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Takemori N, Takemori A, Tanaka Y, Endo Y, Hurst JL, Gómez-Baena G, Harman VM, Beynon RJ. MEERCAT: Multiplexed Efficient Cell Free Expression of Recombinant QconCATs For Large Scale Absolute Proteome Quantification. Mol Cell Proteomics 2017; 16:2169-2183. [PMID: 29055021 PMCID: PMC5724179 DOI: 10.1074/mcp.ra117.000284] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/15/2017] [Indexed: 01/25/2023] Open
Abstract
A major challenge in proteomics is the absolute accurate quantification of large numbers of proteins. QconCATs, artificial proteins that are concatenations of multiple standard peptides, are well established as an efficient means to generate standards for proteome quantification. Previously, QconCATs have been expressed in bacteria, but we now describe QconCAT expression in a robust, cell-free system. The new expression approach rescues QconCATs that previously were unable to be expressed in bacteria and can reduce the incidence of proteolytic damage to QconCATs. Moreover, it is possible to cosynthesize QconCATs in a highly-multiplexed translation reaction, coexpressing tens or hundreds of QconCATs simultaneously. By obviating bacterial culture and through the gain of high level multiplexing, it is now possible to generate tens of thousands of standard peptides in a matter of weeks, rendering absolute quantification of a complex proteome highly achievable in a reproducible, broadly deployable system.
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Affiliation(s)
- Nobuaki Takemori
- From the ‡Proteo-Science Center, Ehime University, Ehime, 791-0295, Japan; .,§Advanced Research Support Center, Ehime University, Ehime, 791-0295, Japan
| | - Ayako Takemori
- From the ‡Proteo-Science Center, Ehime University, Ehime, 791-0295, Japan.,¶The United Graduate School of Agricultural Sciences, Ehime University, Ehime, 790-8566, Japan
| | - Yuki Tanaka
- §Advanced Research Support Center, Ehime University, Ehime, 791-0295, Japan
| | - Yaeta Endo
- From the ‡Proteo-Science Center, Ehime University, Ehime, 791-0295, Japan
| | - Jane L Hurst
- **Mammalian Behaviour and Evolution Group, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE
| | - Guadalupe Gómez-Baena
- ‖Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Victoria M Harman
- ‖Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Robert J Beynon
- ‖Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK;
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52
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Kanno T, Yasutake K, Tanaka K, Hadano S, Ikeda JE. A novel function of N-linked glycoproteins, alpha-2-HS-glycoprotein and hemopexin: Implications for small molecule compound-mediated neuroprotection. PLoS One 2017; 12:e0186227. [PMID: 29016670 PMCID: PMC5633190 DOI: 10.1371/journal.pone.0186227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 09/27/2017] [Indexed: 11/18/2022] Open
Abstract
Therapeutic agents to the central nervous system (CNS) need to be efficiently delivered to the target site of action at appropriate therapeutic levels. However, a limited number of effective drugs for the treatment of neurological diseases has been developed thus far. Further, the pharmacological mechanisms by which such therapeutic agents can protect neurons from cell death have not been fully understood. We have previously reported the novel small-molecule compound, 2-[mesityl(methyl)amino]-N-[4-(pyridin-2-yl)-1H-imidazol-2-yl] acetamide trihydrochloride (WN1316), as a unique neuroprotectant against oxidative injury and a highly promising remedy for the treatment of amyotrophic lateral sclerosis (ALS). One of the remarkable characteristics of WN1316 is that its efficacious doses in ALS mouse models are much less than those against oxidative injury in cultured human neuronal cells. It is also noted that the WN1316 cytoprotective activity observed in cultured cells is totally dependent upon the addition of fetal bovine serum in culture medium. These findings led us to postulate some serum factors being tightly linked to the WN1316 efficacy. In this study, we sieved through fetal bovine serum proteins and identified two N-linked glycoproteins, alpha-2-HS-glycoprotein (AHSG) and hemopexin (HPX), requisites to exert the WN1316 cytoprotective activity against oxidative injury in neuronal cells in vitro. Notably, the removal of glycan chains from these molecules did not affect the WN1316 cytoprotective activity. Thus, two glycoproteins, AHSG and HPX, represent a pivotal glycoprotein of the cytoprotective activity for WN1316, showing a concrete evidence for the novel glycan-independent function of serum glycoproteins in neuroprotective drug efficacy.
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Affiliation(s)
- Takuya Kanno
- NGP Biomedical Research Institute, Neugen Pharma Inc., Meguro, Tokyo, Japan
| | - Kaori Yasutake
- NGP Biomedical Research Institute, Neugen Pharma Inc., Meguro, Tokyo, Japan
| | - Kazunori Tanaka
- NGP Biomedical Research Institute, Neugen Pharma Inc., Meguro, Tokyo, Japan
| | - Shinji Hadano
- Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
| | - Joh-E Ikeda
- NGP Biomedical Research Institute, Neugen Pharma Inc., Meguro, Tokyo, Japan
- Department of Molecular Neurology, Faculty of Medicine, Kitasato University, Sagamihara, Kanagawa, Japan
- Apoptosis Research Centre, Children’s Hospital of Eastern Ontario, Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- * E-mail:
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53
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Jérôme V, Thoring L, Salzig D, Kubick S, Freitag R. Comparison of cell-based versus cell-free mammalian systems for the production of a recombinant human bone morphogenic growth factor. Eng Life Sci 2017; 17:1097-1107. [PMID: 32624737 DOI: 10.1002/elsc.201700005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 06/14/2017] [Accepted: 07/13/2017] [Indexed: 12/18/2022] Open
Abstract
The human bone morphogenetic protein-2 (hBMP2) is a glycoprotein, which induces de novo bone formation. Here, recombinant production in stably transfected Chinese Hamster Ovary (CHO) cells is compared to transient expression in Human Embryo Kidney (HEK) cells and cell-free synthesis in CHO cell lysates containing microsomal structures as sites of post-translational processing. In case of the stably transfected cells, growth rates and viabilities were similar to those of the parent cells, while entry into the death phase of the culture was delayed. The maximum achievable rhBMP2 concentration in these cultures was 153 pg/mL. Up to 280 ng/mL could be produced in the transient expression system. In both cases the rhBMP-2 was found to interact with the producer cells, which presumably contributed to the low yields. In the cell-free system, hBMP2 yields could be increased to almost 40 μg/mL, reached within three hours. The cell-free system thus approached productivities for the active (renatured) protein previously only recorded for bacterial hosts, while assuring comprehensive post-translational processing.
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Affiliation(s)
- Valérie Jérôme
- Chair for Process Biotechnology University of Bayreuth Germany
| | - Lena Thoring
- Department of Cell-free and Cell-based Bioproduction, Fraunhofer Institute for Cell Therapy and Immunology (IZI) Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB) Germany
| | - Denise Salzig
- Chair for Process Biotechnology University of Bayreuth Germany
| | - Stefan Kubick
- Department of Cell-free and Cell-based Bioproduction, Fraunhofer Institute for Cell Therapy and Immunology (IZI) Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB) Germany
| | - Ruth Freitag
- Chair for Process Biotechnology University of Bayreuth Germany
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54
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Takemori N, Takemori A, Tanaka Y, Ishizaki J, Hasegawa H, Shiraishi A, Ohashi Y. High-throughput production of a stable isotope-labeled peptide library for targeted proteomics using a wheat germ cell-free synthesis system. MOLECULAR BIOSYSTEMS 2017; 12:2389-93. [PMID: 27203355 DOI: 10.1039/c6mb00209a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Quantitative proteomic approaches using selected reaction monitoring (SRM) are currently limited by the difficulty in the preparation of reference standards. In this study, we demonstrat the high-throughput production of a reference peptide library using a wheat germ cell-free synthesis system to develop a large-scale SRM assay for targeted proteomics.
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Affiliation(s)
- Nobuaki Takemori
- Division of Proteomics Research, Proteo-Science Center, Ehime University, Ehime, Japan.
| | - Ayako Takemori
- Division of Proteomics Research, Proteo-Science Center, Ehime University, Ehime, Japan.
| | - Yuki Tanaka
- Advanced Research Support Center, Ehime University, Ehime, Japan
| | - Jun Ishizaki
- Department of Hematology, Clinical Immunology and Infectious Diseases, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Hitoshi Hasegawa
- Department of Hematology, Clinical Immunology and Infectious Diseases, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Atsushi Shiraishi
- Department of Ophthalmology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yuichi Ohashi
- Department of Ophthalmology, Ehime University Graduate School of Medicine, Ehime, Japan
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55
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Takeda H, Zhou W, Kido K, Suno R, Iwasaki T, Kobayashi T, Sawasaki T. CP5 system, for simple and highly efficient protein purification with a C-terminal designed mini tag. PLoS One 2017; 12:e0178246. [PMID: 28542437 PMCID: PMC5444806 DOI: 10.1371/journal.pone.0178246] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/10/2017] [Indexed: 02/06/2023] Open
Abstract
There are many strategies to purify recombinant proteins of interest, and affinity purification utilizing monoclonal antibody that targets a linear epitope sequence is one of the essential techniques used in current biochemistry and structural biology. Here we introduce a new protein purification system using a very short CP5 tag. First, we selected anti-dopamine receptor D1 (DRD1) rabbit monoclonal antibody clone Ra62 (Ra62 antibody) as capture antibody, and identified its minimal epitope sequence as a 5-amino-acid sequence at C-terminal of DRD1 (GQHPT-COOH, D1CE sequence). We found that single amino acid substitution in D1CE sequence (GQHVT-COOH) increased dissociation rate up to 10-fold, and named the designed epitope sequence CP5 tag. Using Ra62 antibody and 2 peptides with different affinity, we developed a new affinity protein purification method, CP5 system. Ra62 antibody quickly captures CP5-tagged target protein, and captured CP5-tagged protein was eluted by competing with higher affinity D1CE peptide. By taking the difference of the affinity between D1CE and CP5, sharp elution under mild condition was achieved. Using CP5 system, we successfully purified deubiquitinase CYLD and E3 ubiquitin ligase MARCH3, and detected their catalytic activity. As to G protein-coupled receptors (GPCRs), 9 out of 12 cell-free synthesized ones were purified, demonstrating its purification capability of integral membrane proteins. CP5 tagged CHRM2 expressed by baculovirus-insect cell was also successfully purified by CP5 system. CP5 system offers several distinct advantages in addition to its specificity and elution performance. CP5 tag is easy to construct and handle because of its short length, which has less effect on protein characters. Mild elution of CP5 system is particulaly suitable for preparing delicate proteins such as enzymes and membrane proteins. Our data demonstrate that CP5 system provides a new promising option in protein sample preparation with high yield, purity and activity for downstream applications in functional and structural analysis.
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Affiliation(s)
- Hiroyuki Takeda
- Proteo-Science Center, Ehime University, Matsuyama, Ehime, Japan
| | - Wei Zhou
- Proteo-Science Center, Ehime University, Matsuyama, Ehime, Japan
| | - Kohki Kido
- Proteo-Science Center, Ehime University, Matsuyama, Ehime, Japan
| | - Ryoji Suno
- Department of Medical Chemistry and Cell Biology, Kyoto University Graduate School of Medicine, Yoshida, Sakyo-ku, Kyoto, Japan
| | - Takahiro Iwasaki
- Proteo-Science Center, Ehime University, Matsuyama, Ehime, Japan
| | - Takuya Kobayashi
- Department of Medical Chemistry and Cell Biology, Kyoto University Graduate School of Medicine, Yoshida, Sakyo-ku, Kyoto, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo, Japan
| | - Tatsuya Sawasaki
- Proteo-Science Center, Ehime University, Matsuyama, Ehime, Japan
- * E-mail:
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56
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Kaneko N, Iwasaki T, Ito Y, Takeda H, Sawasaki T, Morikawa S, Nakano N, Kurata M, Masumoto J. Applications of reconstituted inflammasomes in a cell-free system to drug discovery and elucidation of the pathogenesis of autoinflammatory diseases. Inflamm Regen 2017; 37:9. [PMID: 29259708 PMCID: PMC5725934 DOI: 10.1186/s41232-017-0040-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/06/2017] [Indexed: 12/19/2022] Open
Abstract
The inflammasome, typically consisting of a Nod-like receptor, apoptosis-associated speck-like protein, and pro-caspase-1, has recently been identified as a huge intracellular complex, which plays a crucial role in interleukin-1 maturation or specific physiological functions. Two Nod-like receptors, such as nucleotide-binding oligomerization domains-containing protein (Nod)1 and Nod2, interact with the receptor-interacting protein serine-threonine kinase (RIPK)2 accompanied by Iκ-B kinase (IKK) complexes to construct the nodosome, leading to nuclear factor (NF)-κB activation. The aberrant activation of inflammasomes or nodosomes causes autoinflammatory diseases. Therefore, inflammasomes may be attractive targets to treat autoinflammatory diseases. Our aim is to develop reconstituted inflammasomes in a cell-free system to discover specific molecular-target drugs and elucidate the molecular pathogenesis of autoinflammatory diseases. In this review, we describe reconstituted inflammasomes in a cell-free system.
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Affiliation(s)
- Naoe Kaneko
- Department of Pathology, Ehime University Graduate School of Medicine and Proteo-Science Center, Shitsukawa 454, Toon, 791-0295 Ehime Japan
| | - Tomoyuki Iwasaki
- Department of Pathology, Ehime University Graduate School of Medicine and Proteo-Science Center, Shitsukawa 454, Toon, 791-0295 Ehime Japan
| | - Yuki Ito
- Department of Pathology, Ehime University Graduate School of Medicine and Proteo-Science Center, Shitsukawa 454, Toon, 791-0295 Ehime Japan
| | - Hiroyuki Takeda
- Divison of Proteo-Drug-Discovery Sciences, Ehime University Proteo-Science Center, Bunkyocho 3, Matsuyama, 790-8577 Ehime Japan
| | - Tatsuya Sawasaki
- Division of Cell-free Sciences, Ehime University Proteo-Science Center, Bunkyocho 3, Matsuyama, 790-8577 Ehime Japan
| | - Shinnosuke Morikawa
- Department of Pathology, Ehime University Graduate School of Medicine and Proteo-Science Center, Shitsukawa 454, Toon, 791-0295 Ehime Japan
| | - Naoko Nakano
- Department of Pathology, Ehime University Graduate School of Medicine and Proteo-Science Center, Shitsukawa 454, Toon, 791-0295 Ehime Japan
| | - Mie Kurata
- Department of Pathology, Ehime University Graduate School of Medicine and Proteo-Science Center, Shitsukawa 454, Toon, 791-0295 Ehime Japan
| | - Junya Masumoto
- Department of Pathology, Ehime University Graduate School of Medicine and Proteo-Science Center, Shitsukawa 454, Toon, 791-0295 Ehime Japan
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57
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Minkoff BB, Makino SI, Haruta M, Beebe ET, Wrobel RL, Fox BG, Sussman MR. A cell-free method for expressing and reconstituting membrane proteins enables functional characterization of the plant receptor-like protein kinase FERONIA. J Biol Chem 2017; 292:5932-5942. [PMID: 28235802 DOI: 10.1074/jbc.m116.761981] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/09/2017] [Indexed: 01/17/2023] Open
Abstract
There are more than 600 receptor-like kinases (RLKs) in Arabidopsis, but due to challenges associated with the characterization of membrane proteins, only a few have known biological functions. The plant RLK FERONIA is a peptide receptor and has been implicated in plant growth regulation, but little is known about its molecular mechanism of action. To investigate the properties of this enzyme, we used a cell-free wheat germ-based expression system in which mRNA encoding FERONIA was co-expressed with mRNA encoding the membrane scaffold protein variant MSP1D1. With the addition of the lipid cardiolipin, assembly of these proteins into nanodiscs was initiated. FERONIA protein kinase activity in nanodiscs was higher than that of soluble protein and comparable with other heterologously expressed protein kinases. Truncation experiments revealed that the cytoplasmic juxtamembrane domain is necessary for maximal FERONIA activity, whereas the transmembrane domain is inhibitory. An ATP analogue that reacts with lysine residues inhibited catalytic activity and labeled four lysines; mutagenesis demonstrated that two of these, Lys-565 and Lys-663, coordinate ATP in the active site. Mass spectrometric phosphoproteomic measurements further identified phosphorylation sites that were examined using phosphomimetic mutagenesis. The results of these experiments are consistent with a model in which kinase-mediated phosphorylation within the C-terminal region is inhibitory and regulates catalytic activity. These data represent a step further toward understanding the molecular basis for the protein kinase catalytic activity of FERONIA and show promise for future characterization of eukaryotic membrane proteins.
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Affiliation(s)
- Benjamin B Minkoff
- From the Department of Biochemistry and.,the Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
| | | | - Miyoshi Haruta
- From the Department of Biochemistry and.,the Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
| | | | | | | | - Michael R Sussman
- From the Department of Biochemistry and .,the Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706
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58
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Li J, Wang H, Kwon YC, Jewett MC. Establishing a high yieldingstreptomyces-based cell-free protein synthesis system. Biotechnol Bioeng 2017; 114:1343-1353. [DOI: 10.1002/bit.26253] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/06/2017] [Accepted: 01/15/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Jian Li
- Department of Chemical and Biological Engineering; Northwestern University; Evanston Illinois 60208
| | - He Wang
- Department of Chemical and Biological Engineering; Northwestern University; Evanston Illinois 60208
- Masters in Biotechnology Program; Northwestern University; Evanston Illinois
| | - Yong-Chan Kwon
- Department of Chemical and Biological Engineering; Northwestern University; Evanston Illinois 60208
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering; Northwestern University; Evanston Illinois 60208
- Masters in Biotechnology Program; Northwestern University; Evanston Illinois
- Chemistry of Life Processes Institute; Northwestern University; Evanston Illinois
- Member; Robert H. Lurie Comprehensive Cancer Center; Northwestern University; Chicago Illinois
- Simpson Querrey Institute; Northwestern University; Chicago Illinois. Center for Synthetic Biology; Northwestern University; Evanston Illinois
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59
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Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling. Proc Natl Acad Sci U S A 2017; 114:E1336-E1344. [PMID: 28167777 DOI: 10.1073/pnas.1615351114] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To elucidate the dynamic features of a biologically relevant large-scale reaction network, we constructed a computational model of minimal protein synthesis consisting of 241 components and 968 reactions that synthesize the Met-Gly-Gly (MGG) peptide based on an Escherichia coli-based reconstituted in vitro protein synthesis system. We performed a simulation using parameters collected primarily from the literature and found that the rate of MGG peptide synthesis becomes nearly constant in minutes, thus achieving a steady state similar to experimental observations. In addition, concentration changes to 70% of the components, including intermediates, reached a plateau in a few minutes. However, the concentration change of each component exhibits several temporal plateaus, or a quasi-stationary state (QSS), before reaching the final plateau. To understand these complex dynamics, we focused on whether the components reached a QSS, mapped the arrangement of components in a QSS in the entire reaction network structure, and investigated time-dependent changes. We found that components in a QSS form clusters that grow over time but not in a linear fashion, and that this process involves the collapse and regrowth of clusters before the formation of a final large single cluster. These observations might commonly occur in other large-scale biological reaction networks. This developed analysis might be useful for understanding large-scale biological reactions by visualizing complex dynamics, thereby extracting the characteristics of the reaction network, including phase transitions.
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60
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Kasi D, Catherine C, Lee SW, Lee KH, Kim YJ, Ro Lee M, Ju JW, Kim DM. Cell-free translational screening of an expression sequence tag library of Clonorchis sinensis for novel antigen discovery. Biotechnol Prog 2017; 33:832-837. [PMID: 28127897 DOI: 10.1002/btpr.2440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/10/2016] [Indexed: 12/12/2022]
Abstract
The rapidly evolving cloning and sequencing technologies have enabled understanding of genomic structure of parasite genomes, opening up new ways of combatting parasite-related diseases. To make the most of the exponentially accumulating genomic data, however, it is crucial to analyze the proteins encoded by these genomic sequences. In this study, we adopted an engineered cell-free protein synthesis system for large-scale expression screening of an expression sequence tag (EST) library of Clonorchis sinensis to identify potential antigens that can be used for diagnosis and treatment of clonorchiasis. To allow high-throughput expression and identification of individual genes comprising the library, a cell-free synthesis reaction was designed such that both the template DNA and the expressed proteins were co-immobilized on the same microbeads, leading to microbead-based linkage of the genotype and phenotype. This reaction configuration allowed streamlined expression, recovery, and analysis of proteins. This approach enabled us to identify 21 antigenic proteins. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:832-837, 2017.
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Affiliation(s)
- Devi Kasi
- Dept. of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 305-764, Korea
| | - Christy Catherine
- Dept. of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 305-764, Korea
| | - Seung-Won Lee
- Dept. of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 305-764, Korea
| | - Kyung-Ho Lee
- Dept. of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 305-764, Korea
| | - Yu Jung Kim
- Div. of Malaria and Parasitic Diseases, National Institute of Health, Osong, 361-951, Korea
| | - Myeong Ro Lee
- Div. of Malaria and Parasitic Diseases, National Institute of Health, Osong, 361-951, Korea
| | - Jung Won Ju
- Div. of Malaria and Parasitic Diseases, National Institute of Health, Osong, 361-951, Korea
| | - Dong-Myung Kim
- Dept. of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 305-764, Korea
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61
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OsMYC2, an essential factor for JA-inductive sakuranetin production in rice, interacts with MYC2-like proteins that enhance its transactivation ability. Sci Rep 2017; 7:40175. [PMID: 28067270 PMCID: PMC5220304 DOI: 10.1038/srep40175] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/02/2016] [Indexed: 11/08/2022] Open
Abstract
Biosynthesis of sakuranetin, a flavonoid anti-fungal phytoalexin that occurs in rice, is highly dependent on jasmonic acid (JA) signalling and induced by a variety of environmental stimuli. We previously identified OsNOMT, which encodes naringenin 7-O-methyltransferase (NOMT); NOMT is a key enzyme for sakuranetin production. Although OsNOMT expression is induced by JA treatment, the regulation mechanism that activates the biosynthetic pathway of sakuranetin has not yet been elucidated. In this study, we show that JA-inducible basic helix-loop-helix transcriptional factor OsMYC2 drastically enhances the activity of the OsNOMT promoter and is essential for JA-inducible sakuranetin production. In addition, we identified 2 collaborators of OsMYC2, OsMYC2-like protein 1 and 2 (OsMYL1 and OsMYL2) that further activated the OsNOMT promoter in synergy with OsMYC2. Physical interaction of OsMYC2 with OsMYL1 and OsMYL2 further supported the idea that these interactions lead to the enhancement of the transactivation activity of OsMYC2. Our results indicate that JA signalling via OsMYC2 is reinforced by OsMYL1 and OsMYL2, resulting in the inductive production of sakuranetin during defence responses in rice.
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62
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Fogeron ML, Badillo A, Penin F, Böckmann A. Wheat Germ Cell-Free Overexpression for the Production of Membrane Proteins. Methods Mol Biol 2017; 1635:91-108. [PMID: 28755365 DOI: 10.1007/978-1-4939-7151-0_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Due to their hydrophobic nature, membrane proteins are notoriously difficult to express in classical cell-based protein expression systems. Often toxic, they also undergo degradation in cells or aggregate in inclusion bodies, making delicate issues further solubilization and renaturation. These are major bottlenecks in their structural and functional analysis. The wheat germ cell-free (WGE-CF) system offers an effective alternative not only to classical cell-based protein expression systems but also to other cell-free systems for the expression of membrane proteins. The WGE-CF indeed allows the production of milligram amounts of membrane proteins in a detergent-solubilized, homogenous, and active form. Here, we describe the method to produce a viral integral membrane protein, which is the non-structural protein 2 (NS2) of hepatitis C virus, in view of structural studies by solid-state NMR in a native-like lipid environment.
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Affiliation(s)
- Marie-Laure Fogeron
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69007, Lyon, France
| | - Aurélie Badillo
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69007, Lyon, France
| | - François Penin
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69007, Lyon, France
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69007, Lyon, France.
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63
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Perez JG, Stark JC, Jewett MC. Cell-Free Synthetic Biology: Engineering Beyond the Cell. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023853. [PMID: 27742731 DOI: 10.1101/cshperspect.a023853] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell-free protein synthesis (CFPS) technologies have enabled inexpensive and rapid recombinant protein expression. Numerous highly active CFPS platforms are now available and have recently been used for synthetic biology applications. In this review, we focus on the ability of CFPS to expand our understanding of biological systems and its applications in the synthetic biology field. First, we outline a variety of CFPS platforms that provide alternative and complementary methods for expressing proteins from different organisms, compared with in vivo approaches. Next, we review the types of proteins, protein complexes, and protein modifications that have been achieved using CFPS systems. Finally, we introduce recent work on genetic networks in cell-free systems and the use of cell-free systems for rapid prototyping of in vivo networks. Given the flexibility of cell-free systems, CFPS holds promise to be a powerful tool for synthetic biology as well as a protein production technology in years to come.
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Affiliation(s)
- Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611-3068.,Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611-2875
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64
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Murakami M, Kameda K, Tsumoto H, Tsuda T, Masuda K, Utsunomiya R, Mori H, Miura Y, Sayama K. TLN-58, an Additional hCAP18 Processing Form, Found in the Lesion Vesicle of Palmoplantar Pustulosis in the Skin. J Invest Dermatol 2016; 137:322-331. [PMID: 27771329 DOI: 10.1016/j.jid.2016.07.044] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 06/27/2016] [Accepted: 07/20/2016] [Indexed: 10/20/2022]
Abstract
We previously reported that the early vesicle of the palmoplantar pustulosis (PPP) vesicle originated from eccrine sweat in the acrosyringium and that the PPP vesicle contains the antimicrobial peptide human cathelicidin-18/LL-37. The concentration of LL-37 was sufficient to induce the subsequent inflammation in lesions and human keratinocytes, and the PPP vesicles contained additional small fragments of human cathelicidin-18, of approximately 7 kDa, which have not been identified. The aim of the present study was to clarify the additional processed forms found in PPP vesicles and their physiological effects on normal keratinocytes and sweat gland cells. Lesional PPP vesicles were collected from PPP patients, and endogenous human cathelicidin-18/LL-37 was depleted using a LL-37 antibody affinity column. A designed recombinant human cathelicidin-18 peptide was prepared and incubated with the depleted PPP vesicle fluid to confirm the additional processed form. In-gel digestion analysis and protein sequencing confirmed the additional form as TLN-58. TLN-58 up-regulated IL-17C, IL-8, IL-23, IL-1α, and IL-1β mRNA and protein expression in normal human keratinocytes and also showed antibacterial activity against Staphylococcus aureus, Staphylococcus epidermidis, and group A Streptococcus species, similar to LL-37. This additional form could be involved in the continued inflammation in PPP lesions.
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Affiliation(s)
- Masamoto Murakami
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan.
| | - Kenji Kameda
- Advanced Research Support Center, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Hiroki Tsumoto
- Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Teruko Tsuda
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Kana Masuda
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Ryo Utsunomiya
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Hideki Mori
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yuri Miura
- Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Koji Sayama
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
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65
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Production of Recombinant CCN2 Protein in Escherichia coli. Methods Mol Biol 2016. [PMID: 27734367 DOI: 10.1007/978-1-4939-6430-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Recombinant proteins are important tools for understanding molecular functions in vitro. Recent progress in the generation of recombinant proteins is amazing. However, when we plan to produce them, we should choose the best method according to the nature and the use of the target recombinant protein. Degradation and mis-folding are major problems in producing active recombinant CCN2. The method shown in this chapter describes the appropriate conditions under which we can produce CCN2 and its truncated fragments in Escherichia coli.
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66
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67
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Merk H, Rues RB, Gless C, Beyer K, Dong F, Dötsch V, Gerrits M, Bernhard F. Biosynthesis of membrane dependent proteins in insect cell lysates: identification of limiting parameters for folding and processing. Biol Chem 2016; 396:1097-107. [PMID: 25999328 DOI: 10.1515/hsz-2015-0105] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 05/11/2015] [Indexed: 11/15/2022]
Abstract
G protein-coupled receptors, like many other membrane proteins, are notoriously difficult to synthesize in conventional cellular systems. Although expression in insect cells is considered the preferred technique for structural characterizations in particular, inefficient membrane translocation, instability, toxic effects and low yields still pose clear limitations for their production in living cells. Recent studies started to explore alternative strategies for the in vitro production of problematic membrane proteins in cell-free lysates in combination with supplied membranes. We provide a detailed study on the production efficiencies and quality of G protein-coupled receptors, Fab fragments and other proteins synthesized in insect cell lysates containing endogenous microsomes. Effects of different reaction kinetics, redox conditions and sample preparations on the specific activities of synthesized proteins have been analyzed. The extent of glycosylation, membrane translocation and percentages of ligand binding active fractions of synthesized protein samples have been determined. We provide strong evidence that membrane insertion of integral membrane proteins can represent a prime limiting factor for their preparative scale in vitro production. Improved expression protocols resulting into higher production rates yielded more active protein in case of Fab fragments, but not in case of the human endothelin B receptor.
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68
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AGIA Tag System Based on a High Affinity Rabbit Monoclonal Antibody against Human Dopamine Receptor D1 for Protein Analysis. PLoS One 2016; 11:e0156716. [PMID: 27271343 PMCID: PMC4894603 DOI: 10.1371/journal.pone.0156716] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 05/18/2016] [Indexed: 01/11/2023] Open
Abstract
Polypeptide tag technology is widely used for protein detection and affinity purification. It consists of two fundamental elements: a peptide sequence and a binder which specifically binds to the peptide tag. In many tag systems, antibodies have been used as binder due to their high affinity and specificity. Recently, we obtained clone Ra48, a high-affinity rabbit monoclonal antibody (mAb) against dopamine receptor D1 (DRD1). Here, we report a novel tag system composed of Ra48 antibody and its epitope sequence. Using a deletion assay, we identified EEAAGIARP in the C-terminal region of DRD1 as the minimal epitope of Ra48 mAb, and we named this sequence the "AGIA" tag, based on its central sequence. The tag sequence does not include the four amino acids, Ser, Thr, Tyr, or Lys, which are susceptible to post-translational modification. We demonstrated performance of this new tag system in biochemical and cell biology applications. SPR analysis demonstrated that the affinity of the Ra48 mAb to the AGIA tag was 4.90 × 10-9 M. AGIA tag showed remarkably high sensitivity and specificity in immunoblotting. A number of AGIA-fused proteins overexpressed in animal and plant cells were detected by anti-AGIA antibody in immunoblotting and immunostaining with low background, and were immunoprecipitated efficiently. Furthermore, a single amino acid substitution of the second Glu to Asp (AGIA/E2D) enabled competitive dissociation of AGIA/E2D-tagged protein by adding wild-type AGIA peptide. It enabled one-step purification of AGIA/E2D-tagged recombinant proteins by peptide competition under physiological conditions. The sensitivity and specificity of the AGIA system makes it suitable for use in multiple methods for protein analysis.
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69
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Ogawa A, Tabuchi J, Doi Y, Takamatsu M. Biofunction-assisted DNA detection through RNase H-enhanced 3' processing of a premature tRNA probe in a wheat germ extract. Bioorg Med Chem Lett 2016; 26:3658-61. [PMID: 27289318 DOI: 10.1016/j.bmcl.2016.05.091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 12/22/2022]
Abstract
We have developed a novel type of biofunction-assisted, signal-turn-on sensor for simply and homogenously detecting DNA. This sensor system is composed of two types of in vitro-transcribed label-free RNAs (a 3' premature amber suppressor tRNA probe and an amber-mutated mRNA encoding a reporter protein), RNase H, and a wheat germ extract (WGE). A target DNA induces the 3' end maturation of the tRNA probe, which is enhanced by RNase H and leads to the expression of a full-length reporter protein through amber suppression in WGE, while there is almost no expression without the target due to the inactivity of the premature probe. Therefore, the target can be readily detected with the activity of the translated reporter. The catalytic reuse of the target with the help of RNase H in addition to various bioprocesses in WGE enables this sensor system to exhibit relatively high selectivity and sensitivity.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
| | - Junichiro Tabuchi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yasunori Doi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Masashi Takamatsu
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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70
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Németh CE, Marcolongo P, Gamberucci A, Fulceri R, Benedetti A, Zoppi N, Ritelli M, Chiarelli N, Colombi M, Willaert A, Callewaert BL, Coucke PJ, Gróf P, Nagy SK, Mészáros T, Bánhegyi G, Margittai É. Glucose transporter type 10-lacking in arterial tortuosity syndrome-facilitates dehydroascorbic acid transport. FEBS Lett 2016; 590:1630-40. [PMID: 27153185 DOI: 10.1002/1873-3468.12204] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/20/2016] [Accepted: 05/03/2016] [Indexed: 12/25/2022]
Abstract
Loss-of-function mutations in the gene encoding GLUT10 are responsible for arterial tortuosity syndrome (ATS), a rare connective tissue disorder. In this study GLUT10-mediated dehydroascorbic acid (DAA) transport was investigated, supposing its involvement in the pathomechanism. GLUT10 protein produced by in vitro translation and incorporated into liposomes efficiently transported DAA. Silencing of GLUT10 decreased DAA transport in immortalized human fibroblasts whose plasma membrane was selectively permeabilized. Similarly, the transport of DAA through endomembranes was markedly reduced in fibroblasts from ATS patients. Re-expression of GLUT10 in patients' fibroblasts restored DAA transport activity. The present results demonstrate that GLUT10 is a DAA transporter and DAA transport is diminished in the endomembranes of fibroblasts from ATS patients.
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Affiliation(s)
- Csilla E Németh
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Paola Marcolongo
- Department of Molecular and Developmental Medicine, University of Siena, Italy
| | | | - Rosella Fulceri
- Department of Molecular and Developmental Medicine, University of Siena, Italy
| | - Angiolo Benedetti
- Department of Molecular and Developmental Medicine, University of Siena, Italy
| | - Nicoletta Zoppi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, Medical Faculty, University of Brescia, Italy
| | - Marco Ritelli
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, Medical Faculty, University of Brescia, Italy
| | - Nicola Chiarelli
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, Medical Faculty, University of Brescia, Italy
| | - Marina Colombi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, Medical Faculty, University of Brescia, Italy
| | - Andy Willaert
- Center for Medical Genetics, Ghent University, Belgium
| | | | - Paul J Coucke
- Center for Medical Genetics, Ghent University, Belgium
| | - Pál Gróf
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Szilvia K Nagy
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Gábor Bánhegyi
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Éva Margittai
- Institute of Clinical Experimental Research, Semmelweis University, Budapest, Hungary
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71
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Schoborg JA, Clark LG, Choudhury A, Hodgman CE, Jewett MC. Yeast knockout library allows for efficient testing of genomic mutations for cell-free protein synthesis. Synth Syst Biotechnol 2016; 1:2-6. [PMID: 29062921 PMCID: PMC5640588 DOI: 10.1016/j.synbio.2016.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 01/27/2016] [Accepted: 02/12/2016] [Indexed: 12/31/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems from crude lysates have benefitted from modifications to their enzyme composition. For example, functionally deleting enzymes in the source strain that are deleterious to CFPS can improve protein synthesis yields. However, making such modifications can take substantial time. As a proof-of-concept to accelerate prototyping capabilities, we assessed the feasibility of using the yeast knockout collection to identify negative effectors in a Saccharomyces cerevisiae CFPS platform. We analyzed extracts made from six deletion strains that targeted the single deletion of potentially negative effectors (e.g., nucleases). We found a statistically significant increase in luciferase yields upon loss of function of GCN3, PEP4, PPT1, NGL3, and XRN1 with a maximum increase of over 6-fold as compared to the wild type. Our work has implications for yeast CFPS and for rapidly prototyping strains to enable cell-free synthetic biology applications.
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Key Words
- ANOVA, analysis of variance
- ATP, adenosine triphosphate
- CFPS, cell-free protein synthesis
- CRISPR, clustered regularly interspaced short palindromic repeats
- Cell-free biology
- Cell-free protein synthesis
- In vitro translation
- NTP, nucleoside triphosphate
- OD, optical density
- Protein expression
- SC, synthetic complete media
- Saccharomyces cerevisiae
- Synthetic biology
- YKO, yeast knockout
- cAMP, cyclic adenosine monophosphate
- eIF, eukaryotic initiation factor
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Affiliation(s)
- Jennifer A. Schoborg
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Lauren G. Clark
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Alaksh Choudhury
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
- Masters in Biotechnology Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
| | - C. Eric Hodgman
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, 2170 Campus Drive, Evanston, IL 60208-3120, USA
- Masters in Biotechnology Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3120, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 N. St Clair St, Suite 1200, Chicago, IL 60611-3068, USA
- Simpson Querrey Institute, Northwestern University, 303 E. Superior St, Suite 11-131, Chicago, IL 60611-2875, USA
- Corresponding author. 2145 Sheridan Road, Tech E-136, Evanston, IL 60208-3120, USA.2145 Sheridan RoadTech E-136EvanstonIL60208-3120USA
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72
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Ogawa A, Tabuchi J. Biofunction-assisted aptasensors based on ligand-dependent 3' processing of a suppressor tRNA in a wheat germ extract. Org Biomol Chem 2016; 13:6681-5. [PMID: 25962756 DOI: 10.1039/c5ob00794a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a novel type of biofunction-assisted aptasensor that harnesses ligand-dependent 3' processing of a premature amber suppressor tRNA and the subsequent amber suppression of a reporter gene in a wheat germ extract.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
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73
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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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74
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Naimuddin M, Kubo T. A High Performance Platform Based on cDNA Display for Efficient Synthesis of Protein Fusions and Accelerated Directed Evolution. ACS COMBINATORIAL SCIENCE 2016; 18:117-29. [PMID: 26812183 DOI: 10.1021/acscombsci.5b00139] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a high performance platform based on cDNA display technology by developing a new modified puromycin linker-oligonucleotide. The linker consists of four major characteristics: a "ligation site" for hybridization and ligation of mRNA by T4 RNA ligase, a "puromycin arm" for covalent linkage of the protein, a "polyadenosine site" for a longer puromycin arm and purification of protein fusions (optional) using oligo-dT matrices, and a "reverse transcription site" for the formation of stable cDNA protein fusions whose cDNA is covalently linked to its encoded protein. The linker was synthesized by a novel branching strategy and provided >8-fold higher yield than previous linkers. This linker enables rapid and highly efficient ligation of mRNA (>90%) and synthesis of protein fusions (∼ 50-95%) in various cell-free expression systems. Overall, this new cDNA display method provides 10-200 fold higher end-usage fusions than previous methods and benefits higher diversity libraries crucial for directed protein/peptide evolution. With the increased efficiency, this system was able to reduce the time for one selection cycle to <8 h and is potentially amenable to high-throughput systems. We demonstrate the efficiency of this system for higher throughput selections of various biomolecular interactions and achieved 30-40-fold enrichment per selection cycle. Furthermore, a 4-fold higher enrichment of Flag-tag was obtained from a doped mixture compared with that of the previous cDNA display method. A three-finger protein library was evolved to isolate superior nanomolar range binding candidates for vascular endothelial growth factor. This method is expected to provide a beneficial impact to accelerated drug discovery and proteome analysis.
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Affiliation(s)
- Mohammed Naimuddin
- Biomedical
Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
- Janusys Corporation, #508, Saitama
Industrial Technology Center, Skip City, 3-12-18 Kami-Aoki, Kawaguchi, Saitama 333-0844, Japan
| | - Tai Kubo
- Biomedical
Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
- Molecular
Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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75
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Ogawa A, Namba Y, Gakumasawa M. Rational optimization of amber suppressor tRNAs toward efficient incorporation of a non-natural amino acid into protein in a eukaryotic wheat germ extract. Org Biomol Chem 2016; 14:2671-8. [DOI: 10.1039/c5ob02533h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Amber suppressor tRNAs (sup-tRNAs) were rationally optimized toward efficient incorporation of a non-natural amino acid (AcPhe) into protein in a eukaryotic wheat germ extract.
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Affiliation(s)
| | - Yuki Namba
- Proteo-Science Center
- Ehime University
- Matsuyama
- Japan
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76
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Hamada J, Onuma H, Ochi F, Hirai H, Takemoto K, Miyoshi A, Matsushita M, Kadota Y, Ohashi J, Kawamura R, Takata Y, Nishida W, Hashida S, Ishii E, Osawa H. Endoplasmic reticulum stress induced by tunicamycin increases resistin messenger ribonucleic acid through the pancreatic endoplasmic reticulum eukaryotic initiation factor 2α kinase-activating transcription factor 4-CAAT/enhancer binding protein-α homologous protein pathway in THP-1 human monocytes. J Diabetes Investig 2015; 7:312-23. [PMID: 27330716 PMCID: PMC4847884 DOI: 10.1111/jdi.12434] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 09/09/2015] [Accepted: 09/23/2015] [Indexed: 01/06/2023] Open
Abstract
AIMS/INTRODUCTION Resistin, secreted from adipocytes, causes insulin resistance in mice. In humans, the resistin gene is mainly expressed in monocytes and macrophages. Tunicamycin is known to induce endoplasmic reticulum (ER) stress, and reduce resistin gene expression in 3T3-L1 mouse adipocytes. The aim of the present study was to examine whether ER stress affects resistin gene expression in human monocytes. MATERIALS AND METHODS The relationship between resistin messenger ribonucleic acid (mRNA) and ER stress markers mRNA was analyzed by reverse transcription polymerase chain reaction in isolated monocytes of 30 healthy volunteers. The effect of endotoxin/lipopolysaccharides or tunicamycin on resistin gene expression was analyzed in THP-1 human monocytes. Signaling pathways leading to resistin mRNA were assessed by the knockdown using small interfering RNA or overexpression of key molecules involved in unfolded protein response. RESULTS Resistin mRNA was positively associated with immunoglobulin heavy chain-binding protein (BiP) or CAAT/enhancer binding protein-α homologous protein (CHOP) mRNA in human isolated monocytes. In THP-1 cells, lipopolysaccharides increased mRNA of BiP, pancreatic endoplasmic reticulum eukaryotic initiation factor 2α kinase (PERK) and CHOP, as well as resistin. Tunicamycin also increased resistin mRNA. This induction appeared to be dose- and time-dependent. Tunicamycin-induced resistin mRNA was inhibited by chemical chaperone, 4-phenylbutyric acid. The knockdown of either PERK, activating transcription factor 4 (ATF4) or CHOP reduced tunicamycin-induced resistin mRNA. Conversely, overexpression of ATF4 or CHOP increased resistin mRNA. CONCLUSIONS Endoplasmic reticulum stress induced by tunicamycin increased resistin mRNA through the PERK-ATF4-CHOP pathway in THP-1 human monocytes. ER stress could lead to insulin resistance through enhanced resistin gene expression in human monocytes.
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Affiliation(s)
- Junpei Hamada
- Department of Pediatrics Ehime University Graduate School of Medicine Ehime Japan
| | - Hiroshi Onuma
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Fumihiro Ochi
- Department of Pediatrics Ehime University Graduate School of Medicine Ehime Japan
| | - Hiroki Hirai
- Department of Pediatrics Ehime University Graduate School of Medicine Ehime Japan
| | - Koji Takemoto
- Department of Pediatrics Ehime University Graduate School of Medicine Ehime Japan
| | - Akiko Miyoshi
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Manami Matsushita
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Yuko Kadota
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Jun Ohashi
- Department of Biological Sciences Tokyo University Graduate School of Science Tokyo Japan
| | - Ryoichi Kawamura
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Yasunori Takata
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Wataru Nishida
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
| | - Seiichi Hashida
- Institute for Health Sciences Tokushima Bunri University Tokushima Japan
| | - Eiichi Ishii
- Department of Pediatrics Ehime University Graduate School of Medicine Ehime Japan
| | - Haruhiko Osawa
- Department of Diabetes and Molecular Genetics Ehime University Graduate School of Medicine Ehime Japan
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77
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Sogorin EA, Agalarov SC, Spirin AS. Formation of New Polysomes on Free mRNAs in a Cell-Free Translation Systems Is Accompanied by Partial Disassembly of Previously Formed Polysomes. BIOCHEMISTRY (MOSCOW) 2015; 80:1327-30. [PMID: 26567577 DOI: 10.1134/s0006297915100144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A method for detection of the fluorescence-labeled mRNA in translating ribosomal complexes has been developed. It is demonstrated that in the working cell-free translation system with preformed polysomes, formation of new polysomes on free mRNA takes place. For the first time, it is shown that the process is accompanied by partial disassembly of the previously formed polysomes. This result is interpreted as an indication of the direct relationship between processes of translation termination of polysomal ribosomes and translation initiation of free mRNAs.
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Affiliation(s)
- E A Sogorin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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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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79
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Matsunaga S, Masaoka T, Sawasaki T, Morishita R, Iwatani Y, Tatsumi M, Endo Y, Yamamoto N, Sugiura W, Ryo A. A cell-free enzymatic activity assay for the evaluation of HIV-1 drug resistance to protease inhibitors. Front Microbiol 2015; 6:1220. [PMID: 26583013 PMCID: PMC4628118 DOI: 10.3389/fmicb.2015.01220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/19/2015] [Indexed: 12/27/2022] Open
Abstract
Due to their high frequency of genomic mutations, human retroviruses often develop resistance to antiretroviral drugs. The emergence of drug-resistant human immunodeficiency virus type 1 (HIV-1) is a significant obstacle to the effective long-term treatment of HIV infection. The development of a rapid and versatile drug-susceptibility assay would enable acquisition of phenotypic information and facilitate determination of the appropriate choice of antiretroviral agents. In this study, we developed a novel in vitro method, termed the Cell-free drug susceptibility assay (CFDSA), for monitoring phenotypic information regarding the drug resistance of HIV-1 protease (PR). The CFDSA utilizes a wheat germ cell-free protein production system to synthesize enzymatically active HIV-1 PRs directly from PCR products amplified from HIV-1 molecular clones or clinical isolates in a rapid one-step procedure. Enzymatic activity of PRs can be readily measured by AlphaScreen (Amplified Luminescent Proximity Homogeneous Assay Screen) in the presence or absence of clinically used protease inhibitors (PIs). CFDSA measurement of drug resistance was based on the fold resistance to the half-maximal inhibitory concentration (IC50) of various PIs. The CFDSA could serve as a non-infectious, rapid, accessible, and reliable alternative to infectious cell-based phenotypic assays for evaluation of PI-resistant HIV-1.
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Affiliation(s)
- Satoko Matsunaga
- Department of Microbiology, School of Medicine, Yokohama City University Yokohama, Japan
| | - Takashi Masaoka
- Department of Infection and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | | | - Ryo Morishita
- Department of Microbiology, School of Medicine, Yokohama City University Yokohama, Japan ; CellFree Sciences Co., Ltd. Matsuyama, Japan
| | - Yasumasa Iwatani
- Department of Infection and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan ; Department of AIDS Research, Nagoya University Graduate School of Medicine Nagoya, Japan
| | - Masashi Tatsumi
- Department of AIDS Research, AIDS Research Center, National Institute of Infectious Diseases Tokyo, Japan
| | - Yaeta Endo
- Proteo-Science Center, Ehime University Matsuyama, Japan
| | - Naoki Yamamoto
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore Singapore, Singapore
| | - Wataru Sugiura
- Department of Infection and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan ; Department of AIDS Research, Nagoya University Graduate School of Medicine Nagoya, Japan
| | - Akihide Ryo
- Department of Microbiology, School of Medicine, Yokohama City University Yokohama, Japan
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80
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Furukawa H, Oka S, Shimada K, Masuo K, Nakajima F, Funano S, Tanaka Y, Komiya A, Fukui N, Sawasaki T, Tadokoro K, Nose M, Tsuchiya N, Tohma S. Autoantibody Profiles in Collagen Disease Patients with Interstitial Lung Disease (ILD): Antibodies to Major Histocompatibility Complex Class I-Related Chain A (MICA) as Markers of ILD. Biomark Insights 2015; 10:63-73. [PMID: 26327779 PMCID: PMC4539100 DOI: 10.4137/bmi.s28209] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/14/2015] [Accepted: 06/19/2015] [Indexed: 11/05/2022] Open
Abstract
Interstitial lung disease (ILD) is frequently associated with collagen disease. It is then designated as collagen vascular disease-associated ILD (CVD-ILD), and influences patients' prognosis. The prognosis of acute-onset diffuse ILD (AoDILD) occurring in patients with collagen disease is quite poor. Here, we report our investigation of auto-antibody (Ab) profiles to determine whether they may be useful in diagnosing CVD-ILD or AoDILD in collagen disease. Auto-Ab profiles were analyzed using the Lambda Array Beads Multi-Analyte System, granulocyte immunofluorescence test, Proto-Array Human Protein Microarray, AlphaScreen assay, and glutathione S-transferase capture enzyme-linked immunosorbent assay in 34 patients with rheumatoid arthritis (RA) with or without CVD-ILD and in 15 patients with collagen disease with AoDILD. The average anti-major histocompatibility complex class I-related chain A (MICA) Ab levels were higher in RA patients with CVD-ILD than in those without (P = 0.0013). The ratio of the average anti-MICA Ab level to the average anti-human leukocyte antigen class I Ab level (ie, MICA/Class I) was significantly higher in RA patients with CVD-ILD compared with those without (P = 4.47 × 10(-5)). To the best of our knowledge, this is the first report of auto-Ab profiles in CVD-ILD. The MICA/Class I ratio could be a better marker for diagnosing CVD-ILD than KL-6 (Krebs von den lungen-6).
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Affiliation(s)
- Hiroshi Furukawa
- Clinical Research Center for Allergy and Rheumatology, Sagamihara Hospital, National Hospital Organization, Sagamihara, Japan. ; Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shomi Oka
- Clinical Research Center for Allergy and Rheumatology, Sagamihara Hospital, National Hospital Organization, Sagamihara, Japan. ; Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kota Shimada
- Department of Rheumatology, Sagamihara Hospital, National Hospital Organization, Sagamihara, Japan. ; Department of Rheumatic Diseases, Tokyo Metropolitan Tama Medical Center, Fuchu, Japan
| | - Kiyoe Masuo
- Technical Marketing Department, VERITAS Corporation, Tokyo, Japan
| | - Fumiaki Nakajima
- Research and Development Department, Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | | | - Yuki Tanaka
- Intergated Center for Science, Ehime University, Toon
| | - Akiko Komiya
- Clinical Research Center for Allergy and Rheumatology, Sagamihara Hospital, National Hospital Organization, Sagamihara, Japan
| | - Naoshi Fukui
- Clinical Research Center for Allergy and Rheumatology, Sagamihara Hospital, National Hospital Organization, Sagamihara, Japan
| | - Tatsuya Sawasaki
- Cell-Free Science and Technology Research Center, Ehime University, Matsuyama, Japan
| | - Kenji Tadokoro
- Research and Development Department, Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Masato Nose
- Proteo-Medicine Research Center, Ehime University, Toon
| | - Naoyuki Tsuchiya
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shigeto Tohma
- Clinical Research Center for Allergy and Rheumatology, Sagamihara Hospital, National Hospital Organization, Sagamihara, Japan
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81
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Samuel PP, Smith LP, Phillips GN, Olson JS. Apoglobin Stability Is the Major Factor Governing both Cell-free and in Vivo Expression of Holomyoglobin. J Biol Chem 2015. [PMID: 26205820 DOI: 10.1074/jbc.m115.672204] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression levels in animal muscle tissues and in Escherichia coli vary widely for naturally occurring mammalian myoglobins (Mb). To explore this variation, we developed an in vitro transcription and wheat germ extract-based translation assay to examine quantitatively the factors that govern expression of holoMb. We constructed a library of naturally occurring Mbs from two terrestrial and four deep-diving aquatic mammals and three distal histidine mutants designed to enhance apoglobin stability but decrease hemin affinity. A strong linear correlation is observed between cell-free expression levels of holo-metMb variants and their corresponding apoglobin stabilities, which were measured independently by guanidine HCl-induced unfolding titrations using purified proteins. In contrast, there is little dependence of expression on hemin affinity. Our results confirm quantitatively that deep diving mammals have highly stable Mbs that express to higher levels in animal myocytes, E. coli, and the wheat germ cell-free system than Mbs from terrestrial mammals. Our theoretical analyses show that the rate of aggregation of unfolded apoMb is very large, and as a result, the key factor for high level expression of holoMb, and presumably other heme proteins, is an ultra high fraction of folded, native apoglobin that is capable of rapidly binding hemin. This fraction is determined by the overall equilibrium folding constant and not hemin affinity. These results also demonstrate that the cell-free transcription/translation system can be used as a high throughput platform to screen for apoglobin stability without the need to generate large amounts of protein for in vitro unfolding measurements.
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Affiliation(s)
| | | | - George N Phillips
- From BioSciences at Rice and Department of Chemistry, Rice University, Houston, Texas 77005
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82
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Mokuda S, Miyazaki T, Ito Y, Yamasaki S, Inoue H, Guo Y, Kong WS, Kanno M, Takasugi K, Sugiyama E, Masumoto J. The proto-oncogene survivin splice variant 2B is induced by PDGF and leads to cell proliferation in rheumatoid arthritis fibroblast-like synoviocytes. Sci Rep 2015; 5:9795. [PMID: 25997820 PMCID: PMC4441133 DOI: 10.1038/srep09795] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/20/2015] [Indexed: 11/09/2022] Open
Abstract
Survivin is an independent prognostic factor for joint destruction in rheumatoid arthritis (RA). However, the expression and function of survivin in RA synoviocytes remain unclear. We certified the expression of survivin in RA synovial tissues and performed the experiment using RA fibroblast-like synoviocytes (RA-FLS) treated with siRNA. As a result, the expression levels of wild type (WT) survivin and the 2B splice variants in RA synovial tissues were higher than those in osteoarthritis tissue samples, and, these variants were highly expressed in RA-FLS. The expression levels of survivin-WT and -2B in the RA-FLS were upregulated by PDGF. Treatment with siRNA against survivin-2B led to decreased viability of PDGF-treated RA-FLS due to cell cycle suppression and apoptosis promotion, while the siRNA against all survivin isoforms did not affect the viability. Moreover, an overexpression of survivin-2B in RA-FLS led to cell proliferation through cell cycle activation and by conferring resistance to apoptosis. In conclusion, survivin-2B has an important role in RA-FLS proliferation. These data suggest that survivin-2B might contribute to rheumatoid synovial hyperplasia, and have the potential as a novel therapeutic target for RA.
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Affiliation(s)
- Sho Mokuda
- 1] Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan [2] Department of Internal Medicine, Center for Rheumatic Diseases, Dohgo Spa Hospital, Matsuyama, Japan [3] Department of Pathology, Ehime University Proteo-Science Centre and Graduate School of Medicine, Toon, Japan [4] Department of Clinical Immunology and Rheumatology, Hiroshima University Hospital, Hiroshima, Japan
| | - Tatsuhiko Miyazaki
- Department of Pathology, Ehime University Proteo-Science Centre and Graduate School of Medicine, Toon, Japan
| | - Yuki Ito
- Department of Pathology, Ehime University Proteo-Science Centre and Graduate School of Medicine, Toon, Japan
| | - Satoshi Yamasaki
- Department of Clinical Immunology and Rheumatology, Hiroshima University Hospital, Hiroshima, Japan
| | - Hiroko Inoue
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yun Guo
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Weng-Sheng Kong
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masamoto Kanno
- Department of Immunology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kiyoshi Takasugi
- Department of Internal Medicine, Center for Rheumatic Diseases, Dohgo Spa Hospital, Matsuyama, Japan
| | - Eiji Sugiyama
- Department of Clinical Immunology and Rheumatology, Hiroshima University Hospital, Hiroshima, Japan
| | - Junya Masumoto
- Department of Pathology, Ehime University Proteo-Science Centre and Graduate School of Medicine, Toon, Japan
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83
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Nemoto K, Takemori N, Seki M, Shinozaki K, Sawasaki T. Members of the Plant CRK Superfamily Are Capable of Trans- and Autophosphorylation of Tyrosine Residues. J Biol Chem 2015; 290:16665-77. [PMID: 25969537 DOI: 10.1074/jbc.m114.617274] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Indexed: 11/06/2022] Open
Abstract
Protein phosphorylation on Tyr residues is a key post-translational modification in mammals. In plants, recent studies have identified Tyr-specific protein phosphatase and Tyr-phosphorylated proteins in Arabidopsis by phosphoproteomic screenings, implying that plants have a Tyr phosphorylation signal pathway. However, little is known about the protein kinases (PKs) involved in Tyr phosphorylation in plants. Here, we demonstrate that Arabidopsis calcium-dependent protein kinase (CDPK/CPK)-related PKs (CRKs) have high Tyr-autophosphorylation activity and that they can phosphorylate Tyr residue(s) on substrate proteins in Arabidopsis. To identify PKs for Tyr phosphorylation, we examined the autophosphorylation activity of 759 PKs using an Arabidopsis protein array based on a wheat cell-free system. In total, we identified 38 PKs with Tyr-autophosphorylation activity. The CRK family was a major protein family identified. A cell-free substrate screening revealed that these CRKs phosphorylate β-tubulin (TBB) 2, TBB7, and certain transcription factors (TFs) such as ethylene response factor 13 (ERF13). All five CRKs tested showed Tyr-auto/trans-phosphorylation activity and especially two CRKs, CRK2 and CRK3, showed a high ERF13 Tyr-phosphorylation activity. A cell-based transient expression assay revealed that Tyr(16/)Tyr(207) sites in ERF13 were phosphorylated by CRK3 and that Tyr phosphorylation of endogenous TBBs occurs in CRK2 overexpressing cells. Furthermore, crk2 and crk3 mutants showed a decrease in the Tyr phosphorylation level of TBBs. These results suggest that CRKs have Tyr kinase activity, and these might be one of the major PKs responsible for protein Tyr phosphorylation in Arabidopsis plants.
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Affiliation(s)
- Keiichirou Nemoto
- From the Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577 and
| | - Nobuaki Takemori
- From the Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577 and
| | - Motoaki Seki
- the Plant Genomic Network Research Team and CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kazuo Shinozaki
- the Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, and
| | - Tatsuya Sawasaki
- From the Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577 and
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84
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Quast RB, Mrusek D, Hoffmeister C, Sonnabend A, Kubick S. Cotranslational incorporation of non-standard amino acids using cell-free protein synthesis. FEBS Lett 2015; 589:1703-12. [PMID: 25937125 DOI: 10.1016/j.febslet.2015.04.041] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 11/30/2022]
Abstract
Over the last years protein engineering using non-standard amino acids has gained increasing attention. As a result, improved methods are now available, enabling the efficient and directed cotranslational incorporation of various non-standard amino acids to equip proteins with desired characteristics. In this context, the utilization of cell-free protein synthesis is particularly useful due to the direct accessibility of the translational machinery and synthesized proteins without having to maintain a vital cellular host. We review prominent methods for the incorporation of non-standard amino acids into proteins using cell-free protein synthesis. Furthermore, a list of non-standard amino acids that have been successfully incorporated into proteins in cell-free systems together with selected applications is provided.
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Affiliation(s)
- Robert B Quast
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Devid Mrusek
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Christian Hoffmeister
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Andrei Sonnabend
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany.
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85
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Quast RB, Kortt O, Henkel J, Dondapati SK, Wüstenhagen DA, Stech M, Kubick S. Automated production of functional membrane proteins using eukaryotic cell-free translation systems. J Biotechnol 2015; 203:45-53. [PMID: 25828454 DOI: 10.1016/j.jbiotec.2015.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/16/2015] [Accepted: 03/19/2015] [Indexed: 12/14/2022]
Abstract
Due to their high abundance and pharmacological relevance there is a growing demand for the efficient production of functional membrane proteins. In this context, cell-free protein synthesis represents a valuable alternative that allows for the high-throughput synthesis of functional membrane proteins. Here, we demonstrate the potential of our cell-free protein synthesis system, based on lysates from cultured Spodoptera frugiperda 21 cells, to produce pro- and eukaryotic membrane proteins with individual topological characteristics in an automated fashion. Analytical techniques, including confocal laser scanning microscopy, fluorescence detection of eYFP fusion proteins in a microplate reader and in-gel fluorescence of statistically incorporated fluorescent amino acid derivatives were employed. The reproducibility of our automated synthesis approach is underlined by coefficients of variation below 7.2%. Moreover, the functionality of the cell-free synthesized potassium channel KcsA was analyzed electrophysiologically. Finally, we expanded our cell-free membrane protein synthesis system by an orthogonal tRNA/synthetase pair for the site-directed incorporation of p-Azido-l-phenylalanine based on stop codon suppression. Incorporation was optimized by performance of a two-dimensional screening with different Mg(2+) and lysate concentrations. Subsequently, the selective modification of membrane proteins with incorporated p-Azido-l-phenylalanine was exemplified by Staudinger ligation with a phosphine-based fluorescence dye.
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Affiliation(s)
- Robert B Quast
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Oliver Kortt
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Jörg Henkel
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany.
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86
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87
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Shivaprasad PV, Hohn T, Akbergenov R. Biochemical requirements for two Dicer-like activities from wheat germ. PLoS One 2015; 10:e0116736. [PMID: 25615604 PMCID: PMC4304710 DOI: 10.1371/journal.pone.0116736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/14/2014] [Indexed: 12/22/2022] Open
Abstract
RNA silencing pathways were first discovered in plants. Through genetic analysis, it has been established that the key silencing components called Dicer-like (DCL) genes have been shown to cooperatively process RNA substrates of multiple origin into distinct 21, 22 and 24 nt small RNAs. However, only few detailed biochemical analysis of the corresponding complexes has been carried out in plants, mainly due to the large unstable complexes that are hard to obtain or reconstitute in heterologous systems. Reconstitution of activity needs thorough understanding of all protein partners in the complex, something that is still an ongoing process in plant systems. Here, we use biochemical analysis to uncover properties of two previously identified native dicer-like activities from wheat germ. We find that standard wheat germ extract contains Dicer-like enzymes that convert double-stranded RNA (dsRNA) into two classes of small interfering RNAs of 21 and 24 nt in size. The 21 nt dicing activity, likely an siRNA producing complex known as DCL4, is 950 kDa-1.2 mDa in size and is highly unstable during purification processes but has a rather vast range for activity. On the contrary, the 24 nt dicing complex, likely the DCL3 activity, is relatively stable and comparatively smaller in size, but has stricter conditions for effective processing of dsRNA substrates. While both activities could process completely complementary dsRNA albeit with varying abilities, we show that DCL3-like 24 nt producing activity is equally good in processing incompletely complementary RNAs.
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Affiliation(s)
| | - Thomas Hohn
- Department of Plant Physiology, Botanical Institute, University of Basel, Basel, Switzerland
| | - Rashid Akbergenov
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
- * E-mail: (PVS); (RA)
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88
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Ogawa A, Doi Y. Investigation of end processing and degradation of premature tRNAs and their application to stabilization of in vitro transcripts in wheat germ extract. Org Biomol Chem 2015; 13:1008-12. [DOI: 10.1039/c4ob02221a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated the end processing and degradation of premature tRNAs in wheat germ extract (left), which led to the findings of end protectors for efficiently stabilizing an in vitro transcript (purple, right).
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Affiliation(s)
| | - Yasunori Doi
- Proteo-Science Center
- Ehime University
- Matsuyama
- Japan
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89
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Brödel AK, Wüstenhagen DA, Kubick S. Cell-free protein synthesis systems derived from cultured mammalian cells. Methods Mol Biol 2015; 1261:129-40. [PMID: 25502197 DOI: 10.1007/978-1-4939-2230-7_7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present a technology for the production of target proteins using novel cell-free systems derived from cultured human K562 cells and Chinese hamster ovary (CHO) cells. The protocol includes the cultivation of cells, the preparation of translationally active lysates, and the cell-free synthesis of desired proteins. An efficient expression vector based on the internal ribosome entry site (IRES) from the intergenic region (IGR) of the cricket paralysis virus (CrPV) was constructed for both systems. The coupled batch-based platforms enable the synthesis of a broad range of target proteins such as cytosolic proteins, secreted proteins, membrane proteins embedded into endogenous microsomes, and glycoproteins. The glycosylation of erythropoietin demonstrates the successful performance of posttranslational modifications in the novel cell-free systems. Protein yields of approximately 20 μg/ml (K562-based cell-free system) and 50 μg/ml (CHO-based cell-free system) of active firefly luciferase are obtained in the coupled transcription-translation systems within 3 h. As a result, both cell-free protein synthesis systems serve as powerful tools for high-throughput proteomics.
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Affiliation(s)
- Andreas K Brödel
- Department of Cell-free Bioproduction, 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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90
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Terada T, Yokoyama S. Escherichia coli Cell-Free Protein Synthesis and Isotope Labeling of Mammalian Proteins. Methods Enzymol 2015; 565:311-45. [DOI: 10.1016/bs.mie.2015.08.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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91
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Ogawa A. Engineering of ribosomal shunt-modulating eukaryotic ON riboswitches by using a cell-free translation system. Methods Enzymol 2014; 550:109-28. [PMID: 25605383 DOI: 10.1016/bs.mie.2014.10.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A number of natural and artificial bacterial riboswitches have been reported thus far. However, they generally function only in bacteria, not in eukaryotes. This is because of the differences of expression mechanisms (transcription, translation, and so on) between these two main types of organisms. For example, the mechanism of translation initiation is quite different between bacteria and eukaryotes, especially in ribosome loading on mRNA. While the bacterial ribosome binds to a well-conserved, internal sequence some bases before the start codon to initiate translation, the eukaryotic one is loaded on the 5' terminus with the help of certain eukaryotic initiation factors. This means not only that bacterial riboswitches regulating translation initiation are not available in eukaryotic translation systems, but also that it is physically difficult to construct eukaryotic ON riboswitches that regulate the eukaryotic canonical translation initiation, because an aptamer cannot be inserted upstream of the ribosome loading site. However, the mechanism of noncanonical translation initiation via "ribosomal shunt" enables us to design translation initiation-modulating (specifically, ribosomal shunt-modulating) eukaryotic ON riboswitches. This chapter describes a facile method for engineering these ribosomal shunt-modulating eukaryotic ON riboswitches by using a cell-free translation system. Because these riboswitches do not require hybridization switching thanks to a unique shunting mechanism, they have the major advantages of a low energy requirement for upregulation and relatively straightforward design over common hybridization switch-based ON riboswitches.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, Matsuyama, Japan.
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92
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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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93
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Khattak WA, Ullah MW, Ul-Islam M, Khan S, Kim M, Kim Y, Park JK. Developmental strategies and regulation of cell-free enzyme system for ethanol production: a molecular prospective. Appl Microbiol Biotechnol 2014; 98:9561-78. [PMID: 25359472 DOI: 10.1007/s00253-014-6154-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/09/2014] [Accepted: 10/12/2014] [Indexed: 10/24/2022]
Abstract
Most biomanufacturing systems developed for the production of biocommodities are based on whole-cell systems. However, with the advent of innovative technologies, the focus has shifted from whole-cell towards cell-free enzyme system. Since more than a century, researchers are using the cell-free extract containing the required enzymes and their respective cofactors in order to study the fundamental aspects of biological systems, particularly fermentation. Although yeast cell-free enzyme system is known since long ago, it is rarely been studied and characterized in detail. In this review, we hope to describe the major pitfalls encountered by whole-cell system and introduce possible solutions to them using cell-free enzyme systems. We have discussed the glycolytic and fermentative pathways and their regulation at both transcription and translational levels. Moreover, several strategies employed for development of cell-free enzyme system have been described with their potential merits and shortcomings associated with these developmental approaches. We also described in detail the various developmental approaches of synthetic cell-free enzyme system such as compartmentalization, metabolic channeling, protein fusion, and co-immobilization strategies. Additionally, we portrayed the novel cell-free enzyme technologies based on encapsulation and immobilization techniques and their development and commercialization. Through this review, we have presented the basics of cell-free enzyme system, the strategies involved in development and operation, and the advantages over conventional processes. Finally, we have addressed some potential directions for the future development and industrialization of cell-free enzyme system.
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Affiliation(s)
- Waleed Ahmad Khattak
- Department of Chemical Engineering, Kyungpook National University, Daegu, 7020-701, Korea
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94
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Murakami M, Kaneko T, Nakatsuji T, Kameda K, Okazaki H, Dai X, Hanakawa Y, Tohyama M, Ishida-Yamamoto A, Sayama K. Vesicular LL-37 contributes to inflammation of the lesional skin of palmoplantar pustulosis. PLoS One 2014; 9:e110677. [PMID: 25330301 PMCID: PMC4199729 DOI: 10.1371/journal.pone.0110677] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/21/2014] [Indexed: 01/25/2023] Open
Abstract
“Pustulosis palmaris et plantaris”, or palmoplantar pustulosis (PPP), is a chronic pustular dermatitis characterized by intraepidermal palmoplantar pustules. Although early stage vesicles (preceding the pustular phase) formed in the acrosyringium contain the antimicrobial peptides cathelicidin (hCAP-18/LL-37) and dermcidin, the details of hCAP-18/LL-37 expression in such vesicles remain unclear. The principal aim of the present study was to clarify the manner of hCAP-18/LL-37 expression in PPP vesicles and to determine whether this material contributed to subsequent inflammation of lesional skin. PPP vesicle fluid (PPP-VF) induced the expression of mRNAs encoding IL-17C, IL-8, IL-1α, and IL-1β in living skin equivalents, but the level of only IL-8 mRNA decreased significantly upon stimulation of PPP vesicle with depletion of endogenous hCAP-18/LL-37 by affinity chromatography (dep-PPP-VF). Semi-quantitative dot-blot analysis revealed higher concentrations of hCAP-18/LL-37 in PPP-VF compared to healthy sweat (2.87±0.93 µM vs. 0.09±0.09 µM). This concentration of hCAP-18/LL-37 in PPP-VF could upregulate expression of IL-17C, IL-8, IL-1α, and IL-1β at both the mRNA and protein levels. Recombinant hCAP-18 was incubated with dep-PPP-VF. Proteinase 3, which converts hCAP-18 to the active form (LL-37), was present in PPP-VF. Histopathological and immunohistochemical examination revealed that early stage vesicles contained many mononuclear cells but no polymorphonuclear cells, and the mononuclear cells were CD68-positive. The epidermis surrounding the vesicle expresses monocyte chemotactic chemokine, CCL2. In conclusion, PPP-VF contains the proteinase required for LL-37 processing and also may directly upregulate IL-8 in lesional keratinocytes, in turn contributing to the subsequent inflammation of PPP lesional skin.
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Affiliation(s)
- Masamoto Murakami
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
- * E-mail:
| | - Takaaki Kaneko
- Department of Dermatology, Asahikawa Medical College, Asahikawa, Japan
| | - Teruaki Nakatsuji
- Division of Dermatology, University of California San Diego, and VA San Diego Healthcare Center, San Diego, California, United States of America
| | - Kenji Kameda
- Integrated Center for Science, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Hidenori Okazaki
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Xiuju Dai
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yasushi Hanakawa
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Mikiko Tohyama
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
| | | | - Koji Sayama
- Department of Dermatology, Ehime University Graduate School of Medicine, Ehime, Japan
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Abstract
Riboswitches are composed of two regions: one for binding to the ligand (the aptamer domain) and the other for regulating the expression of the gene (the expression platform). In most riboswitches (both natural and artificial), a part of the aptamer domain required for ligand binding is directly involved in the regulation of expression, so that it is difficult to design other ligand-responsive riboswitches based on these riboswitches even by using artificial aptamers obtained through in vitro selection. This chapter describes a method for rationally constructing a foundational ON-riboswitch, which is easily available for the design of other ligand-dependent riboswitches, by introducing a new region (a modulator sequence: MS) in addition to the two basic regions. A facile method for preparing arbitrary molecule-dependent riboswitches based on the foundational riboswitch is also presented.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, Matsuyama, Japan
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96
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Matsubayashi H, Ueda T. Purified cell-free systems as standard parts for synthetic biology. Curr Opin Chem Biol 2014; 22:158-62. [DOI: 10.1016/j.cbpa.2014.09.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/22/2014] [Accepted: 09/23/2014] [Indexed: 10/24/2022]
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97
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Chong S. Overview of cell-free protein synthesis: historic landmarks, commercial systems, and expanding applications. ACTA ACUST UNITED AC 2014; 108:16.30.1-16.30.11. [PMID: 25271714 DOI: 10.1002/0471142727.mb1630s108] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
During the early days of molecular biology, cell-free protein synthesis played an essential role in deciphering the genetic code and contributed to our understanding of translation of protein from messenger RNA. Owing to several decades of major and incremental improvements, modern cell-free systems have achieved higher protein synthesis yields at lower production costs. Commercial cell-free systems are now available from a variety of material sources, ranging from "traditional" E. coli, rabbit reticulocyte lysate, and wheat germ extracts, to recent insect and human cell extracts, to defined systems reconstituted from purified recombinant components. Although each cell-free system has certain advantages and disadvantages, the diversity of the cell-free systems allows in vitro synthesis of a wide range of proteins for a variety of downstream applications. In the post-genomic era, cell-free protein synthesis has rapidly become the preferred approach for high-throughput functional and structural studies of proteins and a versatile tool for in vitro protein evolution and synthetic biology. This unit provides a brief history of cell-free protein synthesis and describes key advances in modern cell-free systems, practical differences between widely used commercial cell-free systems, and applications of this important technology.
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98
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Li J, Gu L, Aach J, Church GM. Improved cell-free RNA and protein synthesis system. PLoS One 2014; 9:e106232. [PMID: 25180701 PMCID: PMC4152126 DOI: 10.1371/journal.pone.0106232] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/04/2014] [Indexed: 12/13/2022] Open
Abstract
Cell-free RNA and protein synthesis (CFPS) is becoming increasingly used for protein production as yields increase and costs decrease. Advances in reconstituted CFPS systems such as the Protein synthesis Using Recombinant Elements (PURE) system offer new opportunities to tailor the reactions for specialized applications including in vitro protein evolution, protein microarrays, isotopic labeling, and incorporating unnatural amino acids. In this study, using firefly luciferase synthesis as a reporter system, we improved PURE system productivity up to 5 fold by adding or adjusting a variety of factors that affect transcription and translation, including Elongation factors (EF-Ts, EF-Tu, EF-G, and EF4), ribosome recycling factor (RRF), release factors (RF1, RF2, RF3), chaperones (GroEL/ES), BSA and tRNAs. The work provides a more efficient defined in vitro transcription and translation system and a deeper understanding of the factors that limit the whole system efficiency.
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Affiliation(s)
- Jun Li
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Liangcai Gu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - John Aach
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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Ogawa A, Tabuchi J, Doi Y. Identification of short untranslated regions that sufficiently enhance translation in high-quality wheat germ extract. Bioorg Med Chem Lett 2014; 24:3724-7. [PMID: 25037913 DOI: 10.1016/j.bmcl.2014.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 06/26/2014] [Accepted: 07/01/2014] [Indexed: 10/25/2022]
Abstract
High-quality wheat germ extract (hqWGE) is very useful for the high-yield production of various types of protein. The most important key to high productivity is the design of mRNA templates. Although the design has been refined for straightforward and efficient translation in hqWGE, there is still room for improvement in untranslated regions (UTRs), especially the 3' UTR length, because a long, cumbersome 3' UTR is commonly used for translation enhancement. Here we examined some short viral 3' cap-independent translation enhancers (3' CITEs) to identify effective ones for efficient translation in hqWGE. We then combined the most effective 3' CITE and a 5' enhancer to further increase the translation efficiency. mRNA with the optimal short 3' and 5' UTRs, both of whose length was less than 150 nt, exhibited a productivity of 1.4 mg/mL in prolonged large-scale protein synthesis in hqWGE, which was comparable to that of control mRNA with a commonly-used long 3' UTR (∼1200 nt).
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
| | - Junichiro Tabuchi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yasunori Doi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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100
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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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