dictyNews Electronic Edition Volume 30, number 16 May 16, 2008 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. ========= Abstracts ========= Kim J, Bates DG, Postlethwaite I, Heslop-Harrison P, Cho K-H Linear time-varying models can reveal nonlinear interactions of biomolecular regulatory networks using multiple time-series data Bioinformatics, in press Motivation: Inherent nonlinearities in biomolecular interactions make the identification of network interactions difficult. One of the principal problems is that all methods based on the use of linear time invariant models will have fundamental limitations in their capability to infer certain nonlinear network interactions. Another difficulty is the multiplicity of possible solutions, since, for a given data set, there may be many different possible networks which generate the same time-series expression profiles. Results: A novel algorithm for the inference of biomolecular interaction networks from temporal expression data is presented. Linear time-varying models, which can represent a much wider class of time-series data than linear time-invariant models, are employed in the algorithm. From time-series expression profiles, the model parameters are identified by solving a nonlinear optimisation problem. In order to systematically reduce the set of possible solutions for the optimisation problem, a filtering process is performed using a phase-portrait analysis with random numerical perturbations. The proposed approach has the advantages of not requiring the system to be in a stable steady-state, of using time-series profiles which have been generated by a single experiment, and of allowing nonlinear network interactions to be identified. The ability of the proposed algorithm to correctly infer network interactions is illustrated by its application to three examples: a nonlinear model for cAMP oscillations in Dictyostelium discoideum, the cell-cycle data for Saccharomyces cerevisiae and a large-scale nonlinear model of a group of synchronised Dictyostelium cells. Submitted by: Pat Heslop-Harrisonr [phh4@le.ac.uk] -------------------------------------------------------------------------------- Dephosphorylation of 2,3-bisphosphoglycerate by MIPP expands the regulatory capacity of the Rapoport–Luebering glycolytic shunt Jaiesoon Cho*†, Jason S. King‡§, Xun Qian*, Adrian J. Harwood‡, and Stephen B. Shears PNAS   vol. 105 (16) pp5998–6003  The Rapoport–Luebering glycolytic bypass comprises evolutionarily conserved reactions that generate and dephosphorylate 2,3-bisphosphoglycerate (2,3-BPG). For>30 years, these reactions have been considered the responsibility of a single enzyme, the 2,3-BPG synthase/2-phosphatase (BPGM). Here, we show that Dictyostelium, birds, and mammals contain an additional 2,3-BPG phosphatase that, unlike BPGM, removes the 3-phosphate. This discovery reveals that the glycolytic pathway can bypass the formation of 3-phosphoglycerate, which is a precursor for serine biosynthesis and an activator of AMP-activated protein kinase. Our 2,3-BPG phosphatase activity is encoded by the previously identified gene for multiple inositol polyphosphate phosphatase (MIPP1), which we now show to have dual substrate specificity. By genetically manipulating Mipp1 expression in Dictyostelium, we demonstrated that this enzyme provides physiologically relevant regulation of cellular 2,3-BPG content. Mammalian erythrocytes possess the highest content of 2,3-BPG, which controls oxygen binding to hemoglobin. We determined that total MIPP1 activity in erythrocytes at 37°C is 0.6 mmol 2,3-BPG hydrolyzed per liter of cells per h, matching previously published estimates of the phosphatase activity of BPGM. MIPP1 is active at 4°C, revealing a clinically significant contribution to 2,3-BPG loss during the storage of erythrocytes for transfusion. Hydrolysis of 2,3-BPG by human MIPP1 is sensitive to physiologic alkalosis; activity decreases 50% when pH rises from 7.0 to 7.4. This phenomenon provides a homeostatic mechanism for elevating 2,3-BPG levels, thereby enhancing oxygen release to tissues. Our data indicate greater biological significance of the Rapoport–Luebering shunt than previously considered. Submitted by: Adrian Harwood [harwoodaj@cf.ac.uk] -------------------------------------------------------------------------------- MPL1, the novel phosphatase with Leucine-Rich-Repeats, is essential for proper ERK2 phosphorylation and cell motility. Marbelys Rodriguez, Bohye Kim, Nam-Sihk Lee, Sudhakar Veeranki, and Leung Kim* Dept of Biological Sciences, Florida International University, Miami, FL 33199 * To whom correspondence should be addressed. Email: kiml@fiu.edu. Eukaryotic Cell, in press The novel Dictyostelium phosphatase Mpl1 contains six Leucine-Rich-Repeats at the amino-terminal end and a phosphatase domain at the carboxyl end. Similarly architectured phosphatases exist among other protozoa such as Entamoeba histolytica, Leishmania major, and Trypanosoma cruzi. Mpl1 was strongly induced after 5 hours of development; ablation by homologous recombination led to defective streaming and aggregation during development. In addition, cAMP pulsed mpl1- cells showed reduced random and directional motility. At the molecular level, mpl1- cells displayed higher prestimulus and persistent post-stimulus ERK2 phosphorylation in response to cAMP stimulation. Consistent with their phenotype of persistent ERK2 phosphorylation, mpl1- cells also displayed an aberrant pattern of cAMP production, resembling that of the regA- cells. Reintroduction of a full length Mpl1 into mpl1- cells restored aggregation, ERK2 regulation, random and directional motility, and cAMP production similar to wild type cells. We propose that MPL1 is a novel phosphatase essential for proper regulation of ERK2 phosphorylation and optimal motility during development. Submitted by: Marbelys Rodriguez [mrodr126@fiu.edu] ============================================================== [End dictyNews, volume 30, number 16]