GENOME-WIDE CHARACTERIZATION AND PHYLOGENETIC AND EXPRESSION ANALYSES OF THE CALEOSIN GENE FAMILY IN SOYBEAN, COMMON BEAN AND BARREL MEDIC

Authors

  • Yue Shen 1. College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi; 2. College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi
  • Qing-Li Jia College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi
  • Ming-Zhe Liu College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi
  • Zhuo-Wei Li College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi
  • Li-Li Wang College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi
  • Cui-Zhu Zhao College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi
  • Zhi-Xi Li College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi
  • Meng Zhang College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi

Abstract

Caleosin are a class of calcium-binding proteins embedded in the phospholipid monolayer of lipid droplets. In addition to maintaining the structure of lipid droplets, caleosin proteins are involved in dormancy and lipid signaling, and are associated with the stress response via their histidine-dependent peroxygenase activity. To date, caleosins have been studied in Arabidopsis thaliana. However, little is known about these genes in legumes, including the most cultivated oilseed crop, soybean. In this paper, 20 caleosin genes in soybean, common bean and barrel medic were studied. Among these, 13 caleosin genes, including 3 in Glycine max, 5 in Phaseolus vulgaris and 5 in Medicago truncatula, are identified for the first time. The structures, characteristics and evolution of the 20 caleosin proteins are analyzed. Expansion patterns show that tandem duplication was the main reason for the caleosin family expansion in the legume. Expression profiles indicate that L-caleosin in soybean and common bean are more important than H-caleosin, which is just the opposite in Arabidopsis thaliana. GmaCLO2, PvuCLO1, PvuCLO3 and MtrCLO3 may play important roles, while GmaCLO6, GmaCLO10 and MtrCLO4 may lose their function in the examined tissues. In addition, according to the results of cis-element analyses, we propose potential functions for the more important caleosin genes in leguminous plants. Our work provides helpful information for further evolution and function analyses of the caleosin gene family in soybean, common bean and barrel medic.

 

Key words: Caleosin; evolution; expression; function; legume

 

Received: September 16, 2015; Revised: December 29, 2015; Accepted: December 29, 2015; Published online: April 27, 2016

Downloads

Download data is not yet available.

References

USDA. Oilseeds: World Markets and Trade. 2014. Available: http://www.fas.usda.gov/data/oilseeds-world-markets-and-trade.

Chapman KD, Dyer JM, Mullen RT. Biogenesis and functions of lipid droplets in plants. Thematic Review Series: Lipid Droplet Synthesis and Metabolism: from Yeast to Man. J Lipid Res. 2012;53(2):215-26.

Chen JC, Tsai CC, Tzen JTC. Cloning and secondary structure analysis of caleosin, a unique calcium-binding protein in oil bodies of plant seeds. Plant Cell Physiol. 1999;40(10):1079-86.

Hernandez-Pinzon I, Patel K, Murphy DJ. The Brassica napus calcium-binding protein, caleosin, has distinct endoplasmic reticulum- and lipid body-associated isoforms. Plant Physiol Biochem. 2001;39(7):615-22.

Murphy DJ. The dynamic roles of intracellular lipid droplets: from archaea to mammals. Protoplasma. 2012;249(3):541-85.

Shen Y, Xie J, Liu R-d, Ni X-f, Wang X-h, Li Z-x, Zhang M. Genomic analysis and expression investigation of caleosin gene family in Arabidopsis. Biochem Biophys Res Commun. 2014;448(4):365-71.

Blée E, Boachon B, Burcklen M, Le Guédard M, Hanano A, Heintz D, Ehlting J, Herrfurth C, Feussner I, Bessoule J-J. The reductase activity of the Arabidopsis caleosin RESPONSIVE TO DESSICATION20 mediates gibberellin-dependent flowering time, abscisic acid sensitivity, and tolerance to oxidative stress. Plant Physiol. 2014;166(1):109-24.

Blée E, Flenet M, Boachon B, Fauconnier ML. A non-canonical caleosin from Arabidopsis efficiently epoxidizes physiological unsaturated fatty acids with complete stereoselectivity. FEBS J. 2012;279(20):3981-95.

Hanano A, Burcklen M, Flenet M, Ivancich A, Louwagie M, Garin J, Blée E. Plant seed peroxygenase is an original heme-oxygenase with an EF-hand calcium binding motif. J Biol Chem. 2006;281(44):33140-51.

Zhao L, Chen Y, Cao Y, Kong X, Hua Y. The integral and extrinsic bioactive proteins in the aqueous extracted soybean oil bodies. J Agr Food Chem. 2013;61(40):9727-33.

Song W, Qin Y, Zhu Y, Yin G, Wu N, Li Y, Hu Y. Delineation of plant caleosin residues critical for functional divergence, positive selection and coevolution. BMC Evol Biol. 2014;14(1):124.

Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463(7278):178-83.

Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet. 2014;46(7):707-13.

Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature. 2011;480(7378):520-4.

Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 2012;40(D1):D1202-D1210.

Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012;40(D1):D1178-D1186.

Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30(9):1236-40.

Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003;31(13):3784-8.

Blom N, Gammeltoft S, Brunak S. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol. 1999;294(5):1351-62.

Bailey TL, Williams N, Misleh C, Li WW. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 2006;34(suppl 2):W369-W373.

Larkin MA, Blackshields G, Brown N, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947-8.

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725-9.

Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59(3):307-21.

Ma H, Zhao J. Genome-wide identification, classification, and expression analysis of the arabinogalactan protein gene family in rice (Oryza sativa L.). J Exp Bot. 2010;61(10):2647-68.

Maher C, Stein L, Ware D. Evolution of Arabidopsis microRNA families through duplication events. Genome Res. 2006;16(4):510-9.

Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 2006;34(suppl 2):W609-W612.

He J, Benedito VA, Wang M, Murray JD, Zhao PX, Tang Y, Udvardi MK. The Medicago truncatula gene expression atlas web server. BMC Bioinformatics. 2009;10(1):441.

Team RC. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2012.

Higo K, Ugawa Y, Iwamoto M, Korenaga T. Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res. 1999;27(1):297-300.

Chen D-H, Chyan C-L, Jiang P-L, Chen C-S, Tzen JTC. The same oleosin isoforms are present in oil bodies of rice embryo and aleurone layer while caleosin exists only in those of the embryo. Plant Physiol Biochem. 2012;60:18-24.

Vermachova M, Purkrtova Z, Santrucek J, Jolivet P, Chardot T, Kodicek M. New protein isoforms identified within Arabidopsis thaliana seed oil bodies combining chymotrypsin/trypsin digestion and peptide fragmentation analysis. Proteomics. 2011;11(16):3430-4.

Blanc G, Hokamp K, Wolfe KH. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 2003;13(2):137-44.

Cheng F, Wu J, Wang X. Genome triplication drove the diversification of Brassica plants. Hortic Res. 2014;1:14024.

McGlew K, Shaw V, Zhang M, Kim RJ, Yang W, Shorrosh B, Suh MC, Ohlrogge J. An annotated database of Arabidopsis mutants of acyl lipid metabolism. Plant Cell Rep. 2015;34(4):519-32.

Wang HW, Zhang B, Hao YJ, Huang J, Tian AG, Liao Y, Zhang JS, Chen SY. The soybean Dof-type transcription factor genes, GmDof4 and GmDof11, enhance lipid content in the seeds of transgenic Arabidopsis plants. Plant J. 2007;52(4):716-29.

Kaplan B, Davydov O, Knight H, Galon Y, Knight MR, Fluhr R, Fromm H. Rapid transcriptome changes induced by cytosolic Ca2+ transients reveal ABRE-related sequences as Ca2+-responsive cis elements in Arabidopsis. Plant Cell. 2006;18(10):2733-48.

Downloads

Published

2016-09-05

How to Cite

1.
Shen Y, Jia Q-L, Liu M-Z, Li Z-W, Wang L-L, Zhao C-Z, Li Z-X, Zhang M. GENOME-WIDE CHARACTERIZATION AND PHYLOGENETIC AND EXPRESSION ANALYSES OF THE CALEOSIN GENE FAMILY IN SOYBEAN, COMMON BEAN AND BARREL MEDIC. Arch Biol Sci [Internet]. 2016Sep.5 [cited 2024Nov.21];68(3):575-8. Available from: https://serbiosoc.org.rs/arch/index.php/abs/article/view/977

Issue

Vol. 68 No. 3 (2016)

Section

Articles

License

Authors grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution 4.0 International License that allows others to share the work with an acknowledgment of the work’s authorship and initial publication in this journal.