Christophe Anjard7, M. Madan Babu8, Siddhartha Basu6, Yulia Bushmanova6, Hanke van der Wel5, Mariko Katoh-Kurasawa4, Christopher Dinh1, Pedro M. Coutinho9, Tamao Saito10, Marek Elias11, Pauline Schaap12, Robert R. Kay8, Bernard Henrissat9, Ludwig Eichinger13, Francisco Rivero14, Nicholas H. Putnam3, Christopher M. West5, William F. Loomis7, Rex L. Chisholm6, Gad Shaulsky3,4, Joan E. Strassmann3, David C. Queller3, Adam Kuspa1,3,4, , and Igor V. Grigoriev2 1Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 2U.S. Department of Energy Joint Genome Institute, Walnut Creek CA 3Department of Ecology and Evolutionary Biology, Rice University, Houston, TX 77005; 4Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 5Department of Biochemistry & Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104 6dictyBase, Center for Genetic Medicine, Northwestern University, 750 N Lake Shore Drive, Chicago, Illinois 60611 7Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, California 92093 8Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK 9Architecture et Fonction des Macromolˇcules Biologiques, UMR6098, CNRS, Universities of Aix-Marseille I & II, 13288 Marseille, France 10Department of Materials and Life Sciences, Sophia University 7-1 Kioi-Cho, Chiyoda-Ku, Tokyo, Japan 102-8554 11Departments of Botany and Parasitology, Faculty of Science, Charles University in Prague, Prague, Czech Republic 12College of Life Sciences, University of Dundee, DD15EH Dundee, UK 13Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany 14Centre for Biomedical Research, The Hull York Medical School and Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK. Genome Biology, in press Background: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. Results: We have produced a draft genome sequence of another group Dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41x coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two Dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate Dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict. Conclusion: The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia. Submitted by Adam Kuspa [akuspa@bcm.edu] -------------------------------------------------------------------------------- Deficiency of huntingtin has pleiotropic effects in the social amoeba Dictyostelium discoideum Michael A. Myre1, Amanda L. Lumsden1, Morgan N. Thompson1, Wilma Wasco2, Marcy E. MacDonald1 and James F. Gusella1 1Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston MA 02114. 2Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown MA 02129. PLoS Genetics, in press Huntingtin is a large HEAT repeat protein first identified in humans, where a polyglutamine tract expansion near the amino terminus causes a gain-of-function mechanism that leads to selective neuronal loss in HuntingtonÕs disease (HD). Genetic evidence in humans and knock-in mouse models suggests that this gain-of-function involves an increase or deregulation of some aspect of huntingtinÕs normal function(s), which remains poorly understood. As huntingtin shows evolutionary conservation, a powerful approach to discovering its normal biochemical role(s) is to study the effects caused by its deficiency in a model organism with a short life-cycle that comprises both cellular and multicellular developmental stages. To facilitate studies aimed at detailed knowledge of huntingtinÕs normal function(s), we generated a null mutant of hd, the HD ortholog in Dictyostelium discoideum. Dictyostelium cells lacking endogenous huntingtin were viable but during development did not exhibit the typical polarized morphology of Dictyostelium cells, streamed poorly to form aggregates by accretion rather than chemotaxis, showed disorganized F-actin staining, exhibited extreme sensitivity to hypoosmotic stress, and failed to form EDTA-resistant cell-cell contacts. Surprisingly, chemotactic streaming could be rescued in the presence of the bivalent cations Ca2+ or Mg2+ but not pulses of cAMP. Although hd- cells completed development, it was delayed and proceeded asynchronously, producing small fruiting bodies with round, defective spores that germinated spontaneously within a glassy sorus. When developed as chimeras with wild-type cells, hd- cells failed to populate the pre-spore region of the slug. In Dictyostelium, huntingtin deficiency is compatible with survival of the organism but renders cells sensitive to low osmolarity which produces pleiotropic cell autonomous defects that affect cAMP signaling, and as a consequence development. Thus, Dictyostelium provides a novel haploid organism model for genetic, cell biological and biochemical studies to delineate the functions of the HD protein. Submitted by Michael Myre [myre@chgr.mgh.harvard.edu] -------------------------------------------------------------------------------- A Dictyostelium SH2 adaptor protein required for correct DIF-1 signaling and pattern formation Christopher Sugden1, Susan Ross1, Sarah J. Annesley4, Christian Cole1, Gareth Bloomfield3, Alasdair Ivens2 Jason Skelton2, Paul R. Fisher4, Geoffrey Barton1 and Jeffrey G. Williams1* 1School of Life Sciences, University of Dundee, Dow St., Dundee, DD1 5EH UK 2Wellcome Trust Sanger Institute, Hinxton, CB10 1SA UK 3MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH UK 4Department of Microbiology, La Trobe University, Bundoora, Victoria 3086, Australia * Corresponding Author j.g.williams@dundee.ac.uk tel 44 1382 385220, fax 44-1382 34421 Dev. Biol., in press Dictyostelium is the only non-metazoan with functionally analysed SH2 domains and studying them can give insights into their evolution and wider potential. LrrB has a novel domain configuration with leucine-rich repeat, 14-3-3 and SH2 protein-protein interaction modules. It is required for the correct expression of several specific genes in early development and here we characterize its role in later, multicellular development. During development in the light, slug formation in LrrB null (lrrB-) mutants is delayed relative to the parental strain, and the slugs are highly defective in phototaxis and thermotaxis. In the dark the mutant arrests development as an elongated mound, in a hitherto unreported process we term dark stalling. The developmental and phototaxis defects are cell autonomous and marker analysis shows that the pstO prestalk sub-region of the slug is aberrant in the lrrB- mutant. Expression profiling, by parallel micro-array and deep RNA sequence analyses, reveals many other alterations in prestalk-specific gene expression in lrrB- slugs, including reduced expression of the ecmB gene and elevated expression of ampA. During culmination ampA is ectopically expressed in the stalk, there is no expression of ampA and ecmB in the lower cup and the mutant fruiting bodies lack a basal disc. The basal disc cup derives from the pstB cells and this population is greatly reduced in the lrrB- mutant. This anatomical feature is a hallmark of mutants aberrant in signalling by DIF-1, the polyketide that induces prestalk and stalk cell differentiation. In a DIF-1 induction assay the lrrB- mutant is profoundly defective in ecmB activation but only marginally defective in ecmA induction. Thus the mutation partially uncouples these two inductive events. In early development LrrB interacts physically and functionally with CldA, another SH2 domain containing protein. However, the CldA null mutant does not phenocopy the lrrB- in its aberrant multicellular development or phototaxis defect, implying that the early and late functions of LrrB are effected in different ways. These observations, coupled with its domain structure, suggest that LrrB is an SH2 adaptor protein active in diverse developmental signaling pathways. Submitted by: Jeff Williams [j.g.williams@dundee.ac.uk] ============================================================== [End dictyNews, volume 36, number 7]