Matching diverse feedstocks to conversion processes for the future bioeconomy

Scown, Corinne D; Baral, Nawa R; Tanjore, Deepti; Rapp, Vi

doi:10.1016/j.copbio.2023.103017

Cited by 2 publications

(1 citation statement)

References 72 publications

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“…These additional precautions will preserve cutset fidelity as enzymatic reactions are translated to encoded genes selected for strain engineering. Algorithms that output potentially overconstrained solutions via strong growth coupling are a powerful approach to obtain strong production phenotypes that are able to meet the stringent titer, rate, and yield demands necessary for an economically viable bioconversion process using renewable carbon streams (41). These approaches will become more valuable as additional catabolic profiles are discovered and introduced into host platforms (35,42,43).…”

Section: Discussionmentioning

confidence: 99%

Bottlenecks in the Implementation of Genome Scale Metabolic Model Based Designs for Bioproduction from Aromatic Carbon Sources

Banerjee,

Menasalvas,

Chen

et al. 2024

Preprint

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Genome scale metabolic models (GSMM) are commonly used to identify gene deletion sets that result in growth coupling, pairing product formation with substrate utilization. While such approaches can improve strain performance beyond levels typically accessible using targeted strain engineering approaches, sustainable feedstocks often pose a challenge for GSMM-based methods due to incomplete underlying metabolic data. Specifically, we address a four-gene deletion design for the lignin-derived non-sugar carbon source, para-coumarate, that proved challenging to implement. We examine the performance of the fully implemented design for p-coumarate to glutamine, a useful biomanufacturing intermediate. In this study glutamine is then converted to indigoidine, an alternative sustainable pigment and a model heterologous product. Through omics, promoter-variation and growth characterization of a fully implemented gene deletion design, we provide evidence that aromatic catabolism in the completed design is rate-limited by fumarate hydratase activity in the citrate cycle and required careful optimization of the final fumarate hydratase protein (PP_0897) expression to achieve growth and production. A metabolic cross-feeding experiment with the completed design strain also revealed an unanticipated nutrient requirement suggesting additional functions for the fumarate hydratase protein. A double sensitivity analysis confirmed a strict requirement for fumarate hydratase activity in the strain where all genes in the growth coupling design have been implemented. While a complete implementation of the design was achieved, this study highlights the challenge of precisely inactivating metabolic reactions encoded by under-characterized proteins especially in the context of multi-gene edits.

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Section: Discussionmentioning

confidence: 99%

Bottlenecks in the Implementation of Genome Scale Metabolic Model Based Designs for Bioproduction from Aromatic Carbon Sources

Banerjee,

Menasalvas,

Chen

et al. 2024

Preprint

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Enhancing Sustainable Energy Through Cutting-Edge Waste Biorefinery Technologies

Lee,

Srinivaas,

et al. 2024

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Biorefineries play a critical role in addressing current global sustainability challenges by converting renewable biomass into valuable products such as biofuels, biochemicals, and bioenergy. The necessity of biorefineries has increased due to the growing demand for eco-friendly alternatives to fossil fuels, mitigating climate change, and reducing environmental impact. Utilizing agricultural byproducts, forest residues, and municipal waste, biorefineries harness feedstock through techniques such as pretreatment, anaerobic digestion, and thermochemical transformation, alongside advanced methods including electrochemical processes, hydrogenation of bio-derived substances, and the implementation of complex biocatalysts within biomass-oriented biorefineries. These processes enhance the efficiency of bioenergy production by breaking down complex biomass into simpler components. The current capacity of biorefineries is expanding globally, with increasing interest in advanced technologies such as gasification, fermentation, and enzymatic conversion. While biorefineries offer significant potential for reducing waste and promoting a circular economy, challenges such as scalability and cost efficiency remain. Future trends include integrating new biotechnological advances and optimizing resource recovery systems to improve yield, profitability, and sustainability in the bioeconomy.

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Matching diverse feedstocks to conversion processes for the future bioeconomy

Cited by 2 publications

References 72 publications

Bottlenecks in the Implementation of Genome Scale Metabolic Model Based Designs for Bioproduction from Aromatic Carbon Sources

Bottlenecks in the Implementation of Genome Scale Metabolic Model Based Designs for Bioproduction from Aromatic Carbon Sources

Enhancing Sustainable Energy Through Cutting-Edge Waste Biorefinery Technologies

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