Trends in Systems Biology for the Analysis and Engineering of Clostridium acetobutylicum Metabolism

Yoo, Minyeong; Nguyen, Ngoc-Phuong-Thao; Soucaille, Philippe

doi:10.1016/j.tim.2019.09.003

Cited by 32 publications

(20 citation statements)

References 102 publications

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“…To address the drawbacks of mutagenesis in theory, various omics technologies (transcriptomics, proteomics, and metabolomics) have been applied to systematically elucidate the complex genotypic/phenotypic changes at different levels [88], providing an amount of targeted genes or proteins that further improve cellular performance by considering the metabolic pathway in its entirety [89].…”

Section: Strain Improvement By Metabolic Engineeringmentioning

confidence: 99%

Pathway dissection, regulation, engineering and application: lessons learned from biobutanol production by solventogenic clostridia

Huang

et al. 2020

Biotechnol Biofuels

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The global energy crisis and limited supply of petroleum fuels have rekindled the interest in utilizing a sustainable biomass to produce biofuel. Butanol, an advanced biofuel, is a superior renewable resource as it has a high energy content and is less hygroscopic than other candidates. At present, the biobutanol route, employing acetone-butanolethanol (ABE) fermentation in Clostridium species, is not economically competitive due to the high cost of feedstocks, low butanol titer, and product inhibition. Based on an analysis of the physiological characteristics of solventogenic clostridia, current advances that enhance ABE fermentation from strain improvement to product separation were systematically reviewed, focusing on: (1) elucidating the metabolic pathway and regulation mechanism of butanol synthesis; (2) enhancing cellular performance and robustness through metabolic engineering, and (3) optimizing the process of ABE fermentation. Finally, perspectives on engineering and exploiting clostridia as cell factories to efficiently produce various chemicals and materials are also discussed.

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Section: Strain Improvement By Metabolic Engineeringmentioning

confidence: 99%

Pathway dissection, regulation, engineering and application: lessons learned from biobutanol production by solventogenic clostridia

Huang

et al. 2020

Biotechnol Biofuels

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“…The characterization of the metabolism of clostridial species and its regulation are the basis of metabolic engineering approaches on the way to high-performance strains for highly efficient industrial solvent production [ 333 ]. By applying omics technologies and metabolic modelling, our understanding of production hosts on the systems level is improved and can guide the rational strain design [ 40 , 326 , 333 ].…”

Section: Systems Biology and Genetic Engineeringmentioning

confidence: 99%

“…While GSM models can describe the general metabolic capabilities of an organism, gene expression varies depending on environmental conditions. The current metabolic phenotype can be accessed on proteome, transcriptome, and metabolome level with single- and multiomics approaches [ 285 , 333 ]. Additionally, fluxomics approaches can use GSM models to calculate and estimate metabolite fluxes.…”

Section: Systems Biology and Genetic Engineeringmentioning

confidence: 99%

“…Continuous cultivation of C. acetobutylicum in a phosphate-limited chemostat allowed the culture to switch from acidogenesis to solventogenesis without triggering sporulation [ 97 ]. The possibility to investigate different metabolic states separately and reproducibly makes continuous cultivation a valuable tool for systems biology studies [ 97 , 332 , 333 ].…”

Section: Systems Biology and Genetic Engineeringmentioning

confidence: 99%

“…Regarding solventogenic clostridia, such phenomena include strain degeneration [ 131 ], solvent tolerance [ 110 ] and the response to inhibitors found in hydrolyzed lignocellulose [ 160 , 176 , 337 ]. A review about systems biology studies of C. acetobutylicum has been published recently and is highly recommended to the reader [ 333 ].…”

Section: Systems Biology and Genetic Engineeringmentioning

confidence: 99%

See 2 more Smart Citations

Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives

Vees

Neuendorf

Pflügl

2020

Journal of Industrial Microbiology and Biotechnology

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The sustainable production of solvents from above ground carbon is highly desired. Several clostridia naturally produce solvents and use a variety of renewable and waste-derived substrates such as lignocellulosic biomass and gas mixtures containing H2/CO2 or CO. To enable economically viable production of solvents and biofuels such as ethanol and butanol, the high productivity of continuous bioprocesses is needed. While the first industrial-scale gas fermentation facility operates continuously, the acetone–butanol–ethanol (ABE) fermentation is traditionally operated in batch mode. This review highlights the benefits of continuous bioprocessing for solvent production and underlines the progress made towards its establishment. Based on metabolic capabilities of solvent producing clostridia, we discuss recent advances in systems-level understanding and genome engineering. On the process side, we focus on innovative fermentation methods and integrated product recovery to overcome the limitations of the classical one-stage chemostat and give an overview of the current industrial bioproduction of solvents.

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An Enhancement of Succinate Production Using a Hybrid of Bacterial Foraging Optimization Algorithm

Siow

Mohamad

Choon

et al. 2021

Proceedings of International Conference on Emerging Technologies and Intelligent Systems

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Genetic modifications, such as gene knockout technique, have become mainstream in metabolic engineering to produce desired amount of targeted metabolites through reconstruction of the metabolic networks. The production, however, does not often achieve desirable outcome. To this end, in-silico methods have been applied to predict potential metabolic network response and optimise production. Previous methods working on relational modelling framework, such as OptKnock and OptGene, however, failed at handling its multivariable and multimodal functions optimization algorithms. This paper proposes hybridising bacterial foraging optimizationg algorithm (BFO) and dynamic flux balance analysis (DFBA) to overcome problems in OptKnock and OptGene with a nature-inspired algorithm and also to couple kinematic variables in the model to predict production of succinate in E.coli model. In-silico results showed that by knocking out genes identifed by BFODFBA, production rate of succinate is better as when compared to OptKnock and OptGene.

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Trends in Systems Biology for the Analysis and Engineering of Clostridium acetobutylicum Metabolism

Cited by 32 publications

References 102 publications

Pathway dissection, regulation, engineering and application: lessons learned from biobutanol production by solventogenic clostridia

Pathway dissection, regulation, engineering and application: lessons learned from biobutanol production by solventogenic clostridia

Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives

An Enhancement of Succinate Production Using a Hybrid of Bacterial Foraging Optimization Algorithm

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