Gene density and organization in a small region of the Arabidopsis thaliana genome

Abstract

We have characterized a 6.4 kb genomic fragment from Arabidopsis thaliana ecotype Columbia overlapping the 5′ end of the AKin10 gene which encodes a protein Ser/Thr kinase. Using, as probes, various restriction fragments located upstream of AKin10, two cDNA clones have been isolated from a cDNA library prepared from young shoot tissue. A comparison between the cDNA and the above genomic sequences allowed us to locate two novel genes, Atcysl and Athypl (for Arabidopsis thaliana cystathionine γ-synthase 1 and hypothetical protein 1). The coding sequences of both genes are interrupted by introns and the exons match the sequences of the corresponding cDNAs. Further analysis of the genomic fragment revealed the presence of an open reading frame (ORF) of 609 nucleotides situated between the two genes. Atcysl, Athypl, AKin10 and the ORF are very close to each other and organized in the same polarity; hence, the intergenic regions probably contain, within less than 0.5 kb, all the regulatory elements necessary to govern initiation and termination of transcription. The deduced protein sequence of Atcysl shows a high degree of similarity with the cystathionine γ-synthase from Escherichia coli. The putative product of the Athypl gene contains seven hydrophobic regions flanked by hydrophilic domains, reminiscent of membrane-spanning proteins. Southern blot hybridization experiments suggest the presence of one copy of Atcysl, Athypl and AKin10 per haploid genome, and Northern blot analysis demonstrates that the three genes are differentially expressed in roots, shoots and leaves.