1
|
Pollack D, Nozoe T, Kussell E. Proteolytic stability and aggregation in a key metabolic enzyme of bacteria. Proc Natl Acad Sci U S A 2024; 121:e2301458121. [PMID: 38683989 PMCID: PMC11087809 DOI: 10.1073/pnas.2301458121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/07/2024] [Indexed: 05/02/2024] Open
Abstract
Proteins that are kinetically stable are thought to be less prone to both aggregation and proteolysis. We demonstrate that the classical lac system of Escherichia coli can be leveraged as a model system to study this relation. β-galactosidase (LacZ) plays a critical role in lactose metabolism and is an extremely stable protein that can persist in growing cells for multiple generations after expression has stopped. By attaching degradation tags to the LacZ protein, we find that LacZ can be transiently degraded during lac operon expression but once expression has stopped functional LacZ is protected from degradation. We reversibly destabilize its tetrameric assembly using α-complementation, and show that unassembled LacZ monomers and dimers can either be degraded or lead to formation of aggregates within cells, while the tetrameric state protects against proteolysis and aggregation. We show that the presence of aggregates is associated with cell death, and that these proteotoxic stress phenotypes can be alleviated by attaching an ssrA tag to LacZ monomers which leads to their degradation. We unify our findings using a biophysical model that enables the interplay of protein assembly, degradation, and aggregation to be studied quantitatively in vivo. This work may yield approaches to reversing and preventing protein-misfolding disease states, while elucidating the functions of proteolytic stability in constant and fluctuating environments.
Collapse
Affiliation(s)
- Dan Pollack
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY10003
| | - Takashi Nozoe
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo153-8902, Japan
- Research Center for Complex Systems Biology, The University of Tokyo, Tokyo153-8902, Japan
- Universal Biology Institute, The University of Tokyo, Tokyo113-0033, Japan
| | - Edo Kussell
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY10003
- Department of Physics, New York University, New York, NY10003
| |
Collapse
|
2
|
Nakashima S, Sato R, Fukami T, Kudo T, Hashiba S, Morinaga G, Nakano M, Ludwig-Schwellinger E, Matsui A, Ishiguro N, Ebner T, Nakajima M. Characterization of Enzymes Involved in Nintedanib Metabolism in Humans. Drug Metab Dispos 2023; 51:733-742. [PMID: 36927840 DOI: 10.1124/dmd.122.001113] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/03/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Nintedanib, which is used to treat idiopathic pulmonary fibrosis and non-small cell lung cancer, is metabolized to a pharmacologically inactive carboxylate derivative, BIBF1202, via hydrolysis and subsequently by glucuronidation to BIBF1202 acyl-glucuronide (BIBF1202-G). Since BIBF1202-G contains an ester bond, it can be hydrolytically cleaved to BIBF1202. In this study, we sought to characterize these metabolic reactions in the human liver and intestine. Nintedanib hydrolysis was detected in human liver microsomes (HLMs) (Clearance [CL int]: 102.8 ± 18.9 µL/min per mg protein) but not in small intestinal preparations. CES1 was suggested to be responsible for nintedanib hydrolysis according to experiments using recombinant hydrolases and hydrolase inhibitors as well as proteomic correlation analysis using 25 individual HLM. BIBF1202 glucuronidation in HLM (3.6 ± 0.3 µL/min per mg protein) was higher than that in human intestinal microsomes (1.5 ± 0.06 µL/min per mg protein). UGT1A1 and gastrointestinal UGT1A7, UGT1A8, and UGT1A10 were able to mediate BIBF1202 glucuronidation. The impact of UGT1A1 on glucuronidation was supported by the finding that liver microsomes from subjects homozygous for the UGT1A1*28 allele showed significantly lower activity than those from subjects carrying the wild-type UGT1A1 allele. Interestingly, BIBF1202-G was converted to BIBF1202 in HLS9 at 70-fold higher rates than the rates of BIBF1202 glucuronidation. An inhibition study and proteomic correlation analysis suggested that β-glucuronidase is responsible for hepatic BIBF1202-G deglucuronidation. In conclusion, the major metabolic reactions of nintedanib in the human liver and intestine were quantitatively and thoroughly elucidated. This information could be helpful to understand the inter- and intraindividual variability in the efficacy of nintedanib. SIGNIFICANCE STATEMENT: To our knowledge, this is the first study to characterize the enzymes responsible for each step of nintedanib metabolism in the human body. This study found that β-glucuronidase may contribute to BIBF1202-G deglucuronidation.
Collapse
Affiliation(s)
- Shimon Nakashima
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (S.N., R.S., T.F., S.H., Ma.N., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (T.F., Ma.N., Mi.N.), Kanazawa University, Kanazawa, Japan; Department of Pharmacokinetics and Nonclinical Safety, Nippon Boehringer Ingelheim Co., Ltd., Hyogo, Japan (T.K., G.M., A.M., N.I.); and Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany (E.L.-S., T.E.)
| | - Rei Sato
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (S.N., R.S., T.F., S.H., Ma.N., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (T.F., Ma.N., Mi.N.), Kanazawa University, Kanazawa, Japan; Department of Pharmacokinetics and Nonclinical Safety, Nippon Boehringer Ingelheim Co., Ltd., Hyogo, Japan (T.K., G.M., A.M., N.I.); and Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany (E.L.-S., T.E.)
| | - Tatsuki Fukami
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (S.N., R.S., T.F., S.H., Ma.N., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (T.F., Ma.N., Mi.N.), Kanazawa University, Kanazawa, Japan; Department of Pharmacokinetics and Nonclinical Safety, Nippon Boehringer Ingelheim Co., Ltd., Hyogo, Japan (T.K., G.M., A.M., N.I.); and Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany (E.L.-S., T.E.)
| | - Takashi Kudo
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (S.N., R.S., T.F., S.H., Ma.N., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (T.F., Ma.N., Mi.N.), Kanazawa University, Kanazawa, Japan; Department of Pharmacokinetics and Nonclinical Safety, Nippon Boehringer Ingelheim Co., Ltd., Hyogo, Japan (T.K., G.M., A.M., N.I.); and Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany (E.L.-S., T.E.)
| | - Shiori Hashiba
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (S.N., R.S., T.F., S.H., Ma.N., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (T.F., Ma.N., Mi.N.), Kanazawa University, Kanazawa, Japan; Department of Pharmacokinetics and Nonclinical Safety, Nippon Boehringer Ingelheim Co., Ltd., Hyogo, Japan (T.K., G.M., A.M., N.I.); and Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany (E.L.-S., T.E.)
| | - Gaku Morinaga
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (S.N., R.S., T.F., S.H., Ma.N., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (T.F., Ma.N., Mi.N.), Kanazawa University, Kanazawa, Japan; Department of Pharmacokinetics and Nonclinical Safety, Nippon Boehringer Ingelheim Co., Ltd., Hyogo, Japan (T.K., G.M., A.M., N.I.); and Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany (E.L.-S., T.E.)
| | - Masataka Nakano
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (S.N., R.S., T.F., S.H., Ma.N., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (T.F., Ma.N., Mi.N.), Kanazawa University, Kanazawa, Japan; Department of Pharmacokinetics and Nonclinical Safety, Nippon Boehringer Ingelheim Co., Ltd., Hyogo, Japan (T.K., G.M., A.M., N.I.); and Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany (E.L.-S., T.E.)
| | - Eva Ludwig-Schwellinger
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (S.N., R.S., T.F., S.H., Ma.N., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (T.F., Ma.N., Mi.N.), Kanazawa University, Kanazawa, Japan; Department of Pharmacokinetics and Nonclinical Safety, Nippon Boehringer Ingelheim Co., Ltd., Hyogo, Japan (T.K., G.M., A.M., N.I.); and Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany (E.L.-S., T.E.)
| | - Akiko Matsui
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (S.N., R.S., T.F., S.H., Ma.N., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (T.F., Ma.N., Mi.N.), Kanazawa University, Kanazawa, Japan; Department of Pharmacokinetics and Nonclinical Safety, Nippon Boehringer Ingelheim Co., Ltd., Hyogo, Japan (T.K., G.M., A.M., N.I.); and Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany (E.L.-S., T.E.)
| | - Naoki Ishiguro
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (S.N., R.S., T.F., S.H., Ma.N., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (T.F., Ma.N., Mi.N.), Kanazawa University, Kanazawa, Japan; Department of Pharmacokinetics and Nonclinical Safety, Nippon Boehringer Ingelheim Co., Ltd., Hyogo, Japan (T.K., G.M., A.M., N.I.); and Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany (E.L.-S., T.E.)
| | - Thomas Ebner
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (S.N., R.S., T.F., S.H., Ma.N., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (T.F., Ma.N., Mi.N.), Kanazawa University, Kanazawa, Japan; Department of Pharmacokinetics and Nonclinical Safety, Nippon Boehringer Ingelheim Co., Ltd., Hyogo, Japan (T.K., G.M., A.M., N.I.); and Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany (E.L.-S., T.E.)
| | - Miki Nakajima
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences (S.N., R.S., T.F., S.H., Ma.N., Mi.N.) and WPI Nano Life Science Institute (WPI-NanoLSI) (T.F., Ma.N., Mi.N.), Kanazawa University, Kanazawa, Japan; Department of Pharmacokinetics and Nonclinical Safety, Nippon Boehringer Ingelheim Co., Ltd., Hyogo, Japan (T.K., G.M., A.M., N.I.); and Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany (E.L.-S., T.E.)
| |
Collapse
|
3
|
Zhu B, Qian C, Tang H, Kitaguchi T, Ueda H. Creating a Thermostable β-Glucuronidase Switch for Homogeneous Immunoassay by Disruption of Conserved Salt Bridges at Diagonal Interfaces. Biochemistry 2023; 62:309-317. [PMID: 35849118 DOI: 10.1021/acs.biochem.2c00165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Escherichia coli β-glucuronidase (GUS) has been used as a reporter enzyme in molecular biology and engineered as an enzyme switch for the development of homogeneous biosensors. In this study, we developed a thermostable GUS enzyme switch based on the thermostable GUS mutant TR3337 by disrupting a conserved salt bridge (H514-E523) between the diagonal subunits of its homotetramer. A combinatorial library (240 variants) was screened using a novel high-throughput strategy, which led to the identification of mutant DLW (H514D/M516L/Y517W) as a functional enzyme switch in a caffeine-recognizing immunosensor. Molecular dynamics simulations were performed to predict the topology change around position 514, and a side-chain flip of D514 (repulsion with E523) was observed in the DLW mutant. Up to 1.8-fold of signal-to-background ratio was confirmed when measured at up to 45 °C, thereby highlighting the DLW mutant as a versatile tool for developing thermostable immunosensors for in vitro and in cellulo applications.
Collapse
Affiliation(s)
- Bo Zhu
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Cheng Qian
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Haoxuan Tang
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Tetsuya Kitaguchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| |
Collapse
|
4
|
Berhanu S, Ueda T, Alix JH. The E. coli DnaK chaperone stimulates the α-complementation of β-galactosidase. J Basic Microbiol 2022; 62:669-688. [PMID: 35289419 DOI: 10.1002/jobm.202100487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/11/2022] [Accepted: 02/20/2022] [Indexed: 11/09/2022]
Abstract
pUC18 and pUC19 are well-known high copy-number plasmid vectors routinely used for DNA cloning purposes. We show here that, in E. coli transformed by native pUC18, the α-complementation of β-galactosidase (i.e., mediated by the peptide LacZα18) is intrinsically weak and slow, but is greatly stimulated by the DnaK/DnaJ/GrpE chaperone system. In contrast, the α-complementation mediated by the peptide LacZα19 (in E. coli transformed by the native pUC19) is much more efficient, and therefore does not require the assistance of the DnaK chaperone machinery. The marked difference between these two LacZα peptides is reproduced in cell-free protein expression system coupled with α-complementation. We conclude that: (i) α-complementation of β-galactosidase is DnaK-mediated depending upon the LacZα peptide donor. (ii) DnaK, sensu stricto, is not necessary for α-complementation, but can enhance it to a great extent. (iii) this observation could be used to establish an easy and inexpensive method for screening small molecules libraries in search of DnaK inhibitors and also for deciphering the DnaK-mediated protein quality control mechanism. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Samuel Berhanu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba Prefecture, Japan
| | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba Prefecture, Japan
| | - Jean-Hervé Alix
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba Prefecture, Japan
| |
Collapse
|
5
|
Santibáñez R, Garrido D, Martin AJM. Atlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages. Bioinformatics 2021; 36:5473-5480. [PMID: 33367504 PMCID: PMC8016457 DOI: 10.1093/bioinformatics/btaa1040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/19/2020] [Accepted: 12/12/2020] [Indexed: 12/31/2022] Open
Abstract
MOTIVATION Cells are complex systems composed of hundreds of genes whose products interact to produce elaborated behaviors. To control such behaviors, cells rely on transcription factors to regulate gene expression, and gene regulatory networks (GRNs) are employed to describe and understand such behavior. However, GRNs are static models, and dynamic models are difficult to obtain due to their size, complexity, stochastic dynamics and interactions with other cell processes. RESULTS We developed Atlas, a Python software that converts genome graphs and gene regulatory, interaction and metabolic networks into dynamic models. The software employs these biological networks to write rule-based models for the PySB framework. The underlying method is a divide-and-conquer strategy to obtain sub-models and combine them later into an ensemble model. To exemplify the utility of Atlas, we used networks of varying size and complexity of Escherichia coli and evaluated in silico modifications, such as gene knockouts and the insertion of promoters and terminators. Moreover, the methodology could be applied to the dynamic modeling of natural and synthetic networks of any bacteria. AVAILABILITY AND IMPLEMENTATION Code, models and tutorials are available online (https://github.com/networkbiolab/atlas). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Rodrigo Santibáñez
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Universidad Mayor, Santiago 8580745, Chile
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Alberto J M Martin
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Universidad Mayor, Santiago 8580745, Chile
| |
Collapse
|
6
|
Schlachter CR, McGee AC, Sitasuwan PN, Horvath GC, Karri NG, Lee LA, Tomashek JJ. Variants of glycosyl hydrolase family 2 β-glucuronidases have increased activity on recalcitrant substrates. Enzyme Microb Technol 2021; 145:109742. [PMID: 33750535 DOI: 10.1016/j.enzmictec.2020.109742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 11/29/2022]
Abstract
Glucuronidated drug metabolites can be quantified from urine samples by first hydrolyzing conjugates with β-glucuronidase (β-GUS) and then separating free drug molecules by liquid chromatography and mass spectrometry detection (LC-MS). To improve the activity and specificity of various β-GUS, we designed enzyme chimeras and generated site-saturation variants based on structural analyses, then screened them for improved activity on drug metabolites important to clinical and forensic drug-testing laboratories. Often, an increase of activity on one substrate of interest was countered by loss of activity against another, and there was no strong correlation of activity on standard β-glucuronidase substrates to activity on recalcitrant drug glucuronides. However, we discovered a chimera of two enzymes from different species of Aspergillus that displays a 27 % increase in activity on morphine-3-glucuronide than the parent proteins. Furthermore, mutations in the M-loop, which is a loop near the active site, resulted in numerous variants with dramatically increased rates of hydrolysis on drug glucuronides. Specifically, the M-loop variant Q451D/A452E of a β-GUS from Brachyspira pilosicoli has a 50-fold and 25-fold increase in activity on the recalcitrant substrates codeine-6-glucuronide and dihydrocodeine-6-glucuronide, respectively, compared to the parent enzyme.
Collapse
Affiliation(s)
- Caleb R Schlachter
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC, 29063, United States
| | - Amanda C McGee
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC, 29063, United States
| | - Pongkwan N Sitasuwan
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC, 29063, United States
| | - Gary C Horvath
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC, 29063, United States
| | - Nanda G Karri
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC, 29063, United States
| | - L Andrew Lee
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC, 29063, United States
| | - John J Tomashek
- Integrated Micro-Chromatography Systems, 110 Centrum Drive, Irmo, SC, 29063, United States.
| |
Collapse
|
7
|
2,5-Disubstituted thiadiazoles as potent β-glucuronidase inhibitors; Synthesis, in vitro and in silico studies. Bioorg Chem 2019; 91:103126. [DOI: 10.1016/j.bioorg.2019.103126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 07/05/2019] [Accepted: 07/11/2019] [Indexed: 01/31/2023]
|
8
|
Ogawa M, Uyeda A, Harada K, Sato Y, Kato Y, Watanabe H, Honda K, Matsuura T. Class III Polyphosphate Kinase 2 Enzymes Catalyze the Pyrophosphorylation of Adenosine-5'-Monophosphate. Chembiochem 2019; 20:2961-2967. [PMID: 31206993 DOI: 10.1002/cbic.201900303] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Indexed: 11/09/2022]
Abstract
Polyphosphate kinase 2 (PPK2) transfer phosphate from inorganic polyphosphate to nucleotides. According to their activity, PPK2 enzymes are classified into three groups. Among them, class III enzymes catalyze both the phosphorylation of nucleotide mono- to diphosphates and di- to triphosphates by using polyphosphate, which is a very inexpensive substrate. Therefore, class III enzymes are very attractive for use in biotechnological applications. Despite several studies on class III enzymes, a detailed mechanism of how phosphate is transferred from the polyphosphate to the nucleotide remains to be elucidated. Herein, it is reported that PPK2 class III enzymes from two different bacterial species catalyze the phosphorylation of adenosine mono- (AMP) into triphosphate (ATP) not only through step-by-step phosphorylation, but also by pyrophosphorylation. These are the first PPK2 enzymes that have been shown to possess polyphosphate-dependent pyrophosphorylation activity.
Collapse
Affiliation(s)
- Marin Ogawa
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Atsuko Uyeda
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazuo Harada
- Department of Applied Environmental Biology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yu Sato
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yasuhiko Kato
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hajime Watanabe
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kohsuke Honda
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomoaki Matsuura
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| |
Collapse
|
9
|
In vitro synthesis of the human calcium transporter Letm1 within cell-sized liposomes and investigation of its lipid dependency. J Biosci Bioeng 2018; 127:544-548. [PMID: 30503650 DOI: 10.1016/j.jbiosc.2018.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/21/2018] [Accepted: 11/01/2018] [Indexed: 01/18/2023]
Abstract
The human mitochondrion-derived calcium transporter Letm1 was synthesized by reconstituted in vitro transcription-translation (IVTT) in cell-sized liposomes and the dependency of Letm1 on phospholipid composition was investigated. Components for IVTT were encapsulated into cell-sized vesicles together with the DNA encoding Letm1, thereby preparing proteoliposomes. The synthesis of Letm1 and pH-dependent calcium transport activity were confirmed by flow cytometry. Finally, we investigated the effect of phospholipid composition on Letm1 transport activity and found that cardiolipin present in the mitochondrial membrane plays an important role on the transport activity of Letm1.
Collapse
|
10
|
Matsuura T, Hosoda K, Shimizu Y. Robustness of a Reconstituted Escherichia coli Protein Translation System Analyzed by Computational Modeling. ACS Synth Biol 2018; 7:1964-1972. [PMID: 30004679 DOI: 10.1021/acssynbio.8b00228] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Robustness against environmental changes is one of the major features of biological systems, but its origin is not well understood. We recently constructed a large-scale computational model of an Escherichia coli-based reconstituted in vitro translation system that enumerates all protein synthesis processes in detail. Our model synthesizes a formyl-Met-Gly-Gly tripeptide (MGG peptide) from 27 initial molecular components through 968 biochemical reactions. Among the 968 kinetic parameters, 483 are nonzero parameters, and the simulator was used to determine how perturbations of 483 individual reactions affect the complex reaction network. We found that even when the kinetic parameter was changed from 100- to 0.01-fold, 94% of the changes hardly affected the two indicators of reaction dynamics in MGG peptide synthesis, which represent the yield of the MGG peptide and the initial lag-time of the peptide synthesis. Moreover, none of the indicators increased proportionally to these changes: e.g., a 100-fold increase in the kinetic parameter increased the yield by only 2.2-fold at most, indicating the insensitivity of the reaction network to perturbation. Robustness and insensitivity are likely to be a common feature of large-scale biological reaction networks.
Collapse
Affiliation(s)
- Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazufumi Hosoda
- Institute for Academic Initiatives, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| |
Collapse
|
11
|
Reduction of the Oxidative Stress Status Using Steviol Glycosides in a Fish Model (Cyprinus carpio). BIOMED RESEARCH INTERNATIONAL 2018; 2017:2352594. [PMID: 28691017 PMCID: PMC5485310 DOI: 10.1155/2017/2352594] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/17/2017] [Accepted: 04/03/2017] [Indexed: 12/20/2022]
Abstract
Steviol glycosides are sweetening compounds from the Stevia rebaudiana Bertoni plant. This product is considered safe for human consumption and was approved as a food additive by the Food and Drugs Administration (FDA) and European Food Safety Authority (EFSA). Its effects on the ecosystem have not been studied in depth; therefore, it is necessary to carry out ecotoxicological studies in organisms such as Cyprinus carpio. The present study aimed to evaluate the antioxidant activity by SGs on diverse tissues in C. carpio using oxidative stress (OS) biomarkers. To test the antioxidant activity, carps were exposed to four systems: (1) SGs free control, (2) CCl4 0.5 mL/kg, (3) SGs 1 g/L, and (4) CCl4 0.5 mL/kg + SGs 1 g/L at 96 h. The following biomarkers were analyzed: lipoperoxidation (LPX), hydroperoxide content (HPC), and protein carbonyl content (PCC), as well as antioxidant activity of superoxide dismutase (SOD) and catalase (CAT). It was found that both (3 and 4) systems' exposure decreases LPX, CHP, PCC, SOD, and CAT with respect to the CCl4 system. The results of this study demonstrate that the concentrations of SGs used are not capable of generating oxidative stress and, on the contrary, would appear to induce an antioxidant effect.
Collapse
|
12
|
Błażejewska K, Kapusta M, Zielińska E, Tukaj Z, Chincinska IA. Mature Luffa Leaves ( Luffa cylindrica L.) as a Tool for Gene Expression Analysis by Agroinfiltration. FRONTIERS IN PLANT SCIENCE 2017; 8:228. [PMID: 28270826 PMCID: PMC5318407 DOI: 10.3389/fpls.2017.00228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/06/2017] [Indexed: 05/23/2023]
Abstract
We exploited the potential of cucurbits for ectopic gene expression. Agroinfiltration is a simple and commonly used method to obtain transient expression of foreign genes in plants. In contrast to in vitro transformation techniques, agroinfiltration can be used for genetic modification of mature plant tissues. Although the cucurbits are commonly used as model plants for molecular biology and biotechnology studies, to date there are no literature sources on the possibility of transient gene expression in mature cucurbit tissues. Our research has shown that mature leaves of Luffa cylindrica L. (luffa), in contrast to other cucurbit species, can be successfully transiently transformed with Agrobacterium tumefaciens. We efficiently transformed luffa leaves with a reporter gene encoding β-glucuronidase (GUS). The GUS activity in transiently transformed leaf tissues was detected within 24 h after the infiltration with bacteria. Additionally, we have shown that the activity of a transiently expressed the GUS gene can be monitored directly in the EDTA-exudates collected from the cut petioles of the agroinfiltrated leaves. The results suggest that luffa leaves can be useful as a plant expression system for studies of physiological and biochemical processes in cucurbits.
Collapse
Affiliation(s)
- Kamila Błażejewska
- Department of Plant Physiology and Biotechnology, Faculty of Biology, University of GdańskGdańsk, Poland
| | - Małgorzata Kapusta
- Department of Plant Cytology and Embryology, Faculty of Biology, University of GdańskGdańsk, Poland
| | - Elżbieta Zielińska
- Department of Plant Physiology and Biotechnology, Faculty of Biology, University of GdańskGdańsk, Poland
| | - Zbigniew Tukaj
- Department of Plant Physiology and Biotechnology, Faculty of Biology, University of GdańskGdańsk, Poland
| | - Izabela A. Chincinska
- Department of Plant Physiology and Biotechnology, Faculty of Biology, University of GdańskGdańsk, Poland
| |
Collapse
|
13
|
Paper-based colorimetric biosensor for antibiotics inhibiting bacterial protein synthesis. J Biosci Bioeng 2017; 123:96-100. [DOI: 10.1016/j.jbiosc.2016.07.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/15/2016] [Accepted: 07/22/2016] [Indexed: 12/13/2022]
|
14
|
Stütz AE, Wrodnigg TM. Carbohydrate-Processing Enzymes of the Lysosome: Diseases Caused by Misfolded Mutants and Sugar Mimetics as Correcting Pharmacological Chaperones. Adv Carbohydr Chem Biochem 2016; 73:225-302. [PMID: 27816107 DOI: 10.1016/bs.accb.2016.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lysosomal storage diseases are hereditary disorders caused by mutations on genes encoding for one of the more than fifty lysosomal enzymes involved in the highly ordered degradation cascades of glycans, glycoconjugates, and other complex biomolecules in the lysosome. Several of these metabolic disorders are associated with the absence or the lack of activity of carbohydrate-processing enzymes in this cell compartment. In a recently introduced therapy concept, for susceptible mutants, small substrate-related molecules (so-called pharmacological chaperones), such as reversible inhibitors of these enzymes, may serve as templates for the correct folding and transport of the respective protein mutant, thus improving its concentration and, consequently, its enzymatic activity in the lysosome. Carbohydrate-processing enzymes in the lysosome, related lysosomal diseases, and the scope and limitations of reported reversible inhibitors as pharmacological chaperones are discussed with a view to possibly extending and improving research efforts in this area of orphan diseases.
Collapse
Affiliation(s)
- Arnold E Stütz
- Glycogroup, Institute of Organic Chemistry, Graz University of Technology, Graz, Austria
| | - Tanja M Wrodnigg
- Glycogroup, Institute of Organic Chemistry, Graz University of Technology, Graz, Austria
| |
Collapse
|
15
|
Sunami T, Ichihashi N, Nishikawa T, Kazuta Y, Yomo T. Effect of Liposome Size on Internal RNA Replication Coupled with Replicase Translation. Chembiochem 2016; 17:1282-9. [DOI: 10.1002/cbic.201500662] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Takeshi Sunami
- Institute for Academic Initiatives; Osaka University; 1-5 Yamadaoka Suita Osaka 565-0871 Japan
- Exploratory Research for Advanced Technology (ERATO); Japan Science and Technology Agency (JST); 1-5 Yamadaoka Suita Osaka 565-0871 Japan
| | - Norikazu Ichihashi
- Exploratory Research for Advanced Technology (ERATO); Japan Science and Technology Agency (JST); 1-5 Yamadaoka Suita Osaka 565-0871 Japan
- Department of Bioinformatics Engineering; Graduate School of Information Science and Technology; Osaka University; 1-5 Yamadaoka Suita Osaka 565-0871 Japan
| | - Takehiro Nishikawa
- Exploratory Research for Advanced Technology (ERATO); Japan Science and Technology Agency (JST); 1-5 Yamadaoka Suita Osaka 565-0871 Japan
| | - Yasuaki Kazuta
- Exploratory Research for Advanced Technology (ERATO); Japan Science and Technology Agency (JST); 1-5 Yamadaoka Suita Osaka 565-0871 Japan
| | - Tetsuya Yomo
- Exploratory Research for Advanced Technology (ERATO); Japan Science and Technology Agency (JST); 1-5 Yamadaoka Suita Osaka 565-0871 Japan
- Department of Bioinformatics Engineering; Graduate School of Information Science and Technology; Osaka University; 1-5 Yamadaoka Suita Osaka 565-0871 Japan
- Graduate School of Frontier Biosciences; Osaka University; 1-5 Yamadaoka Suita Osaka 565-0871 Japan
| |
Collapse
|
16
|
Soga H, Fujii S, Yomo T, Kato Y, Watanabe H, Matsuura T. In vitro membrane protein synthesis inside cell-sized vesicles reveals the dependence of membrane protein integration on vesicle volume. ACS Synth Biol 2014; 3:372-9. [PMID: 24328098 DOI: 10.1021/sb400094c] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Giant unilamellar vesicles (GUVs) are vesicles>1 μm in diameter that provide an environment in which the effect of a confined reaction volume on intravesicular reactions can be investigated. By synthesizing EmrE, a multidrug transporter from Escherichia coli, as a model membrane protein using a reconstituted in vitro transcription-translation system inside GUVs, we investigated the effect of a confined volume on the synthesis and membrane integration of EmrE. Flow cytometry was used to analyze multiple properties of the vesicles and to quantify EmrE synthesis inside GUVs composed of only 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. We found that EmrE was synthesized and integrated into the GUV membrane in its active form. We also found that the ratio of membrane-integrated EmrE to total synthesized EmrE increased with decreasing vesicle volume; this finding is explained by the effect of an increased surface-area-to-volume ratio in smaller vesicles. In vitro membrane synthesis inside GUVs is a useful approach to study quantitatively the properties of membrane proteins and their interaction with the membrane under cell-mimicking environments.
Collapse
Affiliation(s)
- Haruka Soga
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka, Japan
| | - Satoshi Fujii
- Exploratory
Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka, Japan
| | - Tetsuya Yomo
- Exploratory
Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka, Japan
- Department
of Bioinformatic Engineering, Graduate School of Information Science
and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, Japan
| | - Yasuhiko Kato
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka, Japan
| | - Hajime Watanabe
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka, Japan
| | - Tomoaki Matsuura
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka, Japan
- Exploratory
Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka, Japan
| |
Collapse
|
17
|
Okano T, Matsuura T, Suzuki H, Yomo T. Cell-free protein synthesis in a microchamber revealed the presence of an optimum compartment volume for high-order reactions. ACS Synth Biol 2014; 3:347-52. [PMID: 23991849 DOI: 10.1021/sb400087e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The application of microelectromechanical systems (MEMS) to chemistry and biochemistry allows various reactions to be performed in microscale compartments. Here, we aimed to use the glass microchamber to study the compartment size dependency of the protein synthesis, one of the most important reactions in the cell. By encapsulating the cell-free protein synthesis system with different reaction orders in femtoliter microchambers, chamber size dependency of the reaction initiated with a constant copy number of DNA was investigated. We were able to observe the properties specific to the high order reactions in microcompartments with high precision and found the presence of an optimum compartment volume for a high-order reaction using real biological molecules.
Collapse
Affiliation(s)
- Taiji Okano
- Exploratory Research
for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomoaki Matsuura
- Exploratory Research
for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita,
Osaka 565-0871, Japan
| | - Hiroaki Suzuki
- Exploratory Research
for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department
of Precision Mechanics, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Tetsuya Yomo
- Exploratory Research
for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department
of Bioinformatic Engineering, Graduate School of Information
Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate School
of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
18
|
Hassan MI, Waheed A, Grubb JH, Klei HE, Korolev S, Sly WS. High resolution crystal structure of human β-glucuronidase reveals structural basis of lysosome targeting. PLoS One 2013; 8:e79687. [PMID: 24260279 PMCID: PMC3834196 DOI: 10.1371/journal.pone.0079687] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 09/24/2013] [Indexed: 11/19/2022] Open
Abstract
Human β-glucuronidase (GUS) cleaves β-D-glucuronic acid residues from the non-reducing termini of glycosaminoglycan and its deficiency leads to mucopolysaccharidosis type VII (MPSVII). Here we report a high resolution crystal structure of human GUS at 1.7 Å resolution and present an extensive analysis of the structural features, unifying recent findings in the field of lysosome targeting and glycosyl hydrolases. The structure revealed several new details including a new glycan chain at Asn272, in addition to that previously observed at Asn173, and coordination of the glycan chain at Asn173 with Lys197 of the lysosomal targeting motif which is essential for phosphotransferase recognition. Analysis of the high resolution structure not only provided new insights into the structural basis for lysosomal targeting but showed significant differences between human GUS, which is medically important in its own right, and E. coli GUS, which can be selectively inhibited in the human gut to prevent prodrug activation and is also widely used as a reporter gene by plant biologists. Despite these differences, both human and E. coli GUS share a high structure homology in all three domains with most of the glycosyl hydrolases, suggesting that they all evolved from a common ancestral gene.
Collapse
Affiliation(s)
- Md. Imtaiyaz Hassan
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Abdul Waheed
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Jeffery H. Grubb
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Herbert E. Klei
- Research and Development, Bristol-Myers Squibb Company, Princeton, New Jersey, United States of America
| | - Sergey Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - William S. Sly
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
- * E-mail:
| |
Collapse
|
19
|
Naz H, Islam A, Waheed A, Sly WS, Ahmad F, Hassan MI. Humanβ-Glucuronidase: Structure, Function, and Application in Enzyme Replacement Therapy. Rejuvenation Res 2013; 16:352-63. [DOI: 10.1089/rej.2013.1407] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Huma Naz
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Abdul Waheed
- The Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis, University School of Medicine, St. Louis, Missouri
| | - William S. Sly
- The Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis, University School of Medicine, St. Louis, Missouri
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| |
Collapse
|
20
|
Abstract
In vitro methods have enabled the rapid and efficient evolution of proteins and successful generation of novel and highly functional proteins. However, the available methods consider only globular proteins (e.g., antibodies, enzymes) and not membrane proteins despite the biological and pharmaceutical importance of the latter. In this study, we report the development of a method called liposome display that can evolve the properties of membrane proteins entirely in vitro. This method, which involves in vitro protein synthesis inside liposomes, which are cell-sized phospholipid vesicles, was applied to the pore-forming activity of α-hemolysin, a membrane protein derived from Staphylococcus aureus. The obtained α-hemolysin mutant possessed only two point mutations but exhibited a 30-fold increase in its pore-forming activity compared with the WT. Given the ability to synthesize various membrane proteins and modify protein synthesis and functional screening conditions, this method will allow for the rapid and efficient evolution of a wide range of membrane proteins.
Collapse
|
21
|
Nishiyama K, Ichihashi N, Matsuura T, Kazuta Y, Yomo T. α-Complementation in an artificial genome replication system in liposomes. Chembiochem 2012. [PMID: 23193098 DOI: 10.1002/cbic.201200586] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Genome size is considered one of the limiting factors for the replication of primitive life forms. However, the relationship between genome size and replication efficiency has not been tested experimentally. In this study, we examined the effect of genome size on genome replication by using an artificial cell model: a self-replicating RNA genome encapsulated in a liposome. For the reduced genome size we used α-complementation of the lacZ gene. We first characterized α-complementation in the purified translation system and then applied α-complementation to the genome replication system. The reduction in the genome size together with the addition of ω-fragment increased the replication efficiency approximately eightfold. This result provides experimental evidence that genome size can be a limiting factor for primitive self-replication systems; it also implies that this artificial cell model could be a useful experimental model to identify possible mechanisms of genome enlargement.
Collapse
Affiliation(s)
- Kotaro Nishiyama
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Japan
| | | | | | | | | |
Collapse
|
22
|
Matsuura T, Hosoda K, Kazuta Y, Ichihashi N, Suzuki H, Yomo T. Effects of compartment size on the kinetics of intracompartmental multimeric protein synthesis. ACS Synth Biol 2012; 1:431-7. [PMID: 23651340 DOI: 10.1021/sb300041z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The cell contents are encapsulated within a compartment, the volume of which is a fundamental physical parameter that may affect intracompartmental reactions. However, there have been few studies to elucidate whether and how volume changes alone can affect the reaction kinetics. It is difficult to address these questions in vivo, because forced cell volume changes, e.g., by osmotic inflation/deflation, globally alters the internal state. Here, we prepared artificial cell-like compartments with different volumes but with identical constituents, which is not possible with living cells, and synthesized two tetrameric enzymes, β-glucuronidase (GUS) and β-galactosidase (GAL), by cell-free protein synthesis. Tetrameric GUS but not GAL was synthesized more quickly in smaller compartments. The difference between the two was dependent on the rate-limiting step and the reaction order. The observed acceleration mechanism would be applicable to living cells as multimeric protein synthesis in a microcompartment is ubiquitous in vivo.
Collapse
Affiliation(s)
- Tomoaki Matsuura
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Yamadaoka 1-5, Suita, Osaka, Japan
| | | | - Yasuaki Kazuta
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Yamadaoka 1-5, Suita, Osaka, Japan
| | - Norikazu Ichihashi
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Yamadaoka 1-5, Suita, Osaka, Japan
| | - Hiroaki Suzuki
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Yamadaoka 1-5, Suita, Osaka, Japan
| | - Tetsuya Yomo
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Yamadaoka 1-5, Suita, Osaka, Japan
| |
Collapse
|
23
|
Directed Evolution of Proteins through In Vitro Protein Synthesis in Liposomes. J Nucleic Acids 2012; 2012:923214. [PMID: 22957209 PMCID: PMC3431101 DOI: 10.1155/2012/923214] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/10/2012] [Indexed: 11/17/2022] Open
Abstract
Directed evolution of proteins is a technique used to modify protein functions through "Darwinian selection." In vitro compartmentalization (IVC) is an in vitro gene screening system for directed evolution of proteins. IVC establishes the link between genetic information (genotype) and the protein translated from the information (phenotype), which is essential for all directed evolution methods, by encapsulating both in a nonliving microcompartment. Herein, we introduce a new liposome-based IVC system consisting of a liposome, the protein synthesis using recombinant elements (PURE) system and a fluorescence-activated cell sorter (FACS) used as a microcompartment, in vitro protein synthesis system, and high-throughput screen, respectively. Liposome-based IVC is characterized by in vitro protein synthesis from a single copy of a gene in a cell-sized unilamellar liposome and quantitative functional evaluation of the synthesized proteins. Examples of liposome-based IVC for screening proteins such as GFP and β-glucuronidase are described. We discuss the future directions for this method and its applications.
Collapse
|
24
|
Okano T, Matsuura T, Kazuta Y, Suzuki H, Yomo T. Cell-free protein synthesis from a single copy of DNA in a glass microchamber. LAB ON A CHIP 2012; 12:2704-2711. [PMID: 22622196 DOI: 10.1039/c2lc40098g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
To achieve a cell-mimetic reaction environment, we fabricated and tested quartz microchambers for conducting protein synthesis using an in vitro transcription and translation system, the PURE system. By introducing a glass microchamber and blocking the surface of the chamber with amino acids, the concentration of the synthesized marker protein (green fluorescent protein, GFP) was significantly improved compared to that in the poly(dimethylsiloxane) (PDMS) microchamber. The concentration was below the detection limit in the PDMS microchambers, whereas the glass microchambers yielded 700 nM GFP, representing 41% of the bulk reaction. There was no detectable difference when the GFP synthesis was performed in microchambers with sizes ranging from 40 fL to 7 pL, indicating that the present microchamber system can serve as a cell-sized test tube with a variable reaction volume. Finally, we demonstrated that two different proteins, GFP and β-galactosidase, can be expressed from single genes in our experimental setup. Quantized and distinctive signals from proteins synthesized from 0, 1, or 2 copies of genes were obtained. The microchamber presented here can be utilized not only to study the effects of compartment volume on protein synthesis but also for the comprehensive analysis of complex biochemical reactions in cell-mimetic environments.
Collapse
Affiliation(s)
- Taiji Okano
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Suita, Osaka, Japan
| | | | | | | | | |
Collapse
|
25
|
Nishikawa T, Sunami T, Matsuura T, Ichihashi N, Yomo T. Construction of a Gene Screening System Using Giant Unilamellar Liposomes and a Fluorescence-Activated Cell Sorter. Anal Chem 2012; 84:5017-24. [DOI: 10.1021/ac300678w] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
26
|
Dang DT, Schill J, Brunsveld L. Cucurbit[8]uril-mediated protein homotetramerization. Chem Sci 2012. [DOI: 10.1039/c2sc20625k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
27
|
Caschera F, Sunami T, Matsuura T, Suzuki H, Hanczyc MM, Yomo T. Programmed vesicle fusion triggers gene expression. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:13082-13090. [PMID: 21923099 DOI: 10.1021/la202648h] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The membrane properties of phospholipid vesicles can be manipulated to both regulate and initiate encapsulated biochemical reactions and networks. We present evidence for the inhibition and activation of reactions encapsulated in vesicles by the exogenous addition of charged amphiphiles. While the incorporation of cationic amphiphile exerts an inhibitory effect, complementation of additional anionic amphiphiles revitalize the reaction. We demonstrated both the simple hydrolysis reaction of β-glucuronidase and the in vitro gene expression of this enzyme from a DNA template. Furthermore, we show that two vesicle populations decorated separately with positive and negative amphiphiles can fuse selectively to supply feeding components to initiate encapsulated reactions. This mechanism could be one of the rudimentary but effective means to regulate and maintain metabolism in dynamic artificial cell models.
Collapse
Affiliation(s)
- Filippo Caschera
- Center for Fundamental Living Technology (FLinT), Institute of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | | | | | | | | | | |
Collapse
|