综合组学研究描绘了 Rhodococcus opacus PD630 中脂滴的动态变化。
Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630.
机构信息
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.
出版信息
Nucleic Acids Res. 2014 Jan;42(2):1052-64. doi: 10.1093/nar/gkt932. Epub 2013 Oct 22.
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.
费氏中华根瘤菌（Rhodococcus opacus strain PD630，R. opacus PD630）是一种产油细菌，也是少数含有脂滴（lipid droplets，LDs）的原核生物之一。LD 是一种重要的细胞器，用于储存脂质，但也是细胞间能量代谢的重要通讯媒介，然而它仍然是一个了解甚少的细胞细胞器。为了使用简单的模式生物来了解 LD 的动态，我们对 R. opacus PD630 进行了一系列全面的组学研究，包括全基因组、转录组和蛋白质组分析。R. opacus PD630 的基因组编码 8947 个基因，这些基因在脂质运输、合成和代谢方面显著富集，表明其具有超强的碳源生物合成和分解代谢能力。对三种培养条件下的比较转录组分析揭示了导致脂质积累的基因表达变化的全貌。LD 蛋白质组学进一步鉴定了介导脂质合成、储存和其他生物学功能的蛋白质。整合这三个组学揭示了 177 种可能参与脂质代谢和 LD 动态的蛋白质。进一步验证了一种 LD 结构样蛋白 LPD06283 可能影响 LD 形态。我们的组学研究不仅提供了原核 LD 细胞器的首次综合组学研究，而且为促进进一步的原核 LD 研究和生物燃料开发提供了一个系统的平台。
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