A PSTAIRE CDK-like protein localizes in nuclei and cytoplasm of Physarum polycephalum and functions in the mitosis

Genome-wide identification, evolutionary and expression analysis of the cyclin-dependent kinase gene family in peanut

BACKGROUND

Cyclin-dependent kinases (CDKs) are a predominant group of serine/threonine protein kinases that have multi-faceted functions in eukaryotes. The plant CDK members have well-known roles in cell cycle progression, transcriptional regulation, DNA repair, abiotic stress and defense responses, making them promising targets for developing stress adaptable high-yielding crops. There is relatively sparse information available on the CDK family genes of cultivated oilseed crop peanut and its diploid progenitors.

RESULTS

We have identified 52 putative cyclin-dependent kinases (CDKs) and CDK-like (CDKLs) genes in Arachis hypogaea (cultivated peanut) and total 26 genes in each diploid parent of cultivated peanut (Arachis duranensis and Arachis ipaensis). Both CDK and CDKL genes were classified into eight groups based on their cyclin binding motifs and their phylogenetic relationship with Arabidopsis counterparts. Genes in the same subgroup displayed similar exon-intron structure and conserved motifs. Further, gene duplication analysis suggested that segmental duplication events played major roles in the expansion and evolution of CDK and CDKL genes in cultivated peanuts. Identification of diverse cis-acting response elements in CDK and CDKL genes promoter indicated their potential fundamental roles in multiple biological processes. Various gene expression patterns of CDKs and CDKLs in different peanut tissues suggested their involvement during growth and development. In addition, qRT-PCR analysis demonstrated that most representing CDK and CDKL gene family members were significantly down-regulated under ABA, PEG and mannitol treatments.

CONCLUSIONS

Genome-wide analysis offers a comprehensive understanding of the classification, evolution, gene structure, and gene expression profiles of CDK and CDKL genes in cultivated peanut and their diploid progenitors. Additionally, it also provides cell cycle regulatory gene resources for further functional characterization to enhance growth, development and abiotic stress tolerance.

Identification of a novel PSR as the substrate of an SR protein kinase in the true slime mold

Here, a novel cDNA encoding a serine/arginine (SR)-rich protein, designated PSR, was isolated from the true slime mold Physarum polycephalum and expressed in Escherichia coli. The deduced amino acid (aa) sequence reveals that PSR contains RS repeats at its C-terminus, similar to the conventional PSRPK substrate ASF/SF2. To study the novel protein, we generated a variety of mutant constructs by PCR and site-directed mutagenesis. Our analysis indicated that the purified recombinant PSR was phosphorylated by PSRPK in vitro and the SR-rich domain (amino acids 460-469) in the PSR protein was required for phosphorylation. In addition, removal of the docking motif (amino acids 424-450) from PSR significantly reduced the overall catalytic efficiency of the phosphorylation reaction. We also found that the conserved ATP-binding region (62)LGWGHFSTVWLAIDEKNGGREVALK(86) and the serine/threonine protein kinases active-site signature (184)IIHTDLKPENVLL(196) of PSRPK played a crucial role in substrate phosphorylation and Lys(86) and Asp(188) were crucial for PSRPK phosphorylation of PSR. These results suggest that PSR is a novel SR-related protein that is phosphorylated by PSRPK.

Structural and functional relationship between the Ph1 locus protein 5B2 in wheat and CDK2 in mammals

The Ph1 locus in hexaploid wheat is responsible for restricting chromosome pairing at meiosis to true homologues by suppressing homoeologous pairing. Based on detailed modelling studies and predicted ability to form complexes with cyclin-A and cyclin-dependent kinase inhibitor such as p27, Triticum aestivum-5B2 (( Ta ) 5B2) is suggested to be a wheat analogue of human CDK2 enzyme. A blast analysis of the protein data bank using the amino acid sequence of the protein expressed by the 5B2 copy of the cdk-like cluster of genes at the Ph1 locus (( Ta ) 5B2) identified humans CDK2 as a top hit. In this analysis, the canonical cyclin binding motif PSTAIRE of CDK2 is replaced by a novel DARTLRE motif and Thr160 residue, phosphorylation of which is required for positive regulation of CDK2, is replaced by a tyrosine (Tyr174) in ( Ta ) 5B2. Despite these differences, detailed analyses show that all residues known to be important for cyclin binding are either fully conserved or whenever there is alteration in ( Ta ) 5B2, a corresponding but comparable alteration is also observed in plant cyclins notably cyclin-A of Arabidopsis thaliana. Moreover, the Thr160/Tyr174 substitution is also accommodated by suitable alterations in the 3D space around Tyr174 and the 3D model of ( Ta ) 5B2 predicts Tyr174 to play the same role as Thr160 plays in CDK2.