Understanding the C4 dicarboxylic acid metabolism in Clostridium autoethanogenum

The acetogenic bacterium Clostridium autoethanogenum possesses the inherent ability to produce acetate and ethanol during growth on industrial waste gases such as carbon monoxide and carbon dioxide using the Wood-Ljungdahl Pathway (WLP) for carbon fixation. With the urgent need to reduce greenhouse gas emissions and produce chemicals and fuels in a more sustainable manner, autotrophic organisms such as C. autoethanogenum have received considerable industrial interest over recent years. However, the metabolic pathways present in C. autoethanogenum and therefore its capability to produce industrial relevant carbon building-blocks and biofuels have not yet been sufficiently examined. Therefore, the investigation of pathways leading to the production of industrially relevant carbon building blocks is seen as a worthwhile undertaking at the interface of fundamental and applied research. In this project, the metabolism of C4 dicarboxylic acids in C. autoethanogenum in conjunction with the production of succinate was investigated. This analysis revealed a previously unrecognised carbon and energy source, fumarate, and unveiled the combination of the autotrophic WLP with reactions of the branched tricarboxylic acid (TCA), Krebs “cycle” using in vivo NMR techniques. Under the conditions employed, the reducing equivalents gained from the oxidative breakdown of fumarate to acetate were used to partially re-assimilate the CO2 that was liberated during that process. Accordingly, inactivation of the fumarate hydratase led to a disruption of fumarate metabolism. Additionally, through the introduction of a fumarate reductase and its overexpression in the organism, the resulting strain was able to produce succinate in amounts of up to 3.54 g l-1 and yields of up to 0.78 g g-1 fumarate. This study therefore presents an essential basis for the possible establishment of succinate production with C. autoethanogenum and a better understanding of its C4 dicarboxylic acid metabolism

A genome-scale model of Clostridium autoethanogenum reveals optimal bioprocess conditions for high-value chemical production from carbon monoxide

Clostridium autoethanogenum is an industrial microbe used for the commercial-scale production of ethanol from carbon monoxide. While significant progress has been made in the attempted diversification of this bioprocess, further improvements are desirable, particularly in the formation of the high-value platform chemicals, such as 2,3-butanediol. A new, experimentally parameterised genome scale model of C. autoethanogenum predicts dramatically increased 2,3-butanediol production under non-carbon-limited conditions when thermodynamic constraints on hydrogen production are considered

Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

Clostridium autoethanogenum is an acetogenic bacterium capable of producing high value commodity chemicals and biofuels from the C1 gases present in synthesis gas. This common industrial waste gas can act as the sole energy and carbon source for the bacterium that converts the low value gaseous components into cellular building blocks and industrially relevant products via the action of the reductive acetyl-CoA (Wood-Ljungdahl) pathway. Current research efforts are focused on the enhancement and extension of product formation in this organism via synthetic biology approaches. However, crucial to metabolic modelling and directed pathway engineering is a reliable and comprehensively annotated genome sequence

Understanding the C4 dicarboxylic acid metabolism in Clostridium autoethanogenum

The acetogenic bacterium Clostridium autoethanogenum possesses the inherent ability to produce acetate and ethanol during growth on industrial waste gases such as carbon monoxide and carbon dioxide using the Wood-Ljungdahl Pathway (WLP) for carbon fixation. With the urgent need to reduce greenhouse gas emissions and produce chemicals and fuels in a more sustainable manner, autotrophic organisms such as C. autoethanogenum have received considerable industrial interest over recent years. However, the metabolic pathways present in C. autoethanogenum and therefore its capability to produce industrial relevant carbon building-blocks and biofuels have not yet been sufficiently examined. Therefore, the investigation of pathways leading to the production of industrially relevant carbon building blocks is seen as a worthwhile undertaking at the interface of fundamental and applied research. In this project, the metabolism of C4 dicarboxylic acids in C. autoethanogenum in conjunction with the production of succinate was investigated. This analysis revealed a previously unrecognised carbon and energy source, fumarate, and unveiled the combination of the autotrophic WLP with reactions of the branched tricarboxylic acid (TCA), Krebs “cycle” using in vivo NMR techniques. Under the conditions employed, the reducing equivalents gained from the oxidative breakdown of fumarate to acetate were used to partially re-assimilate the CO2 that was liberated during that process. Accordingly, inactivation of the fumarate hydratase led to a disruption of fumarate metabolism. Additionally, through the introduction of a fumarate reductase and its overexpression in the organism, the resulting strain was able to produce succinate in amounts of up to 3.54 g l-1 and yields of up to 0.78 g g-1 fumarate. This study therefore presents an essential basis for the possible establishment of succinate production with C. autoethanogenum and a better understanding of its C4 dicarboxylic acid metabolism

Additional file 1: of Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

Discrepancies occurring between the current and Brown et al. finished genome sequence of C. autoethanogenum. This table shows all of the discrepancies that occur when our finished genome sequence (CLAU) is mapped against the Brown et al. finished genome sequence (BRO). Mutation column describes the mutation occurring in the CLAU genome compared to the BRO genome. Gene / region gives the gene name where the discrepancy occurs, ← / ← or similar denotes that the discrepancy occurred in a non-coding region between the named genes. Homopolymer length indicates the number of the same base occurring consecutively at the site of the discrepancy. Amino acid length gives the annotated protein length of the gene in which the discrepancy occurs, *indicates protein codes for multiple stop codons and ^indicates that no stop codon was found in the annotation. The sequence identity is relative to the CLAU C. autoethanogenum genome sequence when protein BLAST searched on the NCBI database. CLAU, C. autoethanogenum finished genome sequence in present study; CLJU, C. ljungdahlii DSM 13528 finished genome sequence (GCA_000143685.1); BRO, Brown et al. C. autoethanogenum finished genome sequence (GCA_000484505.1); CAUT, Bruno-Barcena et al. C. autoethanogenum draft genome sequence (GCA_000427255.1); NF, not found. (DOCX 73 kb