Abstract
Eukaryotic protein kinases (ePKs) evolved as a family of highly dynamic molecular switches that serve to orchestrate the activity of almost all cellular processes. Some of the functionally characterized ePKs from plants have been found to be components of signaling networks, such as those for the perception of biotic agents, light quality and quantity, plant hormones, and various adverse environmental conditions. To date, only a tiny fraction of plant ePKs have been functionally identified, and even fewer have been identified in maize [Zea mays (Zm)]. In this study, we have identified 1,241 PK-encoding genes in the maize genome. Phylogenetic analyses identified eight gene groups with considerable conservation among groups, and each group could be further divided into multiple families and/or subfamilies. Similar intron/exon structural patterns were observed in the same families/subfamilies, strongly supporting their close evolutionary relationship. Chromosome distribution and genetic analysis revealed that tandem duplications and segmental/whole-genome duplications might represent two of the major mechanisms contributing to the expansion of the PK superfamily in maize. The dynamic expression patterns of ZmPK genes across the 60 different developmental stages of 11 organs showed that some members of this superfamily exhibit tissue-specific expression, whereas others are more ubiquitously expressed, indicative of their important roles in performing diverse developmental and physiological functions during the maize life cycle. Furthermore, RNA-sequence-based gene expression profiling of PKs along a leaf developmental gradient and in mature bundle sheath and mesophyll cells indicated that ZmPK genes are involved in various physiological processes, such as cell-fate decisions, photosynthetic differentiation, and regulation of stomatal development. Our results provide new insights into the function and evolution of maize PKs and will be useful in studies aimed at revealing the global regulatory network of maize development, thereby contributing to the maize molecular breeding with enhanced quality traits.
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Acknowledgments
We are grateful to all researchers who submitted the microarray data to the public expression databases for free access. We thank Yanhui Chen, Yina Lin, Xiaojun Zhong, Si Pan and Xiaoyao Liu in our laboratory for useful discussions.
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11032_2013_9941_MOESM7_ESM.tif
Supplemental Figure S1 Phylogenetic tree of PKs from Arabidopsis, rice and maize. The distance scale is under the figure, and branch lengths are proportional to genetic distance. The Arabidopsis and rice gene names follow those of TAIR and TIGR databases. Sequences in the same clades as known kinase families were classified as such. The red arrowhead indicates the outgroup. The classification for these kinases is shown on the right. Each phylogenetic group is color-coded according to the color key on the lower right. (TIFF 27587 kb)
11032_2013_9941_MOESM8_ESM.tif
Supplemental Figure S2 The map of the intron-exon configuration of ZmPK genes ordered by subfamily. Introns and exons were drawn to scale with the full encoding regions of their respective genes. Exons are depicted as green boxes and introns as connecting thin lines. Non-translated regions, when supported by full-length cDNA sequences, are shown in blue boxes. (TIFF 15270 kb)
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Wei, K., Wang, Y. & Xie, D. Identification and expression profile analysis of the protein kinase gene superfamily in maize development. Mol Breeding 33, 155–172 (2014). https://doi.org/10.1007/s11032-013-9941-x
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DOI: https://doi.org/10.1007/s11032-013-9941-x