Nucleotide Sequence of a cDNA Clone from Arabidopsis thaliana Encoding a Small A-T Tract-Binding Protein

Higher eukaryotes are known to contain proteins that preferentially bind A-T tracts (Russell et al., 1983; Struhl, 1985; Solomon et al., 1986). Winter and Varshavsky (1989) estimated that A-T tracts in Saccharomyces cerevisiae genome occur on average once every 4 kb. The biological significance or function of these sequences is unknown. Here we report the identification of a cDNA of a protein from Arabidopsis thaliana that preferentially binds to A-T tracts (Table I). The A-T tract-binding protein cDNA was isolated and identified during the course of screening of an A. tkaliana ecotype Columbia hgtll expression library with 32P-labeled Arabidopsis cab3 gene promotor fragments containing cis-elements determined earlier by promoter mutation (Mitra et al., 1989). The cDNA was expressed in bacteria and was shown to preferentially bind to A-T tracts of dsDNA in vitro by gel-shift assays and mutational analysis of the binding sequence. The deduced amino acid sequence indicated a single open reading frame coding for a protein containing 161 amino acids with a calculated molecular mass of 18 kD. The amino acid sequence revealed a stretch of eight Gln residues with a Lys between the sixth and seventh Gln, a pattern characteristic of many DNA-binding regulatory proteins. A computer search for similarities with known proteins in severa1 data bases using the Genetics Computer Group FastA program (Devereaux et al., 1984) did not indicate any statistically significant homology with any other proteins in the data bases. Northern blot analysis using total RNA from various Arabidopsis organs indicated that the gene is strongly expressed in leaves and stems, which is a pattern similar to that of photosynthetic genes. However, unlike the photosynthetic genes that usually belong to multigene families, the A-T tract-binding protein is encoded by a single gene in Arabidopsis. A-T tracts within promoter sequences have been postulated to be involved with transcription enhance-