dictyNews Electronic Edition Volume 25, number 15 December 16, 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 dictyNews, the Dicty Reference database and other useful information is available at dictyBase - http://dictybase.org. ============= Abstracts ============= Tamao Saito1,2, Graham W. Taylor3, Ji-ChunYang1, David Neuhaus1, Dmitry Stetsenko1, Atsushi Kato2 and Robert R. Kay1 Biochimica et Biophysica Acta, in press Developing Dictyostelium discoideum amoebae form a stalked fruiting body in which individual cells differentiate into either stalk cells or spores. The major known inducer of stalk cell differentiation is the chlorinated polyketide DIF-1 (1-(3,5-dichloro-2,6-dihydroxy-4-methoxyphenyl)hexan-1-one); however a mutant blocked in the terminal step of DIF-1 biosynthesis still produces one of the prestalk cell subtypes - the pstA cells – as well as s ome mature stalk cells. We therefore searched for additional stalk cell-inducing factors in the medium supporting development of this mutant. These factors were purified by solvent extraction and HPLC and identified by mass spectroscopy and NMR. The mutant lacked detectable DIF-2 and DIF-3 (the pentanone and deschloro homologues of DIF-1) but four major stalk cell-inducing activities were detected, of which three were identified. Two compounds were predicted intermediates in DIF-1 biosynthesis: the desmethyl, and desmethyl-monochloro analogues of DIF-1 (dM-DIF-1 and Cl-THPH respectively), supporting the previously proposed pathway of DIF-1 biosynthesis. The third compound was a novel factor and was identified as 4-methyl-5-pentylbenzene-1,3-diol (MPBD) with the structure confirmed by chemical synthesis. To investigate the potential roles of these compounds as signal molecules, their effects on morphological stalk and spore differentiation were examined in cell culture. All three induced morphological stalk cell differentiation. We found that synthetic MPBD also stimulated spore cell differentiation. Now that these factors are known to be produced and released during development, their biological roles can be pursued further. Submitted by: Tamao Saito [tasaito@sci.hokudai.ac.jp] ----------------------------------------------------------------------------- Retention and Loss of Amino Acid Biosynthetic Pathways Based on Whole-genome Sequences Samuel H. Payne and William F. Loomis Bioinformatics Program, Division of Biological Sciences University of California San Diego, La Jolla CA 92093 USA Eukaryotic Cell, in press Plants and fungi can synthesize each of the 20 amino acids using biosynthetic pathways inherited from their bacterial ancestors. However, the ability to synthesize 9 amino acids (phe, trp, ile, leu, val, lys, his, thr, and met) was lost in a wide variety of eukaryotes that evolved the ability to feed on other organisms. Since the biosynthetic pathways and their respective enzymes are well characterized, orthologs can be recognized in whole genomes to understand when in evolution pathways were lost. The pattern of pathway loss and retention was analyzed in the complete genomes of three early diverging protist parasites, the amoeba Dictyostelium, and six animals. The nine pathways were lost independently in animals, Dictyostelium, Leishmania, Plasmodium and Cryptosporidium.  Seven additional pathways appear to have been lost in one or another parasite demonstrating that they are dispensable in a rich nutritional environment. Our predictions of pathways retained and pathways lost based on computational analyses of whole genomes are validated by minimal media studies in mammals, fish, worms and Dictyostelium. The apparent selective advantages of retaining biosynthetic capabilities for amino acids available in the diet are considered. Submitted by: Bill Loomis [wloomis@ucsd.edu] ============================================================================== [End dictyNews, volume 25, number 15]