RETRACTED: Strategies for design of improved biocatalysts for industrial applications

Madhavan, Aravind; Sindhu, Raveendran; Binod, Parameswaran; Sukumaran, Rajeev; Pandey, Ashok

doi:10.1016/j.biortech.2017.05.031

Cited by 193 publications

(119 citation statements)

References 95 publications

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“…The fact that in the past we have been accessing limited microbial diversity suggests that many desirable enzyme activities may already exist and are accessible through metagenomics‐based activity‐screening protocols . In short, (meta)genome bio‐prospecting has revolutionized enzyme discovery for industrial applications …”

Section: Expanding the Scope And Potential Of Biocatalysismentioning

confidence: 99%

“…[37] In short,( meta)genomeb io-prospecting has revolutionized enzyme discovery [38] forindustrial applications. [39] Most currentc ommercial enzymes originate from mesophilic bacteria or fungi with optimum growth at moderate temperatures (20-45 8C). Microbial exploration has opened up opportunities for exploiting enzymes from unusuale nvironments, such as enzymes from extremophiles.…”

Section: More Enzymes:(meta)genome Miningmentioning

confidence: 99%

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Broadening the Scope of Biocatalysis in Sustainable Organic Synthesis

2019

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This Review is aimed at synthetic organic chemists who may be familiar with organometallic catalysis but have no experience with biocatalysis, and seeks to provide an answer to the perennial question: if it is so attractive, why wasn't it extensively used in the past? The development of biocatalysis in industrial organic synthesis is traced from the middle of the last century. Advances in molecular biology in the last two decades, in particular genome sequencing, gene synthesis and directed evolution of proteins, have enabled remarkable improvements in scope and substantially reduced biocatalyst development times and cost contributions. Additionally, improvements in biocatalyst recovery and reuse have been facilitated by developments in enzyme immobilization technologies. Biocatalysis has become eminently competitive with chemocatalysis and the biocatalytic production of important pharmaceutical intermediates, such as enantiopure alcohols and amines, has become mainstream organic synthesis. The synthetic space of biocatalysis has significantly expanded and is currently being extended even further to include new‐to‐nature biocatalytic reactions.

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Section: Expanding the Scope And Potential Of Biocatalysismentioning

confidence: 99%

Section: More Enzymes:(meta)genome Miningmentioning

confidence: 99%

Broadening the Scope of Biocatalysis in Sustainable Organic Synthesis

2019

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“…To enhance the performance of recombinant proteins, many experimental technologies have been developed, e.g. directed evolution, immobilization, designing better promoters, optimizing codon usage, and changing culture conditions including media and temperature (Agostini, et al, 2012;Madhavan, et al, 2017). However, such empirical optimizations are labor-intensive and time-consuming.…”

Section: Introductionmentioning

confidence: 99%

Structure-aware Protein Solubility Prediction From Sequence Through Graph Convolutional Network And Predicted Contact Map

Chen

Zheng

Zhao

et al. 2020

Preprint

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Motivation: Protein solubility is significant in producing new soluble proteins that can reduce the cost of biocatalysts or therapeutic agents. Therefore, a computational model is highly desired to accurately predict protein solubility from the amino acid sequence. Many methods have been developed, but they are mostly based on the one-dimensional embedding of amino acids that is limited to catch spatially structural information. Results:In this study, we have developed a new structure-aware method to predict protein solubility by attentive graph convolutional network (GCN), where the protein topology attribute graph was constructed through predicted contact maps from the sequence. GraphSol was shown to substantially outperform other sequence-based methods. The model was proven to be stable by consistent R 2 of 0.48 in both the cross-validation and independent test of the eSOL dataset. To our best knowledge, this is the first study to utilize the GCN for sequence-based predictions. More importantly, this architecture could be extended to other protein prediction tasks. Availability: The package is available at http://biomed.nscc-gz.cn Contact:

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“…The advent of novel high-throughput strategies supported by robust modular cloning techniques (Celinska et al 2017; Celińska et al 2018; Engler et al 2008), efficient directed evolution approaches (Dragosits and Mattanovich 2013), and powerful genome editing tools (Sander and Joung 2014; Mans et al 2015; Stovicek et al 2015) allow for generation of numerous variants of the biocatalysts in relatively short time. In spite of great advancement within the field of the biocatalysts generation, high-throughput function-based screening techniques remain the major bottleneck in the novel biocatalysts development pipeline (Quin and Schmidt-Dannert 2012; Madhavan et al 2017). The urgent need for powerful, high-throughput screening methodology was initially realized in the context of directed evolution strategies (Portnoy et al 2011; Tizei et al 2016), which generate large amounts of mutants with uncharacterized genetic background to be screened.…”

Section: Introductionmentioning

confidence: 99%

Rapid micro-assays for amylolytic activities determination: customization and validation of the tests

Borkowska

Białas

Kubiak

et al. 2019

Appl Microbiol Biotechnol

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High-throughput function-based screening techniques remain the major bottleneck in the novel biocatalysts development pipeline. In the present study, we customized protocols for amylolytic activity determination (Somogyi-Nelson and starch-iodine tests) to micro-volume thermalcycler-based assays (linearity range 60–600 μM of reducing sugar, R2 = 0.9855; 0–2 mg/mL of starch, R2 = 0.9921, respectively). Exploitation of a thermalcycler enabled rapid and accurate temperature control, further reduction of reagents and samples volumes, and limited evaporation of the reaction mixtures, meeting several crucial requirements of an adequate enzymatic assay. In the optimized micro-volume Somogyi-Nelson protocol, we were able to reduce the time required for high-temperature heating sixfold (down to 5 min) and further increase sensitivity of the assay (tenfold), when compared to the previous MTP-based protocol. The optimized microassays have complementary scope of specificities: micro-starch-iodine test for endoglucanases, micro-Somogyi-Nelson test for exoglucanases. Due to rapid, micro-volume and high-throughput character, the methods can complement toolbox assisting development of novel biocatalysts and analysis of saccharides-containing samples.Electronic supplementary materialThe online version of this article (10.1007/s00253-018-09610-0) contains supplementary material, which is available to authorized users.

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RETRACTED: Strategies for design of improved biocatalysts for industrial applications

Cited by 193 publications

References 95 publications

Broadening the Scope of Biocatalysis in Sustainable Organic Synthesis

Broadening the Scope of Biocatalysis in Sustainable Organic Synthesis

Structure-aware Protein Solubility Prediction From Sequence Through Graph Convolutional Network And Predicted Contact Map

Rapid micro-assays for amylolytic activities determination: customization and validation of the tests

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