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Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies

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Abstract

Caleosins are a class of Ca2+ binding proteins that appear to be ubiquitous in plants. Some of the main proteins embedded in the lipid monolayer of lipid droplets, caleosins, play critical roles in the degradation of storage lipids during germination and in lipid trafficking. Some of them have been shown to have histidine-dependent peroxygenase activity, which is believed to participate in stress responses in Arabidopsis. In the model plant Arabidopsis thaliana, caleosins have been examined extensively. However, little is known on a genome-wide scale about these proteins in other members of the Brassicaceae. In this study, 51 caleosins in Brassica plants and Arabidopsis lyrata were investigated and analyzed in silico. Among them, 31 caleosins, including 7 in A. lyrata, 11 in Brassica oleracea and 13 in Brassica napus, are herein identified for the first time. Segmental duplication was the main form of gene expansion. Alignment, motif and phylogenetic analyses showed that Brassica caleosins belong to either the H-family or the L-family with different motif structures and physicochemical properties. Our findings strongly suggest that L-caleosins are evolved from H-caleosins. Predicted phosphorylation sites were differentially conserved in H-caleosin and L-caleosins, respectively. ‘RY-repeat’ elements and phytohormone-related cis-elements were identified in different caleosins, which suggest diverse physiological functions. Gene structure analysis indicated that most caleosins (38 out of 44) contained six exons and five introns and their intron phases were highly conserved. Structurally integrated caleosins, such as BrCLO3-3 and BrCLO4-2, showed high expression levels and may have important roles. Some caleosins, such as BrCLO2 and BoCLO8-2, lost motifs of the calcium binding domain, proline knot, potential phosphorylation sites and haem-binding sites. Combined with their low expression, it is suggested that these caleosins may have lost function.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (31270295) and funding provided by Northwest A&F University, China.

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    Authors and Affiliations

    1. College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

      Yue Shen & Zhixi Li

    2. College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

      Yue Shen, Mingzhe Liu, Lili Wang, Zhuowei Li & Meng Zhang

    3. National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada

      David C. Taylor

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    Communicated by S. Hohmann.

    Y. Shen and M. Liu have contributed equally to this publication.

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    Supplemental table 1

    Caleosin genes in A. lyrata, B. rapa, B. oleracea and B. napus (XLS 42 kb)

    Supplemental Fig. 1

    Multiple alignments of caleosins in A. thaliana, A. lyrata, B. rapa, B. oleracea and B. napus. H-form insertion, calcium binding motif and proline-knot domains are boxed with red lines. Putative phosphorylation sites of L-caleosins are marked by a blue box. Putative phosphorylation sites of H-caleosins are marked by a green box. Five fully conserved residues are shown by an upper red circle. The highly conserved histidine sites were indicated by black arrows (PDF 508 kb)

    Supplemental Fig. 2

    Hydrophobicity and the folding prediction of two Arabidopsis caleosins AtCLO1 (AT4G26740) and AtCLO3 (AT2G33380) (PDF 105 kb)

    Supplemental table 2, 3, 4, 5

    Expression data of caleosin genes in different tissues using RNA-seq and ESTs in B. rapa and B. oleracea, and ESTs in B. napus. EST libraries used to construct the synthetic libraries in three Brassica species are also shown (XLS 95 kb)

    Supplemental table 6

    Potential cis-elements of crucial B. napus caleosin genes predicted by PLACE and PlantCARE (XLS 43 kb)

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    Shen, Y., Liu, M., Wang, L. et al. Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies. Mol Genet Genomics 291, 971–988 (2016). https://doi.org/10.1007/s00438-015-1156-x

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