Three types of nuclear genes encoding chloroplast RNA-binding proteins (cp29, cp31 and cp33) are present in Arabidopsis thaliana: presence of cp31 in chloroplasts and its homologue in nuclei/cytoplasms.

Five chloroplast RNA-binding proteins with consensus sequence-type RNA-binding domains have been isolated from tobacco chloroplasts. Here we report three nuclear genes for similar chloroplast RNA-binding proteins (cp29, cp31 and cp33) from Arabidopsis thaliana. Each of the three genes consists of four exons and three introns and their exon/intron junctions were determined by sequencing respective cDNAs. In vitro import assays showed that all three proteins are located in chloroplasts. The three genes are singly-copy each and the transcription start sites were determined to be 80/82 bp (cp29) and 76/88 bp (cp31) upstream from the translational initiation codons. Northern blot analysis revealed that the three genes are transcribed both in leaves and roots, but the transcript level in leaves is higher than in roots. Phylogenetic analysis of chloroplast RNA-binding proteins so far identified shows that these proteins can be classified into three groups. Tobacco and Arabidopsis have these three types of proteins and structural features of each group are conserved between the two plants, suggesting that they are important for chloroplast functions. Interestingly, cp31 (238 amino acids) shares the identical amino acid sequence from the 30th to the last (238th) residues (including two RNA-binding domains) with the Arabidopsis nucleolin-like ribonucleoprotein, FMV3bp [11]. FMV3bp lacks a transit-peptide and must be located in the nucleus or the cytoplasm.