Genome analysis of the cellular slime molds to understand the genetic system controlling cell differentiation

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The cellular slime mold, Dictyostelium discoideum, was used to understand the genetic control of development and differentiation. This organism normally proliferates as unicellular amoebae but gathers and constructs multicellular structures upon starvation. First, large scale analysis of cDNAs was performed to establish the genetic resources. Fourteen cDNA libraries were constructed from the cells at 5 developmental stages, and the nucleotide sequences of 95,884 clones, including 72,703 full-length ones, were determined. The sequences were assembled into 6,790 independent genes, which corresponded to 54% of the predicted 12,500 genes. These resources were then used for reverse-genetic and bioinformatic analyses. The following results were obtained.1. Gene expression patterns during normal development were obtained showing occurrence of the overall drastic changes in expressed genes after cell aggregation. Whole mount in situ hybridization revealed the fine pattern formation in the prestalk region.2. Two hundred and sixty genes were extracted to encode probable transcription factors, and precise expression patterns were obtained by real-time PCR for 40 of them. Thirteen genes were disrupted.3. The Genetic network among 9 probable transcription factors was obtained using the S-system calculation based on the gene expression patterns during development in the wild type and disruption mutants.4. Upstream promoter sequences were obtained by aligning the full-length cDNA and genome sequences, and candidate cis regulatory elements were extracted referring to the expression specificities.