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Juarez A, Villa JA, Lanza VF, Lázaro B, de la Cruz F, Alvarez HM, Moncalián G. Nutrient starvation leading to triglyceride accumulation activates the Entner Doudoroff pathway in Rhodococcus jostii RHA1. Microb Cell Fact 2017; 16:35. [PMID: 28241831 PMCID: PMC5327559 DOI: 10.1186/s12934-017-0651-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 02/22/2017] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Rhodococcus jostii RHA1 and other actinobacteria accumulate triglycerides (TAG) under nutrient starvation. This property has an important biotechnological potential in the production of sustainable oils. RESULTS To gain insight into the metabolic pathways involved in TAG accumulation, we analysed the transcriptome of R jostii RHA1 under nutrient-limiting conditions. We correlate these physiological conditions with significant changes in cell physiology. The main consequence was a global switch from catabolic to anabolic pathways. Interestingly, the Entner-Doudoroff (ED) pathway was upregulated in detriment of the glycolysis or pentose phosphate pathways. ED induction was independent of the carbon source (either gluconate or glucose). Some of the diacylglycerol acyltransferase genes involved in the last step of the Kennedy pathway were also upregulated. A common feature of the promoter region of most upregulated genes was the presence of a consensus binding sequence for the cAMP-dependent CRP regulator. CONCLUSION This is the first experimental observation of an ED shift under nutrient starvation conditions. Knowledge of this switch could help in the design of metabolomic approaches to optimize carbon derivation for single cell oil production.
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Affiliation(s)
- Antonio Juarez
- Institut de Bioenginyeria de Catalunya, Parc Científic de Barcelona, 08028, Barcelona, Spain.,Departamento de Microbiología, Facultad de Biología, Universidad de Barcelona, Avda Diagonal, 643., 08028, Barcelona, Spain
| | - Juan A Villa
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (CSIC-UC), C/Albert Einstein 22, 39011, Santander, Spain
| | - Val F Lanza
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (CSIC-UC), C/Albert Einstein 22, 39011, Santander, Spain
| | - Beatriz Lázaro
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (CSIC-UC), C/Albert Einstein 22, 39011, Santander, Spain
| | - Fernando de la Cruz
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (CSIC-UC), C/Albert Einstein 22, 39011, Santander, Spain
| | - Héctor M Alvarez
- INBIOP (Instituto de Biociencias de la Patagonia), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco, Ruta Provincial No 1, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina
| | - Gabriel Moncalián
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (CSIC-UC), C/Albert Einstein 22, 39011, Santander, Spain.
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Lagrutta LC, Montero-Villegas S, Layerenza JP, Sisti MS, García de Bravo MM, Ves-Losada A. Reversible Nuclear-Lipid-Droplet Morphology Induced by Oleic Acid: A Link to Cellular-Lipid Metabolism. PLoS One 2017; 12:e0170608. [PMID: 28125673 PMCID: PMC5268491 DOI: 10.1371/journal.pone.0170608] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/07/2017] [Indexed: 12/19/2022] Open
Abstract
Neutral lipids—involved in many cellular processes—are stored as lipid droplets (LD), those mainly cytosolic (cLD) along with a small nuclear population (nLD). nLD could be involved in nuclear-lipid homeostasis serving as an endonuclear buffering system that would provide or incorporate lipids and proteins involved in signalling pathways as transcription factors and as enzymes of lipid metabolism and nuclear processes. Our aim was to determine if nLD constituted a dynamic domain. Oleic-acid (OA) added to rat hepatocytes or HepG2 cells in culture produced cellular-phenotypic LD modifications: increases in TAG, CE, C, and PL content and in cLD and nLD numbers and sizes. LD increments were reversed on exclusion of OA and were prevented by inhibition of acyl-CoA synthetase (with Triacsin C) and thus lipid biosynthesis. Under all conditions, nLD corresponded to a small population (2–10%) of total cellular LD. The anabolism triggered by OA, involving morphologic and size changes within the cLD and nLD populations, was reversed by a net balance of catabolism, upon eliminating OA. These catabolic processes included lipolysis and the mobilization of hydrolyzed FA from the LD to cytosolic-oxidation sites. These results would imply that nLD are actively involved in nuclear processes that include lipids. In conclusion, nLD are a dynamic nuclear domain since they are modified by OA through a reversible mechanism in combination with cLD; this process involves acyl-CoA-synthetase activity; ongoing TAG, CE, and PL biosynthesis. Thus, liver nLD and cLD are both dynamic cellular organelles.
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Affiliation(s)
- Lucía C. Lagrutta
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP), La Plata, Buenos Aires, Argentina
| | - Sandra Montero-Villegas
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP), La Plata, Buenos Aires, Argentina
| | - Juan P. Layerenza
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP), La Plata, Buenos Aires, Argentina
| | - Martín S. Sisti
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP), La Plata, Buenos Aires, Argentina
| | - Margarita M. García de Bravo
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP), La Plata, Buenos Aires, Argentina
- Cátedra de Biología, Facultad de Ciencias Médicas, Universidad Nacional de La Plata; La Plata, Buenos Aires, Argentina
| | - Ana Ves-Losada
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP), La Plata, Buenos Aires, Argentina
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- * E-mail:
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53
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Hernández MA, Lara J, Gago G, Gramajo H, Alvarez HM. The pleiotropic transcriptional regulator NlpR contributes to the modulation of nitrogen metabolism, lipogenesis and triacylglycerol accumulation in oleaginous rhodococci. Mol Microbiol 2016; 103:366-385. [DOI: 10.1111/mmi.13564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Martín A. Hernández
- INBIOP (Instituto de Biociencias de la Patagonia), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia San Juan Bosco; Ruta Provincial N° 1, Km 4-Ciudad Universitaria 9000 Comodoro Rivadavia Chubut Argentina
| | - Julia Lara
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Ocampo y Esmeralda 2000 Rosario Santa Fe Argentina
| | - Gabriela Gago
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Ocampo y Esmeralda 2000 Rosario Santa Fe Argentina
| | - Hugo Gramajo
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Ocampo y Esmeralda 2000 Rosario Santa Fe Argentina
| | - Héctor M. Alvarez
- INBIOP (Instituto de Biociencias de la Patagonia), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia San Juan Bosco; Ruta Provincial N° 1, Km 4-Ciudad Universitaria 9000 Comodoro Rivadavia Chubut Argentina
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54
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Bi K, He Z, Gao Z, Zhao Y, Fu Y, Cheng J, Xie J, Jiang D, Chen T. Integrated omics study of lipid droplets from Plasmodiophora brassicae. Sci Rep 2016; 6:36965. [PMID: 27874080 PMCID: PMC5118790 DOI: 10.1038/srep36965] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/20/2016] [Indexed: 12/26/2022] Open
Abstract
Plasmodiophora brassicae causes clubroot disease in cruciferous. In this report, lipid droplets were observed in the resting spores of P. brassicae. 295 lipid droplet-associated proteins were identified and categorized into nine groups. Transcriptome analysis of these proteins during three different zoosporic stages revealed differences in gene expression pattern. GO enrichment analysis revealed that these proteins associated with lipid droplets were mainly linked to biosynthesis and metabolism. GC-MS analysis revealed that lipid droplets contain seven types of free fatty acids: saturated fatty acids C16:0 and C18:0, and unsaturated fatty acids C18:1Δ9, C18:1Δ11, C18:2, C20:4 and C20:5. P. brassicae accumulated a large amount of triacylglycerols (TAGs). We systematically analyzed the putative proteins involved in TAG biosynthesis and its metabolic pathway. KEGG pathway analysis defined 3390 genes, including 167 genes involved in lipid metabolism. Transcriptome analysis revealed that 162 candidate enzymes involved in lipid metabolism were differential expressed. Our omics studies are the first to investigate the lipid droplet organelles in P. brassicae, providing a reference resource to study protist lipid droplets.
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Affiliation(s)
- Kai Bi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Zhangchao He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Zhixiao Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Ying Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Yanping Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
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55
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Manganelli R, Gennaro ML. Protecting from Envelope Stress: Variations on the Phage-Shock-Protein Theme. Trends Microbiol 2016; 25:205-216. [PMID: 27865622 DOI: 10.1016/j.tim.2016.10.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/16/2016] [Accepted: 10/24/2016] [Indexed: 01/03/2023]
Abstract
During envelope stress, critical inner-membrane functions are preserved by the phage-shock-protein (Psp) system, a stress response that emerged from work with Escherichia coli and other Gram-negative bacteria. Reciprocal regulatory interactions and multiple effector functions are well documented in these organisms. Searches for the Psp system across phyla reveal conservation of only one protein, PspA. However, examination of Firmicutes and Actinobacteria reveals that PspA orthologs associate with non-orthologous regulatory and effector proteins retaining functions similar to those in Gram-negative counterparts. Conservation across phyla emphasizes the long-standing importance of the Psp system in prokaryotes, while inter- and intra-phyla variations within the system indicate adaptation to different cell envelope structures, bacterial lifestyles, and/or bacterial morphogenetic strategies.
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Affiliation(s)
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA.
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56
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Gong Z, Zhou W, Shen H, Zhao ZK, Yang Z, Yan J, Zhao M. Co-utilization of corn stover hydrolysates and biodiesel-derived glycerol by Cryptococcus curvatus for lipid production. BIORESOURCE TECHNOLOGY 2016; 219:552-558. [PMID: 27529520 DOI: 10.1016/j.biortech.2016.08.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/07/2016] [Accepted: 08/08/2016] [Indexed: 05/26/2023]
Abstract
In the present study, synergistic effects were observed when glycerol was co-fermented with glucose and xylose for lipid production by the oleaginous yeast Cryptococcus curvatus. Glycerol was assimilated simultaneously with sugars at the beginning of the culture without adaption time. Furthermore, better lipid production results, i.e., lipid yield and lipid productivity of 18.0g/100g and 0.13g/L/h, respectively, were achieved when cells were cultured in blends of corn stover hydrolysates and biodiesel-derived glycerol than those in the hydrolysates alone. The lipid samples had fatty acid compositional profiles similar to those of vegetable oils, suggesting their potential for biodiesel production. This co-utilization strategy provides an extremely simple solution to advance lipid production from both lignocelluloses and biodiesel-derived glycerol in one step.
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Affiliation(s)
- Zhiwei Gong
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan 430081, PR China.
| | - Wenting Zhou
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan 430081, PR China
| | - Hongwei Shen
- Dalian National Laboratory for Clean Energy and Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian 116023, PR China
| | - Zongbao K Zhao
- Dalian National Laboratory for Clean Energy and Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian 116023, PR China
| | - Zhonghua Yang
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan 430081, PR China
| | - Jiabao Yan
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan 430081, PR China
| | - Mi Zhao
- China Carbon Balance Energy and Tech LTD, 1 Jianguomenwai Avenue, Beijing 100004, PR China
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57
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Functional divergence of HBHA from Mycobacterium tuberculosis and its evolutionary relationship with TadA from Rhodococcus opacus. Biochimie 2016; 127:241-8. [DOI: 10.1016/j.biochi.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/06/2016] [Indexed: 12/13/2022]
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58
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Zhang S, Wang Y, Cui L, Deng Y, Xu S, Yu J, Cichello S, Serrero G, Ying Y, Liu P. Morphologically and Functionally Distinct Lipid Droplet Subpopulations. Sci Rep 2016; 6:29539. [PMID: 27386790 PMCID: PMC4937419 DOI: 10.1038/srep29539] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/20/2016] [Indexed: 12/12/2022] Open
Abstract
Lipid droplet (LD), a multi-functional organelle, is often found to associate with other cellular membranous structures and vary in size in a given cell, which may be related to their functional diversity. Here we established a method to separate LD subpopulations from isolated CHO K2 LDs into three different size categories. The subpopulation with smallest LDs was nearly free of ER and other membranous structures while those with larger LDs contained intact ER. These distinct subpopulations of LDs differed in their protein composition and ability to recruit proteins. This method was also applicable to LDs obtained from other sources, such as Huh7 cells, mouse liver and brown adipose tissue, et al. We developed an in vitro assay requiring only isolated LDs, Coenzyme A, and ATP to drive lipid synthesis. The LD subpopulation nearly depleted of ER was able to incorporate fatty acids into triacylglycerol and phospholipids. Together, our data demonstrate that LDs in a given cell are heterogeneous in size and function, and suggest that LDs are one of cellular lipid synthetic organelles.
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Affiliation(s)
- Shuyan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liujuan Cui
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yaqin Deng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shimeng Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinhai Yu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Simon Cichello
- School of Life Sciences, La Trobe University, Melbourne Victoria 3086, Australia
| | | | - Yunshu Ying
- University of Texas Southwestern Medical Center, Dallas 75390, USA
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Chen Y, Geng D, Ehrhardt K, Zhang S. Investigating Evolutionary Dynamics of RHA1 Operons. Evol Bioinform Online 2016; 12:157-63. [PMID: 27398020 PMCID: PMC4927040 DOI: 10.4137/ebo.s39753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/30/2016] [Accepted: 06/01/2016] [Indexed: 12/02/2022] Open
Abstract
Grouping genes as operons is an important genomic feature of prokaryotic organisms. The comprehensive understanding of the operon organizations would be helpful to decipher transcriptional mechanisms, cellular pathways, and the evolutionary landscape of prokaryotic genomes. Although thousands of prokaryotes have been sequenced, genome-wide investigation of the evolutionary dynamics (division and recombination) of operons among these genomes remains unexplored. Here, we systematically analyzed the operon dynamics of Rhodococcus jostii RHA1 (RHA1), an oleaginous bacterium with high potential applications in biofuel, by comparing 340 prokaryotic genomes that were carefully selected from different genera. Interestingly, 99% of RHA1 operons were observed to exhibit evolutionary events of division and recombination among the 340 compared genomes. An operon that encodes all enzymes related to histidine biosynthesis in RHA1 (His-operon) was found to be segmented into smaller gene groups (sub-operons) in diverse genomes. These sub-operons were further reorganized with different functional genes as novel operons that are related to different biochemical processes. Comparatively, the operons involved in the functional categories of lipid transport and metabolism are relatively conserved among the 340 compared genomes. At the pathway level, RHA1 operons found to be significantly conserved were involved in ribosome synthesis, oxidative phosphorylation, and fatty acid synthesis. These analyses provide evolutionary insights of operon organization and the dynamic associations of various biochemical pathways in different prokaryotes.
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Affiliation(s)
- Yong Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, USA
| | - Dandan Geng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Computer and Information Engineering, Tianjin Normal University, Tianjin, China
| | - Kristina Ehrhardt
- Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, USA
- Bioengineering Department, The University of Texas at Dallas, Richardson, TX, USA
| | - Shaoqiang Zhang
- College of Computer and Information Engineering, Tianjin Normal University, Tianjin, China
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60
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Rv2744c Is a PspA Ortholog That Regulates Lipid Droplet Homeostasis and Nonreplicating Persistence in Mycobacterium tuberculosis. J Bacteriol 2016; 198:1645-1661. [PMID: 27002134 DOI: 10.1128/jb.01001-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/16/2016] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), remains a significant cause of morbidity and mortality worldwide, despite the availability of a live attenuated vaccine and anti-TB antibiotics. The vast majority of individuals infected with M. tuberculosis develop an asymptomatic latent infection in which the bacterium survives within host-generated granulomatous lesions in a physiologically altered metabolic state of nonreplicating persistence. The granuloma represents an adverse environment, as M. tuberculosis is exposed to various stressors capable of disrupting the essential constituents of the bacterium. In Gram-negative and Gram-positive bacteria, resistance to cell envelope stressors that perturb the plasma membrane is mediated in part by proteins comprising the phage shock protein (Psp) system. PspA is an important component of the Psp system; in the presence of envelope stress, PspA localizes to the inner face of the plasma membrane, homo-oligomerizes to form a large scaffold-like complex, and helps maintain plasma membrane integrity to prevent a loss of proton motive force. M. tuberculosis and other members of the Mycobacterium genus are thought to encode a minimal functional unit of the Psp system, including an ortholog of PspA. Here, we show that Rv2744c possesses structural and physical characteristics that are consistent with its designation as a PspA family member. However, although Rv2744c is upregulated under conditions of cell envelope stress, loss of Rv2744c does not alter resistance to cell envelope stressors. Furthermore, Rv2744c localizes to the surface of lipid droplets in Mycobacterium spp. and regulates lipid droplet number, size, and M. tuberculosis persistence during anaerobically induced dormancy. Collectively, our results indicate that Rv2744c is a bona fide ortholog of PspA that may function in a novel role to regulate lipid droplet homeostasis and nonreplicating persistence (NRP) in M. tuberculosis IMPORTANCE Mycobacterium tuberculosis is the causative agent of tuberculosis, a disease associated with significant morbidity and mortality worldwide. M. tuberculosis is capable of establishing lifelong asymptomatic infections in susceptible individuals and reactivating during periods of immune suppression to cause active disease. The determinants that are important for persistent infection of M. tuberculosis or for reactivation of this organism from latency are poorly understood. In this study, we describe our initial characterizations of Rv2744c, an ortholog of phage shock protein A (PspA) that regulates the homeostasis of lipid bodies and nonreplicating persistence in M. tuberculosis This function of PspA in M. tuberculosis is novel and suggests that PspA may represent a unique bacterial target upon which to base therapeutic interventions against this organism.
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61
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Amara S, Seghezzi N, Otani H, Diaz-Salazar C, Liu J, Eltis LD. Characterization of key triacylglycerol biosynthesis processes in rhodococci. Sci Rep 2016; 6:24985. [PMID: 27126051 PMCID: PMC4850399 DOI: 10.1038/srep24985] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/01/2016] [Indexed: 11/09/2022] Open
Abstract
Oleaginous microorganisms have considerable potential for biofuel and commodity chemical production. Under nitrogen-limitation, Rhodococcus jostii RHA1 grown on benzoate, an analog of lignin depolymerization products, accumulated triacylglycerols (TAGs) to 55% of its dry weight during transition to stationary phase, with the predominant fatty acids being C16:0 and C17:0. Transcriptomic analyses of RHA1 grown under conditions of N-limitation and N-excess revealed 1,826 dysregulated genes. Genes whose transcripts were more abundant under N-limitation included those involved in ammonium assimilation, benzoate catabolism, fatty acid biosynthesis and the methylmalonyl-CoA pathway. Of the 16 atf genes potentially encoding diacylglycerol O-acyltransferases, atf8 transcripts were the most abundant during N-limitation (~50-fold more abundant than during N-excess). Consistent with Atf8 being a physiological determinant of TAG accumulation, a Δatf8 mutant accumulated 70% less TAG than wild-type RHA1 while atf8 overexpression increased TAG accumulation 20%. Genes encoding type-2 phosphatidic acid phosphatases were not significantly expressed. By contrast, three genes potentially encoding phosphatases of the haloacid dehalogenase superfamily and that cluster with, or are fused with other Kennedy pathway genes were dysregulated. Overall, these findings advance our understanding of TAG metabolism in mycolic acid-containing bacteria and provide a framework to engineer strains for increased TAG production.
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Affiliation(s)
- Sawsan Amara
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Nicolas Seghezzi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Hiroshi Otani
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Carlos Diaz-Salazar
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jie Liu
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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Wang Y, Zhou XM, Ma X, Du Y, Zheng L, Liu P. Construction of Nanodroplet/Adiposome and Artificial Lipid Droplets. ACS NANO 2016; 10:3312-3322. [PMID: 26910792 DOI: 10.1021/acsnano.5b06852] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The lipid droplet (LD) is a cellular organelle that consists of a neutral lipid core with a monolayer-phospholipid membrane and associated proteins. Recent LD studies demonstrate its importance in metabolic diseases and biofuel development. However, the mechanisms governing its formation and dynamics remain elusive. Therefore, we developed an in vitro system to facilitate the elucidation of these mechanisms. We generated sphere-shaped structures with a neutral lipid core and a monolayer-phospholipid membrane by mechanically mixing neutral lipids and phospholipids followed by a two-step purification. We named the nanodroplet "adiposome". We then recruited LD structure-like/resident proteins to the adiposome, including the bacterial MLDS, Caenorhabditis elegans MDT-28/PLIN-1, or mammalian perilipin-2. In addition, adipose triglyceride lipase (ATGL) and apolipoprotein A1 (apo A-I) were recruited to adiposome. We termed the functional protein-coated adiposomes, Artificial Lipid Droplets (ALDs). With this experimental system, different proteins can be recruited to build ALDs for some biological goals and potential usage in drug delivery.
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Affiliation(s)
- Yang Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
| | - Xiao-Ming Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
| | - Xuejing Ma
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Yalan Du
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
- Department of Histology and Embryology, University of South China , Hengyang, Hunan 421001, China
| | - Lemin Zheng
- The Institute of Cardiovascular Sciences and Institute of Systems Biomedicine, School of Basic Medical Sciences, and Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, Peking University Health Science Center , Beijing 100191, China
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100049, China
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63
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Targeting Fat: Mechanisms of Protein Localization to Lipid Droplets. Trends Cell Biol 2016; 26:535-546. [PMID: 26995697 DOI: 10.1016/j.tcb.2016.02.007] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 12/18/2022]
Abstract
How proteins specifically localize to the phospholipid monolayer surface of lipid droplets (LDs) is being unraveled. We review here the major known pathways of protein targeting to LDs and suggest a classification framework based on the localization origin for the protein. Class I proteins often have a membrane-embedded, hydrophobic 'hairpin' motif, and access LDs from the endoplasmic reticulum (ER) either during LD formation or after formation via ER-LD membrane bridges. Class II proteins access the LD surface from the cytosol and bind through amphipathic helices or other hydrophobic domains. Other proteins require lipid modifications or protein-protein interactions to bind to LDs. We summarize knowledge for targeting and removal of the different classes, and highlight areas needing investigation.
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Indest KJ, Eberly JO, Hancock DE, Jung CM, Carr MR, Blakeney GA. Rhodococcus jostii RHA1 TadA-homolog deletion mutants accumulate less polyhydroxyalkanoates (PHAs) than the parental strain. J GEN APPL MICROBIOL 2016; 62:213-6. [DOI: 10.2323/jgam.2016.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Karl J. Indest
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Jed O. Eberly
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Dawn E. Hancock
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Carina M. Jung
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Matthew R. Carr
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
| | - Gary A. Blakeney
- U.S. Army Engineer Research and Development Center, Environmental Laboratory
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Metabolic engineering Corynebacterium glutamicum to produce triacylglycerols. Metab Eng 2015; 33:86-97. [PMID: 26645801 DOI: 10.1016/j.ymben.2015.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/04/2015] [Accepted: 11/17/2015] [Indexed: 01/09/2023]
Abstract
In this study, we metabolically engineered Corynebacterium glutamicum to produce triacylglycerols (TAGs) by completing and constraining a de novo TAG biosynthesis pathway. First, the plasmid pZ8_TAG4 was constructed which allows the heterologous expression of four genes: three (atf1 and atf2, encoding the diacylglycerol acyltransferase; pgpB, encoding the phosphatidic acid phosphatase) to complete the TAG biosynthesis pathway, and one gene (tadA) for lipid body assembly. Second, we applied four metabolic strategies to increase TAGs accumulation: (i) boosting precursor supply by heterologous expression of tesA (encoding thioesterase to form free fatty acid to reduce the feedback inhibition by acyl-ACP) and fadD (encoding acyl-CoA synthetase to enhance acyl-CoA supply), (ii) reduction of TAG degradation and precursor consumption by deleting four cellular lipases (cg0109, cg0110, cg1676 and cg1320) and the diacylglycerol kinase (cg2849), (iii) enhancement of fatty acid biosynthesis by deletion of fasR (cg2737, TetR-type transcriptional regulator of genes for the fatty acid biosynthesis), and (iv) elimination of the observed by-product formation of organic acids by blocking the acetic acid (pqo) and lactic acid production (ldh) pathways. The final strain (CgTesRtcEfasEbp/pZ8_TAG4) achieved a 7.5% yield of total fatty acids (2.38 ± 0.05 g/L intracellular fatty acids and 0.64 ± 0.09 g/L extracellular fatty acids) from 4% glucose in shake flasks after process optimization. This corresponds to maximum intracellular fatty acids content of 17.8 ± 0.5% of the dry cell.
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66
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Seoudi RS, Dowd A, Del Borgo M, Kulkarni K, Perlmutter P, Aguilar MI, Mechler A. Amino acid sequence controls the self-assembled superstructure morphology of N-acetylated tri-β3-peptides. PURE APPL CHEM 2015. [DOI: 10.1515/pac-2015-0108] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractPeptides based on unnatural β3-amino acids offer a versatile platform for the design of self-assembling nanostructures due to the folding stability of the 14-helix and the high symmetry of the side chains inherent in this geometry. We have previously described that N-terminal acetylation (Ac-) forms a supramolecular self-assembly motif that allows β3-peptides to assemble head-to-tail into a helical nanorod which then further bundles into hierarchical superstructures. Here we investigate the effect of the topography of the 14-helical nanorod on lateral self-assembly. Specifically, we report on the variations in the superstructure of three isomeric peptides comprising the same three β3-amino acid residues: β3-leucine (L), β3-isoleucine (I) β3-alanine (A) to give peptides Ac-β3[LIA], Ac-β3[IAL] and Ac-β3[ALI]. AFM imaging shows markedly different superstructures for the three peptides. Well defined synchrotron far-infrared spectra reveal uniform geometries with a high degree of similarity between the isomeric peptides in the amide modes of the 400–650 wavenumber range. Far-IR also confirms that the C-terminal carboxyl group is free in the assemblies, thus it is solvated in the dispersant. Hence, the differences in the superstructures formed by the fibers are defined primarily by van der Waals energy minimization between the varied cross sectional morphologies of the core nanorods.
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Affiliation(s)
| | | | - Mark Del Borgo
- 3Department of Biochemistry and Molecular Biology, Monash University, Australia
| | - Ketav Kulkarni
- 3Department of Biochemistry and Molecular Biology, Monash University, Australia
| | | | | | - Adam Mechler
- 1La Trobe Institute for Molecular Science, Department of Chemistry and Physics, La Trobe University, Melbourne, Victoria, Australia
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67
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Alvarez HM. Triacylglycerol and wax ester-accumulating machinery in prokaryotes. Biochimie 2015; 120:28-39. [PMID: 26343555 DOI: 10.1016/j.biochi.2015.08.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/31/2015] [Indexed: 12/13/2022]
Abstract
Gram negative bacteria as well as Gram positive actinobacteria possess the ability to accumulate variable amounts of wax esters (WE) and/or triacylglycerols (TAG) under nitrogen limiting conditions. In recent years many advances have been made to obtain insight into neutral lipid biosynthesis and accumulation in prokaryotes. The clinical and industrial relevance of bacterial WE/TAG significantly promoted basic and applied research in this field. The recent integrated omic studies as well as the functional characterization of diverse genes are contributing to unravel the composition of the WE/TAG-accumulating machinery in bacteria. This will be a valuable data for designing new drugs against bacteria with clinical importance, such as Mycobacterium tuberculosis, or for transferring and optimizing lipid accumulation in bacterial hosts naturally unable to produce such lipids, such as Escherichia coli. In this article, recent investigations addressing WE/TAG biosynthesis and storage in prokaryotes are presented. A comprehensive view of the current knowledge on the different genes/proteins involved in WE/TAG biosynthesis is included.
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Affiliation(s)
- Héctor M Alvarez
- Centro Regional de Investigación y Desarrollo Científico Tecnológico (CRIDECIT), Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco, CIT-CHUBUT, CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina.
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Bouchez I, Pouteaux M, Canonge M, Genet M, Chardot T, Guillot A, Froissard M. Regulation of lipid droplet dynamics in Saccharomyces cerevisiae depends on the Rab7-like Ypt7p, HOPS complex and V1-ATPase. Biol Open 2015; 4:764-75. [PMID: 25948753 PMCID: PMC4571102 DOI: 10.1242/bio.20148615] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
It has now been clearly shown that lipid droplets (LDs) play a dynamic role in the cell. This was reinforced by LD proteomics which suggest that a significant number of trafficking proteins are associated with this organelle. Using microscopy, we showed that LDs partly co-localize with the vacuole in S. cerevisiae. Immunoblot experiments confirmed the association of the vacuolar Rab GTPase Rab7-like Ypt7p with LDs. We observed an increase in fatty acid content and LD number in ypt7Δ mutant and also changes in LD morphology and intra LD fusions, revealing a direct role for Ypt7p in LD dynamics. Using co-immunoprecipitation, we isolated potential Ypt7p partners including, Vma13p, the H subunit of the V1 part of the vacuolar (H+) ATPase (V-ATPase). Deletion of the VMA13 gene, as well as deletion of three other subunits of the V1 part of the V-ATPase, also increased the cell fatty acid content and LD number. Mutants of the Homotypic fusion and vacuole protein sorting (HOPS) complex showed similar phenotypes. Here, we demonstrated that LD dynamics and membrane trafficking between the vacuole and LDs are regulated by the Rab7-like Ypt7p and are impaired when the HOPS complex and the V1 domain of the V-ATPase are defective.
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Affiliation(s)
- Isabelle Bouchez
- Institut Jean-Pierre Bourgin IJPB, UMR 1318 INRA, Saclay Plant Sciences, route de St Cyr (RD 10), 78026, Versailles cedex, France Institut Jean-Pierre Bourgin IJPB, UMR 1318 AgroParisTech, route de St Cyr (RD 10), 78026, Versailles cedex, France
| | - Marie Pouteaux
- Institut Jean-Pierre Bourgin IJPB, UMR 1318 INRA, Saclay Plant Sciences, route de St Cyr (RD 10), 78026, Versailles cedex, France Institut Jean-Pierre Bourgin IJPB, UMR 1318 AgroParisTech, route de St Cyr (RD 10), 78026, Versailles cedex, France
| | - Michel Canonge
- Institut Jean-Pierre Bourgin IJPB, UMR 1318 INRA, Saclay Plant Sciences, route de St Cyr (RD 10), 78026, Versailles cedex, France Institut Jean-Pierre Bourgin IJPB, UMR 1318 AgroParisTech, route de St Cyr (RD 10), 78026, Versailles cedex, France
| | - Mélanie Genet
- Institut Jean-Pierre Bourgin IJPB, UMR 1318 INRA, Saclay Plant Sciences, route de St Cyr (RD 10), 78026, Versailles cedex, France Institut Jean-Pierre Bourgin IJPB, UMR 1318 AgroParisTech, route de St Cyr (RD 10), 78026, Versailles cedex, France
| | - Thierry Chardot
- Institut Jean-Pierre Bourgin IJPB, UMR 1318 INRA, Saclay Plant Sciences, route de St Cyr (RD 10), 78026, Versailles cedex, France Institut Jean-Pierre Bourgin IJPB, UMR 1318 AgroParisTech, route de St Cyr (RD 10), 78026, Versailles cedex, France
| | - Alain Guillot
- MICALIS PAPPSO, UMR 1319 INRA, Domaine de Vilvert 78352, Jouy-en-Josas cedex, France MICALIS PAPPSO, UMR 1319 AgroParisTech, Domaine de Vilvert 78352, Jouy-en-Josas cedex, France
| | - Marine Froissard
- Institut Jean-Pierre Bourgin IJPB, UMR 1318 INRA, Saclay Plant Sciences, route de St Cyr (RD 10), 78026, Versailles cedex, France Institut Jean-Pierre Bourgin IJPB, UMR 1318 AgroParisTech, route de St Cyr (RD 10), 78026, Versailles cedex, France
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69
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Chlamydia trachomatis Infection Leads to Defined Alterations to the Lipid Droplet Proteome in Epithelial Cells. PLoS One 2015; 10:e0124630. [PMID: 25909443 PMCID: PMC4409204 DOI: 10.1371/journal.pone.0124630] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/16/2015] [Indexed: 11/19/2022] Open
Abstract
The obligate intracellular bacterium Chlamydia trachomatis is a major human pathogen and a main cause of genital and ocular diseases. During its intracellular cycle, C. trachomatis replicates inside a membrane-bound vacuole termed an “inclusion”. Acquisition of lipids (and other nutrients) from the host cell is a critical step in chlamydial replication. Lipid droplets (LD) are ubiquitous, ER-derived neutral lipid-rich storage organelles surrounded by a phospholipids monolayer and associated proteins. Previous studies have shown that LDs accumulate at the periphery of, and eventually translocate into, the chlamydial inclusion. These observations point out to Chlamydia-mediated manipulation of LDs in infected cells, which may impact the function and thereby the protein composition of these organelles. By means of a label-free quantitative mass spectrometry approach we found that the LD proteome is modified in the context of C. trachomatis infection. We determined that LDs isolated from C. trachomatis-infected cells were enriched in proteins related to lipid metabolism, biosynthesis and LD-specific functions. Interestingly, consistent with the observation that LDs intimately associate with the inclusion, a subset of inclusion membrane proteins co-purified with LD protein extracts. Finally, genetic ablation of LDs negatively affected generation of C. trachomatis infectious progeny, consistent with a role for LD biogenesis in optimal chlamydial growth.
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70
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Jiang X, Huang L, Xing D. Photoactivation of Dok1/ERK/PPARγ signaling axis inhibits excessive lipolysis in insulin-resistant adipocytes. Cell Signal 2015; 27:1265-75. [PMID: 25813581 DOI: 10.1016/j.cellsig.2015.03.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/07/2015] [Accepted: 03/16/2015] [Indexed: 12/19/2022]
Abstract
Insulin resistance is a hallmark of the metabolic syndrome and type 2 diabetes. Increased plasma FFA level is an important cause of obesity-associated insulin resistance. Over-activated ERK is closely related with FFA release from adipose tissues in patients with type 2 diabetes. Nevertheless, there are no effective strategies to lower plasma FFA level. Low-power laser irradiation (LPLI) has been reported to regulate multiple biological processes. However, whether LPLI could ameliorate metabolic disorders and the molecular mechanisms involved remain unknown. In this study, we first demonstrated that LPLI suppresses excessive lipolysis of insulin-resistant adipocytes by activating tyrosine kinases-1(Dok1)/ERK/PPARγ pathway. Our data showed that LPLI inhibits ERK phosphorylation through the activation of Dok1, resulting in decreased phospho-PPARγ level. Non-phosphorylated PPARγ maintains in nucleus to promote the expression of adipogenic genes, reversing excessive lipolysis in insulin-resistant adipocytes. In summary, the present research highlights the important roles of Dok1/ERK/PPARγ pathway in lowering FFA release from adipocytes, and our research extends the knowledge of the biological effects induced by LPLI.
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Affiliation(s)
- Xiaoxiao Jiang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Lei Huang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
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71
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Dávila Costa JS, Leichert L, Alvarez HM, Herrero OM. Label-free and redox proteomic analyses of the triacylglycerol-accumulating Rhodococcus jostii RHA1. Microbiology (Reading) 2015; 161:593-610. [DOI: 10.1099/mic.0.000028] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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72
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Yu J, Zhang S, Cui L, Wang W, Na H, Zhu X, Li L, Xu G, Yang F, Christian M, Liu P. Lipid droplet remodeling and interaction with mitochondria in mouse brown adipose tissue during cold treatment. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:918-28. [PMID: 25655664 DOI: 10.1016/j.bbamcr.2015.01.020] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/22/2014] [Accepted: 01/16/2015] [Indexed: 01/17/2023]
Abstract
Brown adipose tissue (BAT) maintains animal body temperature by non-shivering thermogenesis, which is through uncoupling protein 1 (UCP1) that uncouples oxidative phosphorylation and utilizes β-oxidation of fatty acids released from triacylglycerol (TAG) in lipid droplets (LDs). Increasing BAT activity and "browning" other tissues such as white adipose tissue (WAT) can enhance the expenditure of excess stored energy, and in turn reduce prevalence of metabolic diseases. Although many studies have characterized the biology of BAT and brown adipocytes, BAT LDs especially their activation induced by cold exposure remain to be explored. We have isolated LDs from mouse interscapular BAT and characterized the full proteome using mass spectrometry. Both morphological and biochemical experiments showed that the LDs could tightly associate with mitochondria. Under cold treatment mouse BAT started expressing LD structure protein PLIN-2/ADRP and increased expression of PLIN1. Both hormone sensitive lipase (HSL) and adipose TAG lipase (ATGL) were increased in LDs. In addition, isolated BAT LDs showed increased levels of the mitochondrial protein UCP1, and prolonged cold exposure could stimulate BAT mitochondrial cristae biogenesis. These changes were in agreement with the data from transcriptional analysis. Our results provide the BAT LD proteome for the first time and show that BAT LDs facilitate heat production by coupling increasing TAG hydrolysis through recruitment of ATGL and HSL to the organelle and expression of another LD resident protein PLIN2/ADRP, as well as by tightly associating with activated mitochondria. These findings will benefit the study of BAT activation and the interaction between LDs and mitochondria.
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Affiliation(s)
- Jinhai Yu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liujuan Cui
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Weiyi Wang
- Department of Physiology and Pathophysiology, Peking University Health Science Center, Beijing 100191, China
| | - Huimin Na
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaotong Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linghai Li
- Department of Anesthesiology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Guoheng Xu
- Department of Physiology and Pathophysiology, Peking University Health Science Center, Beijing 100191, China
| | - Fuquan Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Mark Christian
- Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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Dynamics of the lipid droplet proteome of the Oleaginous yeast rhodosporidium toruloides. EUKARYOTIC CELL 2015; 14:252-64. [PMID: 25576482 DOI: 10.1128/ec.00141-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Lipid droplets (LDs) are ubiquitous organelles that serve as a neutral lipid reservoir and a hub for lipid metabolism. Manipulating LD formation, evolution, and mobilization in oleaginous species may lead to the production of fatty acid-derived biofuels and chemicals. However, key factors regulating LD dynamics remain poorly characterized. Here we purified the LDs and identified LD-associated proteins from cells of the lipid-producing yeast Rhodosporidium toruloides cultured under nutrient-rich, nitrogen-limited, and phosphorus-limited conditions. The LD proteome consisted of 226 proteins, many of which are involved in lipid metabolism and LD formation and evolution. Further analysis of our previous comparative transcriptome and proteome data sets indicated that the transcription level of 85 genes and protein abundance of 77 proteins changed under nutrient-limited conditions. Such changes were highly relevant to lipid accumulation and partially confirmed by reverse transcription-quantitative PCR. We demonstrated that the major LD structure protein Ldp1 is an LD marker protein being upregulated in lipid-rich cells. When overexpressed in Saccharomyces cerevisiae, Ldp1 localized on the LD surface and facilitated giant LD formation, suggesting that Ldp1 plays an important role in controlling LD dynamics. Our results significantly advance the understanding of the molecular basis of lipid overproduction and storage in oleaginous yeasts and will be valuable for the development of superior lipid producers.
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74
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The effects of putative lipase and wax ester synthase/acyl-CoA:diacylglycerol acyltransferase gene knockouts on triacylglycerol accumulation in Gordonia sp. KTR9. J Ind Microbiol Biotechnol 2014; 42:219-27. [PMID: 25487758 DOI: 10.1007/s10295-014-1552-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/19/2014] [Indexed: 10/24/2022]
Abstract
Previously, we demonstrated triacylglycerol (TAG) accumulation and the in vivo ability to catalyze esters from exogenous short chain alcohol sources in Gordonia sp. strain KTR9. In this study, we investigated the effects that putative lipase (KTR9_0186) and wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT; KTR9_3844) gene knockouts had on TAG accumulation. Gene disruption of KTR9_0186 resulted in a twofold increase in TAG content in nitrogen starved cells. Lipase mutants subjected to carbon starvation, following nitrogen starvation, retained 75 % more TAGs and retained pigmentation. Transcriptome expression data confirmed the deletion of KTR9_0186 and identified the up-regulation of key genes involved in fatty acid degradation, a likely compensatory mechanism for reduced TAG mobilization. In vitro assays with purified KTR9_3844 demonstrated WS/DGAT activity with short chain alcohols and C16 and C18 fatty acid Co-As. Collectively, these results indicate that Gordonia sp. KTR9 has a suitable tractable genetic background for TAG production as well as the enzymatic capacity to catalyze fatty acid esters from short chain alcohols.
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75
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Muller EEL, Sheik AR, Wilmes P. Lipid-based biofuel production from wastewater. Curr Opin Biotechnol 2014; 30:9-16. [DOI: 10.1016/j.copbio.2014.03.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/27/2014] [Accepted: 03/28/2014] [Indexed: 11/15/2022]
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76
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Hernández MA, Comba S, Arabolaza A, Gramajo H, Alvarez HM. Overexpression of a phosphatidic acid phosphatase type 2 leads to an increase in triacylglycerol production in oleaginous Rhodococcus strains. Appl Microbiol Biotechnol 2014; 99:2191-207. [PMID: 25213912 DOI: 10.1007/s00253-014-6002-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 01/28/2023]
Abstract
Oleaginous Rhodococcus strains are able to accumulate large amounts of triacylglycerol (TAG). Phosphatidic acid phosphatase (PAP) enzyme catalyzes the dephosphorylation of phosphatidic acid (PA) to yield diacylglycerol (DAG), a key precursor for TAG biosynthesis. Studies to establish its role in lipid metabolism have been mainly focused in eukaryotes but not in bacteria. In this work, we identified and characterized a putative PAP type 2 (PAP2) encoded by the ro00075 gene in Rhodococcus jostii RHA1. Heterologous expression of ro00075 in Escherichia coli resulted in a fourfold increase in PAP activity and twofold in DAG content. The conditional deletion of ro00075 in RHA1 led to a decrease in the content of DAG and TAG, whereas its overexpression in both RHA1 and Rhodococcus opacus PD630 promoted an increase up to 10 to 15 % by cellular dry weight in TAG content. On the other hand, expression of ro00075 in the non-oleaginous strain Rhodococcus fascians F7 promoted an increase in total fatty acid content up to 7 % at the expense of free fatty acid (FFA), DAG, and TAG fractions. Moreover, co-expression of ro00075/atf2 genes resulted in a fourfold increase in total fatty acid content by a further increase of the FFA and TAG fractions. The results of this study suggest that ro00075 encodes for a PAP2 enzyme actively involved in TAG biosynthesis. Overexpression of this gene, as single one or with an atf gene, provides an alternative approach to increase the biosynthesis and accumulation of bacterial oils as a potential source of raw material for biofuel production.
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Affiliation(s)
- Martín A Hernández
- Centro Regional de Investigación y Desarrollo Científico Tecnológico, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco, Ruta Provincial N° 1, Km 4-Ciudad Universitaria, 9000, Comodoro Rivadavia, Chubut, Argentina
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Peramuna A, Summers ML. Composition and occurrence of lipid droplets in the cyanobacterium Nostoc punctiforme. Arch Microbiol 2014; 196:881-90. [PMID: 25135835 DOI: 10.1007/s00203-014-1027-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 08/03/2014] [Accepted: 08/06/2014] [Indexed: 12/12/2022]
Abstract
Inclusions of neutral lipids termed lipid droplets (LDs) located throughout the cell were identified in the cyanobacterium Nostoc punctiforme by staining with lipophylic fluorescent dyes. LDs increased in number upon entry into stationary phase and addition of exogenous fructose indicating a role for carbon storage, whereas high-light stress did not increase LD numbers. LD accumulation increased when nitrate was used as the nitrogen source during exponential growth as compared to added ammonia or nitrogen-fixing conditions. Analysis of isolated LDs revealed enrichment of triacylglycerol (TAG), α-tocopherol, and C17 alkanes. LD TAG from exponential phase growth contained mainly saturated C16 and C18 fatty acids, whereas stationary phase LD TAG had additional unsaturated fatty acids characteristic of whole cells. This is the first characterization of cyanobacterial LD composition and conditions leading to their production. Based upon their abnormally large size and atypical location, these structures represent a novel sub-organelle in cyanobacteria.
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Affiliation(s)
- Anantha Peramuna
- Department of Biology, California State University Northridge, 18111 Nordhoff St., Northridge, CA, 91330-8303, USA
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78
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Liu Y, Zhang C, Shen X, Zhang X, Cichello S, Guan H, Liu P. Microorganism lipid droplets and biofuel development. BMB Rep 2014; 46:575-81. [PMID: 24355300 PMCID: PMC4133864 DOI: 10.5483/bmbrep.2013.46.12.271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Indexed: 01/28/2023] Open
Abstract
Lipid droplet (LD) is a cellular organelle that stores neutral lipids as a source of energy and carbon. However, recent research has emerged that the organelle is involved in lipid synthesis, transportation, and metabolism, as well as mediating cellular protein storage and degradation. With the exception of multi-cellular organisms, some unicellular microorganisms have been observed to contain LDs. The organelle has been isolated and characterized from numerous organisms. Triacylglycerol (TAG) accumulation in LDs can be in excess of 50% of the dry weight in some microorganisms, and a maximum of 87% in some instances. These microorganisms include eukaryotes such as yeast and green algae as well as prokaryotes such as bacteria. Some organisms obtain carbon from CO2 via photosynthesis, while the majority utilizes carbon from various types of biomass. Therefore, high TAG content generated by utilizing waste or cheap biomass, coupled with an efficient conversion rate, present these organisms as bio-tech ‘factories’ to produce biodiesel. This review summarizes LD research in these organisms and provides useful information for further LD biological research and microorganism biodiesel development. [BMB Reports 2013; 46(12): 575-581]
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Affiliation(s)
| | | | | | | | | | - Hongbin Guan
- Marine College, Shandong University at Weihai, 180 Wenhua Xilu, Weihai, Shandong 264209, China
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese, Academy of Sciences, Beijing 100101, China
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79
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Identification of a novel ATP-binding cassette transporter involved in long-chain fatty acid import and its role in triacylglycerol accumulation in Rhodococcus jostii RHA1. Microbiology (Reading) 2014; 160:1523-1532. [DOI: 10.1099/mic.0.078477-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Members of the genus Rhodococcus are specialists in the biosynthesis and accumulation of triacylglycerols (TAGs). As no transport protein related to TAG metabolism has yet been characterized in these bacteria, we used the available genomic information of Rhodococcus jostii RHA1 to perform a broad survey of genes coding for putative lipid transporter proteins in this oleaginous micro-organism. Among the seven genes encoding putative lipid transporters, ro05645 (now called ltp1: lipid transporter protein) coding for an ATP-binding cassette protein was found clustered with others genes encoding enzymes catalysing the three putative acylation reactions of the Kennedy pathway for TAG synthesis. Overexpression of ltp1 in the RHA1 strain led to an increase of approximately sixfold and threefold in biomass and TAG production, respectively, when cells were cultivated on palmitic acid and oleic acid. Moreover, overexpression of ltp1 also promoted a significant increase in the uptake of a fluorescently labelled long-chain fatty acid (LCFA), as compared with the WT strain RHA1, and its further incorporation into the TAG fraction. Gluconate-grown cells showed increasing amounts of intracellular free fatty acids, but not of TAG, after overexpressing ltp1. Thus, for the first time to our knowledge, a transporter functionally related to TAG metabolism was identified in oleaginous rhodococci. Our results suggested that Ltp1 is an importer of LCFAs that plays a functional role in lipid homeostasis of R. jostii RHA1.
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Abstract
Lipid droplets (LDs) are an intracellular organelle, consisting of a neutral lipid core covered by a monolayer of phospholipids and proteins. It primarily mediates lipid storage, metabolism, and transportation. Recently, research of LDs has emerged as a rapidly developing field due to the strong linkage between ectopic lipid accumulation and metabolic syndromes. Recently, more than 30 proteomic studies of isolated LDs have identified many important LD proteins that have highlighted and have also predicted the potential biological roles of the organelle, motivating the field to develop quite rapidly. This chapter summarizes methods used in proteomic studies for three representative species reported and discusses their advantages and disadvantages. We believe that this chapter provides useful information and methods for future LD proteomic studies especially for LDs in other species.
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81
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Garay LA, Boundy-Mills KL, German JB. Accumulation of high-value lipids in single-cell microorganisms: a mechanistic approach and future perspectives. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:2709-27. [PMID: 24628496 PMCID: PMC3983371 DOI: 10.1021/jf4042134] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 01/12/2014] [Accepted: 03/16/2014] [Indexed: 05/08/2023]
Abstract
In recent years attention has been focused on the utilization of microorganisms as alternatives for industrial and nutritional applications. Considerable research has been devoted to techniques for growth, extraction, and purification of high-value lipids for their use as biofuels and biosurfactants as well as high-value metabolites for nutrition and health. These successes argue that the elucidation of the mechanisms underlying the microbial biosynthesis of such molecules, which are far from being completely understood, now will yield spectacular opportunities for industrial scale biomolecular production. There are important additional questions to be solved to optimize the processing strategies to take advantage of the assets of microbial lipids. The present review describes the current state of knowledge regarding lipid biosynthesis, accumulation, and transport mechanisms present in single-cell organisms, specifically yeasts, microalgae, bacteria, and archaea. Similarities and differences in biochemical pathways and strategies of different microorganisms provide a diverse toolset to the expansion of biotechnologies for lipid production. This paper is intended to inspire a generation of lipid scientists to insights that will drive the biotechnologies of microbial production as uniquely enabling players of lipid biotherapeutics, biofuels, biomaterials, and other opportunity areas into the 21st century.
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Affiliation(s)
- Luis A. Garay
- Department
of Food Science
and Technology, University of California, Davis, One Shields Avenue, Davis California 95616-8598, United States
| | - Kyria L. Boundy-Mills
- Department
of Food Science
and Technology, University of California, Davis, One Shields Avenue, Davis California 95616-8598, United States
| | - J. Bruce German
- Department
of Food Science
and Technology, University of California, Davis, One Shields Avenue, Davis California 95616-8598, United States
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82
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Tan JSY, Seow CJP, Goh VJ, Silver DL. Recent advances in understanding proteins involved in lipid droplet formation, growth and fusion. J Genet Genomics 2014; 41:251-9. [PMID: 24894352 DOI: 10.1016/j.jgg.2014.03.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 03/03/2014] [Accepted: 03/05/2014] [Indexed: 01/29/2023]
Abstract
Lipid droplets (LDs) were once viewed as simple, inert lipid micelles. However, they are now known to be organelles with a rich proteome involved in a myriad of cellular processes. LDs are heterogeneous in nature with different sizes and compositions of phospholipids, neutral lipids and proteins. This review takes a focused look at the roles of proteins involved in the regulation of LD formation, expansion, and morphology. The related proteins are summarized such as the fat-specific protein (Fsp27), fat storage-inducing transmembrane (FIT) proteins, seipin and ADP-ribosylation factor 1-coat protein complex I (Arf-COPI). Finally, we present important challenges in LD biology for a deeper understanding of this dynamic organelle to be achieved.
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Affiliation(s)
- Jolene S Y Tan
- Signature Research Program in Cardiovascular & Metabolic Disorders, Duke-NUS Graduate Medical School Singapore, Singapore 169857, Singapore
| | - Colin J P Seow
- Signature Research Program in Cardiovascular & Metabolic Disorders, Duke-NUS Graduate Medical School Singapore, Singapore 169857, Singapore
| | - Vera J Goh
- Signature Research Program in Cardiovascular & Metabolic Disorders, Duke-NUS Graduate Medical School Singapore, Singapore 169857, Singapore
| | - David L Silver
- Signature Research Program in Cardiovascular & Metabolic Disorders, Duke-NUS Graduate Medical School Singapore, Singapore 169857, Singapore.
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83
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MacEachran DP, Sinskey AJ. The Rhodococcus opacus TadD protein mediates triacylglycerol metabolism by regulating intracellular NAD(P)H pools. Microb Cell Fact 2013; 12:104. [PMID: 24209886 PMCID: PMC3827869 DOI: 10.1186/1475-2859-12-104] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 11/05/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Gram-positive actinomycete Rhodococcus opacus is widely studied for its innate ability to store large amounts of carbon in the form of triacylglycerol (TAG). Several groups have demonstrated that R. opacus PD630 is capable of storing anywhere from 50 to 76% of its cell dry weight as TAG. While numerous studies have focused on phenomenological aspects of this process, few have sought to identify the underlying molecular and biochemical mechanisms responsible for the biosynthesis and storage of this molecule. RESULTS Herein we further our previous efforts to illuminate the black box that is lipid metabolism in actinomycetes using a genetic approach. Utilizing a simple, colorimetric genetic screen, we have identified a gene, referred to herein as tadD (triacylglycerol accumulation deficient), which is critical for TAG biosynthesis in R. opacus PD630. Furthermore, we demonstrate that the purified protein product of this gene is capable of oxidizing glyceraldehyde-3-phosphate, while simultaneously reducing NAD(P)+ to NAD(P)H. Supporting this biochemical data, we observed that the ratio of NAD(P)H to NAD(P)+ is elevated in wildtype cultures grown under lipid production conditions as compared to cultures grown under vegetative growth conditions, while the mutant strain demonstrated no change irrespective of growth conditions. Finally, we demonstrate that over-expressing a putative phosphorylative glyceraldehyde-3-phosphate dehydrogenase leads to decreased TAG production during growth on TAG accumulation conditions. CONCLUSION Taken together, the data support the identification of a key metabolic branch point separating vegetative growth and lipid accumulation lifestyles in Rhodococcus.
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Affiliation(s)
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street Bldg, 68-370, Cambridge, MA 02142, USA.
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84
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Chen Y, Ding Y, Yang L, Yu J, Liu G, Wang X, Zhang S, Yu D, Song L, Zhang H, Zhang C, Huo L, Huo C, Wang Y, Du Y, Zhang H, Zhang P, Na H, Xu S, Zhu Y, Xie Z, He T, Zhang Y, Wang G, Fan Z, Yang F, Liu H, Wang X, Zhang X, Zhang MQ, Li Y, Steinbüchel A, Fujimoto T, Cichello S, Yu J, Liu P. Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. Nucleic Acids Res 2013; 42:1052-64. [PMID: 24150943 PMCID: PMC3902926 DOI: 10.1093/nar/gkt932] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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.
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Affiliation(s)
- Yong Chen
- 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
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85
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Chen Y, Yang L, Ding Y, Zhang S, He T, Mao F, Zhang C, Zhang H, Huo C, Liu P. Tracing evolutionary footprints to identify novel gene functional linkages. PLoS One 2013; 8:e66817. [PMID: 23825567 PMCID: PMC3692504 DOI: 10.1371/journal.pone.0066817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 05/13/2013] [Indexed: 11/19/2022] Open
Abstract
Systematic determination of gene function is an essential step in fully understanding the precise contribution of each gene for the proper execution of molecular functions in the cell. Gene functional linkage is defined as to describe the relationship of a group of genes with similar functions. With thousands of genomes sequenced, there arises a great opportunity to utilize gene evolutionary information to identify gene functional linkages. To this end, we established a computational method (called TRACE) to trace gene footprints through a gene functional network constructed from 341 prokaryotic genomes. TRACE performance was validated and successfully tested to predict enzyme functions as well as components of pathway. A so far undescribed chromosome partitioning-like protein ro03654 of an oleaginous bacteria Rhodococcus sp. RHA1 (RHA1) was predicted and verified experimentally with its deletion mutant showing growth inhibition compared to RHA1 wild type. In addition, four proteins were predicted to act as prokaryotic SNARE-like proteins, and two of them were shown to be localized at the plasma membrane. Thus, we believe that TRACE is an effective new method to infer prokaryotic gene functional linkages by tracing evolutionary events.
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Affiliation(s)
- Yong Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (PL); (YC)
| | - Li Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yunfeng Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shuyan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tong He
- School of Applied Mathematics, Central University of Finance and Economics, Beijing, China
| | - Fenglou Mao
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Congyan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huina Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chaoxing Huo
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (PL); (YC)
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86
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Qu G, Wang X, Liu Q, Liu R, Yin N, Ma J, Chen L, He J, Liu S, Jiang G. The ex vivo and in vivo biological performances of graphene oxide and the impact of surfactant on graphene oxide's biocompatibility. J Environ Sci (China) 2013; 25:873-881. [PMID: 24218816 DOI: 10.1016/s1001-0742(12)60252-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Graphene oxide (GO) displays promising properties for biomedical applications including drug delivery and cancer therapeutics. However, GO exposure also raises safety concerns such as potential side effects on health. Here, the biological effects of GO suspended in phosphate buffered saline (PBS) with or without 1% nonionic surfactant Tween 80 were investigated. Based on the ex vivo experiments, Tween 80 significantly affected the interaction between GO and peripheral blood from mice. GO suspension in PBS tended to provoke the aggregation of diluted blood cells, which could be prevented by the addition of Tween 80. After intravenous administration, GO suspension with or without 1% Tween 80 was quickly eliminated by the mononuclear phagocyte system. Nevertheless, GO suspension without Tween 80 showed greater accumulation in lungs than that containing 1% Tween 80. In contrast, less GO was found in livers for GO suspension compared to Tween 80 assisted GO suspension. Organs including hearts, livers, lungs, spleens, kidneys, brains, and testes did not reveal histological alterations. The indexes of peripheral blood showed no change upon GO exposure. Our results together demonstrated that Tween 80 could greatly alter GO's biological performance and determine the pattern of its biodistribution in mice.
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Affiliation(s)
- Guangbo Qu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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87
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88
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Yang L, Ding Y, Chen Y, Zhang S, Huo C, Wang Y, Yu J, Zhang P, Na H, Zhang H, Ma Y, Liu P. The proteomics of lipid droplets: structure, dynamics, and functions of the organelle conserved from bacteria to humans. J Lipid Res 2012; 53:1245-53. [PMID: 22534641 DOI: 10.1194/jlr.r024117] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Lipid droplets are cellular organelles that consists of a neutral lipid core covered by a monolayer of phospholipids and many proteins. They are thought to function in the storage, transport, and metabolism of lipids, in signaling, and as a specialized microenvironment for metabolism in most types of cells from prokaryotic to eukaryotic organisms. Lipid droplets have received a lot of attention in the last 10 years as they are linked to the progression of many metabolic diseases and hold great potential for the development of neutral lipid-derived products, such as biofuels, food supplements, hormones, and medicines. Proteomic analysis of lipid droplets has yielded a comprehensive catalog of lipid droplet proteins, shedding light on the function of this organelle and providing evidence that its function is conserved from bacteria to man. This review summarizes many of the proteomic studies on lipid droplets from a wide range of organisms, providing an evolutionary perspective on this organelle.
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Affiliation(s)
- Li Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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89
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Zhang P, Na H, Liu Z, Zhang S, Xue P, Chen Y, Pu J, Peng G, Huang X, Yang F, Xie Z, Xu T, Xu P, Ou G, Zhang SO, Liu P. Proteomic study and marker protein identification of Caenorhabditis elegans lipid droplets. Mol Cell Proteomics 2012; 11:317-28. [PMID: 22493183 DOI: 10.1074/mcp.m111.016345] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Lipid droplets (LDs) are a neutral lipid storage organelle that is conserved across almost all species. Many metabolic syndromes are directly linked to the over-storage of neutral lipids in LDs. The study of LDs in Caenorhabditis elegans (C. elegans) has been difficult because of the lack of specific LD marker proteins. Here we report the purification and proteomic analysis of C. elegans lipid droplets for the first time. We identified 306 proteins, 63% of these proteins were previously known to be LD-proteins, suggesting a similarity between mammalian and C. elegans LDs. Using morphological and biochemical analyses, we show that short-chain dehydrogenase, DHS-3 is almost exclusively localized on C. elegans LDs, indicating that it can be used as a LD marker protein in C. elegans. These results will facilitate further mechanistic studies of LDs in this powerful genetic system, C. elegans.
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Affiliation(s)
- Peng Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
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