The Arabidopsis cyclophilin gene family

Abstract

Database searching has allowed the identification of a number of previously unreported single and multidomain isoform members of the Arabidopsis cyclophilin gene family. In addition to the cyclophilin-like peptidyl-prolyl cis-trans isomerase domain, the latter contain a variety of other domains with characterized functions. Transcriptional analysis showed they are expressed throughout the plant, and different isoforms are present in all parts of the cell including the cytosol, nucleus, mitochondria, secretory pathway, and chloroplast. The abundance and diversity of cyclophilin isoforms suggests that, like their animal counterparts, plant cyclophilins are likely to be important proteins involved in a wide variety of cellular processes. As well as fulfilling the basic role of protein folding, they may also play important roles in mRNA processing, protein degradation, and signal transduction and thus may be crucial during both development and stress responsiveness.

Figure 1.

Primary domain structure of representative isoforms of the SD and MD Arabidopsis cyclophilin proteins. TMD, transmembrane domain; TPR, tetratricopeptide repeat; S/K-R/E, Ser/Lys-Arg/Glu-rich region; U, U-box domain; WD40, WD40 repeat; RRM, RNA recognition motif; R, Arg- rich region; NLS, nuclear localization signal; EK, Glu-Lys-rich region; RS, Arg-Ser rich region; LZ, Leu zipper.

Figure 2.

Multiple alignment of the deduced protein sequences of the Arabidopsis cyclophilin family. Multidomain isoform sequences have been truncated to improve the alignment (see Table I for details of sequence used). Backgrounds indicate percentage of amino acid similarity: black, 100%; dark gray, 80%; light gray, 60%. Amino acids in red represent those required for PPiase catalysis, those in blue for CsA binding (Zydowsky et al., 1992). Secondary structure features are those of human Cyclophilin A (Kallen et al., 1991). Roman numerals on the left-hand side correspond to the cladistic subdivision used in Figure 3.

Figure 3.

A, Structure of human cyclophilin A as elucidated by x-ray diffraction analysis. The variable insertion region corresponding to the α-I/β-III junction is indicated by the red arrow (Kallen et al., 1991; ; image obtained from the Swiss-3D image database at the ExPASY website [http://ca.expasy.org]). B, Unrooted cladogram of the Arabidopsis cyclophilin protein family and human cyclophilin A obtained using the sequence alignment of Figure 2. The branch lengths are proportional to divergence, with the scale of 0.1 representing 10% change. Colors represent predicted cellular location (black, cytosol; green, chloroplast; blue, mitochondria; red, secretory pathway; orange, nucleus).

Figure 4.

RT-PCR analysis of the expression patterns of the newly identified cyclophilin genes in tissues of Arabidopsis (Columbia). Figure 4 shows ethidium bromide-stained gels of PCR amplification using cDNA produced from leaf (L), flower buds (F), roots (R), and stems (S). The UBQ5 gene was used as a control for amplification.