Comparative functional genomics of the TPR gene family in Arabidopsis, rice and maize

The tetratricopeptide repeat (TPR) proteins found in all kingdoms of life can mediate protein-protein interactions in a variety of biological systems through binding to specific peptide ligands, such as cell cycle control, transcription, protein transport and protein folding. Although the proteins are ubiquitous, no comprehensive overview of them in Arabidopsis thaliana (At), Oryza sativa (Os), Zea mays (Zm) and Populus trichocarpa (Pt) has been available in the literature till now. Through whole genome investigation, 177 Arabidopsis, 216 rice, 211 maize and 243 poplar TPR genes were identified and categorized into 28 subfamilies and 11 groups based on their domain compositions and phylogenetic relationships, respectively. Phylogenetic analysis revealed that most genes in the same subfamilies are classified into at least two groups, implying that TPR proteins have acquired functional diversity by extensive domain shuffling and/or emerged multiple times independently during evolution. Structural analysis of ZmTPR080 showed that eight TPR motifs as two anti-parallel a-helices form an amphipathic groove capable of accepting a target protein peptide. Similar expression patterns across development stages suggested functional conservation between homologous pairs, for example, AtTPR050/ZmTPR049 may have similar functions in the regulation of flowering. Under drought stress, 26 OsTPRs showed strong alterations of their expression levels in rice leaf, while 10 and 49 ZmTPRs were significantly differentially expressed in maize leaf and cob, respectively.