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Biocatalysis and Bioengineering

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (20 February 2023) | Viewed by 9407

Special Issue Editor

Dr. Samuel De Visser

E-Mail Website
Guest Editor
Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
Interests: computational chemistry; density functional theory; QM/MM; reaction mechanisms; biomimetic models; enzyme catalysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Enzymes are versatile catalysts in Nature that are able to convert substrates into useful products using environmentally benign reaction mechanisms. There are still many gaps in the understanding of chemical reaction mechanisms of enzymes and research into these topics is broad. In addition, engineers are using the knowledge of enzymatic reaction mechanisms to engineer these natural systems and give them novel functions, e.g. for the synthesis of biofuels or small compounds such as drugs. This Special Issue will cover the latest achievements and work done in the fields of biocatalysis and bioengineering.

Prof. Dr. Samuel De Visser
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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Keywords

  • enzymatic reaction mechanisms
  • enzyme catalysis
  • bioengineering
  • structure and function of enzymes

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Published Papers (3 papers)

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Research

13 pages, 2819 KiB  
Article
Construction of Biocatalysts Using the P450 Scaffold for the Synthesis of Indigo from Indole
by Yanqing Li, Yingwu Lin, Fang Wang, Jinghan Wang, Osami Shoji and Jiakun Xu
Int. J. Mol. Sci. 2023, 24(3), 2395; https://doi.org/10.3390/ijms24032395 - 25 Jan 2023
Cited by 5 | Viewed by 2376
Abstract
With the increasing demand for blue dyes, it is of vital importance to develop a green and efficient biocatalyst to produce indigo. This study constructed a hydrogen peroxide-dependent catalytic system for the direct conversion of indole to indigo using P450BM3 with the assistance [...] Read more.
With the increasing demand for blue dyes, it is of vital importance to develop a green and efficient biocatalyst to produce indigo. This study constructed a hydrogen peroxide-dependent catalytic system for the direct conversion of indole to indigo using P450BM3 with the assistance of dual-functional small molecules (DFSM). The arrangements of amino acids at 78, 87, and 268 positions influenced the catalytic activity. F87G/T268V mutant gave the highest catalytic activity with kcat of 1402 min−1 and with a yield of 73%. F87A/T268V mutant was found to produce the indigo product with chemoselectivity as high as 80%. Moreover, F87G/T268A mutant was found to efficiently catalyze indole oxidation with higher activity (kcat/Km = 1388 mM−1 min−1) than other enzymes, such as the NADPH-dependent P450BM3 (2.4-fold), the Ngb (32-fold) and the Mb (117-fold). Computer simulation results indicate that the arrangements of amino acid residues in the active site can significantly affect the catalytic activity of the protein. The DFSM-facilitated P450BM3 peroxygenase system provides an alternative, simple approach for a key step in the bioproduction of indigo. Full article
(This article belongs to the Special Issue Biocatalysis and Bioengineering)
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13 pages, 2320 KiB  
Article
Discovery of New Phenylacetone Monooxygenase Variants for the Development of Substituted Indigoids through Biocatalysis
by Nicolás Núñez-Navarro, Javier Salazar Muñoz, Francisco Castillo, César A. Ramírez-Sarmiento, Ignacio Poblete-Castro, Flavia C. Zacconi and Loreto P. Parra
Int. J. Mol. Sci. 2022, 23(20), 12544; https://doi.org/10.3390/ijms232012544 - 19 Oct 2022
Cited by 3 | Viewed by 2607
Abstract
Indigoids are natural pigments obtained from plants by ancient cultures. Romans used them mainly as dyes, whereas Asian cultures applied these compounds as treatment agents for several diseases. In the modern era, the chemical industry has made it possible to identify and develop [...] Read more.
Indigoids are natural pigments obtained from plants by ancient cultures. Romans used them mainly as dyes, whereas Asian cultures applied these compounds as treatment agents for several diseases. In the modern era, the chemical industry has made it possible to identify and develop synthetic routes to obtain them from petroleum derivatives. However, these processes require high temperatures and pressures and large amounts of solvents, acids, and alkali agents. Thus, enzyme engineering and the development of bacteria as whole-cell biocatalysts emerges as a promising green alternative to avoid the use of these hazardous materials and consequently prevent toxic waste generation. In this research, we obtained two novel variants of phenylacetone monooxygenase (PAMO) by iterative saturation mutagenesis. Heterologous expression of these two enzymes, called PAMOHPCD and PAMOHPED, in E. coli was serendipitously found to produce indigoids. These interesting results encourage us to characterize the thermal stability and enzyme kinetics of these new variants and to evaluate indigo and indirubin production in a whole-cell system by HPLC. The highest yields were obtained with PAMOHPCD supplemented with L-tryptophan, producing ~3000 mg/L indigo and ~130.0 mg/L indirubin. Additionally, both enzymes could oxidize and produce several indigo derivatives from substituted indoles, with PAMOHPCD being able to produce the well-known Tyrian purple. Our results indicate that the PAMO variants described herein have potential application in the textile, pharmaceutics, and semiconductors industries, prompting the use of environmentally friendly strategies to obtain a diverse variety of indigoids. Full article
(This article belongs to the Special Issue Biocatalysis and Bioengineering)
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21 pages, 4605 KiB  
Article
Biochemical Basis of Xylooligosaccharide Utilisation by Gut Bacteria
by Ravindra Pal Singh, Raja Bhaiyya, Raksha Thakur, Jayashree Niharika, Chandrajeet Singh, Dimitrios Latousakis, Gerhard Saalbach, Sergey A. Nepogodiev, Praveen Singh, Sukesh Chander Sharma, Shantanu Sengupta, Nathalie Juge and Robert A. Field
Int. J. Mol. Sci. 2022, 23(6), 2992; https://doi.org/10.3390/ijms23062992 - 10 Mar 2022
Cited by 7 | Viewed by 3539
Abstract
Xylan is one of the major structural components of the plant cell wall. Xylan present in the human diet reaches the large intestine undigested and becomes a substrate to species of the gut microbiota. Here, we characterised the capacity of Limosilactobacillus reuteri and [...] Read more.
Xylan is one of the major structural components of the plant cell wall. Xylan present in the human diet reaches the large intestine undigested and becomes a substrate to species of the gut microbiota. Here, we characterised the capacity of Limosilactobacillus reuteri and Blautia producta strains to utilise xylan derivatives. We showed that L. reuteri ATCC 53608 and B. producta ATCC 27340 produced β-D-xylosidases, enabling growth on xylooligosaccharide (XOS). The recombinant enzymes were highly active on artificial (p-nitrophenyl β-D-xylopyranoside) and natural (xylobiose, xylotriose, and xylotetraose) substrates, and showed transxylosylation activity and tolerance to xylose inhibition. The enzymes belong to glycoside hydrolase family 120 with Asp as nucleophile and Glu as proton donor, as shown by homology modelling and confirmed by site-directed mutagenesis. In silico analysis revealed that these enzymes were part of a gene cluster in L. reuteri but not in Blautia strains, and quantitative proteomics identified other enzymes and transporters involved in B. producta XOS utilisation. Based on these findings, we proposed a model for an XOS metabolism pathway in L. reuteri and B. producta strains. Together with phylogenetic analyses, the data also revealed the extended xylanolytic potential of the gut microbiota. Full article
(This article belongs to the Special Issue Biocatalysis and Bioengineering)
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