Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy

Pavan, Marilene; Reinmets, Kristina; Garg, Shivani; Mueller, Alexander P.; Marcellin, Esteban; Köpke, Michael; Valgepea, Kaspar

doi:10.1016/j.ymben.2022.01.015

Cited by 45 publications

(36 citation statements)

References 251 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, improved recycling of solid waste (e.g., municipal solid waste [MSW], plastic waste) is becoming increasingly important to maintain biosustainability. Gas fermentation offers a sustainable route for the production of renewable chemicals and fuels by recycling gaseous one-carbon (C1) waste feedstocks using gas-fermenting organisms [e.g., industrial waste gases, syngas from gasified MSW or biomass (CO + H 2 +CO 2 )] ( Liew et al, 2016 ; Redl et al, 2017 ; Fackler et al, 2021 ; Pavan et al, 2022 ). Acetogen bacteria are particularly attractive for gas fermentation as they can accept gas (CO) as their sole energy and carbon source ( Wood 1991 ) and use the most efficient pathway to fix CO 2 ( Drake et al, 2006 ; Fast and Papoutsakis 2012 ; Cotton et al, 2018 ), the Wood-Ljungdahl pathway (WLP) ( Wood 1991 ; Ragsdale and Pierce, 2008 ).…”

Section: Introductionmentioning

confidence: 99%

“…Acetogen bacteria are particularly attractive for gas fermentation as they can accept gas (CO) as their sole energy and carbon source ( Wood 1991 ) and use the most efficient pathway to fix CO 2 ( Drake et al, 2006 ; Fast and Papoutsakis 2012 ; Cotton et al, 2018 ), the Wood-Ljungdahl pathway (WLP) ( Wood 1991 ; Ragsdale and Pierce, 2008 ). Acetogens can natively convert carbon into acetic acid, ethanol, or 2,3-butanediol among other products while metabolic engineering for expanding their product spectrum is advancing rapidly ( Köpke and Simpson 2020 ; Bourgade et al, 2021 ; Fackler et al, 2021 ; Pavan et al, 2022 ). Notably, the acetogen Clostridium autoethanogenum is used as a commercial-scale gas fermentation cell factory ( Köpke and Simpson, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Faster Growth Enhances Low Carbon Fuel and Chemical Production Through Gas Fermentation

Lima

Ingelman

Brahmbhatt

et al. 2022

Front. Bioeng. Biotechnol.

Self Cite

View full text Add to dashboard Cite

Gas fermentation offers both fossil carbon-free sustainable production of fuels and chemicals and recycling of gaseous and solid waste using gas-fermenting microbes. Bioprocess development, systems-level analysis of biocatalyst metabolism, and engineering of cell factories are advancing the widespread deployment of the commercialised technology. Acetogens are particularly attractive biocatalysts but effects of the key physiological parameter–specific growth rate (μ)—on acetogen metabolism and the gas fermentation bioprocess have not been established yet. Here, we investigate the μ-dependent bioprocess performance of the model-acetogen Clostridium autoethanogenum in CO and syngas (CO + CO2+H2) grown chemostat cultures and assess systems-level metabolic responses using gas analysis, metabolomics, transcriptomics, and metabolic modelling. We were able to obtain steady-states up to μ ∼2.8 day−1 (∼0.12 h−1) and show that faster growth supports both higher yields and productivities for reduced by-products ethanol and 2,3-butanediol. Transcriptomics data revealed differential expression of 1,337 genes with increasing μ and suggest that C. autoethanogenum uses transcriptional regulation to a large extent for facilitating faster growth. Metabolic modelling showed significantly increased fluxes for faster growing cells that were, however, not accompanied by gene expression changes in key catabolic pathways for CO and H2 metabolism. Cells thus seem to maintain sufficient “baseline” gene expression to rapidly respond to CO and H2 availability without delays to kick-start metabolism. Our work advances understanding of transcriptional regulation in acetogens and shows that faster growth of the biocatalyst improves the gas fermentation bioprocess.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Faster Growth Enhances Low Carbon Fuel and Chemical Production Through Gas Fermentation

Lima

Ingelman

Brahmbhatt

et al. 2022

Front. Bioeng. Biotechnol.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Exploring the physiological boundaries of acetogens has been informative for understanding regulation of their energy-limited metabolism (Valgepea et al, 2017a; Mahamkali et al, 2020; Jin et al, 2021; Klask et al, 2020). Additionally, various bioprocess approaches, multi-omics analysis, construction of metabolic models, and development of genetic tools are being pursued for development of cell factories with enhanced substrate conversion, product distribution, and expanded product spectrum (Valgepea et al, 2018; Lemgruber et al, 2019; Heffernan et al, 2020; Smith et al, 2020; Fackler et al, 2021; Jin et al, 2021; Bourgade et al, 2021; Diender et al, 2021; Molitor et al, 2019; Pavan et al, 2022). Notably, the effects of μ on acetogen metabolism and the gas fermentation bioprocess have not been established.…”

Section: Discussionmentioning

confidence: 99%

“…Acetogen bacteria are particularly attractive for gas fermentation as they accept gas as their sole energy and carbon source (Wood 1991) and use the most efficient pathway to fix CO 2 (Drake 2006; Fast and Papoutsakis 2012; Cotton et al, 2018), the Wood-Ljungdahl pathway (WLP) (Wood 1991; Ragsdale and Pierce, 2008). Acetogens generally convert carbon into acetic acid, ethanol, or 2,3-butanediol while metabolic engineering for expanding their product spectrum is advancing rapidly (Bourgade et al, 2021; Köpke and Simpson 2020; Fackler et al, 2021; Pavan et al, 2022). Notably, the acetogen Clostridium autoethanogenum is used as a commercial-scale gas fermentation cell factory (Köpke and Simpson, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Gas fermentation offers a sustainable route for the production of renewable chemicals and fuels by recycling gaseous one-carbon (C1) waste feedstocks using gas-fermenting organisms (e.g. industrial waste gases, syngas from gasified MSW or biomass [CO+H 2 +CO 2 ]) (Liew et al, 2016; Redl et al, 2017; Fackler et al, 2021; Pavan et al, 2022). Acetogen bacteria are particularly attractive for gas fermentation as they accept gas as their sole energy and carbon source (Wood 1991) and use the most efficient pathway to fix CO 2 (Drake 2006; Fast and Papoutsakis 2012; Cotton et al, 2018), the Wood-Ljungdahl pathway (WLP) (Wood 1991; Ragsdale and Pierce, 2008).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Faster growth enhances low carbon fuel and chemical production through gas fermentation

Lima

Ingelman

Brahmbhatt

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

Gas fermentation offers both fossil carbon-free sustainable production of fuels and chemicals and recycling of gaseous and solid waste using gas-fermenting microbes. Bioprocess development, systems-level analysis of biocatalyst metabolism, and engineering of cell factories are advancing the widespread deployment of the commercialised technology. Acetogens are particularly attractive biocatalysts but effects of the key physiological parameter – specific growth rate (μ) – on acetogen metabolism and the gas fermentation bioprocess have not been established yet. Here, we investigate the (μ-dependent bioprocess performance of the model-acetogen Clostridium autoethanogenum in CO and syngas (CO+CO2+H2) grown chemostat cultures and assess systems-level metabolic responses using gas analysis, metabolomics, transcriptomics, and metabolic modelling. We were able to obtain steady-states up to μ ~2.8 day-1 (~0.12 h-1) and show that faster growth supports both higher yields and productivities for reduced by-products ethanol and 2,3-butanediol. Transcriptomics data revealed differential expression of 1,337 genes with increasing (μ) and suggest that C. autoethanogenum uses transcriptional regulation to a large extent for facilitating faster growth. Metabolic modelling showed significantly increased fluxes for faster growing cells that were, however, not accompanied by gene expression changes in key catabolic pathways for CO and H2 metabolism. Cells thus seem to maintain sufficient 'baseline' gene expression to rapidly respond to CO and H2 availability without delays to kick-start metabolism. Our work advances understanding of transcriptional regulation in acetogens and shows that faster growth of the biocatalyst improves the gas fermentation bioprocess.

show abstract

From Rags to Riches: Exploiting the Calvin‐Benson‐Bassham Cycle for Biomanufacturing

Federici,

Orsi,

Nikel

2023

ChemCatChem

View full text Add to dashboard Cite

Industrial chemical production largely relies on fossil fuels, resulting in the unavoidable release of carbon dioxide (CO2) into the atmosphere. The concept of a circular carbon bioeconomy has been proposed to address this issue, wherein CO2 is captured and used as raw material for manufacturing new chemicals. Microbial cell factories and, in particular, autotrophic microorganisms capable of utilizing CO2 as the sole carbon source, emerged as potential catalysts for upcycling CO2 to valuable products. The Calvin‐Benson‐Bassham cycle (CBBc), the best‐known CO2 fixation pathway, is widely distributed in Nature. While extensively studied, microbial engineering programmes based on the CBBc remains relatively underexplored. In this review, we discuss avenues towards biotechnological exploitation of the CBBc to engineer CO2‐utilizing microbial cell factories, with a focus on chemically‐derived electron donors. We also highlight the advantages and challenges of implementing the CBBc in heterotrophic microbial hosts and its potential to advance a true circular carbon bioeconomy. Moreover, based on the pathway’s architecture, we argue about the ideal value‐added products to generate from this metabolic route. Studying and engineering the CBBc in both natural‐ and synthetic‐autotrophs will enhance our understanding on this CO2 fixation pathway, enabling further exploration of biomanufacturing avenues with CO2 as feedstock.

show abstract

Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy

Cited by 45 publications

References 251 publications

Faster Growth Enhances Low Carbon Fuel and Chemical Production Through Gas Fermentation

Faster Growth Enhances Low Carbon Fuel and Chemical Production Through Gas Fermentation

Faster growth enhances low carbon fuel and chemical production through gas fermentation

From Rags to Riches: Exploiting the Calvin‐Benson‐Bassham Cycle for Biomanufacturing

Contact Info

Product

Resources

About