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Peng Y, Zhu M, Gong Y, Wang C. Identification and functional prediction of lncRNAs associated with intramuscular lipid deposition in Guangling donkeys. Front Vet Sci 2024; 11:1410109. [PMID: 39036793 PMCID: PMC11258529 DOI: 10.3389/fvets.2024.1410109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 05/30/2024] [Indexed: 07/23/2024] Open
Abstract
Many studies have shown that long non-coding RNAs (lncRNAs) play key regulatory roles in various biological processes. However, the importance and molecular regulatory mechanisms of lncRNAs in donkey intramuscular fat deposition remain to be further investigated. In this study, we used published transcriptomic data from the longissimus dorsi muscle of Guangling donkeys to identify lncRNAs and obtained 196 novel lncRNAs. Compared with the coding genes, the novel lncRNAs and the known lncRNAs exhibited some typical features, such as shorter transcript length and smaller exons. A total of 272 coding genes and 52 lncRNAs were differentially expressed between the longissimus dorsi muscles of the low-fat and high-fat groups. The differentially expressed genes were found to be involved in various biological processes related to lipid metabolism. The potential target genes of differentially expressed lncRNAs were predicted by cis and trans. Functional analysis of lncRNA targets showed that some lncRNAs may act on potential target genes involved in lipid metabolism processes and regulate lipid deposition in the longissimus dorsi muscle. This study provides valuable information for further investigation of the molecular mechanisms of lipid deposition traits in donkeys, which may improve meat traits and facilitate the selection process of donkeys in future breeding.
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Affiliation(s)
- Yongdong Peng
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | | | | | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
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2
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Chance R, Kang AS. Eukaryotic ribosome display for antibody discovery: A review. Hum Antibodies 2024; 32:107-120. [PMID: 38788063 DOI: 10.3233/hab-240001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Monoclonal antibody biologics have significantly transformed the therapeutic landscape within the biopharmaceutical industry, partly due to the utilisation of discovery technologies such as the hybridoma method and phage display. While these established platforms have streamlined the development process to date, their reliance on cell transformation for antibody identification faces limitations related to library diversification and the constraints of host cell physiology. Cell-free systems like ribosome display offer a complementary approach, enabling antibody selection in a completely in vitro setting while harnessing enriched cellular molecular machinery. This review aims to provide an overview of the fundamental principles underlying the ribosome display method and its potential for advancing antibody discovery and development.
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Chen J, Cai B, Tian C, Jiang D, Shi H, Huang Y, Zhu C, Li G, Deng S. RNA Sequencing (RNA-Seq) Analysis Reveals Liver Lipid Metabolism Divergent Adaptive Response to Low- and High-Salinity Stress in Spotted Scat ( Scatophagus argus). Animals (Basel) 2023; 13:ani13091503. [PMID: 37174540 PMCID: PMC10177406 DOI: 10.3390/ani13091503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Spotted scat (Scatophagus argus) can tolerate a wide range of salinity fluctuations. It is a good model for studying environmental salinity adaptation. Lipid metabolism plays an important role in salinity adaptation in fish. To elucidate the mechanism of lipid metabolism in the osmoregulation, the liver transcriptome was analyzed after 22 d culture with a salinity of 5 ppt (Low-salinity group: LS), 25 ppt (Control group: Ctrl), and 35 ppt (High-salinity group: HS) water by using RNA sequencing (RNA-seq) in spotted scat. RNA-seq analysis showed that 1276 and 2768 differentially expressed genes (DEGs) were identified in the LS vs. Ctrl and HS vs. Ctrl, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the pathways of steroid hormone biosynthesis, steroid biosynthesis, glycerophospholipid metabolism, glycerolipid metabolism, and lipid metabolism were significantly enriched in the LS vs. Ctrl. The genes of steroid biosynthesis (sqle, dhcr7, and cyp51a1), steroid hormone biosynthesis (ugt2a1, ugt2a2, ugt2b20, and ugt2b31), and glycerophospholipid metabolism (cept1, pla2g4a, and ptdss2) were significantly down-regulated in the LS vs. Ctrl. The pathways related to lipid metabolisms, such as fatty acid metabolism, fatty acid biosynthesis, peroxisome proliferator-activated receptor (PPAR) signaling pathway, adipocytokine signaling pathway, fatty acid degradation, and unsaturated fatty acid biosynthesis, were significantly enriched in the HS vs. Ctrl. The genes of unsaturated fatty acid biosynthesis (scd1, hacd3, fads2, pecr, and elovl1) and adipocytokine signaling pathway (g6pc1, socs1, socs3, adipor2, pck1, and pparα) were significantly up-regulated in the HS vs. Ctrl. These results suggest that the difference in liver lipid metabolism is important to adapt to low- and high-salinity stress in spotted scat, which clarifies the molecular regulatory mechanisms of salinity adaptation in euryhaline fish.
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Affiliation(s)
- Jieqing Chen
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Bosheng Cai
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Changxu Tian
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Dongneng Jiang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Zhanjiang 524088, China
| | - Hongjuan Shi
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Zhanjiang 524088, China
| | - Yang Huang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Zhanjiang 524088, China
| | - Chunhua Zhu
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Zhanjiang 524088, China
| | - Guangli Li
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Siping Deng
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Zhanjiang 524088, China
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Vegni J, Sun Y, Seemann SE, Zappaterra M, Davoli R, Dall’Olio S, Gorodkin J, Zambonelli P. RNA-Seq Study on the Longissimus thoracis Muscle of Italian Large White Pigs Fed Extruded Linseed with or without Antioxidants and Polyphenols. Animals (Basel) 2023; 13:ani13071187. [PMID: 37048443 PMCID: PMC10093021 DOI: 10.3390/ani13071187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The addition of n-3 polyunsaturated fatty acids (n-3 PUFAs) to the swine diet increases their content in muscle cells, and the additional supplementation of antioxidants promotes their oxidative stability. However, to date, the functionality of these components within muscle tissue is not well understood. Using a published RNA-seq dataset and a selective workflow, the study aimed to find the differences in gene expression and investigate how differentially expressed genes (DEGs) were implicated in the cellular composition and metabolism of muscle tissue of 48 Italian Large White pigs under different dietary conditions. A functional enrichment analysis of DEGs, using Cytoscape, revealed that the diet enriched with extruded linseed and supplemented with vitamin E and selenium promoted a more rapid and massive immune system response because the overall function of muscle tissue was improved, while those enriched with extruded linseed and supplemented with grape skin and oregano extracts promoted the presence and oxidative stability of n-3 PUFAs, increasing the anti-inflammatory potential of the muscular tissue.
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Affiliation(s)
- Jacopo Vegni
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
| | - Ying Sun
- Center for Non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Copenhagen, Denmark
| | - Stefan E. Seemann
- Center for Non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Copenhagen, Denmark
| | - Martina Zappaterra
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
| | - Roberta Davoli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
| | - Stefania Dall’Olio
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
| | - Jan Gorodkin
- Center for Non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Copenhagen, Denmark
- Correspondence: (J.G.); (P.Z.); Tel.: +45-23375667 (J.G.); +39-051-2088055 (P.Z.)
| | - Paolo Zambonelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
- Correspondence: (J.G.); (P.Z.); Tel.: +45-23375667 (J.G.); +39-051-2088055 (P.Z.)
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Nishiguchi R, Tanaka T, Hayashida J, Nakagita T, Zhou W, Takeda H. Evaluation of Cell-Free Synthesized Human Channel Proteins for In Vitro Channel Research. MEMBRANES 2022; 13:48. [PMID: 36676855 PMCID: PMC9861611 DOI: 10.3390/membranes13010048] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Despite channel proteins being important drug targets, studies on channel proteins remain limited, as the proteins are difficult to express and require correct complex formation within membranes. Although several in vitro synthesized recombinant channels have been reported, considering the vast diversity of the structures and functions of channel proteins, it remains unclear which classes of channels cell-free synthesis can be applied to. In this study, we synthesized 250 clones of human channels, including ion channel pore-forming subunits, gap junction proteins, porins, and regulatory subunits, using a wheat cell-free membrane protein production system, and evaluated their synthetic efficiency and function. Western blotting confirmed that 95% of the channels were successfully synthesized, including very large channels with molecular weights of over 200 kDa. A subset of 47 voltage-gated potassium ion channels was further analyzed using a planar lipid bilayer assay, out of which 80% displayed a voltage-dependent opening in the assay. We co-synthesized KCNB1 and KCNS3, a known heteromeric complex pair, and demonstrated that these channels interact on a liposome. These results indicate that cell-free protein synthesis provides a promising solution for channel studies to overcome the bottleneck of in vitro protein production.
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Affiliation(s)
- Rei Nishiguchi
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
| | - Toyohisa Tanaka
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
| | - Jun Hayashida
- Nissan Chemical Corporation, Shiraoka 1470, Shiraoka 349-0294, Saitama, Japan
| | - Tomoya Nakagita
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
| | - Wei Zhou
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
| | - Hiroyuki Takeda
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
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6
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Herianto S, Chien PJ, Ho JAA, Tu HL. Liposome-based artificial cells: From gene expression to reconstitution of cellular functions and phenotypes. BIOMATERIALS ADVANCES 2022; 142:213156. [PMID: 36302330 DOI: 10.1016/j.bioadv.2022.213156] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Bottom-up approaches in creating artificial cells that can mimic natural cells have significant implications for both basic research and translational application. Among various artificial cell models, liposome is one of the most sophisticated systems. By encapsulating proteins and associated biomolecules, they can functionally reconstitute foundational features of biological cells, such as the ability to divide, communicate, and undergo shape deformation. Yet constructing liposome artificial cells from the genetic level, which is central to generate self-sustained systems remains highly challenging. Indeed, many studies have successfully established the expression of gene-coded proteins inside liposomes. Further, recent endeavors to build a direct integration of gene-expressed proteins for reconstituting molecular functions and phenotypes in liposomes have also significantly increased. Thus, this review presents the development of liposome-based artificial cells to demonstrate the process of gene-expressed proteins and their reconstitution to perform desired molecular and cell-like functions. The molecular and cellular phenotypes discussed here include the self-production of membrane phospholipids, division, shape deformation, self-DNA/RNA replication, fusion, and intercellular communication. Together, this review gives a comprehensive overview of gene-expressing liposomes that can stimulate further research of this technology and achieve artificial cells with superior properties in the future.
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Affiliation(s)
- Samuel Herianto
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan; Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Po-Jen Chien
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ja-An Annie Ho
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan; BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan; Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
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7
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Wang Y, Jin B, Li B, Luo Y, Ma M, Chen Y, Liu H, Xie H, Yang T, Zhao X, Ding P. Cell-free protein synthesis of influenza virus hemagglutinin HA2-integrated virosomes for siRNA delivery. Int J Pharm 2022; 623:121890. [PMID: 35690307 DOI: 10.1016/j.ijpharm.2022.121890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/13/2022] [Accepted: 06/01/2022] [Indexed: 10/18/2022]
Abstract
It is well known that the difficulty of siRNA therapeutic application is the lack of safe and effective delivery vector. Virosome is a nano vesicle composed of lipid membrane and membrane protein. It retains fusion protein without virus genetic material, and therefore has the reduced immunogenicity compared with viral vector. Virosomes have the potential to deliver protein and nucleic acid drugs, but the traditional preparation method of virosomes is quite limited. In this study, we firstly proposed to synthesize influenza virus hemagglutinin HA2 virosomes by cell-free protein synthesis. In this study, liposomes provided the hydrophobic lipid bilayer environment for the formation of HA2 protein multimer, which inhibited the aggregation of hydrophobic HA2 and improved HA2 protein expression. Chitosan as a rigid core adsorbed siRNA and improved the encapsulation efficiency of siRNA. In conclusion, the cell-free protein synthesis was used to prepare HA2 virosomes, which paves the way for constructing a novel nano vector with high delivery efficiency and biosafety for the delivery of siRNA.
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Affiliation(s)
- Yichen Wang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Bo Jin
- The First Hospital, China Medical University, Department of Medical Oncology, Shenyang 110001, China
| | - Bao Li
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yucen Luo
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Mengrui Ma
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yongfeng Chen
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Hui Liu
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Huichao Xie
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Tianzhi Yang
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, Husson University, Bangor, ME 04401, USA
| | - Xiaoyun Zhao
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Pingtian Ding
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China; College of Pharmacy, Shenzhen Technology University, Shenzhen 518118, China.
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8
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Islam MS, Gaston JP, Baker MAB. Fluorescence Approaches for Characterizing Ion Channels in Synthetic Bilayers. MEMBRANES 2021; 11:857. [PMID: 34832086 PMCID: PMC8619978 DOI: 10.3390/membranes11110857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022]
Abstract
Ion channels are membrane proteins that play important roles in a wide range of fundamental cellular processes. Studying membrane proteins at a molecular level becomes challenging in complex cellular environments. Instead, many studies focus on the isolation and reconstitution of the membrane proteins into model lipid membranes. Such simpler, in vitro, systems offer the advantage of control over the membrane and protein composition and the lipid environment. Rhodopsin and rhodopsin-like ion channels are widely studied due to their light-interacting properties and are a natural candidate for investigation with fluorescence methods. Here we review techniques for synthesizing liposomes and for reconstituting membrane proteins into lipid bilayers. We then summarize fluorescence assays which can be used to verify the functionality of reconstituted membrane proteins in synthetic liposomes.
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Affiliation(s)
- Md. Sirajul Islam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - James P. Gaston
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
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9
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Peng Y, Li H, Liu Z, Zhang C, Li K, Gong Y, Geng L, Su J, Guan X, Liu L, Zhou R, Zhao Z, Guo J, Liang Q, Li X. Chromosome-level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi-C technology. Mol Ecol Resour 2021; 21:2093-2108. [PMID: 33829635 DOI: 10.1111/1755-0998.13397] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
The Arctic fox (Vulpes lagopus) is the only fox species occurring in the Arctic and has adapted to its extreme climatic conditions. Currently, the molecular basis of its adaptation to the extreme climate has not been characterized. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first V. lagopus genome assembly, which is assembled into chromosome fragments. The genome assembly has a total length of 2.345 Gb with a contig N50 of 31.848 Mb and a scaffold N50 of 131.537 Mb, consisting of 25 pseudochromosomal scaffolds. The V. lagopus genome had approximately 32.33% repeat sequences. In total, 21,278 protein-coding genes were predicted, of which 99.14% were functionally annotated. Compared with 12 other mammals, V. lagopus was most closely related to V. Vulpes with an estimated divergence time of ~7.1 Ma. The expanded gene families and positively selected genes potentially play roles in the adaptation of V. lagopus to Arctic extreme environment. This high-quality assembled genome will not only promote future studies of genetic diversity and evolution in foxes and other canids but also provide important resources for conservation of Arctic species.
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Affiliation(s)
- Yongdong Peng
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhengzhu Liu
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Chuansheng Zhang
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Keqiang Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Mathematics and Information Science, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yuanfang Gong
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Liying Geng
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jingjing Su
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, China
| | - Xuemin Guan
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Lei Liu
- College of Animal Science and Technology, Shandong Agricultural University, Tai-an, China
| | - Ruihong Zhou
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Ziya Zhao
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jianxu Guo
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing, China
| | - Xianglong Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
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10
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Fogeron ML, Lecoq L, Cole L, Harbers M, Böckmann A. Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology. Front Mol Biosci 2021; 8:639587. [PMID: 33842544 PMCID: PMC8027086 DOI: 10.3389/fmolb.2021.639587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic biology using CFPS to develop new proteins for technical applications and therapy. Out of the available CFPS systems, wheat germ cell-free protein synthesis (WG-CFPS) merges the highest yields with the use of a eukaryotic ribosome, making it an excellent approach for the synthesis of complex eukaryotic proteins including, for example, protein complexes and membrane proteins. Separating the translation reaction from other cellular processes, CFPS offers a flexible means to adapt translation reactions to protein needs. There is a large demand for such potent, easy-to-use, rapid protein expression systems, which are optimally serving protein requirements to drive biochemical and structural biology research. We summarize here a general workflow for a wheat germ system providing examples from the literature, as well as applications used for our own studies in structural biology. With this review, we want to highlight the tremendous potential of the rapidly evolving and highly versatile CFPS systems, making them more widely used as common tools to recombinantly prepare particularly challenging recombinant eukaryotic proteins.
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Affiliation(s)
- Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Matthias Harbers
- CellFree Sciences, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
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Cell-Free Expression of a Plant Membrane Protein BrPT2 From Boesenbergia Rotunda. Mol Biotechnol 2021; 63:316-326. [PMID: 33565047 DOI: 10.1007/s12033-021-00304-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2021] [Indexed: 10/22/2022]
Abstract
Prenylation of aromatic natural products by membrane-bound prenyltransferases (PTs) is an important biosynthesis step of many bioactive compounds. At present, only a few plant flavonoid-related PT genes have been functionally characterized, mainly due to the difficulties of expressing these membrane proteins. Rapid and effective methods to produce functional plant membrane proteins are thus indispensable. Here, we evaluated expression systems through cell-based and cell-free approaches to express Boesenbergia rotunda BrPT2 encoding a membrane-bound prenyltransferase. We attempted to express BrPT2 in Escherichia coli and tobacco plants but failed to detect this protein using the Western-blot technique, whereas an intact single band of 43 kDa was detected when BrPT2 was expressed using a cell-free protein synthesis system (PURE). Under in vitro enzymatic condition, the synthesized BrPT2 successfully catalyzed pinostrobin chalcone to pinostrobin. Molecular docking analysis showed that pinostrobin chalcone interacts with BrPT2 at two cavities: (1) the main binding site at the central cavity and (2) the allosteric binding site located away from the central cavity. Our findings suggest that cell-free protein synthesis could be an alternative for rapid production of valuable difficult-to-express membrane proteins.
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12
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Shen J, Wu G, Tsai AL, Zhou M. Structure and Mechanism of a Unique Diiron Center in Mammalian Stearoyl-CoA Desaturase. J Mol Biol 2020; 432:5152-5161. [PMID: 32470559 PMCID: PMC7483794 DOI: 10.1016/j.jmb.2020.05.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/16/2020] [Accepted: 05/22/2020] [Indexed: 12/11/2022]
Abstract
Stearoyl-CoA desaturase 1 (SCD1) is a membrane-embedded metalloenzyme that catalyzes the formation of a double bond on a saturated acyl-CoA. SCD1 has a diiron center and its proper function requires an electron transport chain composed of NADH (or NADPH), cytochrome b5 reductase (b5R), and cytochrome b5 (cyt b5). Since SCD1 is a key regulator in fat metabolism and is required for survival of cancer cells, there is intense interest in targeting SCD1 for various metabolic diseases and cancers. Crystal structures of human and mouse SCD1 were reported recently; however, both proteins have two zinc ions instead of two iron ions in the catalytic center, and as a result, the enzymes are inactive. Here we report a general approach for incorporating iron into heterologously expressed proteins in HEK293 cells. We produced mouse SCD1 that contains a diiron center and visualized its diiron center by solving its crystal structure to 3.5 Å. We assembled the entire electron transport chain using the purified soluble domains of cyt b5 and b5R, and the purified mouse SCD1, and we showed that three proteins coordinate to produce proper products. These results established an in vitro system that allows precise perturbations of the electron transport chain for the understanding of the catalytic mechanism in SCD1.
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Affiliation(s)
- Jiemin Shen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Gang Wu
- Division of Hematology, Internal Medicine, University of Texas Medical School at Houston, 6431 Fannin, Houston, TX 77030, USA
| | - Ah-Lim Tsai
- Division of Hematology, Internal Medicine, University of Texas Medical School at Houston, 6431 Fannin, Houston, TX 77030, USA.
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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13
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Ghoneum A, Gonzalez D, Abdulfattah AY, Said N. Metabolic Plasticity in Ovarian Cancer Stem Cells. Cancers (Basel) 2020; 12:E1267. [PMID: 32429566 PMCID: PMC7281273 DOI: 10.3390/cancers12051267] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/15/2020] [Accepted: 05/15/2020] [Indexed: 12/18/2022] Open
Abstract
Ovarian Cancer is the fifth most common cancer in females and remains the most lethal gynecological malignancy as most patients are diagnosed at late stages of the disease. Despite initial responses to therapy, recurrence of chemo-resistant disease is common. The presence of residual cancer stem cells (CSCs) with the unique ability to adapt to several metabolic and signaling pathways represents a major challenge in developing novel targeted therapies. The objective of this study is to investigate the transcripts of putative ovarian cancer stem cell (OCSC) markers in correlation with transcripts of receptors, transporters, and enzymes of the energy generating metabolic pathways involved in high grade serous ovarian cancer (HGSOC). We conducted correlative analysis in data downloaded from The Cancer Genome Atlas (TCGA), studies of experimental OCSCs and their parental lines from Gene Expression Omnibus (GEO), and Cancer Cell Line Encyclopedia (CCLE). We found positive correlations between the transcripts of OCSC markers, specifically CD44, and glycolytic markers. TCGA datasets revealed that NOTCH1, CD133, CD44, CD24, and ALDH1A1, positively and significantly correlated with tricarboxylic acid cycle (TCA) enzymes. OVCAR3-OCSCs (cancer stem cells derived from a well-established epithelial ovarian cancer cell line) exhibited enrichment of the electron transport chain (ETC) mainly in complexes I, III, IV, and V, further supporting reliance on the oxidative phosphorylation (OXPHOS) phenotype. OVCAR3-OCSCs also exhibited significant increase in CD36, ACACA, SCD, and CPT1A, with CD44, CD133, and ALDH1A1 exhibiting positive correlations with lipid metabolic enzymes. TCGA data show positive correlations between OCSC markers and glutamine metabolism enzymes, whereas in OCSC experimental models of GSE64999, GSE28799, and CCLE, the number of positive and negative correlations observed was significantly lower and was different between model systems. Appropriate integration and validation of data model systems with those in patients' specimens is needed not only to bridge our knowledge gap of metabolic programing of OCSCs, but also in designing novel strategies to target the metabolic plasticity of dormant, resistant, and CSCs.
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Affiliation(s)
- Alia Ghoneum
- Departments of Cancer Biology, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA; (A.G.); (D.G.); (A.Y.A.)
| | - Daniela Gonzalez
- Departments of Cancer Biology, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA; (A.G.); (D.G.); (A.Y.A.)
| | - Ammar Yasser Abdulfattah
- Departments of Cancer Biology, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA; (A.G.); (D.G.); (A.Y.A.)
- Faculty of Medicine, University of Alexandria, Alexandria 21131, Egypt
| | - Neveen Said
- Departments of Cancer Biology, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA; (A.G.); (D.G.); (A.Y.A.)
- Departments of Pathology, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA
- Departments of Urology, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA
- Comprehensive Cancer Center, Wake Forest Baptist Health Sciences, Winston Salem, NC 27157, USA
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14
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Gregorio NE, Levine MZ, Oza JP. A User's Guide to Cell-Free Protein Synthesis. Methods Protoc 2019; 2:E24. [PMID: 31164605 PMCID: PMC6481089 DOI: 10.3390/mps2010024] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 02/06/2023] Open
Abstract
Cell-free protein synthesis (CFPS) is a platform technology that provides new opportunities for protein expression, metabolic engineering, therapeutic development, education, and more. The advantages of CFPS over in vivo protein expression include its open system, the elimination of reliance on living cells, and the ability to focus all system energy on production of the protein of interest. Over the last 60 years, the CFPS platform has grown and diversified greatly, and it continues to evolve today. Both new applications and new types of extracts based on a variety of organisms are current areas of development. However, new users interested in CFPS may find it challenging to implement a cell-free platform in their laboratory due to the technical and functional considerations involved in choosing and executing a platform that best suits their needs. Here we hope to reduce this barrier to implementing CFPS by clarifying the similarities and differences amongst cell-free platforms, highlighting the various applications that have been accomplished in each of them, and detailing the main methodological and instrumental requirement for their preparation. Additionally, this review will help to contextualize the landscape of work that has been done using CFPS and showcase the diversity of applications that it enables.
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Affiliation(s)
- Nicole E Gregorio
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Max Z Levine
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| | - Javin P Oza
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
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15
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Lu M, Zhao X, Xing H, Xun Z, Yang T, Cai C, Wang D, Ding P. Liposome-chaperoned cell-free synthesis for the design of proteoliposomes: Implications for therapeutic delivery. Acta Biomater 2018; 76:1-20. [PMID: 29625253 DOI: 10.1016/j.actbio.2018.03.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/20/2018] [Accepted: 03/27/2018] [Indexed: 12/12/2022]
Abstract
Cell-free (CF) protein synthesis has emerged as a powerful technique platform for efficient protein production in vitro. Liposomes have been widely studied as therapeutic carriers due to their biocompatibility, biodegradability, low toxicity, flexible surface manipulation, easy preparation, and higher cargo encapsulation capability. However, rapid immune clearance, insufficient targeting capacity, and poor cytoplasmic delivery efficiency substantially restrict their clinical application. The incorporation of functional membrane proteins (MPs) or peptides allows the transfer of biological properties to liposomes and imparts them with improved circulation, increased targeting, and efficient intracellular delivery. Liposome-chaperoned CF synthesis enables production of proteoliposomes in one-step reaction, which not only substantially simplifies the production procedure but also keeps protein functionality intact. Building off these observations, proteoliposomes with integrated MPs represent an excellent candidate for therapeutic delivery. In this review, we describe recent advances in CF synthesis with emphasis on detailing key factors for improving CF expression efficiency. Furthermore, we provide insights into strategies for rational design of proteoliposomal nanodelivery systems via CF synthesis. STATEMENT OF SIGNIFICANCE Liposome-chaperoned CF synthesis has emerged as a powerful approach for the design of recombinant proteoliposomes in one-step reaction. The incorporation of bioactive MPs or peptides into liposomes via CF synthesis can facilitate the development of proteoliposomal nanodelivery systems with improved circulation, increased targeting, and enhanced cellular delivery capacity. Moreover, by adapting lessons learned from natural delivery vehicles, novel bio-inspired proteoliposomes with enhanced delivery properties could be produced in CF systems. In this review, we first give an overview of CF synthesis with focus on enhancing protein expression in liposome-chaperoned CF systems. Furthermore, we intend to provide insight into harnessing CF-synthesized proteoliposomes for efficient therapeutic delivery.
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16
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Abstract
The terminal alkyne is a readily derivatized functionality valued for its diverse applications in material synthesis, pharmaceutical science, and chemical biology. The synthetic biology routes to terminal alkynes are highly desired and yet underexplored. Some marine natural products contain a terminal alkyne functionality, and the discovery of the biosynthetic gene clusters for jamaicamide B and carmabin A marked the beginning of a new era in the understanding and engineering of terminal alkyne biosynthesis. In this chapter, we will overview recent advances in understanding the biosynthetic machinery for terminal alkyne synthesis. We will first describe how to elucidate terminal alkyne biosynthetic mechanism through heterologous expression, purification, and in vitro biochemical assays of individual pathway proteins. This will be followed by the description of an in vivo reporting system for the characterization of a membrane-bound bifunctional desaturase/acetylenase involved in terminal alkyne formation. The chapter will also cover the strategies for discovering additional protein homologs for terminal alkyne synthesis from microbes as well as the applications of click chemistry to identify and quantify terminal alkyne-bearing metabolites from microbial cultures. We will conclude this chapter with current challenges and future directions in this field.
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Affiliation(s)
- Xuejun Zhu
- University of California, Berkeley, CA, United States
| | - Wenjun Zhang
- University of California, Berkeley, CA, United States; Chan Zuckerberg Biohub, San Francisco, CA, United States.
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17
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Nanazashvili M, Sánchez-Rodríguez JE, Fosque B, Bezanilla F, Sackin H. LRET Determination of Molecular Distances during pH Gating of the Mammalian Inward Rectifier Kir1.1b. Biophys J 2018; 114:88-97. [PMID: 29320699 PMCID: PMC5773755 DOI: 10.1016/j.bpj.2017.10.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/23/2017] [Accepted: 10/19/2017] [Indexed: 01/31/2023] Open
Abstract
Gating of the mammalian inward rectifier Kir1.1 at the helix bundle crossing (HBC) by intracellular pH is believed to be mediated by conformational changes in the C-terminal domain (CTD). However, the exact motion of the CTD during Kir gating remains controversial. Crystal structures and single-molecule fluorescence resonance energy transfer of KirBac channels have implied a rigid body rotation and/or a contraction of the CTD as possible triggers for opening of the HBC gate. In our study, we used lanthanide-based resonance energy transfer on single-Cys dimeric constructs of the mammalian renal inward rectifier, Kir1.1b, incorporated into anionic liposomes plus PIP2, to determine unambiguous, state-dependent distances between paired Cys residues on diagonally opposite subunits. Functionality and pH dependence of our proteoliposome channels were verified in separate electrophysiological experiments. The lanthanide-based resonance energy transfer distances measured in closed (pH 6) and open (pH 8) conditions indicated neither expansion nor contraction of the CTD during gating, whereas the HBC gate widened by 8.8 ± 4 Å, from 6.3 ± 2 to 15.1 ± 6 Å, during opening. These results are consistent with a Kir gating model in which rigid body rotation of the large CTD around the permeation axis is correlated with opening of the HBC hydrophobic gate, allowing permeation of a 7 Å hydrated K ion.
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Affiliation(s)
- Mikheil Nanazashvili
- Department of Physiology and Biophysics, The Chicago Medical School, Rosalind Franklin University, North Chicago, Illinois
| | - Jorge E Sánchez-Rodríguez
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois; Departamento de Física, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Ben Fosque
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Henry Sackin
- Department of Physiology and Biophysics, The Chicago Medical School, Rosalind Franklin University, North Chicago, Illinois.
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18
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Wang M, Chen H, Ailati A, Chen W, Chilton FH, Todd Lowther W, Chen YQ. Substrate specificity and membrane topologies of the iron-containing ω3 and ω6 desaturases from Mortierella alpina. Appl Microbiol Biotechnol 2017; 102:211-223. [PMID: 29082420 DOI: 10.1007/s00253-017-8585-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/06/2017] [Accepted: 10/09/2017] [Indexed: 11/28/2022]
Abstract
Polyunsaturated fatty acids (PUFAs) are essential lipids for cell function, normal growth, and development, serving as key structural components of biological membranes and modulating critical signal transduction events. Omega-3 (n-3) long chain PUFAs (LC-PUFAs) such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) have been shown to protect against inflammatory diseases and enhance brain development and function. This had led to a marked increase in demand for fish and fish oils in human diets, supplements, and aquaculture and created a need for new, sustainable n-3 LC-PUFA sources. We have studied for the first time homogenous preparations of the membrane-type ω6 and ω3 fatty acid desaturases from the fungus Mortierella alpina, as a model system to produce PUFAs. These desaturases possess a di-iron metal center and are selective for 18:1 n-9 and 18:2 n-6 acyl-CoA substrates, respectively. Sequence alignments and membrane topology predictions support that these enzymes have unique cap regions that may include the rearrangement and repositioning of the active site, especially when compared to the mammalian stearoyl-coenzyme A desaturase-1 (SCD1) and the related sphingolipid α-hydroxylase (Scs7p) that act upon different substrates.
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Affiliation(s)
- Mingxuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, USA
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Aisikaer Ailati
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, USA
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Floyd H Chilton
- Department of Physiology and Pharmacology, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, USA
| | - W Todd Lowther
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, USA.
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China. .,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China. .,Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Blvd., Winston-Salem, NC, 27157, USA.
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19
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Yilmaz JL, Lim ZL, Beganovic M, Breazeale S, Andre C, Stymne S, Vrinten P, Senger T. Determination of Substrate Preferences for Desaturases and Elongases for Production of Docosahexaenoic Acid from Oleic Acid in Engineered Canola. Lipids 2017; 52:207-222. [PMID: 28197856 PMCID: PMC5325871 DOI: 10.1007/s11745-017-4235-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/16/2017] [Indexed: 11/25/2022]
Abstract
Production of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in plant seed oils has been pursued to improve availability of these omega-3 fatty acids that provide important human health benefits. Canola (Brassica napus), through the introduction of 10 enzymes, can convert oleic acid (OLA) into EPA and ultimately DHA through a pathway consisting of two elongation and five desaturation steps. Herein we present an assessment of the substrate specificity of the seven desaturases and three elongases that were introduced into canola by expressing individual proteins in yeast. In vivo feeding experiments were conducted with 14 potential fatty acid intermediates in an OLA to DHA pathway to determine the fatty acid substrate profiles for each enzyme. Membrane fractions were prepared from yeast expression strains and shown to contain active enzymes. The elongases, as expected, extended acyl-CoA substrates in the presence of malonyl-CoA. To distinguish between enzymes that desaturate CoA- and phosphatidylcholine-linked fatty acid substrates, we developed a novel in vitro method. We show that a delta-12 desaturase from Phytophthora sojae, an omega-3 desaturase from Phytophthora infestans and a delta-4 desaturase from Thraustochytrium sp., all prefer phosphatidylcholine-linked acyl substrates with comparatively low use of acyl-CoA substrates. To further validate our method, a delta-9 desaturase from Saccharomyces cerevisiae was confirmed to use acyl-CoA as substrate, but could not use phosphatidylcholine-linked substrates. The results and the assay methods presented herein will be useful in efforts to improve modeling of fatty acid metabolism and production of EPA and DHA in plants.
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Affiliation(s)
| | - Ze Long Lim
- Bioriginal Food and Science Corporation, Saskatoon, SK, S7N 0W9, Canada
| | - Mirela Beganovic
- Scandinavian Biotechnology Research (ScanBiRes) AB, 230 53, Alnarp, Sweden
| | | | - Carl Andre
- BASF Plant Science LP, Research Triangle Park, NC, 27709, USA
| | - Sten Stymne
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 230 53, Alnarp, Sweden
| | - Patricia Vrinten
- Bioriginal Food and Science Corporation, Saskatoon, SK, S7N 0W9, Canada
| | - Toralf Senger
- BASF Plant Science LP, Research Triangle Park, NC, 27709, USA
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20
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Schmitt C, Lippert AH, Bonakdar N, Sandoghdar V, Voll LM. Compartmentalization and Transport in Synthetic Vesicles. Front Bioeng Biotechnol 2016; 4:19. [PMID: 26973834 PMCID: PMC4770187 DOI: 10.3389/fbioe.2016.00019] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/11/2016] [Indexed: 12/03/2022] Open
Abstract
Nanoscale vesicles have become a popular tool in life sciences. Besides liposomes that are generated from phospholipids of natural origin, polymersomes fabricated of synthetic block copolymers enjoy increasing popularity, as they represent more versatile membrane building blocks that can be selected based on their specific physicochemical properties, such as permeability, stability, or chemical reactivity. In this review, we focus on the application of simple and nested artificial vesicles in synthetic biology. First, we provide an introduction into the utilization of multicompartmented vesosomes as compartmentalized nanoscale bioreactors. In the bottom-up development of protocells from vesicular nanoreactors, the specific exchange of pathway intermediates across compartment boundaries represents a bottleneck for future studies. To date, most compartmented bioreactors rely on unspecific exchange of substrates and products. This is either based on changes in permeability of the coblock polymer shell by physicochemical triggers or by the incorporation of unspecific porin proteins into the vesicle membrane. Since the incorporation of membrane transport proteins into simple and nested artificial vesicles offers the potential for specific exchange of substances between subcompartments, it opens new vistas in the design of protocells. Therefore, we devote the main part of the review to summarize the technical advances in the use of phospholipids and block copolymers for the reconstitution of membrane proteins.
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Affiliation(s)
- Christine Schmitt
- Division of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anna H. Lippert
- Max-Planck-Institute for the Science of Light, Erlangen, Germany
| | - Navid Bonakdar
- Max-Planck-Institute for the Science of Light, Erlangen, Germany
| | - Vahid Sandoghdar
- Max-Planck-Institute for the Science of Light, Erlangen, Germany
| | - Lars M. Voll
- Division of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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21
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Niwa T, Sasaki Y, Uemura E, Nakamura S, Akiyama M, Ando M, Sawada S, Mukai SA, Ueda T, Taguchi H, Akiyoshi K. Comprehensive study of liposome-assisted synthesis of membrane proteins using a reconstituted cell-free translation system. Sci Rep 2015; 5:18025. [PMID: 26667602 PMCID: PMC4678891 DOI: 10.1038/srep18025] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/03/2015] [Indexed: 02/02/2023] Open
Abstract
Membrane proteins play pivotal roles in cellular processes and are key targets for drug discovery. However, the reliable synthesis and folding of membrane proteins are significant problems that need to be addressed owing to their extremely high hydrophobic properties, which promote irreversible aggregation in hydrophilic conditions. Previous reports have suggested that protein aggregation could be prevented by including exogenous liposomes in cell-free translation processes. Systematic studies that identify which membrane proteins can be rescued from irreversible aggregation during translation by liposomes would be valuable in terms of understanding the effects of liposomes and developing applications for membrane protein engineering in the context of pharmaceutical science and nanodevice development. Therefore, we performed a comprehensive study to evaluate the effects of liposomes on 85 aggregation-prone membrane proteins from Escherichia coli by using a reconstituted, chemically defined cell-free translation system. Statistical analyses revealed that the presence of liposomes increased the solubility of >90% of the studied membrane proteins, and ultimately improved the yields of the synthesized proteins. Bioinformatics analyses revealed significant correlations between the liposome effect and the physicochemical properties of the membrane proteins.
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Affiliation(s)
- Tatsuya Niwa
- Department of Biomolecular Engineering, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Eri Uemura
- Department of Biomolecular Engineering, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Shugo Nakamura
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Minato Akiyama
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Mitsuru Ando
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Japan Science and Technology Agency (JST), The Exploratory Research for Advanced Technology (ERATO), Bio-nanotransporter Project, Katsura Int'tech Center, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
| | - Shinichi Sawada
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Japan Science and Technology Agency (JST), The Exploratory Research for Advanced Technology (ERATO), Bio-nanotransporter Project, Katsura Int'tech Center, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
| | - Sada-atu Mukai
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Japan Science and Technology Agency (JST), The Exploratory Research for Advanced Technology (ERATO), Bio-nanotransporter Project, Katsura Int'tech Center, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
| | - Takuya Ueda
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, FSB401, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Hideki Taguchi
- Department of Biomolecular Engineering, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,Japan Science and Technology Agency (JST), The Exploratory Research for Advanced Technology (ERATO), Bio-nanotransporter Project, Katsura Int'tech Center, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
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22
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Zapf T, Tan CD, Reinelt T, Huber C, Shaohua D, Geifman‐Shochat S, Paulsen H, Sinner E. Funktionelle Synthese des Lichtsammelkomplexes II in Polymermembran‐Architekturen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Thomas Zapf
- Department für Nanobiotechnologie, Institut für Synthetische Bioarchitekturen, Universität für Bodenkultur, Muthgasse 11/2, 1190 Wien (Österreich)
| | - Cherng‐Wen Darren Tan
- Department für Nanobiotechnologie, Institut für Synthetische Bioarchitekturen, Universität für Bodenkultur, Muthgasse 11/2, 1190 Wien (Österreich)
| | - Tobias Reinelt
- Department für Nanobiotechnologie, Institut für Synthetische Bioarchitekturen, Universität für Bodenkultur, Muthgasse 11/2, 1190 Wien (Österreich)
| | - Christoph Huber
- Department für Nanobiotechnologie, Institut für Synthetische Bioarchitekturen, Universität für Bodenkultur, Muthgasse 11/2, 1190 Wien (Österreich)
| | - Ding Shaohua
- CAS Key Lab of Bio‐Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou (China)
| | | | - Harald Paulsen
- Institut für allgemeine Botanik, Johannes Gutenberg‐Universität Mainz (Deutschland)
| | - Eva‐Kathrin Sinner
- Department für Nanobiotechnologie, Institut für Synthetische Bioarchitekturen, Universität für Bodenkultur, Muthgasse 11/2, 1190 Wien (Österreich)
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23
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Zemella A, Thoring L, Hoffmeister C, Kubick S. Cell-Free Protein Synthesis: Pros and Cons of Prokaryotic and Eukaryotic Systems. Chembiochem 2015; 16:2420-31. [PMID: 26478227 PMCID: PMC4676933 DOI: 10.1002/cbic.201500340] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 01/07/2023]
Abstract
From its start as a small-scale in vitro system to study fundamental translation processes, cell-free protein synthesis quickly rose to become a potent platform for the high-yield production of proteins. In contrast to classical in vivo protein expression, cell-free systems do not need time-consuming cloning steps, and the open nature provides easy manipulation of reaction conditions as well as high-throughput potential. Especially for the synthesis of difficult to express proteins, such as toxic and transmembrane proteins, cell-free systems are of enormous interest. The modification of the genetic code to incorporate non-canonical amino acids into the target protein in particular provides enormous potential in biotechnology and pharmaceutical research and is in the focus of many cell-free projects. Many sophisticated cell-free systems for manifold applications have been established. This review describes the recent advances in cell-free protein synthesis and details the expanding applications in this field.
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Affiliation(s)
- Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Christian Hoffmeister
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
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24
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Zapf T, Tan CD, Reinelt T, Huber C, Shaohua D, Geifman‐Shochat S, Paulsen H, Sinner E. Synthesis and Functional Reconstitution of Light‐Harvesting Complex II into Polymeric Membrane Architectures. Angew Chem Int Ed Engl 2015; 54:14664-8. [DOI: 10.1002/anie.201506304] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 07/28/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Thomas Zapf
- Department for Nanobiotechnology, Institute of Synthetic Bioarchitectures, University of Natural Resources and Life Science, Muthgasse 11/2, 1190 Vienna (Austria)
| | - Cherng‐Wen Darren Tan
- Department for Nanobiotechnology, Institute of Synthetic Bioarchitectures, University of Natural Resources and Life Science, Muthgasse 11/2, 1190 Vienna (Austria)
| | - Tobias Reinelt
- Department for Nanobiotechnology, Institute of Synthetic Bioarchitectures, University of Natural Resources and Life Science, Muthgasse 11/2, 1190 Vienna (Austria)
| | - Christoph Huber
- Department for Nanobiotechnology, Institute of Synthetic Bioarchitectures, University of Natural Resources and Life Science, Muthgasse 11/2, 1190 Vienna (Austria)
| | - Ding Shaohua
- CAS Key Lab of Bio‐Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Keling Road 88, 215163 Suzhou (China)
| | - Susana Geifman‐Shochat
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore (Singapore)
| | - Harald Paulsen
- Institute of General Botany, Johannes Gutenberg University Mainz, Johannes‐von‐Müller‐Weg 6, 55128 Mainz (Germany)
| | - Eva‐Kathrin Sinner
- Department for Nanobiotechnology, Institute of Synthetic Bioarchitectures, University of Natural Resources and Life Science, Muthgasse 11/2, 1190 Vienna (Austria)
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25
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Zapf T, Zafiu C, Zaba C, Tan CWD, Hunziker W, Sinner EK. Nanoscopic leg irons: harvesting of polymer-stabilized membrane proteins with antibody-functionalized silica nanoparticles. Biomater Sci 2015. [PMID: 26215897 DOI: 10.1039/c5bm00133a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Silica-based nanoparticles (SiNPs) are presented to harvest complex membrane proteins, which have been embedded into unilammelar polymersomes via in vitro membrane assisted protein synthesis (iMAP). Size-optimized SiNPs have been surface-modified with polymer-targeting antibodies, which are employed to harvest the protein-containing polymersomes. The polymersomes mimic the cellular membrane. They are chemically defined and preserve their structural-functional integrity as virtually any membrane protein species can be synthesized into such architecture via the ribosomal context of a cellular lysate. The SiNPs resemble 'heavy leg irons' catching the polymersomes in order to enable gravity-based generic purification and concentration of such proteopolymersomes from the crude mixture of cellular lysates.
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Affiliation(s)
- Thomas Zapf
- Department for Nanobiotechnology, Institute of Synthetic Bioarchitectures, University of Natural Resources and Life Science, Muthgasse 11/2, 1190 Vienna, Austria.
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26
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Kovácsová G, Gustavsson E, Wang J, Kreir M, Peuker S, Westenhoff S. Cell-free expression of a functional pore-only sodium channel. Protein Expr Purif 2015; 111:42-7. [PMID: 25770647 PMCID: PMC4430601 DOI: 10.1016/j.pep.2015.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/01/2015] [Accepted: 03/04/2015] [Indexed: 01/10/2023]
Abstract
Voltage-gated sodium channels participate in the propagation of action potentials in excitable cells. Eukaryotic Navs are pseudo homotetrameric polypeptides, comprising four repeats of six transmembrane segments (S1-S6). The first four segments form the voltage-sensing domain and S5 and S6 create the pore domain with the selectivity filter. Prokaryotic Navs resemble these characteristics, but are truly tetrameric. They can typically be efficiently synthesized in bacteria, but production in vitro with cell-free synthesis has not been demonstrated. Here we report the cell-free expression and purification of a prokaryotic tetrameric pore-only sodium channel. We produced milligram quantities of the functional channel protein as characterized by size-exclusion chromatography, infrared spectroscopy and electrophysiological recordings. Cell-free expression enables advanced site-directed labelling, post-translational modifications, and special solubilization schemes. This enables next-generation biophysical experiments to study the principle of sodium ion selectivity and transport in sodium channels.
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Affiliation(s)
- Gabriela Kovácsová
- Department of Chemistry, University of Gothenburg, P.O. Box 462, SE-40530 Gothenburg, Sweden
| | - Emil Gustavsson
- Department of Chemistry, University of Gothenburg, P.O. Box 462, SE-40530 Gothenburg, Sweden
| | - Jiajun Wang
- Nanion Technologies GmbH, Gabrielenstraße 9, 80636 Munich, Germany
| | - Mohamed Kreir
- Nanion Technologies GmbH, Gabrielenstraße 9, 80636 Munich, Germany
| | - Sebastian Peuker
- Department of Chemistry, University of Gothenburg, P.O. Box 462, SE-40530 Gothenburg, Sweden.
| | - Sebastian Westenhoff
- Department of Chemistry, University of Gothenburg, P.O. Box 462, SE-40530 Gothenburg, Sweden.
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27
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Bai Y, McCoy JG, Levin EJ, Sobrado P, Rajashankar KR, Fox BG, Zhou M. X-ray structure of a mammalian stearoyl-CoA desaturase. Nature 2015; 524:252-6. [PMID: 26098370 PMCID: PMC4689147 DOI: 10.1038/nature14549] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 05/05/2015] [Indexed: 12/25/2022]
Abstract
Stearoyl-CoA desaturase (SCD) is conserved in all eukaryotes and introduces the first double bond into saturated fatty acyl-CoAs1–4. Since the monounsaturated products of SCD are key precursors of membrane phospholipids, cholesterol esters, and triglycerides, SCD is pivotal in fatty acid metabolism. Humans have two SCD homologs (SCD1 and SCD5), while mice have four (SCD1–SCD4). SCD1-deficient mice do not become obese or diabetic when fed a high-fat diet because of improved lipid metabolic profiles and insulin sensitivity5,6. Thus, SCD1 is a pharmacological target in the treatment of obesity, diabetes, and other metabolic diseases7. SCD1 is an integral membrane protein located in the endoplasmic reticulum, and catalyzes the formation of a cis-double bond between the 9th and 10th carbons of stearoyl- or palmitoyl-CoA8,9. The reaction requires molecular oxygen, which is activated by a diiron center, and cytochrome b5, which regenerates the diiron center10. To better understand the structural basis of these characteristics of SCD function, we crystallized and solved the structure of mouse SCD1 bound to stearoyl-CoA at 2.6 Å resolution. The structure shows a novel fold comprising four transmembrane helices capped by a cytosolic domain, and a plausible pathway for lateral substrate access and product egress. The acyl chain of the bound stearoyl-CoA is enclosed in a tunnel buried in the cytosolic domain, and the geometry of the tunnel and configuration of the bound acyl chain provide a structural basis for the regioselectivity and stereospecificity of the desaturation reaction. The dimetal center is coordinated by a unique configuration of nine conserved histidine residues that implies a potentially novel metal center and mechanism for oxygen activation. The structure also illustrates a possible route for electron transfer from cytochrome b5 to the diiron center.
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Affiliation(s)
- Yonghong Bai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jason G McCoy
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Elena J Levin
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Pablo Sobrado
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kanagalaghatta R Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Brian G Fox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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Folding membrane proteins in vitro: A table and some comments. Arch Biochem Biophys 2014; 564:314-26. [DOI: 10.1016/j.abb.2014.06.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/17/2014] [Accepted: 06/23/2014] [Indexed: 12/23/2022]
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29
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Takemori N, Takemori A, Matsuoka K, Morishita R, Matsushita N, Aoshima M, Takeda H, Sawasaki T, Endo Y, Higashiyama S. High-throughput synthesis of stable isotope-labeled transmembrane proteins for targeted transmembrane proteomics using a wheat germ cell-free protein synthesis system. MOLECULAR BIOSYSTEMS 2014; 11:361-5. [PMID: 25431973 DOI: 10.1039/c4mb00556b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a wheat germ cell-free protein synthesis system, we developed a high-throughput method for the synthesis of stable isotope-labeled full-length transmembrane proteins as proteoliposomes to mimic the in vivo environment, and we successfully constructed an internal standard library for targeted transmembrane proteomics by using mass spectrometry.
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30
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Sachse R, Dondapati SK, Fenz SF, Schmidt T, Kubick S. Membrane protein synthesis in cell-free systems: From bio-mimetic systems to bio-membranes. FEBS Lett 2014; 588:2774-81. [DOI: 10.1016/j.febslet.2014.06.007] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/30/2014] [Accepted: 06/02/2014] [Indexed: 01/28/2023]
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31
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Harbers M. Wheat germ systems for cell-free protein expression. FEBS Lett 2014; 588:2762-73. [PMID: 24931374 DOI: 10.1016/j.febslet.2014.05.061] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/25/2014] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
Cell-free protein expression plays an important role in biochemical research. However, only recent developments led to new methods to rapidly synthesize preparative amounts of protein that make cell-free protein expression an attractive alternative to cell-based methods. In particular the wheat germ system provides the highest translation efficiency among eukaryotic cell-free protein expression approaches and has a very high success rate for the expression of soluble proteins of good quality. As an open in vitro method, the wheat germ system is a preferable choice for many applications in protein research including options for protein labeling and the expression of difficult-to-express proteins like membrane proteins and multiple protein complexes. Here I describe wheat germ cell-free protein expression systems and give examples how they have been used in genome-wide expression studies, preparation of labeled proteins for structural genomics and protein mass spectroscopy, automated protein synthesis, and screening of enzymatic activities. Future directions for the use of cell-free expression methods are discussed.
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Affiliation(s)
- Matthias Harbers
- RIKEN Center for Life Science Technologies, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan; CellFree Sciences Co., Ltd., 75-1, Ono-cho, Leading Venture Plaza 201, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan.
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32
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33
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Zheng X, Dong S, Zheng J, Li D, Li F, Luo Z. Expression, stabilization and purification of membrane proteins via diverse protein synthesis systems and detergents involving cell-free associated with self-assembly peptide surfactants. Biotechnol Adv 2014; 32:564-74. [PMID: 24566241 DOI: 10.1016/j.biotechadv.2014.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 06/13/2013] [Accepted: 02/17/2014] [Indexed: 12/21/2022]
Abstract
G-protein coupled receptors (GPCRs) are involved in regulating most of physiological actions and metabolism in the bodies, which have become most frequently addressed therapeutic targets for various disorders and diseases. Purified GPCR-based drug discoveries have become routine that approaches to structural study, novel biophysical and biochemical function analyses. However, several bottlenecks that GPCR-directed drugs need to conquer the problems including overexpression, solubilization, and purification as well as stabilization. The breakthroughs are to obtain efficient protein yield and stabilize their functional conformation which are both urgently requiring of effective protein synthesis system methods and optimal surfactants. Cell-free protein synthesis system is superior to the high yields and post-translation modifications, and early signs of self-assembly peptide detergents also emerged to superiority in purification of membrane proteins. We herein focus several predominant protein synthesis systems and surfactants involving the novel peptide detergents, and uncover the advantages of cell-free protein synthesis system with self-assembling peptide detergents in purification of functional GPCRs. This review is useful to further study in membrane proteins as well as the new drug exploration.
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Affiliation(s)
- Xuan Zheng
- College of Basic Medical Sciences, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Shuangshuang Dong
- College of Basic Medical Sciences, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Jie Zheng
- College of laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Duanhua Li
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Feng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, China
| | - Zhongli Luo
- College of Basic Medical Sciences, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China.
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34
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Lai G, Renthal R. Integral Membrane Protein Fragment Recombination after Transfer from Nanolipoprotein Particles to Bicelles. Biochemistry 2013; 52:9405-12. [DOI: 10.1021/bi401391c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Ginny Lai
- Department
of Biology, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Robert Renthal
- Department
of Biology, University of Texas at San Antonio, San Antonio, Texas 78249, United States
- Department
of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
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35
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Zhang X, Sheng J, Huang L, Du L, Cai J, Cen P, Xu Z. High-level soluble expression of one model olfactory receptor (ODR-10) in Escherichia coli cell-free system. World J Microbiol Biotechnol 2013; 30:893-901. [DOI: 10.1007/s11274-013-1502-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Accepted: 09/18/2013] [Indexed: 01/06/2023]
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36
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Liu YJ, Hansen GPR, Venancio-Marques A, Baigl D. Cell-free preparation of functional and triggerable giant proteoliposomes. Chembiochem 2013; 14:2243-7. [PMID: 24115581 DOI: 10.1002/cbic.201300501] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Indexed: 01/15/2023]
Abstract
Heat, we leak: We express a membrane protein outside well-defined giant liposomes obtained by gravity-transferred sucrose-in-oil droplets into a cell-free, reconstituted expression system. We show that the presence of the liposome is necessary during expression for efficient protein insertion into the membrane and that temperature can trigger the resulting membrane function.
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Affiliation(s)
- Yan-Jun Liu
- Department of Chemistry, Ecole Normale Superieure, 24 rue Lhomond, 75005 Paris (France) http://www.baigllab.com/; Université Pierre et Marie Curie Paris 6, 4 place Jussieu, 75005 Paris (France); UMR 8640, CNRS, 3 rue Michel-Ange, 75016 Paris (France)
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37
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Ritz S, Hulko M, Zerfass C, May S, Hospach I, Krasteva N, Nelles G, Sinner EK. Cell-free expression of a mammalian olfactory receptor and unidirectional insertion into small unilamellar vesicles (SUVs). Biochimie 2013; 95:1909-16. [PMID: 23816872 DOI: 10.1016/j.biochi.2013.06.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/20/2013] [Indexed: 01/29/2023]
Abstract
Although the identification of the multigene family encoding mammalian olfactory receptors were identified more than 20 years ago, we are far from understanding olfactory perception because of the difficulties in functional expression of these receptors in heterologous cell systems. Cell-free (CF) or in vitro expression systems offer an elegant alternative route to cell based protein expression, as the functional expression of membrane proteins can be directly achieved from the genetic template without the need of cell cultivation and protein isolation. Here we investigated in detail the cell-free expression and membrane insertion of the olfactory receptor OR5 in dependence of different experimental conditions like probing different origins of the cell-free expression system (from bacteria, via plants and insects toward mammalian system) and lipid composition of the respective extracts. We provided substantial biochemical indications by radioactive labeling based on [(35)S]-methionine, followed by proteolytic digestion, and we found that the insertion of the olfactory receptor OR5 into liposomes resulted in an unidirectional orientation with the binding side exposed into the aqueous space, resembling the native orientation in the cilia of the olfactory neurons. We report the different results in synthesis capacity for the different in vitro systems employed as we like to demonstrate the first in vitro kit toward and ex situ and ex vivo odorant receptor array.
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Affiliation(s)
- Sandra Ritz
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany.
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38
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Carraher C, Nazmi AR, Newcomb RD, Kralicek A. Recombinant expression, detergent solubilisation and purification of insect odorant receptor subunits. Protein Expr Purif 2013; 90:160-9. [PMID: 23770557 DOI: 10.1016/j.pep.2013.06.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/31/2013] [Accepted: 06/04/2013] [Indexed: 12/16/2022]
Abstract
Insect odorant receptors (ORs) are seven transmembrane domain proteins that comprise a novel family of ligand-gated non-selective cation channels. The functional channel is made up of an odour activated ligand-binding OR and the OR co-receptor, Orco. However, the structure, stoichiometry and mechanism of activation of the receptor complex are not well understood. Here we demonstrate that baculovirus-mediated Sf9 cell expression and wheat germ cell-free expression, but not Escherichia coli cell-based or cell-free expression, can be used successfully to over-express a selection of insect ORs. From a panel of 19 detergents, 1%w/v Zwittergent 3-16 was able to solubilise five Drosophila melanogaster ORs produced from both eukaryotic expression systems. A large-scale purification protocol was then developed for DmOrco and the ligand-binding receptor, DmOr22a. The proteins were nickel-affinity purified using a deca-histidine tag in a buffer containing 0.2 mM Zwittergent 3-16, followed by size exclusion chromatography. These purified ORs appear to form similarly sized protein-detergent complexes when isolated from both expression systems. Circular dichroism analysis of both purified proteins suggests they are folded correctly. We also provide evidence that when DmOrco is expressed in Sf9 cells it undergoes post translational modification, probably glycosylation. Finally we show that the recombinant ORs can be incorporated into pre-formed liposomes. The ability to recombinantly express and purify insect ORs to homogeneity on a preparative scale, as well as insert them into liposomes, is a major step forward in enabling future structural and functional studies, as well as their use in OR based biosensors.
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Affiliation(s)
- Colm Carraher
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
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39
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Chen H, Gu Z, Zhang H, Wang M, Chen W, Lowther WT, Chen YQ. Expression and purification of integral membrane fatty acid desaturases. PLoS One 2013; 8:e58139. [PMID: 23520490 PMCID: PMC3592867 DOI: 10.1371/journal.pone.0058139] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 02/01/2013] [Indexed: 01/08/2023] Open
Abstract
Fatty acid desaturase enzymes perform dehydrogenation reactions leading to the insertion of double bonds in fatty acids, and are divided into soluble and integral membrane classes. Crystal structures of soluble desaturases are available; however, membrane desaturases have defied decades of efforts due largely to the difficulty of generating recombinant desaturase proteins for crystallographic analysis. Mortierella alpina is an oleaginous fungus which possesses eight membrane desaturases involved in the synthesis of saturated, monounsaturated and polyunsaturated fatty acids. Here, we describe the successful expression, purification and enzymatic assay of three M. alpina desaturases (FADS15, FADS12, and FADS9-I). Estimated yields of desaturases with purity >95% are approximately 3.5% (Ca. 4.6 mg/L of culture) for FADS15, 2.3% (Ca. 2.5 mg/L of culture) for FADS12 and 10.7% (Ca. 37.5 mg/L of culture) for FADS9-I. Successful expression of high amounts of recombinant proteins represents a critical step towards the structural elucidation of membrane fatty acid desaturases.
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Affiliation(s)
- Haiqin Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, People’s Republic of China
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Zhennan Gu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, People’s Republic of China
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, People’s Republic of China
| | - Mingxuan Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, People’s Republic of China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, People’s Republic of China
| | - W. Todd Lowther
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Yong Q. Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province, People’s Republic of China
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
- * E-mail:
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40
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Jarecki BW, Makino SI, Beebe ET, Fox BG, Chanda B. Function of Shaker potassium channels produced by cell-free translation upon injection into Xenopus oocytes. Sci Rep 2013; 3:1040. [PMID: 23301161 PMCID: PMC3539143 DOI: 10.1038/srep01040] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 12/06/2012] [Indexed: 11/21/2022] Open
Abstract
Voltage-gated ion channels are a class of membrane proteins that temporally orchestrate the ion flux critical for chemical and electrical signaling in excitable cells. Current methods to investigate the function of these channels rely on heterologous expression in living systems or reconstitution into artificial membranes; however these approaches have inherent drawbacks which limit potential biophysical applications. Here, we describe a new integrated approach combining cell-free translation of membrane proteins and in vivo expression using Xenopus laevis oocytes. In this method, proteoliposomes containing Shaker potassium channels are synthesized in vitro and injected into the oocytes, yielding functional preparations as shown by electrophysiological and fluorescence measurements within few hours. This strategy for studying eukaryotic ion channels is contrasted with existing, laborious procedures that require membrane protein extraction and reconstitution into synthetic lipid systems.
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Affiliation(s)
- Brian W Jarecki
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53706, USA
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41
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Friddin MS, Smithers NP, Beaugrand M, Marcotte I, Williamson PTF, Morgan H, de Planque MRR. Single-channel electrophysiology of cell-free expressed ion channels by direct incorporation in lipid bilayers. Analyst 2013; 138:7294-8. [DOI: 10.1039/c3an01540h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Casteleijn MG, Urtti A, Sarkhel S. Expression without boundaries: Cell-free protein synthesis in pharmaceutical research. Int J Pharm 2013; 440:39-47. [DOI: 10.1016/j.ijpharm.2012.04.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/01/2012] [Accepted: 04/03/2012] [Indexed: 11/15/2022]
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Aly KA, Beebe ET, Chan CH, Goren MA, Sepúlveda C, Makino SI, Fox BG, Forest KT. Cell-free production of integral membrane aspartic acid proteases reveals zinc-dependent methyltransferase activity of the Pseudomonas aeruginosa prepilin peptidase PilD. Microbiologyopen 2012; 2:94-104. [PMID: 23255525 PMCID: PMC3584216 DOI: 10.1002/mbo3.51] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/30/2012] [Accepted: 11/05/2012] [Indexed: 12/25/2022] Open
Abstract
Integral membrane aspartic acid proteases are receiving growing recognition for their fundamental roles in cellular physiology of eukaryotes and prokaryotes, and may be medically important pharmaceutical targets. The Gram-negative Pseudomonas aeruginosa PilD and the archaeal Methanococcus voltae FlaK were synthesized in the presence of unilamellar liposomes in a cell-free translation system. Cosynthesis of PilD with its full-length substrate, PilA, or of FlaK with its full-length substrate, FlaB2, led to complete cleavage of the substrate signal peptides. Scaled-up synthesis of PilD, followed by solubilization in dodecyl-β-d-maltoside and chromatography, led to a pure enzyme that retained both of its known biochemical activities: cleavage of the PilA signal peptide and S-adenosyl methionine-dependent methylation of the mature pilin. X-ray fluorescence scans show for the first time that PilD is a zinc-binding protein. Zinc is required for the N-terminal methylation of the mature pilin, but not for signal peptide cleavage. Taken together, our work identifies the P. aeruginosa prepilin peptidase PilD as a zinc-dependent N-methyltransferase and provides a new platform for large-scale synthesis of PilD and other integral membrane proteases important for basic microbial physiology and virulence.
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Affiliation(s)
- Khaled A Aly
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Long AR, O'Brien CC, Alder NN. The cell-free integration of a polytopic mitochondrial membrane protein into liposomes occurs cotranslationally and in a lipid-dependent manner. PLoS One 2012; 7:e46332. [PMID: 23050015 PMCID: PMC3457961 DOI: 10.1371/journal.pone.0046332] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 08/31/2012] [Indexed: 01/19/2023] Open
Abstract
The ADP/ATP Carrier (AAC) is the most abundant transporter of the mitochondrial inner membrane. The central role that this transporter plays in cellular energy production highlights the importance of understanding its structure, function, and the basis of its pathologies. As a means of preparing proteoliposomes for the study of membrane proteins, several groups have explored the use of cell-free translation systems to facilitate membrane protein integration directly into preformed unilamellar vesicles without the use of surfactants. Using AAC as a model, we report for the first time the detergent-free reconstitution of a mitochondrial inner membrane protein into liposomes using a wheat germ-based in vitro translation system. Using a host of independent approaches, we demonstrate the efficient integration of AAC into vesicles with an inner membrane-mimetic lipid composition and, more importantly, that the integrated AAC is functionally active in transport. By adding liposomes at different stages of the translation reaction, we show that this direct integration is obligatorily cotranslational, and by synthesizing stable ribosome-bound nascent chain intermediates, we show that the nascent AAC polypeptide interacts with lipid vesicles while ribosome-bound. Finally, we show that the presence of the phospholipid cardiolipin in the liposomes specifically enhances AAC translation rate as well as the efficiency of vesicle association and integration. In light of these results, the possible mechanisms of liposome-assisted membrane protein integration during cell-free translation are discussed with respect to the mode of integration and the role of specific lipids.
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Affiliation(s)
- Ashley R. Long
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Catherine C. O'Brien
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Nathan N. Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
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45
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Qi Q, Gibson A, Fu X, Zheng M, Kuehn R, Wang Y, Wang Y, Navarro S, Morrell JA, Jiang D, Simmons G, Bell E, Ivleva NB, McClerren AL, Loida P, Ruff TG, Petracek ME, Preuss SB. Involvement of the N-terminal B-box domain of Arabidopsis BBX32 protein in interaction with soybean BBX62 protein. J Biol Chem 2012; 287:31482-93. [PMID: 22801428 PMCID: PMC3438981 DOI: 10.1074/jbc.m112.346940] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 06/21/2012] [Indexed: 01/29/2023] Open
Abstract
Previous studies have demonstrated that Arabidopsis thaliana BBX32 (AtBBX32) represses light signaling in A. thaliana and that expression of AtBBX32 in soybean increases grain yield in multiple locations and multiyear field trials. The BBX32 protein is a member of the B-box zinc finger family from A. thaliana and contains a single conserved Zn(2+)-binding B-box domain at the N terminus. Although the B-box domain is predicted to be involved in protein-protein interactions, the mechanism of interaction is poorly understood. Here, we provide in vitro and in vivo evidence demonstrating the physical and functional interactions of AtBBX32 with another B-box protein, soybean BBX62 (GmBBX62). Deletion analysis and characterization of the purified B-box domain indicate that the N-terminal B-box region of AtBBX32 interacts with GmBBX62. Computational modeling and site-directed mutagenesis of the AtBBX32 B-box region identified specific residues as critical for mediating the interaction between AtBBX32 and GmBBX62. This study defines the plant B-box as a protein interaction domain and offers novel insight into its role in mediating specific protein-protein interactions between different plant B-box proteins.
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Affiliation(s)
- Qungang Qi
- From the Monsanto Company, Chesterfield, Missouri 63017 and
| | - Ann Gibson
- From the Monsanto Company, Chesterfield, Missouri 63017 and
| | - Xiaoran Fu
- From the Monsanto Company, Chesterfield, Missouri 63017 and
| | - Meiying Zheng
- From the Monsanto Company, Chesterfield, Missouri 63017 and
| | | | - Yongcheng Wang
- From the Monsanto Company, Chesterfield, Missouri 63017 and
| | - Yanfei Wang
- From the Monsanto Company, Chesterfield, Missouri 63017 and
| | | | | | - Dongming Jiang
- From the Monsanto Company, Chesterfield, Missouri 63017 and
| | - Grant Simmons
- From the Monsanto Company, Chesterfield, Missouri 63017 and
| | - Erin Bell
- the Monsanto Company, St. Louis, Missouri 63167
| | | | | | - Paul Loida
- From the Monsanto Company, Chesterfield, Missouri 63017 and
| | - Thomas G. Ruff
- From the Monsanto Company, Chesterfield, Missouri 63017 and
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Haferkamp I, Linka N. Functional expression and characterisation of membrane transport proteins. PLANT BIOLOGY (STUTTGART, GERMANY) 2012; 14:675-90. [PMID: 22639981 DOI: 10.1111/j.1438-8677.2012.00591.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Membrane transporters set the framework organising the complexity of plant metabolism in cells, tissues and organisms. Their substrate specificity and controlled activity in different cells is a crucial part for plant metabolism to run pathways in concert. Transport proteins catalyse the uptake and exchange of ions, substrates, intermediates, products and cofactors across membranes. Given the large number of metabolites, a wide spectrum of transporters is required. The vast majority of in silico annotated membrane transporters in plant genomes, however, has not yet been functionally characterised. Hence, to understand the metabolic network as a whole, it is important to understand how transporters connect and control the metabolic pathways of plant cells. Heterologous expression and in vitro activity studies of recombinant transport proteins have highly improved their functional analysis in the last two decades. This review provides a comprehensive overview of the recent advances in membrane protein expression and functional characterisation using various host systems and transport assays.
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Affiliation(s)
- I Haferkamp
- Plant Physiology, Technical University of Kaiserslautern, Kaiserslautern, Germany Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - N Linka
- Plant Physiology, Technical University of Kaiserslautern, Kaiserslautern, Germany Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Roos C, Kai L, Proverbio D, Ghoshdastider U, Filipek S, Dötsch V, Bernhard F. Co-translational association of cell-free expressed membrane proteins with supplied lipid bilayers. Mol Membr Biol 2012; 30:75-89. [PMID: 22716775 DOI: 10.3109/09687688.2012.693212] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Routine strategies for the cell-free production of membrane proteins in the presence of detergent micelles and for their efficient co-translational solubilization have been developed. Alternatively, the expression in the presence of rationally designed lipid bilayers becomes interesting in particular for biochemical studies. The synthesized membrane proteins would be directed into a more native-like environment and cell-free expression of transporters, channels or other membrane proteins in the presence of supplied artificial membranes could allow their subsequent functional analysis without any exposure to detergents. In addition, lipid-dependent effects on activity and stability of membrane proteins could systematically be studied. However, in contrast to the generally efficient detergent solubilization, the successful stabilization of membrane proteins with artificial membranes appears to be more difficult. A number of strategies have therefore been explored in order to optimize the co-translational association of membrane proteins with different forms of supplied lipid bilayers including liposomes, bicelles, microsomes or nanodiscs. In this review, we have compiled the current state-of-the-art of this technology and we summarize parameters which have been indicated as important for the co-translational association of cell-free synthesized membrane proteins with supplied membranes.
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Affiliation(s)
- Christian Roos
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Germany
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Functional analysis of membranous Fo-a subunit of F1Fo-ATP synthase by in vitro protein synthesis. Biochem J 2012; 442:631-8. [PMID: 22166005 DOI: 10.1042/bj20111284] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The a subunit of F(1)F(o) (F(1)F(o)-ATP synthase) is a highly hydrophobic protein with five putative transmembrane helices which plays a central role in H(+)-translocation coupled with ATP synthesis/hydrolysis. In the present paper, we show that the a subunit produced by the in vitro protease-free protein synthesis system (the PURE system) is integrated into a preformed F(o) a-less F(1)F(o) complex in Escherichia coli membrane vesicles and liposomes. The resulting F(1)F(o) has a H(+)-coupled ATP synthesis/hydrolysis activity that is approximately half that of the native F(1)F(o). By using this procedure, we analysed five mutations of F(1)F(o), where the conserved residues in the a subunit (Asn(90), Asp(112), Arg(169), Asn(173) and Gln(217)) were individually replaced with alanine. All of the mutant F(o) a subunits were successfully incorporated into F(1)F(o), showing the advantage over conventional expression in E. coli by which three (N90A, D112A, and Q217A) mutant a subunits were not found in F(1)F(o). The N173A mutant retained full activity and the mutants D112A and Q217A had weak, but detectable, activity. No activity was observed for the R169A and N90A mutants. Asn(90) is located in the middle of putative second transmembrane helix and likely to play an important role in H(+)-translocation. The present study exemplifies that the PURE system provides an alternative approach when in vivo expression of membranous components in protein complexes turns out to be difficult.
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Goren MA, Fox BG, Bangs JD. Amino acid determinants of substrate selectivity in the Trypanosoma brucei sphingolipid synthase family. Biochemistry 2011; 50:8853-61. [PMID: 21899277 DOI: 10.1021/bi200981a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The substrate selectivity of four Trypanosoma brucei sphingolipid synthases was examined. TbSLS1, an inositol phosphorylceramide (IPC) synthase, and TbSLS4, a bifunctional sphingomyelin (SM)/ethanolamine phosphorylceramide (EPC) synthase, were inactivated by Ala substitutions of a conserved triad of residues His210, His253, and Asp257 thought to form part of the active site. TbSLS4 also catalyzed the reverse reaction, production of ceramide from sphingomyelin, but none of the Ala substitutions of the catalytic triad in TbSLS4 were able to do so. Site-directed mutagenesis identified residues proximal to the conserved triad that were responsible for the discrimination between charge and size of the different head groups. For discrimination between anionic (phosphoinositol) and zwitterionic (phosphocholine, phosphoethanolamine) head groups, doubly mutated V172D/S252F TbSLS1 and D172V/F252S TbSLS3 showed reciprocal conversion between IPC and bifunctional SM/EPC synthases. For differentiation of zwitterionic headgroup size, N170A TbSLS1 and A170N/N187D TbSLS4 showed reciprocal conversion between EPC and bifunctional SM/EPC synthases. These studies provide a mapping of the SLS active site and demonstrate that differences in catalytic specificity of the T. brucei enzyme family are controlled by natural variations in as few as three residue positions.
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Affiliation(s)
- Michael A Goren
- Department of Biochemistry,School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53706, USA
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Nozawa A, Ogasawara T, Matsunaga S, Iwasaki T, Sawasaki T, Endo Y. Production and partial purification of membrane proteins using a liposome-supplemented wheat cell-free translation system. BMC Biotechnol 2011; 11:35. [PMID: 21481249 PMCID: PMC3090341 DOI: 10.1186/1472-6750-11-35] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 04/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recently, some groups have reported on cell-free synthesis of functional membrane proteins (MPs) in the presence of exogenous liposomes (liposomes). Previously, we reported synthesis of a functional AtPPT1 plant phosphate transporter that was associated with liposomes during translation. However, it is unclear whether or not lipid/MP complex formation is common to all types of MPs in the wheat cell-free system. RESULTS AtPPT1 was synthesized using a wheat cell-free system with or without liposomes. AtPPT1 synthesized with liposomes showed high transport activity, but the activity of AtPPT1 synthesized without liposomes was less than 10% activity of that with liposomes. To test whether co-translational association with liposomes is observed in the synthesis of other MPs, we used 40 mammalian MPs having one to 14 transmembrane domains (TMDs) and five soluble proteins as a control. The association rate of all 40 MPs into liposomes was more than 40% (mean value: 59%), while that of the five soluble proteins was less than 20% (mean value: 12%). There were no significant differences in association rate among MPs regardless of the number of TMDs and synthesis yield. These results indicate that the wheat cell-free system is a highly productive method for lipid/MP complex formation and is suitable for large-scale preparation. The liposome association of green fluorescent protein (GFP)-fusion MPs were also tested and recovered as lipid/MP complex after floatation by Accudenz density gradient ultracentrifugation (DGU). Employment of GFP-MPs revealed optimal condition for Accudenz floatation. Using the optimized Accudenz DGU condition, P2RX4/lipid complexes were partially purified and detected as a major band by Coomassie Brilliant Blue (CBB)-staining after SDS-PAGE. CONCLUSION Formation of lipid/AtPPT1 complex during the cell-free synthesis reaction is critical for synthesis of a functional MP. The lipid/MP complex during the translation was observed in all 40 MPs tested. At least 29 MPs, as judged by their higher productivity compared to GFP, might be suitable for a large-scale preparation. MPs synthesized by this method form lipid/MP complexes, which could be readily partially purified by Accudenz DGU. Wheat cell-free protein synthesis in the presence of liposomes will be a useful method for preparation of variety type of MPs.
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Affiliation(s)
- Akira Nozawa
- Cell-Free Science and Technology Research Center and the Venture Business, Laboratory, Ehime University, 3 Bunkyo-Cho, Matsuyama, Ehime 790-8577, Japan
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