dictyNews Electronic Edition Volume 34, number 9 March 12, 2010 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 ========= A myosin IK-Abp1-PakB circuit acts as a switch to regulate phagocytosis efficiency Régis Dieckmann, Yosuke von Heyden, Claudia Kistler, Navin Gopaldass, Stéphanie Hausherr, Scott William Crawley, Eva C. Schwarz, Ralph P. Diensthuber, Graham P. Côté, Georgios Tsiavaliaris, and Thierry Soldati Molecular Biology of the Cell, in press Actin dynamics and myosin contractile forces are necessary for formation and closure of the phagocytic cup. In Dictyostelium, the actin-binding protein Abp1 and myosinIK are enriched in the closing cup and especially at an actin-dense constriction furrow formed around the neck of engulfed budded yeasts. This phagocytic furrow consists of concentric overlapping rings of MyoK, Abp1, Arp3, coronin and myosin II, following an order strikingly reminiscent of the overall organization of the lamellipodium of migrating cells. Mutation analyses of MyoK revealed that both a C-terminal farnesylation membrane anchor and a Gly-Pro-Arg domain that interacts with profilin and Abp1, were necessary for proper localization in the furrow and efficient phagocytosis. Consequently, we measured the binding affinities of these interactions and unraveled further interactions with profilins, dynamin A and PakB. Due to the redundancy of the interaction network, we hypothesize that MyoK and Abp1 are restricted to regulatory roles and might affect the dynamic of cup progression. Indeed, phagocytic uptake was regulated antagonistically by MyoK and Abp1. MyoK is phosphorylated by PakB and positively regulates phagocytosis, whereas binding of Abp1 negatively regulates PakB and MyoK. We conclude that a MyoK-Abp1-PakB circuit acts as a switch regulating phagocytosis efficiency of large particles. Submitted by Thierry Soldati [Thierry.Soldati@unige.ch] -------------------------------------------------------------------------------- Bimodal analysis reveals a general scaling law governing non-directed and chemotactic cell motility J. Scott Gruver1*, Alka A. Potdar2,4*, Junhwan Jeon2,4, Jiqing Sai3, Bridget Anderson5, Donna Webb3,5,6, Ann Richmond3,7, Vito Quaranta3, Peter T. Cummings2,4,8, and Chang Chung1,5, # 1Department of Pharmacology, 2Vanderbilt Integrative Cancer Biology Center, 3Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN 37232, 4Department of Chemical and Biomolecular Engineering, 5Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, 6Vanderbilt Kennedy Center for Research on Human Development, Nashville TN, 37235, 7Department of Veterans Affairs (Nashville, TN), 8Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831 Biophy. J., in press Cell motility is a fundamental process with relevance to embryonic development, immune response, and metastasis. Cells move either spontaneously, in a non-directed fashion, or in response to chemotactic signals, in a directed fashion. Even though they are often studied separately, both forms of motility share many complex processes at the molecular and subcellular scale, e.g., orchestrated cytoskeletal rearrangements and polarization. In addition, at the cellular level both types of motility include persistent runs interspersed with reorientation pauses(1-4). Because there is a great range of variability in motility among different cell types, a key challenge in the field is to integrate these multi-scale processes into a coherent framework. We analyzed the motility of Dictyostelium cells with bimodal analysis, a method that compares time spent in persistent versus reorientation mode. Unexpectedly, we found that reorientation time is coupled with persistent time in an inverse correlation and, surprisingly, the inverse correlation holds for both non-directed and chemotactic motility, so that the full range of Dictyostelium motility can be described by a single scaling relationship. Additionally, we found an identical scaling relationship for three human cell lines, indicating that the coupling of reorientation and persistence holds across species and making it possible to describe the complexity of cell motility in a surprisingly general and simple manner. With this new perspective, we analyzed the motility of Dictyostelium mutants, and found four in which the coupling between two modes was altered. Our results point to a fundamental underlying principle, described by a simple scaling law, unifying mechanisms of eukaryotic cell motility at several scales. Submitted by Chang Chung [chang.chung@vanderbilt.edu] -------------------------------------------------------------------------------- New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data Anup Parikh, Eryong Huang, Christopher Dinh, Blaz Zupan, Adam Kuspa, Devika Subramanian and Gad Shaulsky Baylor College of Medicine, University of Ljubljana and Rice University BMC Bioinformatics, in press Background Identifying candidate genes in genetic networks is important for understanding regulation and biological function. Large gene expression datasets contain relevant information about genetic networks, but mining the data is not a trivial task. Algorithms that infer Bayesian networks from expression data are powerful tools for learning complex genetic networks, since they can incorporate prior knowledge and uncover higher-order dependencies among genes. However, these algorithms are computationally demanding, so novel techniques that allow targeted exploration for discovering new members of known pathways are essential. Results Here we describe a Bayesian network approach that addresses a specific network within a large dataset to discover new components. Our algorithm draws individual genes from a large gene-expression repository, and ranks them as potential members of a known pathway. We apply this method to discover new components of the cAMP-dependent protein kinase (PKA) pathway, a central regulator of Dictyostelium discoideum development. The PKA network is well studied in D. discoideum but the transcriptional networks that regulate PKA activity and the transcriptional outcomes of PKA function are largely unknown. Most of the genes highly ranked by our method encode either known components of the PKA pathway or are good candidates. We tested 5 uncharacterized highly ranked genes by creating mutant strains and identified a candidate cAMP-response element-binding protein, yet undiscovered in D. discoideum, and a histidine kinase, a candidate upstream regulator of PKA activity. Conclusions The single-gene expansion method is useful in identifying new components of known pathways. The method takes advantage of the Bayesian framework to incorporate prior biological knowledge and discovers higher-order dependencies among genes while greatly reducing the computational resources required to process high-throughput datasets. Submitted by Gad Shaulsky [gadi@bcm.edu] -------------------------------------------------------------------------------- Conserved Developmental Transcriptomes in Evolutionary Divergent Species Anup Parikh*, Edward Roshan Mirada*, Mariko Katoh-Kurasawa, Danny Fuller, Gregor Rot, Lan Zagar, Tomaz Curk, Richard Sucgang, Rui Chen, Blaz Zupan, William F. Loomis, Adam Kuspa and Gad Shaulsky * equal contribution Baylor College of Medicine, UC San Diego, and University of Ljubljana Genome Biology, in press Background Evolutionary divergent organisms often share developmental anatomies despite vast differences between their genome sequences. The social amoebae Dictyostelium discoideum and Dictyostelium purpureum have similar developmental morphologies although their genomes are as divergent as those of man and jawed fish. Results Here we show that the anatomical similarities are accompanied by extensive transcriptome conservation. Using RNA sequencing we compared the abundance and developmental regulation of all the transcripts in the two species. In both species, most genes are developmentally regulated and the greatest expression changes occur during the transition from unicellularity to multicellularity. The developmental regulation of transcription is highly conserved between orthologs in the two species. In addition to timing of expression, the level of mRNA production is also conserved between orthologs and is consistent with the intuitive notion that transcript abundance correlates with the amount of protein required. Furthermore, the conservation of transcriptomes extends to cell-type specific expression. Conclusions These findings suggest that developmental programs are remarkably conserved at the transcriptome level, considering the great evolutionary distance between the genomes. Moreover, this transcriptional conservation may be responsible for the similar developmental anatomies of Dictyostelium discoideum and Dictyostelium purpureum. Submitted by Gad Shaulsky [gadi@bcm.edu] ============================================================== [End dictyNews, volume 34, number 9]