<i>Bacillus subtilis</i> as a robust host for biochemical production utilizing biomass

Park, Seo A; Bhatia, Shashi Kant; Park, Hyun A.; Kim, Seo Yeong; Sudheer, Pamidimarri D. V. N.; Yang, Yung‐Hun; Choi, Kwon‐Young

doi:10.1080/07388551.2021.1888069

Cited by 33 publications

(21 citation statements)

References 106 publications

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“…B. subtilis is one of the most important industrial protein producers and a promising generally recognized as safe (GRAS) chassis for the biosynthesis of various biochemicals ( 29 , 30 ). Here, we show an example on how AutoESD can be used to design editing sequences for engineering B. subtilis to produce meso-2,3-butanediol (2,3-BD), a platform chemical and promising alternative biofuel ( 31 ).…”

Section: Resultsmentioning

confidence: 99%

AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms

Yang

Mao

Wang

et al. 2022

Nucleic Acids Research

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Advances in genetic manipulation and genome engineering techniques have enabled on-demand targeted deletion, insertion, and substitution of DNA sequences. One important step in these techniques is the design of editing sequences (e.g. primers, homologous arms) to precisely target and manipulate DNA sequences of interest. Experimental biologists can employ multiple tools in a stepwise manner to assist editing sequence design (ESD), but this requires various software involving non-standardized data exchange and input/output formats. Moreover, necessary quality control steps might be overlooked by non-expert users. This approach is low-throughput and can be error-prone, which illustrates the need for an automated ESD system. In this paper, we introduce AutoESD (https://autoesd.biodesign.ac.cn/), which designs editing sequences for all steps of genetic manipulation of many common homologous-recombination techniques based on screening-markers. Notably, multiple types of manipulations for different targets (CDS or intergenic region) can be processed in one submission. Moreover, AutoESD has an entirely cloud-based serverless architecture, offering high reliability, robustness and scalability which is capable of parallelly processing hundreds of design tasks each having thousands of targets in minutes. To our knowledge, AutoESD is the first cloud platform enabling precise, automated, and high-throughput ESD across species, at any genomic locus for all manipulation types.

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Section: Resultsmentioning

confidence: 99%

AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms

Yang

Mao

Wang

et al. 2022

Nucleic Acids Research

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“…36 B. subtilis has been well studied for a variety of in vitro industry applications in areas such as pharmaceutical/nutraceutical production, recombinant protein production and secretion, and production of functional peptides and oligopeptides. [37][38][39][40] However, these inducible systems have limited control for both in vitro and in vivo applications due to potential host toxicity, cost and carbon-source dependence. 41 Temperature-sensitive repressors (TSRs) are a class of repressors that bind an operatorpromoter region with temperature dependence and show promise for in vivo control with local heating for localized delivery.…”

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

Magnetothermal control of temperature-sensitive repressors in superparamagnetic iron nanoparticle-coatedBacillus subtilis

Greeson

Madsen

Makela

et al. 2022

Preprint

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Superparamagnetic iron oxide nanoparticles (SPIONs) are used as contrast agents in magnetic resonance imaging (MRI) and magnetic particle imaging (MPI) and resulting images can be used to guide magnetothermal heating. Alternating magnetic fields (AMF) cause local temperature increases in regions with SPIONs, and we investigated the ability of magnetic hyperthermia to regulate temperature-sensitive repressors (TSRs) of bacterial transcription. The TSR, TlpA39, was derived from a Gram-negative bacterium, and used here for thermal control of reporter gene expression in Gram-positive, Bacillus subtilis. In vitro heating of B. subtilis with TlpA39 controlling bacterial luciferase expression, resulted in a 14.6-fold (12-hour; h) and 1.8-fold (1-h) increase in reporter transcripts with a 9.0-fold (12-h) and 11.1-fold (1-h) increase in bioluminescence. To develop magnetothermal control, B. subtilis cells were coated with three SPION variations. Electron microscopy coupled with energy dispersive X-ray spectroscopy revealed an external association with, and retention of, SPIONs on B. subtilis. Furthermore, using long duration AMF we demonstrated magnetothermal induction of the TSRs in SPION-coated B. subtilis with a maximum of 4.6-fold increases in bioluminescence. After intramuscular injections of SPION-coated B. subtilis, histology revealed that SPIONs remained in the same locations as the bacteria. For in vivo studies, 1-h of AMF is the maximum exposure due to anesthesia constraints. Both in vitro and in vivo, there was no change in bioluminescence after 1-h of AMF treatment. Pairing TSRs with magnetothermal energy using SPIONs for localized heating with AMF can lead to transcriptional control that expands options for targeted bacteriotherapies.

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“…Much technological research and many innovations have contributed to the development of whole‐cell biocatalyst (WCB), which has tremendous potential for commercial application to produce biofuels 18,19 . The development of technologies such as omics, protein engineering and flux management using metabolic models has helped to develop microbial strains capable of bio‐transforming non‐native feedstocks into the respective biofuels 20 . This progress in WCB can help to achieve independence from conventional fossil fuel usage, which further can limit environmental deterioration and help in attaining global ecosystem balance 19 …”

Section: Introductionmentioning

confidence: 99%

“…18,19 The development of technologies such as omics, protein engineering and flux management using metabolic models has helped to develop microbial strains capable of bio-transforming nonnative feedstocks into the respective biofuels. 20 This progress in WCB can help to achieve independence from conventional fossil fuel usage, which further can limit environmental deterioration and help in attaining global ecosystem balance. 19 This review focuses on giving a brief background on the concept of WCB, and an overview of the different types of microbial systems developed to produce biofuels.…”

mentioning

confidence: 99%

Whole‐cell biocatalysis: Advancements toward the biosynthesis of fuels

Madavi

Chauhan

Keshri

et al. 2021

Biofuels Bioprod Bioref

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The availability of robust microbial systems has facilitated the implementation of greener technology replacing existing less sustainable chemical technologies. Whole-cell biocatalysis has empowered the biological production of chemicals and biofuels, replacing labor-intensive traditional chemical catalysis. Whole-cell biocatalysis offers new avenues to use sustainable raw/waste biomass as a substrate for biotransformation into industrially important compounds. Using a native or nonnative microbial cell system as a chassis for developing a suitable cell catalyst requires multiple-level adjustments owing to the target product. Enzymes, the critical entity of biocatalysis, are an important factor influencing biocatalysis efficiency; whole cells provide optimal conditions to the enzymes or enzyme cascades for maximum productivity. Advancements in system biology and metabolic engineering techniques have led to the rational design of whole-cell catalysts for the suitable production of green fuels. Traditional enzyme catalysts are limited by issues such as enzyme stability and repeatability, laborious downstream processing and enzyme production technicalities, but whole-cell biocatalysis could bypass those bottlenecks. Thus, the application of whole cells in the catalysis and production of fuels has progressed greatly in the past couple of decades. This review focuses on detailing the concept of whole-cell biocatalysis and its advances in the production of biofuels such as alcohols and fatty acidbased, terpenoid-derived and carbon-free fuels. The technical advancements in various hosts such as Escherichia coli, Saccharomyces cerevisiae, Corynebacterium glutamicum and Synechococcus elongatus to establish whole-cell biocatalysis are summarized. In addition, system engineering toward the optimum production of various biofuels is added to the discussion.

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Bacillus subtilis as a robust host for biochemical production utilizing biomass

Cited by 33 publications

References 106 publications

AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms

AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms

Magnetothermal control of temperature-sensitive repressors in superparamagnetic iron nanoparticle-coatedBacillus subtilis

Whole‐cell biocatalysis: Advancements toward the biosynthesis of fuels

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