Directed evolution of cytochrome P450 enzymes for biocatalysis: exploiting the catalytic versatility of enzymes with relaxed substrate specificity

2015 ◽  
Vol 467 (1) ◽  
pp. 1-15 ◽  
Author(s):  
James B.Y.H. Behrendorff ◽  
Weiliang Huang ◽  
Elizabeth M.J. Gillam

Cytochrome P450 enzymes are renowned for their ability to insert oxygen into an enormous variety of compounds with a high degree of chemo- and regio-selectivity under mild conditions. This property has been exploited in Nature for an enormous variety of physiological functions, and representatives of this ancient enzyme family have been identified in all kingdoms of life. The catalytic versatility of P450s makes them well suited for repurposing for the synthesis of fine chemicals such as drugs. Although these enzymes have not evolved in Nature to perform the reactions required for modern chemical industries, many P450s show relaxed substrate specificity and exhibit some degree of activity towards non-natural substrates of relevance to applications such as drug development. Directed evolution and other protein engineering methods can be used to improve upon this low level of activity and convert these promiscuous generalist enzymes into specialists capable of mediating reactions of interest with exquisite regio- and stereo-selectivity. Although there are some notable successes in exploiting P450s from natural sources in metabolic engineering, and P450s have been proven repeatedly to be excellent material for engineering, there are few examples to date of practical application of engineered P450s. The purpose of the present review is to illustrate the progress that has been made in altering properties of P450s such as substrate range, cofactor preference and stability, and outline some of the remaining challenges that must be overcome for industrial application of these powerful biocatalysts.

2020 ◽  
Author(s):  
Li Ma ◽  
Fengwei Li ◽  
Xingwang Zhang ◽  
Hui Chen ◽  
Qian Huang ◽  
...  

AbstractDirected evolution (DE) inspired by natural evolution (NE) has been achieving tremendous successes in protein/enzyme engineering. However, the conventional ‘one-protein-for-one-task’ DE cannot match the ‘multi-proteins-for-multi-tasks’ NE in terms of screening throughput and efficiency, thus often failing to meet the fast-growing demands for biocatalysts with desired properties. In this study, we design a novel ‘multi-enzyme-for-multi-substrate’ (MEMS) DE model and establish the proof-of-concept by running a NE-mimicking and higher-throughput screening on the basis of ‘two-P450s-against-seven-substrates’ (2P×7S) in one pot. With the significantly improved throughput and hit-rate, we witness a series of convergent evolution events of the two archetypal cytochrome P450 enzymes (P450 BM3 and P450cam) in laboratory. Further structural analysis of the two functionally convergent P450 variants provide important insights into how distinct active-sites can reach a common catalytic goal.


2015 ◽  
Vol 51 (12) ◽  
pp. 2208-2224 ◽  
Author(s):  
Gheorghe-Doru Roiban ◽  
Manfred T. Reetz

Cytochrome P450 enzymes (CYPs) have been used for more than six decades as catalysts for the CH-activating oxidative hydroxylation of organic compounds with formation of added-value products.


2006 ◽  
Vol 397 (3) ◽  
pp. 399-406 ◽  
Author(s):  
Scott J. Garforth ◽  
Yan Yun Wu ◽  
Vinayaka R. Prasad

Human and mouse telomerases show a high degree of similarity in both the protein and RNA components. Human telomerase is more active and more processive than the mouse telomerase. There are two key differences between hTR [human TR (telomerase RNA)] and mTR (mouse TR) structures. First, the mouse telomerase contains only 2 nt upstream of its template region, whereas the human telomerase contains 45 nt. Secondly, the template region of human telomerase contains a 5-nt alignment domain, whereas that of mouse has only 2 nt. We hypothesize that these differences are responsible for the differential telomerase activities. Mutations were made in both the hTR and mTR, changing the template length and the length of the RNA upstream of the template, and telomerase was reconstituted in vitro using mouse telomerase reverse transcriptase generated by in vitro translation. We show that the sequences upstream of the template region, with a potential to form a double-stranded helix (the P1 helix) as in hTR, increase telomerase activity. The longer alignment domain increases telomerase activity only in the context of the P1 helix. Thus the TR contributes to regulating the level of activity of mammalian telomerases.


Author(s):  
Inha Cho ◽  
Zhijun Jia ◽  
Frances H. Arnold

<p>Directed evolution of cytochrome P450 enzymes fine-tunes site selectivity of new-to-nature C‒H amidation for modular, sustainable and scalable preparation of enantio-enriched β-, γ- and δ-lactams.<br></p><p></p>


2020 ◽  
Author(s):  
Inha Cho ◽  
Zhijun Jia ◽  
Frances H. Arnold

<p>Please note that this work has been retracted by the authors.</p><p><br></p><p>After publication of the Report “Site-selective enzymatic C‒H amidation for synthesis of diverse lactams” in <i>Science </i>(<i>1, also linked in metadata</i>), efforts to reproduce the work showed that the enzymes do not catalyze the reactions with the activities and selectivities claimed. Careful examination of the first author’s lab notebook then revealed missing contemporaneous entries and raw data for key experiments. The authors therefore have retracted the article from <i>Science</i> and are now retracting the preprint from ChemRxiv. The original paper can be accessed by selecting “Version 1” of the preprint below, or by accessing <a href="https://doi.org/10.26434/chemrxiv.7711418.v1">https://doi.org/10.26434/chemrxiv.7711418.v1</a>. </p><p><br></p><p><b><i> Inha Cho, Zhi-Jun Jia, Frances H. Arnold*</i></b></p><p><b><i><br></i></b></p><p>Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.</p><p><br></p><p>*Corresponding author. Email: [email protected]</p><p><b><br></b></p><p><b>References</b></p><p>1. I. Cho, Z.-J. Jia, F. H. Arnold, <i>Science</i> <b>364</b>, 575 (2019). DOI: 10.1126/science.aaw9068<br></p><p><br></p><p><br></p><p>*******************************************************************************************</p><p><br></p><p>Directed evolution of cytochrome P450 enzymes fine-tunes site selectivity of new-to-nature C‒H amidation for modular, sustainable and scalable preparation of enantio-enriched β-, γ- and δ-lactams.<br></p><p></p>


2019 ◽  
Vol 295 (3) ◽  
pp. 833-849 ◽  
Author(s):  
Zhong Li ◽  
Yuanyuan Jiang ◽  
F. Peter Guengerich ◽  
Li Ma ◽  
Shengying Li ◽  
...  

Cytochrome P450 enzymes (P450s) are broadly distributed among living organisms and play crucial roles in natural product biosynthesis, degradation of xenobiotics, steroid biosynthesis, and drug metabolism. P450s are considered as the most versatile biocatalysts in nature because of the vast variety of substrate structures and the types of reactions they catalyze. In particular, P450s can catalyze regio- and stereoselective oxidations of nonactivated C–H bonds in complex organic molecules under mild conditions, making P450s useful biocatalysts in the production of commodity pharmaceuticals, fine or bulk chemicals, bioremediation agents, flavors, and fragrances. Major efforts have been made in engineering improved P450 systems that overcome the inherent limitations of the native enzymes. In this review, we focus on recent progress of different strategies, including protein engineering, redox-partner engineering, substrate engineering, electron source engineering, and P450-mediated metabolic engineering, in efforts to more efficiently produce pharmaceuticals and other chemicals. We also discuss future opportunities for engineering and applications of the P450 systems.


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