Harnessing the power of directed evolution to improve genome editing systems

Su, Qiwen; Zhou, Minjie; Cheng, Cristina; Niu, Jia

doi:10.1016/j.cbpa.2021.02.004

Cited by 3 publications

(5 citation statements)

References 56 publications

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“…Due to the limitation of the receptor availability and practicability, the specificity and sensitivity of CRISPR-Cas12a-based biosensors need to be further improved. In addition, the use of evolutionary techniques to screen multiple functional recognition elements or improve various genome editing systems will play an important role in further promoting the research and application of the CRISPR-Cas12a biosensors ( Su et al, 2021 ). Currently, the detection method based on CRISPR-Cas12a is still in the laboratory stage.…”

Section: Challenges and Prospectsmentioning

confidence: 99%

CRISPR/Cas12a-based technology: A powerful tool for biosensing in food safety

Mao

Chen

Wang

et al. 2022

Trends in Food Science & Technology

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Section: Challenges and Prospectsmentioning

confidence: 99%

CRISPR/Cas12a-based technology: A powerful tool for biosensing in food safety

Mao

Chen

Wang

et al. 2022

Trends in Food Science & Technology

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“…因此, CRISPR/Cas9 在放线菌当中的应用仍有很多的不足和阻碍. 这些问题可以通过使用生物信息学工具进行精确设计, 以及人工优化 Cas9 蛋白降低脱靶现象的发生得以解决 [49] . 总之 , 由于 CRISPR/Cas9 系统的灵活性以及其在较短的时间内产生无缝和无标记突变的能力, 基于 CRISPR/Cas9 的基因编辑方法有望超越传统放线菌体系中的常规遗传改造方法, 不仅广泛应用于天然产物的发现和开发, 还将应用于有助于分子生物学、微生物遗传学、合成生物学等学科的深度发展 .…”

Section: 需求与展望unclassified

Application of CRISPR/Cas9 Gene Editing System in Obtaining Natural Products in Actinomycetes

Qiao¹,

Chen²,

Liu³

et al. 2021

Chinese Journal of Organic Chemistry

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As important source of clinical drugs, the natural products in actinomycetes and their derivatives have been developed on a large scale and used in clinical practice. In order to achieve efficient synthesis of active natural products, structural derivation of new natural products, and targeted mining of unknown natural products, researches mainly focus on the biosynthetic gene clusters from actinomycetes, which should be rationally engineered by advanced biotechnology. CRISPR/ Cas, which represents the clustered regularly interspaced short palindromic repeats and the associated protein, is an adaptive immune system developed by some bacteria and archaea in the long-term natural evolution process to resist the invasion of foreign genetic materials. As a representative of gene editing system, the clustered regularly interspaced short palindromic repeats and the associated protein 9 (CRISPR/Cas9) has been widely used in the targeted editing of deoxyribonucleic acid (DNA) fragments, which provides unlimited possibilities for the development of biotechnology. This paper reviews the application of the CRISPR/Cas9 system in the genetic manipulation of actinomycetes, including the recent research progress in capture, editing and reconstruction of gene clusters, in situ homologous recombination and metabolic regulation, which involves the novel CRISPR/Cas9-mediated gene editing methods and the representative successful cases. This paper will provide valuable information for the efficient use of CRISPR/Cas9 to obtain natural products in actinomycetes.

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“…Directed evolution involves methods of controlling the process of evolution to achieve particular goals. In another sense, “it replaces the guesswork of forecasting with a strategic decision‐making process” (Su et al, 2021), or in a different perception, it encourages mistakes to stimulate evolution. Contrasting the natural evolution process, directed evolution encompasses discrete cycles of mutagenesis, transformation, screening or selection, and gene harvesting and manipulation (Wang et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

“…From “TRIZ Forecasting” (the mid‐1980s) to “Directed Evolution” (1994) designation, laboratory (or in vitro) evolution has emerged as one of the most simplified, reliable, and efficient tool for proteins and metabolic pathways engineering (Cobb et al, 2013; Zlotin & Zusman, 2020). While the concept traces back to 1960s, the methodology has expeditiously been evolved during the last decade, resulting in the development of a wide variety of laboratory engineered proteins, biocatalysts, peptides, and small drug molecules with enhanced characteristics such as (a) high substrate specificity; (b) improved stability; (c) better and expanded substrate binding, inhibition, catalytic activity (Kcat) and product tolerance; and/or (d) enhanced gene expression with increased protein yield/overall pathway flux (Bloom et al, 2005; Boersma et al, 2007; Brakmann, 2001; Rubin‐Pitel et al, 2007; Su et al, 2021; Yang et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Forty years of directed evolution and its continuously evolving technology toolbox: A review of the patent landscape

Iqbal¹,

Sadaf

2022

Biotech & Bioengineering

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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. While 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 40 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.

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Harnessing the power of directed evolution to improve genome editing systems

Cited by 3 publications

References 56 publications

CRISPR/Cas12a-based technology: A powerful tool for biosensing in food safety

CRISPR/Cas12a-based technology: A powerful tool for biosensing in food safety

Application of CRISPR/Cas9 Gene Editing System in Obtaining Natural Products in Actinomycetes

Forty years of directed evolution and its continuously evolving technology toolbox: A review of the patent landscape

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