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      Combined Optimization of Codon Usage and Glycine Supplementation Enhances the Extracellular Production of a β-Cyclodextrin Glycosyltransferase from Bacillus sp. NR5 UPM in Escherichia coli

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          Abstract

          Two optimization strategies, codon usage modification and glycine supplementation, were adopted to improve the extracellular production of Bacillus sp. NR5 UPM β-cyclodextrin glycosyltransferase (CGT-BS) in recombinant Escherichia coli. Several rare codons were eliminated and replaced with the ones favored by E. coli cells, resulting in an increased codon adaptation index (CAI) from 0.67 to 0.78. The cultivation of the codon modified recombinant E. coli following optimization of glycine supplementation enhanced the secretion of β-CGTase activity up to 2.2-fold at 12 h of cultivation as compared to the control. β-CGTase secreted into the culture medium by the transformant reached 65.524 U/mL at post-induction temperature of 37 °C with addition of 1.2 mM glycine and induced at 2 h of cultivation. A 20.1-fold purity of the recombinant β-CGTase was obtained when purified through a combination of diafiltration and nickel-nitrilotriacetic acid (Ni-NTA) affinity chromatography. This combined strategy doubled the extracellular β-CGTase production when compared to the single approach, hence offering the potential of enhancing the expression of extracellular enzymes, particularly β-CGTase by the recombinant E. coli.

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          Protein Identification and Analysis Tools on the ExPASy Server

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            Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation.

            To investigate the possible influence of the local rates of translation on protein folding, 16 consecutive rare (in Escherichia coli) codons in the chloramphenicol acetyltransferase (CAT) gene have been replaced by frequent ones. Site-directed silent mutagenesis reduced the pauses in translation of CAT in E. coli S30 extract cell-free system and led to the acceleration of the overall rate of CAT protein synthesis. At the same time, the silently mutated protein (with unaltered protein sequence) synthesized in the E. coli S30 extract system was shown to possess 20% lower specific activity. The data suggest that kinetics of protein translation can affect the in vivo protein-folding pathway, leading to increased levels of protein misfolding.
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              Codon usage: Nature's roadmap to expression and folding of proteins

              Biomedical and biotechnological research relies on processes leading to the successful expression and production of key biological products. High-quality proteins are required for many purposes, including protein structural and functional studies. Protein expression is the culmination of multistep processes involving regulation at the level of transcription, mRNA turnover, protein translation, and post-translational modifications leading to the formation of a stable product. Although significant strides have been achieved over the past decade, advances toward integrating genomic and proteomic information are essential, and until such time, many target genes and their products may not be fully realized. Thus, the focus of this review is to provide some experimental support and a brief overview of how codon usage bias has evolved relative to regulating gene expression levels.
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                Author and article information

                Journal
                Int J Mol Sci
                Int J Mol Sci
                ijms
                International Journal of Molecular Sciences
                MDPI
                1422-0067
                30 May 2020
                June 2020
                : 21
                : 11
                : 3919
                Affiliations
                [1 ]Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; nikmardiana@ 123456unikl.edu.my (N.I.M.N.-P.); mfarhan@ 123456unimap.edu.my (M.F.M.S.); suraini@ 123456upm.edu.my (S.A.-A.); faizal_ibrahim@ 123456upm.edu.my (M.F.I.); ezyana@ 123456upm.edu.my (E.K.B.)
                [2 ]Section of Bioengineering Technology, University Kuala Lumpur Branch Campus Malaysian Institute of Chemical & Bioengineering Technology, Taboh Naning, Alor Gajah 78000, Melaka, Malaysia
                [3 ]School of Bioprocess Engineering, Universiti Malaysia Perlis, Kompleks Pusat Pengajian Jejawi 3, Arau 02600, Perlis, Malaysia
                [4 ]Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang 43400, Selangor, Malaysia; noorjahan@ 123456upm.edu.my
                Author notes
                [* ]Correspondence: yatiramli@ 123456upm.edu.my ; Tel.: +603-97691948
                Author information
                https://orcid.org/0000-0002-4202-9069
                https://orcid.org/0000-0002-4611-1684
                https://orcid.org/0000-0002-5214-225X
                https://orcid.org/0000-0002-8015-8654
                Article
                ijms-21-03919
                10.3390/ijms21113919
                7313058
                32486212
                45562548-e247-41e8-94b9-5f9943bb9b8d
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 25 March 2020
                : 05 May 2020
                Categories
                Article

                Molecular biology
                cyclodextrin glycosyltransferase,codon usage,cyclodextrin,glycine,inducer,extracellular enzyme

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