DGE-seq analysis of MUR3-related Arabidopsis mutants provides insight into how dysfunctional xyloglucan affects cell elongation.
Our previous study of the Arabidopsis mur3-3 mutant and mutant plants in which the mur3-3 phenotypes are suppressed (xxt2mur3-3, xxt5mur3-3, xxt1xxt2mur3-3 and 35Spro:XLT2:mur3-3) showed that hypocotyl cell elongation is decreased in plants that synthesize galactose-deficient xyloglucan. To obtain genome-wide insight into the transcriptome changes and regulatory networks that may be involved in this decreased elongation, we performed digital gene expression analyses of the etiolated hypocotyls of wild type (WT), mur3-3 and the four suppressor lines. Numerous differentially expressed genes (DEGs) were detected in comparisons between WT and mur3-3 (1423), xxt2mur3-3 and mur3-3 (675), xxt5mur3-3 and mur3-3 (1272), xxt1xxt2mur3-3 and mur3-3 (1197) and 35Spro:XLT2:mur3-3 vs mur3-3 (121). 550 overlapped DEGs were detected among WT vs mur3-3, xxt2mur3-3 vs mur3-3, xxt5mur3-3 vs mur3-3, and xxt1xxt2mur3-3 vs mur3-3 comparisons. These DEGs include 46 cell wall-related genes, 24 transcription factors, 6 hormone-related genes, 9 protein kinase genes and 9 aquaporin genes. The expression of all of the 550 overlapped genes is restored to near wild-type levels in the four mur3-3 suppressor lines. qRT-PCR of fifteen of these 550 genes showed that their expression levels are consistent with the digital gene expression data. Overexpression of some of these genes (XTH4, XTH30, PME3, EXPA11, MYB88, ROT3, AT5G37790, WAG2 and TIP2;3) that are down-regulated in mur3-3 partially rescued the short hypocotyl phenotype but not the aerial phenotype of mur3-3, indicating that different mechanisms exist between hypocotyl cell elongation and leaf cell elongation.
Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, PR China; Graduate School of Chinese Academy of Agricultural Science, Beijing 100081, PR China. Electronic address: xuzc1110@163.com.
Zongchang
Z
Xu
Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, PR China; Graduate School of Chinese Academy of Agricultural Science, Beijing 100081, PR China. Electronic address: menglihua@yeah.net.
Meng
M
Wang
Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, PR China. Electronic address: shidc@qibebt.ac.cn.
Dachuan
D
Shi
Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China. Electronic address: zhougk@qibebt.ac.cn.
Gongke
G
Zhou
Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, PR China. Electronic address: tian15288861055@163.com.
Tiantian
T
Niu
Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-4712 USA; Department of Plant Biology, University of Georgia, Athens, GA 30602-4712 USA. Electronic address: hahn@ccrc.uga.edu.
Michael G
MG
Hahn
Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602-4712 USA. Electronic address: mao@ccrc.uga.edu.
Malcolm A
MA
O'Neill
Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, PR China. Electronic address: kongyingzhen@caas.cn.
Yingzhen
Y
Kong
D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D049108:Cell Enlargement; D005700:Galactosyltransferases / Q000235:genetics / Q000502:physiology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000502:physiology; D005936:Glucans / Q000378:metabolism / Q000502:physiology*; D009154:Mutation; D060888:Real-Time Polymerase Chain Reaction; D014990:Xylans / Q000378:metabolism
D005936:Glucans; D014990:Xylans; C029353:xyloglucan; D005700:Galactosyltransferases; C478982:MUR3 protein, Arabidopsis
Arabidopsis; Cell elongation; DGE-seq; Hypocotyl; MUR3; Xyloglucan