TY - JOUR
T1 - Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630
AU - Chen, Yong
AU - Ding, Yunfeng
AU - Yang, Li
AU - Yu, Jinhai
AU - Liu, Guiming
AU - Wang, Xumin
AU - Zhang, Shuyan
AU - Yu, Dan
AU - Song, Lai
AU - Zhang, Hangxiao
AU - Zhang, Congyan
AU - Huo, Linhe
AU - Huo, Chaoxing
AU - Wang, Yang
AU - Du, Yalan
AU - Zhang, Huina
AU - Zhang, Peng
AU - Na, Huimin
AU - Xu, Shimeng
AU - Zhu, Yaxin
AU - Xie, Zhensheng
AU - He, Tong
AU - Zhang, Yue
AU - Wang, Guoliang
AU - Fan, Zhonghua
AU - Yang, Fuquan
AU - Liu, Honglei
AU - Wang, Xiaowo
AU - Zhang, Xuegong
AU - Zhang, Michael Q.
AU - Li, Yanda
AU - Steinbüchel, Alexander
AU - Toyoshi, Fujimoto
AU - Simon, Cichello
AU - Yu, Jun
AU - Liu, Pingsheng
N1 - Funding Information:
Ministry of Science and Technology of China [2009CB919000, 2011CBA00906, 2012CB316500, 2012DFG32160]; National Natural Science Foundation of China [30971431, 31000365, 61273228, 31100068, 91019016]. Funding for open access charge: Ministry of Science and Technology of China.
PY - 2014/1/1
Y1 - 2014/1/1
N2 - Rhodococcus opacus strain PD630 (R. opacus PD630), is an oleaginous bacterium, and also is one of few prokaryotic organisms that contain lipid droplets (LDs). LD is an important organelle for lipid storage but also intercellular communication regarding energy metabolism, and yet is a poorly understood cellular organelle. To understand the dynamics of LD using a simple model organism, we conducted a series of comprehensive omics studies of R. opacus PD630 including complete genome, transcriptome and proteome analysis. The genome of R. opacus PD630 encodes 8947 genes that are significantly enriched in the lipid transport, synthesis and metabolic, indicating a super ability of carbon source biosynthesis and catabolism. The comparative transcriptome analysis from three culture conditions revealed the landscape of gene-altered expressions responsible for lipid accumulation. The LD proteomes further identified the proteins that mediate lipid synthesis, storage and other biological functions. Integrating these three omics uncovered 177 proteins that may be involved in lipid metabolism and LD dynamics. A LD structure-like protein LPD06283 was further verified to affect the LD morphology. Our omics studies provide not only a first integrated omics study of prokaryotic LD organelle, but also a systematic platform for facilitating further prokaryotic LD research and biofuel development.
AB - Rhodococcus opacus strain PD630 (R. opacus PD630), is an oleaginous bacterium, and also is one of few prokaryotic organisms that contain lipid droplets (LDs). LD is an important organelle for lipid storage but also intercellular communication regarding energy metabolism, and yet is a poorly understood cellular organelle. To understand the dynamics of LD using a simple model organism, we conducted a series of comprehensive omics studies of R. opacus PD630 including complete genome, transcriptome and proteome analysis. The genome of R. opacus PD630 encodes 8947 genes that are significantly enriched in the lipid transport, synthesis and metabolic, indicating a super ability of carbon source biosynthesis and catabolism. The comparative transcriptome analysis from three culture conditions revealed the landscape of gene-altered expressions responsible for lipid accumulation. The LD proteomes further identified the proteins that mediate lipid synthesis, storage and other biological functions. Integrating these three omics uncovered 177 proteins that may be involved in lipid metabolism and LD dynamics. A LD structure-like protein LPD06283 was further verified to affect the LD morphology. Our omics studies provide not only a first integrated omics study of prokaryotic LD organelle, but also a systematic platform for facilitating further prokaryotic LD research and biofuel development.
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U2 - 10.1093/nar/gkt932
DO - 10.1093/nar/gkt932
M3 - Article
C2 - 24150943
AN - SCOPUS:84893274031
SN - 0305-1048
VL - 42
SP - 1052
EP - 1064
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - 2
ER -