title: Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630.
abstract: 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.
authors.affiliation: National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China, University of the Chinese Academy of Sciences, Beijing 100049, China, Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China, Department of Histology and Embryology, University of South China, Hengyang Hunan Province 421001, China, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China, School of Applied Mathematics, Central University of Finance and Economics, Beijing 102206, China, Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Dallas, TX 75083-0688, USA, Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Corrensstrasse 3, D-48149 Münster, Germany, Environmental Sciences Department, King Abdulaziz University, Jeddah 21589, Saudi Arabia, Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa, Nagoya 466-8550, Japan and School of Life Sciences, La Trobe University, Melbourne, Victoria, 3086, Australia.
authors.forename: Yong
authors.initials: Y
authors.lastname: Chen
authors.forename: Yunfeng
authors.initials: Y
authors.lastname: Ding
authors.forename: Li
authors.initials: L
authors.lastname: Yang
authors.forename: Jinhai
authors.initials: J
authors.lastname: Yu
authors.forename: Guiming
authors.initials: G
authors.lastname: Liu
authors.forename: Xumin
authors.initials: X
authors.lastname: Wang
authors.forename: Shuyan
authors.initials: S
authors.lastname: Zhang
authors.forename: Dan
authors.initials: D
authors.lastname: Yu
authors.forename: Lai
authors.initials: L
authors.lastname: Song
authors.forename: Hangxiao
authors.initials: H
authors.lastname: Zhang
authors.forename: Congyan
authors.initials: C
authors.lastname: Zhang
authors.forename: Linhe
authors.initials: L
authors.lastname: Huo
authors.forename: Chaoxing
authors.initials: C
authors.lastname: Huo
authors.forename: Yang
authors.initials: Y
authors.lastname: Wang
authors.forename: Yalan
authors.initials: Y
authors.lastname: Du
authors.forename: Huina
authors.initials: H
authors.lastname: Zhang
authors.forename: Peng
authors.initials: P
authors.lastname: Zhang
authors.forename: Huimin
authors.initials: H
authors.lastname: Na
authors.forename: Shimeng
authors.initials: S
authors.lastname: Xu
authors.forename: Yaxin
authors.initials: Y
authors.lastname: Zhu
authors.forename: Zhensheng
authors.initials: Z
authors.lastname: Xie
authors.forename: Tong
authors.initials: T
authors.lastname: He
authors.forename: Yue
authors.initials: Y
authors.lastname: Zhang
authors.forename: Guoliang
authors.initials: G
authors.lastname: Wang
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Fan
authors.forename: Fuquan
authors.initials: F
authors.lastname: Yang
authors.forename: Honglei
authors.initials: H
authors.lastname: Liu
authors.forename: Xiaowo
authors.initials: X
authors.lastname: Wang
authors.forename: Xuegong
authors.initials: X
authors.lastname: Zhang
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
authors.forename: Yanda
authors.initials: Y
authors.lastname: Li
authors.forename: Alexander
authors.initials: A
authors.lastname: Steinbüchel
authors.forename: Toyoshi
authors.initials: T
authors.lastname: Fujimoto
authors.forename: Simon
authors.initials: S
authors.lastname: Cichello
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Pingsheng
authors.initials: P
authors.lastname: Liu
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D015870:Gene Expression; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D023281:Genomics; D050356:Lipid Metabolism; D008055:Lipids; D015388:Organelles / Q000378:metabolism / Q000648:ultrastructure; D040901:Proteomics; D012240:Rhodococcus / Q000235:genetics / Q000378:metabolism* / Q000648:ultrastructure; D014280:Triglycerides / Q000096:biosynthesis / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D008055:Lipids; D014280:Triglycerides