Genome-wide analysis of the cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins

Abstract

Cyclins are primary regulators of the activity of cyclin-dependent kinases, which are known to play critical roles in controlling eukaryotic cell cycle progression. While there has been extensive research on cell cycle mechanisms and cyclin function in animals and yeasts, only a small number of plant cyclins have been characterized functionally. In this paper, we describe an exhaustive search for cyclin genes in the Arabidopsis genome and among available sequences from other vascular plants. Based on phylogenetic analysis, we define 10 classes of plant cyclins, four of which are plant-specific, and a fifth is shared between plants and protists but not animals. Microarray and reverse transcriptase-polymerase chain reaction analyses further provide expression profiles of cyclin genes in different tissues of wild-type Arabidopsis plants. Comparative phylogenetic studies of 174 plant cyclins were also performed. The phylogenetic results imply that the cyclin gene family in plants has experienced more gene duplication events than in animals. Expression patterns and phylogenetic analyses of Arabidopsis cyclin genes suggest potential gene redundancy among members belonging to the same group. We discuss possible divergence and conservation of some plant cyclins. Our study provides an opportunity to rapidly assess the position of plant cyclin genes in terms of evolution and classification, serving as a guide for further functional study of plant cyclins.

Figure 1.

Unrooted NJ tree of the Arabidopsis and human cyclins, with bootstrap values higher than 50% shown for each clade. Ten and 13 families of cyclins are recognizable in Arabidopsis and human, respectively, five of which (A, B, C, H, and L) are shared by both species. The remaining five types of Arabidopsis cyclins are named as CycJ18-, D_plant-, T-, SDS-, and L-type, respectively. Twenty-two proteins from human are highlighted by gray boxes. Three proteins from protists are in inverted boxes: NP_703528, EAA22167, and AAG44389 from Plasmodium falciparum, P. yoelii yoelii, and Trypanosoma cruzi, respectively. Eighteen newly named Arabidopsis cyclins are in open boxes.

Figure 2.

Phylogenetic relationships and domain structure of the 49 Arabidopsis cyclins. With 0.01 as the E-value cutoff, almost all of the A-, B-, D-, and SDS-type of cyclins contain both cyclin_N and cyclin_C domains, whereas all other types of cyclins lack cyclin_C domain. D-box was found in nine A- and nine B-cyclins.

Figure 3.

Analysis of expression of some cyclin genes using RT-PCR. The APT1 gene was used as an internal control. Thirty-four cycles PCR reactions were performed for those genes with asterisks (*), while 29 cycles were done for all the other genes. The microarray data, if available, are listed below the corresponding RT-PCR bands to show the general consistency of results from these two methods and the high sensitivity of RT-PCR. The abbreviation for the organs is the same as in Table I.

Figure 4.

NJ tree of 49 A-, two B-, two SDS-, and four D-type cyclins from plants. Forty-seven core members of A-type were clustered into three groups, i.e. CycA1, CycA2, and CycA3, while the remaining two CycA-like proteins from rice, Orasa;CycA3;3 and Orasa;CycA3;3, were resolved as sisters to all other A- and B-type cyclins. Sequences from Arabidopsis are in open boxes, while those from rice are in light shading. Cyclin nomenclature is according to Renaudin et al. (1996). Adica, Adiantum capillus; Arath, Arabidopsis; Brana, Brassica napus; Catro, Catharantus roseus; Dauca, Daucus carota; Glyma, Glycine max; Lyces, Lycopersicon esculentum; Medsa, Medicago sativa; Nicta, Nicotiana tabacum; Orysa, Oryza sativa; Picba, Picea abies; Pissa, Pisum sativum; Silla, Silene latifolia; Zeama, Zea mays. For more information, such as synonym(s), accession number, locus name, and signature motif, please see the Supplemental Table I.

Figure 5.

NJ tree of 45 B-type cyclins from plants, with two A-, two SDS-, and four D-type cyclins as outgroups. Three major groups, CycB1, CycB2, and CycB3, are recognizable, although the relationships among them are not resolved. Sequences from Arabidopsis are in open boxes, while those from rice in light shading. Cyclin nomenclature is according to Renaudin et al. (1996). Antma, Antirrhinum majus; Arath, Arabidopsis; Catro, Catharantus roseus; Cheru, Chenopodium rubrum; Dauca, Daucus carota; Glyma, Glycine max; Luplu, Lupinus luteus; Lyces, Lycopersicon esculentum; Medsa, Medicago sativa; Nicta, Nicotiana tabacum; Orysa, Oryza sativa; Petcr, Petroselinum crispum; Pethy, Petunia x hybrida; Picma, Picea mariana; Pissa, Pisum sativum; Sesro, Sesbania rostrata; Zeama, Zea mays. For more information, such as synonym(s), accession number, locus name, and signature motif, please see the Supplemental Table I.

Figure 6.

Unrooted NJ tree of 51 D-type cyclins from plants. Six groups of cyclins, CycD1-, CycD2-/CycD4-, CycD3-, CycD5-, CycD6-, and CycD7-type cyclins, are recognizable, although the relationships among then are not resolved. Sequences from Arabidopsis are in open boxes, while those from rice are in light shading. Cyclin nomenclature is according to Renaudin et al. (1996). Antma, Antirrhinum majus; Arath, Arabidopsis; Cheru, Chenopodium rubrum; Dauca, Daucus carota; Hiltu, Helianthus tuberosus; Lagsi, Lagenaria siceraria; Lyces, Lycopersicon esculentum; Medsa, Medicago sativa; Nicta, Nicotiana tabacum; Orysa, Oryza sativa; Pissa, Pisum sativum; Phypa, Physcomitrella patens; Popal, Populus alba; Poptr, Populus tremula x Populus tremuloides; Triea, Triticum aestivum; Zeama, Zea mays. For more information, such as synonym(s), accession number, locus name, and signature motif, please see the Supplemental Table I.

Figure 7.

Unrooted NJ tree of two C-, two H-, two L-, and 11 T-type cyclins from plants, with four monophyletic groups formed for each type. Sequences from Arabidopsis are in open boxes, while those from rice are in light shading. For more information, such as synonym(s), accession number, locus name, and signature motif, please see Supplemental Table I.

Figure 8.

Unrooted NJ tree of 15 U-type cyclins from plants. Four groups, CycU1-, CycU2-, CycU3-, and CycU4-type cyclins, were formed. Sequences from Arabidopsis are in open boxes, while those from rice are in light shading. For more information, such as synonym(s), accession number, locus name, and signature motif, please see Supplemental Table I.