Genome-Scale Metabolic Model of
            <i>Caldicellulosiruptor bescii</i>
            Reveals Optimal Metabolic Engineering Strategies for Bio-based Chemical Production

Zhang, Ke; Zhao, Weishu; Rodionov, Dmitry A.; Rubinstein, Gabriel M.; Nguyen, Diep N.; Tanwee, Tania N. N.; Crosby, James R.; Bing, Ryan G.; Kelly, Robert M.; Adams, Michael W. W.; Zhang, Ying

doi:10.1128/msystems.01351-20

Cited by 11 publications

(5 citation statements)

References 61 publications

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“…This study elucidated the transcriptional regulatory network and mechanisms controlling expression of CU genes in C. bescii , thereby improving the functional annotations of carbohydrate transporters and catabolic enzymes to inform a metabolic model of C. bescii ( 31 ). The developed C. bescii model containing the targeted reconstruction of CU pathways supports metabolic engineering strategies for this biotechnology-important thermophilic bacterium capable of unpretreated lignocellulose conversion to bioproducts.…”

Section: Resultsmentioning

confidence: 99%

“…As result, the reconstructed regulatory network of CU genes refined and improved a metabolic reconstruction describing how C. bescii degrades plant biomass and obtains carbon and energy for growth via cytoplasmic CU pathways. The refined CU pathway reconstructions were further used to construct the first metabolic model of C. bescii ( 31 ), thus opening opportunities for metabolic engineering of this species to produce bio-based chemicals from plant biomass.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii

et al. 2021

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To develop functional metabolic engineering platforms for nonmodel microorganisms, a comprehensive understanding of the physiological and metabolic characteristics is critical. Caldicellulosiruptor bescii and other species in this genus have untapped potential for conversion of unpretreated plant biomass into industrial fuels and chemicals. The highly interactive and complex machinery used by C. bescii to acquire and process complex carbohydrates contained in lignocellulose was elucidated here to complement related efforts to develop a metabolic engineering platform with this bacterium.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii

et al. 2021

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“…Specifically, Caldicellulosiruptor spp. have only two types of hydrogenases: bifurcating [Fe–Fe] hydrogenase and [Ni–Fe] hydrogenase (Cha et al 2013a , 2016 ; Zhang et al 2021 ). NADH and ferredoxin are catabolized by the bifurcating [Fe–Fe] hydrogenase, resulting in the production of H 2 (Cha et al 2016 ; Zhang et al 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…have only two types of hydrogenases: bifurcating [Fe–Fe] hydrogenase and [Ni–Fe] hydrogenase (Cha et al 2013a , 2016 ; Zhang et al 2021 ). NADH and ferredoxin are catabolized by the bifurcating [Fe–Fe] hydrogenase, resulting in the production of H 2 (Cha et al 2016 ; Zhang et al 2021 ). On the other hand, the [Ni–Fe] hydrogenase is a membrane-bound heterodimer and is widely found in nature (Alfano and Cavazza 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Metabolic engineering of Caldicellulosiruptor bescii for hydrogen production

Cha,

Kim,

Lee

et al. 2024

Appl Microbiol Biotechnol

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Hydrogen is an alternative fuel for transportation vehicles because it is clean, sustainable, and highly flammable. However, the production of hydrogen from lignocellulosic biomass by microorganisms presents challenges. This microbial process involves multiple complex steps, including thermal, chemical, and mechanical treatment of biomass to remove hemicellulose and lignin, as well as enzymatic hydrolysis to solubilize the plant cell walls. These steps not only incur costs but also result in the production of toxic hydrolysates, which inhibit microbial growth. A hyper-thermophilic bacterium of Caldicellulosiruptor bescii can produce hydrogen by decomposing and fermenting plant biomass without the need for conventional pretreatment. It is considered as a consolidated bioprocessing (CBP) microorganism. This review summarizes the basic scientific knowledge and hydrogen-producing capacity of C. bescii. Its genetic system and metabolic engineering strategies to improve hydrogen production are also discussed. Key points • Hydrogen is an alternative and eco-friendly fuel. • Caldicellulosiruptor bescii produces hydrogen with a high yield in nature. • Metabolic engineering can make C. bescii to improve hydrogen production.

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“…Genomescale metabolic models (GSMs), which is based on steady-states of metabolites [18], have been used inform many metabolic engineering requirements [19,20]. For example, Zhang., et al [21] used GSM to examine bottlenecks in ethanol production by Caldicellulosiruptor bescii. Underpinning these computational approaches is the relationship between genotype and phenotype, commonly known as genotype-phenotype relationship [22][23][24][25], where genomic perturbations (such as knockouts) results in changes in the fluxome.…”

Section: Introductionmentioning

confidence: 99%

Consistency between Saccharomyces cerevisiae S288C Genome Scale Models (iND750 and iMM904)

Wong¹,

Sim²,

Ling³

2023

Act Scie Micro

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Saccharomyces cerevisiae is an important experimental organism for industrial and scientific research with S. cerevisiae S288C as the first eukaryote genome sequenced. Genome-scale metabolic models (GSMs) are computational tools to explore metabolic engineering requirements. Currently, there are 2 major GSMs of S. cerevisiae S288C, iND750 and iMM904, which raises the question of whether they are consistent to each other. Here, we compare iND750 and iMM904 by examining the fluxomic changes resulting from single reaction knockouts. 40.5% to 50.3% (n = 637) of the reactions are common in both GSMs. Of which, 64 (10.0% of common reactions, or between 4.1% and 5.2% of the total reactions in each GSM) reaction knockouts resulted in significant fluxomic changes. This is significantly lower (t = -15.882, df = 30, p-value = 3.82E-16) from expected using randomization test, suggesting that iND750 and iMM904 are likely to be consistent with each other from the perspective of common reactions.

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Genome-Scale Metabolic Model of Caldicellulosiruptor bescii Reveals Optimal Metabolic Engineering Strategies for Bio-based Chemical Production

Cited by 11 publications

References 61 publications

Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii

Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii

Metabolic engineering of Caldicellulosiruptor bescii for hydrogen production

Consistency between Saccharomyces cerevisiae S288C Genome Scale Models (iND750 and iMM904)

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