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Tashiro M, Kiyota H, Kawai-Noma S, Saito K, Ikeuchi M, Iijima Y, Umeno D. Bacterial Production of Pinene by a Laboratory-Evolved Pinene-Synthase. ACS Synth Biol 2016; 5:1011-20. [PMID: 27247193 DOI: 10.1021/acssynbio.6b00140] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Successful feeding of the substrate geranylpyrophosphate (GPP) to monoterpene synthase is critical to the efficient microbial production of monoterpenes. Overexpression of GPP synthases, metabolic channeling from GPP synthase to terpene synthases, and down-tuning of endogenous competitors have been successfully used to increase the production of monoterpene. Nevertheless, the production of monoterpenes has remained considerably lower than that of hemi-/sesqui-terpenoids. We tested whether it is effective to improve the cellular activity of monoterpene synthases. To this end, we developed a high-throughput screening system to monitor for elevated GPP consumption. Through a single round of mutagenesis and screening, we isolated a pinene synthase variant that outperformed the wild-type (parent) enzyme in multiple contexts in Escherichia coli and cyanobacteria. The purified variant exhibited drastically altered metal dependency, enabling to keep the activity in the cytosol that is manganese-deficient. Coexpression of this variant with mevalonate pathway enzymes, isopentenylpyrophosphate isomerase, and GPP synthase yielded 140 mg/L pinene in a flask culture.
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Goto S, Umino S, Amakai W, Fujiwara K, Sugo T, Kojima T, Kawai-Noma S, Umeno D, Saito K. Impregnation structure of cobalt ferrocyanide microparticles by the polymer chain grafted onto nylon fiber. J NUCL SCI TECHNOL 2016. [DOI: 10.1080/00223131.2016.1143886] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Nakamura Y, Fujiwara K, Sugo T, Kawai-Noma S, Umeno D, Saito K. Preparation of Extractant-Impregnated Fiber for Recovery of Palladium from Hydrochloric Acid Solution. KAGAKU KOGAKU RONBUN 2016. [DOI: 10.1252/kakoronbunshu.42.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Tashiro Y, Kimura Y, Furubayashi M, Tanaka A, Terakubo K, Saito K, Kawai-Noma S, Umeno D. Directed evolution of the autoinducer selectivity of Vibrio fischeri LuxR. J GEN APPL MICROBIOL 2016; 62:240-247. [DOI: 10.2323/jgam.2016.04.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Ike K, Arasawa Y, Koizumi S, Mihashi S, Kawai-Noma S, Saito K, Umeno D. Evolutionary Design of Choline-Inducible and -Repressible T7-Based Induction Systems. ACS Synth Biol 2015; 4:1352-60. [PMID: 26289535 DOI: 10.1021/acssynbio.5b00107] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
By assembly and evolutionary engineering of T7-phage-based transcriptional switches made from endogenous components of the bet operon on the Escherichia coli chromosome, genetic switches inducible by choline, a safe and inexpensive compound, were constructed. The functional plasticity of the BetI repressor was revealed by rapid and high-frequency identification of functional variants with various properties, including those with high stringency, high maximum expression level, and reversed phenotypes, from a pool of BetI mutants. The plasmid expression of BetI mutants resulted in the choline-inducible (Bet-ON) or choline-repressible (Bet-OFF) switching of genes under the pT7/betO sequence at unprecedentedly high levels, while keeping the minimal leaky expression in uninduced conditions.
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Tominaga M, Ike K, Kawai-Noma S, Saito K, Umeno D. Rapid and liquid-based selection of genetic switches using nucleoside kinase fused with aminoglycoside phosphotransferase. PLoS One 2015; 10:e0120243. [PMID: 25790096 PMCID: PMC4366196 DOI: 10.1371/journal.pone.0120243] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/20/2015] [Indexed: 11/18/2022] Open
Abstract
The evolutionary design of genetic switches and circuits requires iterative rounds of positive (ON-) and negative (OFF-) selection. We previously reported a rapid OFF selection system based on the kinase activity of herpes simplex virus thymidine kinase (hsvTK) on the artificial mutator nucleoside dP. By fusing hsvTK with the kanamycin resistance marker aminoglycoside-(3')-phosphotransferase (APH), we established a novel selector system for genetic switches. Due to the bactericidal nature of kanamycin and nucleoside-based lethal mutagenesis, both positive and negative selection could be completed within several hours. Using this new selector system, we isolated a series of homoserine lactone-inducible genetic switches with different expression efficiencies from libraries of the Vibrio fischeri lux promoter in two days, using only liquid handling.
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Tominaga M, Kawai-Noma S, Kawagishi I, Sowa Y, Saito K, Umeno D. Liquid-based iterative recombineering method tolerant to counter-selection escapes. PLoS One 2015; 10:e0119818. [PMID: 25775434 PMCID: PMC4361647 DOI: 10.1371/journal.pone.0119818] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/16/2015] [Indexed: 11/24/2022] Open
Abstract
Selection-based recombineering is a flexible and proven technology to precisely modify bacterial genomes at single base resolution. It consists of two steps of homologous recombination followed by selection/counter-selection. However, the shortage of efficient counter-selectable markers limits the throughput of this method. Additionally, the emergence of ‘selection escapees’ can affect recombinant pools generated through this method, and they must be manually removed at each step of selection-based recombineering. Here, we report a series of efforts to improve the throughput and robustness of selection-based recombineering and to achieve seamless and automatable genome engineering. Using the nucleoside kinase activity of herpes simplex virus thymidine kinase (hsvTK) on the non-natural nucleoside dP, a highly efficient, rapid, and liquid-based counter-selection system was established. By duplicating hsvtk gene, combined with careful control of the population size for the subsequent round, we effectively eliminated selection escapes, enabling seamless and multiple insertions/replacement of gene-size fragments in the chromosome. Four rounds of recombineering could thus be completed in 10 days, requiring only liquid handling and without any need for colony isolation or genotype confirmation. The simplicity and robustness of our method make it broadly accessible for multi-locus chromosomal modifications.
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Sasaki TA, Uchiyama S, Fujiwara K, Sugo T, Umeno D, Saito K. Nd/Dy Resolution by SPE-Based Elution Chromatography with Bis(2-ethylhexyl) Phosphate (HDEHP)-Impregnated Fiber-Packed Bed. KAGAKU KOGAKU RONBUN 2015. [DOI: 10.1252/kakoronbunshu.41.220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Furubayashi M, Li L, Katabami A, Saito K, Umeno D. Directed evolution of squalene synthase for dehydrosqualene biosynthesis. FEBS Lett 2014; 588:3375-81. [PMID: 25093296 DOI: 10.1016/j.febslet.2014.07.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 07/20/2014] [Accepted: 07/22/2014] [Indexed: 10/24/2022]
Abstract
Squalene synthase (SQS) catalyzes the first step of sterol/hopanoid biosynthesis in various organisms. It has been long recognized that SQSs share a common ancestor with carotenoid synthases, but it is not known how these enzymes selectively produce their own product. In this study, SQSs from yeast, human, and bacteria were independently subjected to directed evolution for the production of the C30 carotenoid backbone, dehydrosqualene. This was accomplished via high-throughput screening with Pantoea ananatis phytoene desaturase, which can selectively convert dehydrosqualene into yellow carotenoid pigments. Genetic analysis of the resultant mutants revealed various mutations that could effectively convert SQS into a "dehydrosqualene synthase." All of these mutations are clustered around the residues that have been proposed to be important for NADPH binding.
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Furubayashi M, Saito K, Umeno D. Evolutionary analysis of the functional plasticity of Staphylococcus aureus C30 carotenoid synthase. J Biosci Bioeng 2014; 117:431-6. [DOI: 10.1016/j.jbiosc.2013.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/02/2013] [Accepted: 10/04/2013] [Indexed: 11/16/2022]
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Okamura Y, Fujiwara K, Ishihara R, Sugo T, Kojima T, Umeno D, Saito K. Cesium removal in freshwater using potassium cobalt hexacyanoferrate-impregnated fibers. Radiat Phys Chem Oxf Engl 1993 2014. [DOI: 10.1016/j.radphyschem.2013.04.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Sasaki TA, Uchiyama S, Fujiwara K, Sugo T, Umeno D, Saito K. Similarity of Rare Earth Extraction by Acidic Extractant Bis(2-ethylhexyl) Phosphate (HDEHP) Supported on a Dodecylamino-Group-Containing Graft Chain and by HDEHP Dissolved in Dodecane. KAGAKU KOGAKU RONBUN 2014. [DOI: 10.1252/kakoronbunshu.40.404] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Ever-increasing repertories of RNA-based switching devices are enabling synthetic biologists to construct compact, self-standing, and easy-to-integrate regulatory circuits. However, it is rather rare that the existing RNA-based expression controllers happen to have the exact specification needed for particular applications from the beginning. Evolutionary design of is powerful strategy for quickly tuning functions/specification of genetic switches. Presented here are the steps required for rapid and efficient enrichment of genetic switches with desired specification using recently developed nucleoside kinase-based dual selection system. Here, the library of genetic switches, created by randomizing either the part or the entire sequence coding switching components, is subjected to OFF (negative) selection and ON (positive) selection in various conditions. The entire selection process is completed only by liquid handling, facilitating the parallel and continuous operations of multiple selection projects. This automation-liable platform for genetic selection of functional switches has potential applications for development of RNA-based biosensors, expression controllers, and their integrated forms (genetic circuits).
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Tanaka R, Ishihara R, Miyoshi K, Umeno D, Saito K, Asai S, Yamada S, Hirota H. Simple Method for High-Density Impregnation of Aliquat 336 onto Porous Sheet and Binding Performance of Resulting Sheet for Palladium Ions. SEP SCI TECHNOL 2013. [DOI: 10.1080/01496395.2013.829101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Furubayashi M, Li L, Katabami A, Saito K, Umeno D. Construction of carotenoid biosynthetic pathways using squalene synthase. FEBS Lett 2013; 588:436-42. [PMID: 24333579 DOI: 10.1016/j.febslet.2013.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 11/28/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022]
Abstract
The first committed steps of steroid/hopanoid pathways involve squalene synthase (SQS). Here, we report the Escherichia coli production of diaponeurosporene and diapolycopene, yellow C30 carotenoid pigments, by expressing human SQS and Staphylococcus aureus dehydrosqualene (C30 carotenoid) desaturase (CrtN). We suggest that the carotenoid pigments are synthesized mainly via the desaturation of squalene rather than the direct synthesis of dehydrosqualene through the non-reductive condensation of prenyl diphosphate precursors, indicating the possible existence of a "squalene route" and a "lycopersene route" for C30 and C40 carotenoids, respectively. Additionally, this finding yields a new method of colorimetric screening for the cellular activity of squalene synthases, which are major targets for cholesterol-lowering drugs.
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Ishihara R, Uchiyama S, Ikezawa H, Yamada S, Hirota H, Umeno D, Saito K. Effect of Dose on Mole Percentages of Polymer Brush and Root Grafted onto Porous Polyethylene Sheet by Radiation-Induced Graft Polymerization. Ind Eng Chem Res 2013. [DOI: 10.1021/ie4011436] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Iwanade A, Umeno D, Saito K, Sugo T. Dependence of protein binding capacity of dimethylamino-γ-butyric-acid (DMGABA)-immobilized porous membrane on composition of solvent used for DMGABA immobilization. Radiat Phys Chem Oxf Engl 1993 2013. [DOI: 10.1016/j.radphyschem.2013.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Wada G, Ishihara R, Miyoshi K, Umeno D, Saito K, Asai S, Yamada S, Hirota H. Crosslinked-Chelating Porous Sheet with High Dynamic Binding Capacity of Metal Ions. SOLVENT EXTRACTION AND ION EXCHANGE 2013. [DOI: 10.1080/07366299.2012.735555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Uchiyama S, Ishihara R, Umeno D, Saito K, Yamada S, Hirota H, Asai S. Determination of Mole Percentages of Brush and Root of Polymer Chain Grafted onto Porous Sheet. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 2013. [DOI: 10.1252/jcej.12we274] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sugiyama M, Ikeda K, Umeno D, Saito K, Kikuchi T, Ando K. Removal of Urea from Water Using Urease-Immobilized Fibers. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 2013. [DOI: 10.1252/jcej.12we267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Shimoda Y, Sekiya Y, Umeno D, Saito K, Furumoto G, Shirataki H, Shinohara N, Kubota N. Protein-Binding Characteristics of Anion-Exchange Particles Prepared by Radiation-Induced Graft Polymerization at Low Temperatures. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 2013. [DOI: 10.1252/jcej.13we056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Hirayama Y, Okamura Y, Fujiwara K, Sugo T, Umeno D, Saito K. Effect of Salt Concentration of Cesium Solution on Cesium-Binding Capacity of Potassium Cobalt-Hexacyanoferrate-Impregnated Fiber. KAGAKU KOGAKU RONBUN 2013. [DOI: 10.1252/kakoronbunshu.39.28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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48
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Ishihara R, Asai S, Otosaka S, Yamada S, Hirota H, Miyoshi K, Umeno D, Saito K. Dependence of Lanthanide-Ion Binding Performance on HDEHP Concentration in HDEHP Impregnation to Porous Sheet. SOLVENT EXTRACTION AND ION EXCHANGE 2012. [DOI: 10.1080/07366299.2011.609382] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Tashiro Y, Katabami A, Saito K, Umeno D. A system for the rapid determination of the mutation spectrum in Escherichia coli. ANAL SCI 2012; 28:95-101. [PMID: 22322800 DOI: 10.2116/analsci.28.95] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The first step toward elucidating the mutagenic effects of chemicals and pathways is to determine the specificity of the mutations generated spontaneously or in response to treatment with mutagens. We constructed a set of plasmid-encoded probes for the specific detection of each type of base substitution mutation. Using these probes, we were able to quickly determine both the mutation rate and the specificity of the mutations caused by different types of mutagens and mutagenic conditions. We also developed a PCR-based method to rapidly and robustly determine the mutation spectrum in response to various mutagenic samples in parallel. This system allows one to not only analyze the mutation specificity of various chemicals, but also to search for novel genetic elements that promote the specific mutation events.
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Harayama T, Okamura Y, Shimoda Y, Umeno D, Saito K, Shinohara N, Kubota N. Protein Resolution in Elution Chromatography Using Novel Cation-Exchange Polymer-Brush-Immobilized Particles. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 2012. [DOI: 10.1252/jcej.12we011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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