1
|
Iqbal Z, Sadaf S. A patent-based consideration of latest platforms in the art of directed evolution: a decade long untold story. Biotechnol Genet Eng Rev 2022; 38:133-246. [PMID: 35200115 DOI: 10.1080/02648725.2021.2017638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Directed (or in vitro) evolution of proteins and metabolic pathways requires tools for creating genetic diversity and identifying protein variants with new or improved functional properties. Besides simplicity, reliability, speed, versatility, universal applicability and economy of the technique, the new science of synthetic biology requires improved means for construction of smart and high-quality mutant libraries to better navigate the sequence diversity. In vitro CRISPR/Cas9-mediated mutagenic (ICM) system and machine-learning (ML)-assisted approaches to directed evolution are now in the field to achieve the goal. This review describes the gene diversification strategies, screening and selection methods, in silico (computer-aided), Cas9-mediated and ML-based approaches to mutagenesis, developed especially in the last decade, and their patent position. The objective behind is to emphasize researchers the need for noting which mutagenesis, screening or selection method is patented and then selecting a suitable restriction-free approach to sequence diversity. Techniques and evolved products subject to patent rights need commercial license if their use is for purposes other than private or experimental research.
Collapse
Affiliation(s)
- Zarina Iqbal
- IP Litigation Department, PakPat World Intellectual Property Protection Services, Lahore, Pakistan
| | - Saima Sadaf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| |
Collapse
|
2
|
Iqbal Z, Sadaf S. Forty Years of Directed Evolution and its Continuously Evolving Technology Toolbox - A Review of the Patent Landscape. Biotechnol Bioeng 2021; 119:693-724. [PMID: 34923625 DOI: 10.1002/bit.28009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 11/10/2022]
Abstract
Generating functional protein variants with novel or improved characteristics has been a goal of the biotechnology industry and life sciences, for decades. Rational design and directed evolution are two major pathways to achieve the desired ends. Whilst rational protein design approach has made substantial progress, the idea of using a method based on cycles of mutagenesis and natural selection to develop novel binding proteins, enzymes and structures has attracted great attention. Laboratory evolution of proteins/enzymes requires new tools and analytical approaches to create genetic diversity and identifying variants with desired traits. In this pursuit, construction of sufficiently large libraries of target molecules to search for improved variants and the need for new protocols to alter the properties of target molecules has been a continuing challenge in the directed evolution experiments. This review will discuss the in vivo and in vitro gene diversification tools, library screening or selection approaches, and artificial intelligence/machine-learning-based strategies to mutagenesis developed in the last forty years to accelerate the natural process of evolution in creating new functional protein variants, optimization of microbial strains and transformation of enzymes into industrial machines. Analyzing patent position over these techniques and mechanisms also constitutes an integral and distinctive part of this review. The aim is to provide an up-to-date resource/technology toolbox for research-based and pharmaceutical companies to discover the boundaries of competitor's intellectual property (IP) portfolio, their freedom-to-operate in the relevant IP landscape, and the need for patent due diligence analysis to rule out whether use of a particular patented mutagenesis method, library screening/selection technique falls outside the safe harbor of experimental use exemption. While so doing, we have referred to some recent cases that emphasize the significance of selecting a suitable gene diversification strategy in directed evolution experiments. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Zarina Iqbal
- PakPat World Intellectual Property Protection Services, Lahore, 54000, Pakistan
| | - Saima Sadaf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
| |
Collapse
|
3
|
Biyani M, Biyani M, Nishigaki K. Biomolecular display technology: a new tool for drug discovery. Anim Biotechnol 2020. [DOI: 10.1016/b978-0-12-811710-1.00019-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
4
|
Ghimire Gautam S, Komatsu M, Nishigaki K. Strong Inhibition of Beta-Amyloid Peptide Aggregation Realized by Two-Steps Evolved Peptides. Chem Biol Drug Des 2014; 85:356-68. [DOI: 10.1111/cbdd.12400] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 07/12/2014] [Accepted: 07/21/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Sunita Ghimire Gautam
- Department of Functional Materials Science; Graduate School of Science and Engineering; Saitama University; 255 Shimo-okubo Sakura-Ku Saitama-Shi 338-8570 Japan
| | - Masayuki Komatsu
- Department of Functional Materials Science; Graduate School of Science and Engineering; Saitama University; 255 Shimo-okubo Sakura-Ku Saitama-Shi 338-8570 Japan
| | - Koichi Nishigaki
- Department of Functional Materials Science; Graduate School of Science and Engineering; Saitama University; 255 Shimo-okubo Sakura-Ku Saitama-Shi 338-8570 Japan
| |
Collapse
|
5
|
Biomolecular Display Technology. Anim Biotechnol 2014. [DOI: 10.1016/b978-0-12-416002-6.00020-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
6
|
Yanagawa H. Exploration of the Origin and Evolution of Globular Proteins by mRNA Display. Biochemistry 2013; 52:3841-51. [DOI: 10.1021/bi301704x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Hiroshi Yanagawa
- Department of Biosciences and Informatics,
Faculty
of Sciences and Technology, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| |
Collapse
|
7
|
Peptide-Modulated Activity Enhancement of Acidic Protease Cathepsin E at Neutral pH. INTERNATIONAL JOURNAL OF PEPTIDES 2012; 2012:316432. [PMID: 23365585 PMCID: PMC3534310 DOI: 10.1155/2012/316432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/20/2012] [Accepted: 10/27/2012] [Indexed: 11/17/2022]
Abstract
Enzymes are regulated by their activation and inhibition. Enzyme activators can often be effective tools for scientific and medical purposes, although they are more difficult to obtain than inhibitors. Here, using the paired peptide method, we report on protease-cathepsin-E-activating peptides that are obtained at neutral pH. These selected peptides also underwent molecular evolution, after which their cathepsin E activation capability improved. Thus, the activators we obtained could enhance cathepsin-E-induced cancer cell apoptosis, which indicated their potential as cancer drug precursors.
Collapse
|
8
|
Kitamura K, Komatsu M, Biyani M, Futakami M, Kawakubo T, Yamamoto K, Nishigaki K. Proven in vitro evolution of protease cathepsin E-inhibitors and -activators at pH 4.5 using a paired peptide method. J Pept Sci 2012; 18:711-9. [PMID: 23109368 DOI: 10.1002/psc.2453] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 07/08/2012] [Accepted: 08/20/2012] [Indexed: 12/25/2022]
Abstract
Improving a particular function of molecules is often more difficult than identifying such molecules ab initio. Here, a method to acquire higher affinity and/or more functional peptides was developed as a progressive library selection method. The primary library selection products were utilized to build a secondary library composed of blocks of 4 amino acids, of which selection led to peptides with increased activity. These peptides were further converted to randomly generate paired peptides. Cathepsin E-inhibitors thus obtained exhibited the highest activities and affinities (pM order). This was also the case with cathepsin E-activating peptides, proving the methodological effectiveness. The primary, secondary, and tertiary library selections can be regarded as module-finding, module-shuffling, and module-pairing, respectively, which resembles the progression of the natural evolution of proteins. The mode of peptide binding to their target proteins is discussed in analogy to antibodies and epitopes of an antigen.
Collapse
Affiliation(s)
- Koichiro Kitamura
- Janusys Corporation, #508, Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama, 333-0844, Japan; Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama, 338-8570, Japan; Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS), Saitama Small Enterprise Promotion Corporation, #552, Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama, 333-0844, Japan; City Area Program Saitama Metropolitan Area, Saitama small and medium Enterprises Development Corporation, 2-3-2 Kamiochiai, Chuo-ku, Saitama City, Saitama, 338-0001, Japan
| | | | | | | | | | | | | |
Collapse
|
9
|
Kumar A, Singh S. Directed evolution: tailoring biocatalysts for industrial applications. Crit Rev Biotechnol 2012; 33:365-78. [DOI: 10.3109/07388551.2012.716810] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|
10
|
Abstract
The cDNA display method is a robust in vitro display technology that converts an unstable mRNA-protein fusion (mRNA display) to a stable mRNA/cDNA-protein fusion (cDNA display) whose cDNA is covalently linked to its encoded protein using a well-designed puromycin linker. We provide technical details for preparing cDNA display molecules and for the synthesis of the puromycin linker for the purpose of screening the functional proteins and peptides.
Collapse
Affiliation(s)
- Shingo Ueno
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | | |
Collapse
|
11
|
Biyani M, Futakami M, Kitamura K, Kawakubo T, Suzuki M, Yamamoto K, Nishigaki K. In Vitro Selection of Cathepsin E-Activity-Enhancing Peptide Aptamers at Neutral pH. INTERNATIONAL JOURNAL OF PEPTIDES 2011; 2011:834525. [PMID: 21527983 PMCID: PMC3064998 DOI: 10.1155/2011/834525] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 01/17/2011] [Indexed: 12/14/2022]
Abstract
The aspartic protease cathepsin E has been shown to induce apoptosis in cancer cells under physiological conditions. Therefore, cathepsin E-activity-enhancing peptides functioning in the physiological pH range are valuable potential cancer therapeutic candidates. Here, we have used a general in vitro selection method (evolutionary rapid panning analysis system (eRAPANSY)), based on inverse substrate-function link (SF-link) selection to successfully identify cathepsin E-activity-enhancing peptide aptamers at neutral pH. A successive enrichment of peptide activators was attained in the course of selection. One such peptide activated cathepsin E up to 260%, had a high affinity (K(D); ∼300 nM), and had physiological activity as demonstrated by its apoptosis-inducing reaction in cancerous cells. This method is expected to be widely applicable for the identification of protease-activity-enhancing peptide aptamers.
Collapse
Affiliation(s)
- Madhu Biyani
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama 338-8570, Japan
- City Area Program Saitama Metropolitan Area, Saitama Small and Medium Enterprises Development Corporation, 2-3-2 Kamiochiai, Chuo-Ku, Saitama 338-0001, Japan
| | - Masae Futakami
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama 338-8570, Japan
- City Area Program Saitama Metropolitan Area, Saitama Small and Medium Enterprises Development Corporation, 2-3-2 Kamiochiai, Chuo-Ku, Saitama 338-0001, Japan
| | - Koichiro Kitamura
- City Area Program Saitama Metropolitan Area, Saitama Small and Medium Enterprises Development Corporation, 2-3-2 Kamiochiai, Chuo-Ku, Saitama 338-0001, Japan
- Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS) Group, Saitama Small Enterprise Promotion Corporation, no. 552 Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama 333-0844, Japan
- Janusys Corporation, no. 508 Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama 333-0844, Japan
| | - Tomoyo Kawakubo
- Proteolysis Research Laboratory, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Miho Suzuki
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama 338-8570, Japan
| | - Kenji Yamamoto
- Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS) Group, Saitama Small Enterprise Promotion Corporation, no. 552 Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama 333-0844, Japan
- Proteolysis Research Laboratory, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Koichi Nishigaki
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama 338-8570, Japan
- City Area Program Saitama Metropolitan Area, Saitama Small and Medium Enterprises Development Corporation, 2-3-2 Kamiochiai, Chuo-Ku, Saitama 338-0001, Japan
- Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS) Group, Saitama Small Enterprise Promotion Corporation, no. 552 Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama 333-0844, Japan
| |
Collapse
|
12
|
Kinoshita Y, Tayama T, Kitamura K, Salimullah M, Uchida H, Suzuki M, Husimi Y, Nishigaki K. Novel concept microarray enabling PCR and multistep reactions through pipette-free aperture-to-aperture parallel transfer. BMC Biotechnol 2010; 10:71. [PMID: 20923572 PMCID: PMC2959086 DOI: 10.1186/1472-6750-10-71] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 10/06/2010] [Indexed: 11/15/2022] Open
Abstract
Background The microarray has contributed to developing the omic analysis. However, as it depends basically on the surface reaction, it is hard to perform bulk reactions and sequential multistep reactions. On the other hand, the popular microplate technology, which has a great merit of being able to perform parallel multistep reactions, has come to its limit in increasing the number of wells (currently, up to 9600) and reducing the volume to deal with due to the difficulty in operations. Results Here, we report a novel microarray technology which enables us to explore advanced applications, termed microarray-with-manageable volumes (MMV). The technical essence is in the pipette-free direct parallel transfer from well to well performed by centrifugation, evading the evaporation and adsorption-losses during handling. By developing the MMV plate, accompanying devices and techniques, generation of multiple conditions (256 kinds) and performance of parallel multistep reactions, including PCR and in vitro translation reactions, have been made possible. These were demonstrated by applying the MMV technology to searching lysozyme-crystallizing conditions and selecting peptides aimed for Aβ-binding or cathepsin E-inhibition. Conclusions With the introduction of a novel concept microarray (MMV) technology, parallel and multistep reactions in sub-μL scale have become possible.
Collapse
Affiliation(s)
- Yasunori Kinoshita
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Aita T. A trade-off relationship between energetic cost and entropic cost for in vitro evolution. Biosystems 2010; 101:194-9. [PMID: 20650304 DOI: 10.1016/j.biosystems.2010.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 07/08/2010] [Accepted: 07/09/2010] [Indexed: 11/28/2022]
Abstract
In this paper, we consider two complementary cost functions for the landscape exploring processes to obtain the global optimum sequence through in vitro evolution protocol: one is the entropic cost C(etp), which is based on the deviation from the uniformity of a mutant distribution in sequence space, and the other is the energetic cost C(eng), which is based on the total number of sequences to be generated and evaluated. Based on a prior knowledge about the structure of a given fitness landscapes, the conductor of the experiment can think up the efficient search algorithm (ESA), which requires the minimum number of points (=sequences) to be searched up to the global optimum. For five typical fitness landscapes, we considered their respective (putative) ESA, C(etp)(*) and C(eng)(*) based on the ESA. As a result, we found a trade-off relationship between C(etp)(*) and C(eng)(*) for every case, that is, C(eng)(*)+C(etp)(*) is approximately equal to the logarithm of the volume of the sequence space. C(etp)(*) and C(eng)(*) are interpreted in terms of the information-theoretic concepts.
Collapse
Affiliation(s)
- Takuyo Aita
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan.
| |
Collapse
|
14
|
Çakar ZP. Metabolic and evolutionary engineering research in Turkey and beyond. Biotechnol J 2009; 4:992-1002. [DOI: 10.1002/biot.200800332] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
15
|
Kitamura K, Yoshida C, Kinoshita Y, Kadowaki T, Takahashi Y, Tayama T, Kawakubo T, Naimuddin M, Salimullah M, Nemoto N, Hanada K, Husimi Y, Yamamoto K, Nishigaki K. Development of systemic in vitro evolution and its application to generation of peptide-aptamer-based inhibitors of cathepsin E. J Mol Biol 2008; 387:1186-98. [PMID: 19150354 DOI: 10.1016/j.jmb.2008.12.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 11/16/2008] [Accepted: 12/11/2008] [Indexed: 12/27/2022]
Abstract
Proteases are involved in various biological functions. Thus, inhibition of their activities is scientifically interesting and medically important. However, there is no systematic method established to date to generate endopeptidase inhibitory peptides. Here, we report a general system to identify endopeptidase inhibitory peptides based on the use of in vitro evolution. Using this system, we generated peptides that inhibit cathepsin E (CE) specifically at a submicromolar IC(50). This system generates protease inhibitor peptides utilizing techniques of cDNA display, selection-by-function, Y-ligation-based block shuffling, and others. We further demonstrated the importance and effectiveness of a secondary library for obtaining small-sized and active peptides. CE inhibitory peptides generated by this method were characterized by a small size (8 to 12 aa) and quite different sequences, suggesting that they bind to different sites on CE. Typical CE inhibitory peptide aptamers obtained here (P(i)101; SCGG IIII SCIA) have half an inhibition activity (K(i); 5 nM) of pepstatin A (potent CE inhibitor) without inhibiting cathepsin D (structurally similar to CE). The general applicability of this system suggests that it may be useful to identify inhibitory peptides for various kinds of proteases and that it may therefore contribute to protein science and drug discovery. The peptide binding to a protein is discussed in comparison with the antibody binding to an antigen.
Collapse
Affiliation(s)
- Koichiro Kitamura
- Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS), Saitama Small Enterprise Promotion Corporation, #552, Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama 333-0844, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Yoshida C, Kuniwake A, Naimuddin M, Nishigaki K. Molecular design guided by a local map of sequence space: DNA aptamers that inhibit cathepsin E. Oligonucleotides 2008; 18:1-8. [PMID: 18321158 DOI: 10.1089/oli.2007.0102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
It has been strongly demanded by a number of people to elevate activities of molecules of a particular function. Currently, there is no general guide available for this purpose. Here we present a novel approach for this; a local sequence space map-directed method for exploring molecules of a higher activity. This approach exploits the knowledge of a local sequence space so far established and obtains the shape of sequence space (map) by intra- and extrapolating the known landscape, which was drawn through the principal coordinates analysis. In this method, we successfully obtained 16 DNA aptamers of cathepsin E (CE) inhibitory activity that have comparable or higher activities than the ancestral ones on which the designed molecules were based. Some of them had a 30% higher activity than the previously reported top one (SFR-6-3). This high efficiency in obtaining functional molecules (16 out of 21 newly designed ones) is by no means usual because most of molecules generated at random are known to have no function, showing the effectiveness of the map-based approach. The selected molecules were confirmed to have the i-motif structure, consistent to the fact that they have a C-rich sequence and their CE-inhibitory activities were measured at an acidic pH, both of which are favorable for the i-motif. This structure of CE-inhibitory aptamers was inferred to contribute to the structural stability but not to the function itself directly.
Collapse
Affiliation(s)
- Chuya Yoshida
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Saitama Japan
| | | | | | | |
Collapse
|
17
|
Klein-Marcuschamer D, Ajikumar PK, Stephanopoulos G. Engineering microbial cell factories for biosynthesis of isoprenoid molecules: beyond lycopene. Trends Biotechnol 2007; 25:417-24. [PMID: 17681626 DOI: 10.1016/j.tibtech.2007.07.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Revised: 05/24/2007] [Accepted: 07/20/2007] [Indexed: 11/23/2022]
Abstract
The isoprenoid superfamily of compounds holds great potential for delivering commercial therapeutics, neutraceuticals and fine chemicals. As such, it has attracted widespread attention and prompted research aimed at metabolic engineering of the pathway for isoprenoid overproduction. The carotenoids in particular, because of their convenient colorimetric screening properties, have facilitated the investigation of new tools for pathway optimization. Because all isoprenoids share common metabolic precursors, genetic platforms resulting from work with carotenoids can be applied to the biosynthesis of other valuable products. In this review we summarize the many tools and methods that have been developed for isoprenoid pathway engineering, and the potential of these technologies for producing other molecules of this family, especially terpenoids.
Collapse
|
18
|
Futakami M, Salimullah M, Miura T, Tokita S, Nishigaki K. Novel Mutation Assay with High Sensitivity based on Direct Measurement of Genomic DNA Alterations: Comparable Results to the Ames Test. ACTA ACUST UNITED AC 2007; 141:675-86. [PMID: 17383979 DOI: 10.1093/jb/mvm074] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Almost all of the methodologies developed to date to assay the potential mutagenicity of chemical substances are based on detection of altered phenotypic traits. The alternative approach of directly screening the whole genome for mutations is not feasible because of the logistics of carrying out mass sequencing of genes. Here we describe a novel and highly sensitive mutation assay, which we term the 'genome profiling-based mutation assay' (GPMA) that directly detects mutations generated in genomic DNA. We used GPMA to detect mutations caused by known mutagens such as AF2 and ethidium bromide even at concentrations of 30 ppb. The number of mutations detected was dependent on the number of generations in culture and the concentrations of the mutagens. Almost complete agreement was observed between GPMA and the Ames test in the discrimination of mutagens (63 out of 64). Owing to the high sensitivity of GPMA, the effects of long-term and low-dose exposures and the influence of chemicals of low solubility can also be screened. Thus, genotype-based GPMA can complement the Ames test, which is the standard technology in this field and is based on phenotypic traits.
Collapse
Affiliation(s)
- Masae Futakami
- Department of Functional Materials Science, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | | | | | | | | |
Collapse
|
19
|
Saito H, Minamisawa T, Shiba K. Motif programming: a microgene-based method for creating synthetic proteins containing multiple functional motifs. Nucleic Acids Res 2007; 35:e38. [PMID: 17287291 PMCID: PMC1874597 DOI: 10.1093/nar/gkm017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The presence of peptide motifs within the proteins provides the synthetic biologist with the opportunity to fabricate novel proteins through the programming of these motifs. Here we describe a method that enables one to combine multiple peptide motifs to generate a combinatorial protein library. With this method, a set of sense and antisense oligonucleotide primers were prepared. These primers were mixed and polymerized, so that the resultant DNA consisted of combinatorial polymers of multiple microgenes created from the stochastic assembly of the sense and antisense primers. With this motif-mixing method, we prepared a protein library from the BH1-4 motifs shared among Bcl-2 family proteins. Among the 41 clones created, 70% of clones had a stable, presumably folded expression product in human cells, which was detectable by immunohistochemistry and western blot. The proteins obtained varied with respect to both the number and the order of the four motifs. The method enables homology-independent polymerization of DNA blocks that coded motif sequences, and the frequency of each motif within a library can be adjusted in a tailor-made manner. This motif programming has a potential for creating a library with a large proportion of folded/functional proteins.
Collapse
Affiliation(s)
- Hirohide Saito
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan and CREST, Japan Science and Technology Agency (JST), c/o Cancer Institute
| | - Tamiko Minamisawa
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan and CREST, Japan Science and Technology Agency (JST), c/o Cancer Institute
| | - Kiyotaka Shiba
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Koto-ku, Tokyo 135-8550, Japan and CREST, Japan Science and Technology Agency (JST), c/o Cancer Institute
- *To whom correspondence should be addressed. +81 3 3570 0489+81 3 3570 0461
| |
Collapse
|
20
|
Naimuddin M, Kitamura K, Kinoshita Y, Honda-Takahashi Y, Murakami M, Ito M, Yamamoto K, Hanada K, Husimi Y, Nishigaki K. Selection-by-function: efficient enrichment of cathepsin E inhibitors from a DNA library. J Mol Recognit 2007; 20:58-68. [PMID: 17173335 DOI: 10.1002/jmr.812] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A method for efficient enrichment of protease inhibitors out of a DNA library was developed by introducing SF-link technology. A two-step selection strategy was designed consisting of the initial enrichment of aptamers based on binding function while the second enrichment step was based on the inhibitory activity to a protease, cathepsin E (CE). The latter was constructed by covalently linking of a biotinylated peptide substrate to each of the ssDNA molecule contained in the preliminarily selected DNA library, generating 'SF-link'. Gradual enrichment of inhibitory DNAs was attained in the course of selection. One molecule, SFR-6-3, showed an IC(50) of around 30 nM, a K(d) of around 15 nM and high selectivity for CE. Sequence and structure analysis revealed a C-rich sequence without any guanine and possibly an i-motif structure, which must be novel to be found in in vitro-selected aptamers. SF-link technology, which is novel as the screening technology, provided a remarkable enrichment of specific protease inhibitors and has a potential to be further developed.
Collapse
Affiliation(s)
- Mohammed Naimuddin
- Rational Evolutionary Design of Advanced Biomolecules (REDS), Saitama Small Enterprise Promotion Corporation, SKIP city, 3-12-18 Kamiaoki, Kawaguchi, Saitama 333-0844, Japan.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Kashiwagi K, Isogai Y, Nishiguchi KI, Shiba K. Frame shuffling: a novel method for in vitro protein evolution. Protein Eng Des Sel 2006; 19:135-40. [PMID: 16415043 DOI: 10.1093/protein/gzj008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe 'frame shuffling', a novel method for preparing artificial protein libraries. With this method, a Y-family DNA polymerase known to introduce frame shift mutations at high rates is utilized to scramble the reading frames of a parental gene. The resultant progeny produce mutant proteins having segmental sequence changes. Such frame-shuffled mutant proteins exhibit physicochemical properties that differ from those of proteins obtained using conventional mutagenesis.
Collapse
Affiliation(s)
- Kenji Kashiwagi
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Ariake, Koto-ku, Tokyo, Japan
| | | | | | | |
Collapse
|
22
|
Chatterjee R, Yuan L. Directed evolution of metabolic pathways. Trends Biotechnol 2006; 24:28-38. [PMID: 16298446 DOI: 10.1016/j.tibtech.2005.11.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2005] [Revised: 09/08/2005] [Accepted: 11/07/2005] [Indexed: 10/25/2022]
Abstract
The modification of cellular metabolism is of biotechnological and commercial significance because naturally occurring metabolic pathways are the source of diverse compounds used in fields ranging from medicine to bioremediation. Directed evolution is the experimental improvement of biocatalysts or cellular properties through iterative genetic diversification and selection procedures. The creation of novel metabolic functions without disrupting the balanced intracellular pool of metabolites is the primary challenge of pathway manipulation. The introduction of coordinated changes across multiple genetic elements, in conjunction with functional selection, presents an integrated approach for the modification of metabolism with benign physiological consequences. Directed evolution formats take advantage of the dynamic structures of genomes and genomic sub-structures and their ability to evolve in multiple directions in response to external stimuli. The elucidation, design and application of genome-restructuring mechanisms are key elements in the directed evolution of cellular metabolic pathways.
Collapse
|
23
|
MURAYAMA S, YOSHIDA C, AOYAMA T, URATA S, NISHIGAKI K. Stochastic Prediction of Peptide Secondary Structure Based on Molecular Dynamics Simulation Performed for Nano-second–Effectiveness of the %stickiness Approach Represented by Triangle Map Mode. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2006. [DOI: 10.2477/jccj.5.213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
24
|
Otten LG, Quax WJ. Directed evolution: selecting today's biocatalysts. ACTA ACUST UNITED AC 2005; 22:1-9. [PMID: 15857778 DOI: 10.1016/j.bioeng.2005.02.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2004] [Revised: 11/21/2004] [Accepted: 11/22/2004] [Indexed: 10/25/2022]
Abstract
Directed evolution has become a full-grown tool in molecular biology nowadays. The methods that are involved in creating a mutant library are extensive and can be divided into several categories according to their basic ideas. Furthermore, both screening and selection can be used to target the enzyme towards the desired direction. Nowadays, this technique is broadly used in two major applications: (industrial) biocatalysis and research. In the first field enzymes are engineered in order to produce suitable biocatalysts with high catalytic activity and stability in an industrial environment. In the latter area methods are established to quickly engineer new enzymes for every possible catalytic step, thereby creating a universal biotechnological toolbox. Furthermore, directed evolution can be used to try to understand the natural evolutionary processes. This review deals with new mutagenesis and recombination strategies published recently. A full overview of new methods for creating more specialised mutant libraries is given. The importance of selection in directed evolution strategies is being exemplified by some current successes including the beta-lactam acylases.
Collapse
Affiliation(s)
- Linda G Otten
- University of Groningen, University Centre for Pharmacy, Pharmaceutical Biology, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | |
Collapse
|
25
|
Abstract
Systematic approaches to directed evolution of proteins have been documented since the 1970s. The ability to recruit new protein functions arises from the considerable substrate ambiguity of many proteins. The substrate ambiguity of a protein can be interpreted as the evolutionary potential that allows a protein to acquire new specificities through mutation or to regain function via mutations that differ from the original protein sequence. All organisms have evolutionarily exploited this substrate ambiguity. When exploited in a laboratory under controlled mutagenesis and selection, it enables a protein to "evolve" in desired directions. One of the most effective strategies in directed protein evolution is to gradually accumulate mutations, either sequentially or by recombination, while applying selective pressure. This is typically achieved by the generation of libraries of mutants followed by efficient screening of these libraries for targeted functions and subsequent repetition of the process using improved mutants from the previous screening. Here we review some of the successful strategies in creating protein diversity and the more recent progress in directed protein evolution in a wide range of scientific disciplines and its impacts in chemical, pharmaceutical, and agricultural sciences.
Collapse
Affiliation(s)
- Ling Yuan
- Department of Plant and Soil Sciences, and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA.
| | | | | | | |
Collapse
|
26
|
Osuna J, Yáñez J, Soberón X, Gaytán P. Protein evolution by codon-based random deletions. Nucleic Acids Res 2004; 32:e136. [PMID: 15459282 PMCID: PMC521680 DOI: 10.1093/nar/gnh135] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2004] [Revised: 09/10/2004] [Accepted: 09/15/2004] [Indexed: 11/14/2022] Open
Abstract
A method to delete in-phase codons throughout a defined target region of a gene has been developed. This approach, named the codon-based random deletion (COBARDE) method, is able to delete complete codons in a random and combinatorial mode. Robustness, automation and fine-tuning of the mutagenesis rate are essential characteristics of the method, which is based on the assembly of oligonucleotides and on the use of two transient orthogonal protecting groups during the chemical synthesis. The performance of the method for protein function evolution was demonstrated by changing the substrate specificity of TEM-1 beta-lactamase. Functional ceftazidime-resistant beta-lactamase variants containing several deleted residues inside the catalytically important omega-loop region were found. The results show that the COBARDE method is a useful new molecular tool to access previously unexplorable sequence space.
Collapse
Affiliation(s)
- Joel Osuna
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología/UNAM, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México
| | | | | | | |
Collapse
|
27
|
Tabuchi I, Soramoto S, Ueno S, Husimi Y. Multi-line split DNA synthesis: a novel combinatorial method to make high quality peptide libraries. BMC Biotechnol 2004; 4:19. [PMID: 15341664 PMCID: PMC520752 DOI: 10.1186/1472-6750-4-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2004] [Accepted: 09/01/2004] [Indexed: 11/30/2022] Open
Abstract
Background We developed a method to make a various high quality random peptide libraries for evolutionary protein engineering based on a combinatorial DNA synthesis. Results A split synthesis in codon units was performed with mixtures of bases optimally designed by using a Genetic Algorithm program. It required only standard DNA synthetic reagents and standard DNA synthesizers in three lines. This multi-line split DNA synthesis (MLSDS) is simply realized by adding a mix-and-split process to normal DNA synthesis protocol. Superiority of MLSDS method over other methods was shown. We demonstrated the synthesis of oligonucleotide libraries with 1016 diversity, and the construction of a library with random sequence coding 120 amino acids containing few stop codons. Conclusions Owing to the flexibility of the MLSDS method, it will be able to design various "rational" libraries by using bioinformatics databases.
Collapse
Affiliation(s)
- Ichiro Tabuchi
- Tokyo Evolution Research Center, 1-1-45-504, Okubo, Shinjuku-ku, Tokyo 169-0072, Japan
- Department of Functional Materials Science, Saitama University,255 Shimo-Okubo, Saitama 338-8570, Japan
| | - Sayaka Soramoto
- Department of Functional Materials Science, Saitama University,255 Shimo-Okubo, Saitama 338-8570, Japan
| | - Shingo Ueno
- Department of Functional Materials Science, Saitama University,255 Shimo-Okubo, Saitama 338-8570, Japan
| | - Yuzuru Husimi
- Department of Functional Materials Science, Saitama University,255 Shimo-Okubo, Saitama 338-8570, Japan
| |
Collapse
|
28
|
|
29
|
|
30
|
Kitamura K, Yoshida C, Nishigaki K. GFPs of insertion mutation generated by molecular size-altering block shuffling. FEBS Lett 2004; 555:483-8. [PMID: 14675760 DOI: 10.1016/s0014-5793(03)01308-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Insertion and deletion analyses of a protein have been less common than point mutation analyses, partly due to the lack in effective methods. This is the case with the green fluorescent protein (GFP), which is so widely applied in molecular biology and other fields. In this paper we first introduce a systematic approach for generating insertion/deletion mutants of GFP. A new technology of Y-ligation-based block shuffling (YLBS) was successfully applied to produce size-altered GFPs, providing insertion-containing GFPs of fluorescence, though no deletion type of fluorescence was obtained so far as examined. The analysis of these proteins suggested that size alteration (deletion/insertion) is acceptable so far as some type of rearrangement in a local structure can accommodate it. This paper demonstrates that YLBS can generate insertion and deletion mutant libraries systematically, which are beneficial in the study of structure-function relationship.
Collapse
Affiliation(s)
- Koichiro Kitamura
- Department of Functional Materials Science, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | | | | |
Collapse
|