title: Conserved structure and varied expression reveal key roles of phosphoglucan phosphatase gene starch excess 4 in barley.
abstract: As one of the phosphoglucan phosphatases, starch excess 4 (SEX4) encoded by SEX4 gene has recently been intensively studied because of its vital role in the degradation of leaf starch. In this study, we isolated and chromosomally mapped barley SEX4, characterized its gene and protein structure, predicted the cis-elements of its promoter, and analysed its expression based on real-time quantitative PCR and publically available microarray data. The full length of barely SEX4 (HvSEX4) was 4,598 bp and it was mapped on the long arm of chromosome 4H (4HL). This gene contained 14 exons and 13 introns in all but two of the species analysed, Arabidopsis (13 exons and 12 introns) and Oryza brachyantha (12 exons and 11 introns). An exon-intron junction composed of intron 4 to intron 7 and exon 5 to exon 8 was highly conserved among the analysed species. SEX4 is characterized with conserved functional domains (dual specificity phosphatase domain and carbohydrate-binding module 48) and varied chloroplast transit peptide and C-terminal. Expression analyses indicated that: (1) SEX4 was mainly expressed in anthers of barley, young leaf and anthers of rice, and leaf of Arabidopsis; (2) it exhibited a diurnal pattern in barley, rice and Arabidopsis; (3) significant difference in the expression of SEX4 was not detected for either barley or rice under any of the investigated stresses; and (4) it was significantly down-regulated at middle stage and up-regulated at late stage under cold treatment, down-regulated at early stage under heat treatment, and up-regulated at late stage under salt treatment in Arabidopsis. The strong relationships detected in the current study between SEX4 and glucan, water dikinases (GWD) or phosphoglucan, water dikinases (PWD) were discussed. Collectively, our results provide insights into genetic manipulation of SEX4, especially in monocotyledon and uncovering the possible roles of SEX4 in plant development.
authors.affiliation: Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Ma
authors.forename: Qian-Tao
authors.initials: QT
authors.lastname: Jiang
authors.forename: Long
authors.initials: L
authors.lastname: Wei
authors.forename: Qiang
authors.initials: Q
authors.lastname: Yang
authors.forename: Xiao-Wei
authors.initials: XW
authors.lastname: Zhang
authors.forename: Yuan-Ying
authors.initials: YY
authors.lastname: Peng
authors.forename: Guo-Yue
authors.initials: GY
authors.lastname: Chen
authors.forename: Yu-Ming
authors.initials: YM
authors.lastname: Wei
authors.forename: Chunji
authors.initials: C
authors.lastname: Liu
authors.forename: You-Liang
authors.initials: YL
authors.lastname: Zheng
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D002940:Circadian Rhythm / Q000187:drug effects / Q000235:genetics; D017124:Conserved Sequence; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant; D005936:Glucans / Q000378:metabolism*; D001467:Hordeum / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity / Q000235:genetics; D012275:Oryza / Q000187:drug effects / Q000235:genetics; D010744:Phosphoric Monoester Hydrolases / Q000235:genetics* / Q000378:metabolism; D010766:Phosphorylation / Q000187:drug effects; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D012965:Sodium Chloride / Q000494:pharmacology; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics
chemical_list: D005936:Glucans; D010940:Plant Proteins; D012965:Sodium Chloride; D010744:Phosphoric Monoester Hydrolases
references.citation: BMC Evol Biol. 2009 Jun 22;9:138
references.pmid: 19545434
references.citation: Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15379-84
references.pmid: 20679247
references.citation: Nat Protoc. 2007;2(4):953-71
references.pmid: 17446895
references.citation: Proc Natl Acad Sci U S A. 2014 May 20;111(20):7272-7
references.pmid: 24799671
references.citation: Genetica. 2011 Oct;139(10):1283-92
references.pmid: 22290495
references.citation: Plant Biotechnol J. 2012 Sep;10(7):871-82
references.pmid: 22672098
references.citation: Front Plant Sci. 2013 May 27;4:147
references.pmid: 23750161
references.citation: Plant Physiol. 2014 Apr 29;165(2):866-879
references.pmid: 24781197
references.citation: Plant Mol Biol. 2010 Oct;74(3):307-11
references.pmid: 20658259
references.citation: PLoS One. 2014 Jan 31;9(1):e87333
references.pmid: 24498076
references.citation: Mol Biol Evol. 2013 Dec;30(12):2725-9
references.pmid: 24132122
references.citation: Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9732-7
references.pmid: 16772378
references.citation: Plant Physiol. 2009 Jun;150(2):962-76
references.pmid: 19395406
references.citation: Nature. 2012 May 30;485(7400):635-41
references.pmid: 22660326
references.citation: Planta. 2013 Dec;238(6):1081-93
references.pmid: 24002549
references.citation: Methods. 2001 Dec;25(4):402-8
references.pmid: 11846609
references.citation: Nucleic Acids Res. 1999 Jan 1;27(1):297-300
references.pmid: 9847208
references.citation: Carbohydr Polym. 2012 Jul 1;89(3):979-91
references.pmid: 24750889
references.citation: Annu Rev Plant Biol. 2010;61:209-34
references.pmid: 20192737
references.citation: Plant Cell. 2011 Nov;23(11):4096-111
references.pmid: 22100529
references.citation: Nature. 2011 Nov 16;480(7378):520-4
references.pmid: 22089132
references.citation: Plant Physiol. 2010 Feb;152(2):711-22
references.pmid: 20018599
references.citation: Plant J. 2006 May;46(3):400-13
references.pmid: 16623901
references.citation: Plant Physiol. 2009 May;150(1):190-204
references.pmid: 19321714
references.citation: Science. 2014 Jul 18;345(6194):1251788
references.pmid: 25035500
references.citation: New Phytol. 2014 Jul;203(2):495-507
references.pmid: 24697163
references.citation: Trends Plant Sci. 2014 Jul;19(7):471-8
references.pmid: 24534096
references.citation: Nat Rev Genet. 2012 Mar 13;13(4):227-32
references.pmid: 22411467
references.citation: Plant Cell. 2009 Jan;21(1):334-46
references.pmid: 19141707
references.citation: Genome. 2007 Oct;50(10):898-906
references.pmid: 18059553
references.citation: J Cell Biol. 2007 Jul 30;178(3):477-88
references.pmid: 17646401
references.citation: Genetica. 2013 Jun;141(4-6):227-38
references.pmid: 23690246
references.citation: Biotechnol Adv. 2014 Jan-Feb;32(1):87-106
references.pmid: 23827783
references.citation: Plant J. 2009 Jan;57(1):1-13
references.pmid: 18764922
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417
references.citation: Nucleic Acids Res. 1980 Oct 10;8(19):4321-5
references.pmid: 7433111