Quantitative proteomic survey of endoplasmic reticulum in mouse liver.
To gain a better understanding of the critical function of the endoplasmic reticulum (ER) in liver, we carried out a proteomic survey of mouse liver ER. The ER proteome was profiled with a new three-dimensional, gel-based strategy. From 6152 and 6935 MS spectra, 903 and 1042 proteins were identified with at least two peptides matches at 95% confidence in the rough (r) and smooth (s) ER, respectively. Comparison of the rER and sER proteomes showed that calcium-binding proteins are significantly enriched in the sER suggesting that the ion-binding function of the ER is compartmentalized. Comparison of the rat and mouse ER proteomes showed that 662 proteins were common to both, comprising 53.5% and 49.3% of those proteomes, respectively. We proposed that these proteins were stably expressed proteins that were essential for the maintenance of ER function. GO annotation with a hypergeometric model proved this hypothesis. Unexpectedly, 210 unknown proteins and some proteins previously reported to occur in the cytosol were highly enriched in the ER. This study provides a reference map for the ER proteome of liver. Identification of new ER proteins will enhance our current understanding of the ER and also suggest new functions for this organelle.
Song
Yanping
Y
State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, PR China.
Jiang
Ying
Y
Ying
Wantao
W
Gong
Yan
Y
Yan
Yujuan
Y
Yang
Dong
D
Ma
Jie
J
Xue
Xiaofang
X
Zhong
Fan
F
Wu
Songfeng
S
Hao
Yunwei
Y
Sun
Aihua
A
Li
Tao
T
Sun
Wei
W
Wei
Handong
H
Zhu
Yunping
Y
Qian
Xiaohong
X
He
Fuchu
F
D000818:Animals; D016000:Cluster Analysis; D003577:Cytochrome P-450 Enzyme System / Q000378:metabolism; D057225:Data Mining; D030562:Databases, Protein; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D018870:Endoplasmic Reticulum, Rough / Q000737:chemistry* / Q000378:metabolism; D018871:Endoplasmic Reticulum, Smooth / Q000737:chemistry* / Q000378:metabolism; D008099:Liver / Q000737:chemistry* / Q000378:metabolism; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D010455:Peptides / Q000737:chemistry; D020543:Proteome / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D051381:Rats; D018709:Statistics, Nonparametric; D013347:Subcellular Fractions / Q000737:chemistry / Q000378:metabolism
D010455:Peptides; D020543:Proteome; D003577:Cytochrome P-450 Enzyme System