1. Volume 4, Issue 5, Pages 505-515.e5 (May 2017)
Maintenance of ATP Homeostasis Triggers Metabolic Shifts in Gas-Fermenting Acetogens 
Kaspar Valgepea, Renato de Souza Pinto Lemgruber, Kieran Meaghan, Robin William Palfreyman, Tanus Abdalla, Björn Daniel Heijstra, James Bruce Behrendorff, Ryan Tappel, Michael Köpke, Séan Dennis Simpson, Lars Keld Nielsen, Esteban Marcellin 
Cell Systems 
Volume 4, Issue 5, Pages e5 (May 2017)
DOI: /j.cels
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2. Cell Systems 2017 4, 505-515.e5DOI: (10.1016/j.cels.2017.04.008)
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3. Figure 1
Steady-State By-product Patterns in Syngas-Fermenting C. autoethanogenum Chemostats
(A) Four biomass levels studied within the 15 chemostats. Data are represented as the average ± SD between biological replicates indicated by numbers. RPM, rounds per minute.
(B) C-molar by-product yields per biomass for all individual steady states.
(C) Distribution of carbon between acetate and ethanol for all individual steady states.
(D) Carbon balance (CB) for low-, medium-, and high-biomass concentration conditions. Refer to Table 1 for carbon recoveries at each condition.
EtOH, ethanol; 2,3-BDO, 2R,3R-butanediol. See also Figure S1.
Cell Systems 2017 4, e5DOI: ( /j.cels )
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4. Figure 2
Transcriptome Analysis of Steady-State Syngas-Fermenting C. autoethanogenum Chemostats
(A) Differentially expressed transcripts (q < 0.05) between high- and low-biomass chemostats. Refer to (B) for gene IDs and STAR Methods for details on transcript expression fold-change (FC) calculation. See also Table S1.
(B) Hierarchical clustering of the 107 differentially expressed genes. Color denotes expression distance of the average of the respective biomass level from the average of all biomass levels. See also Table S2.
(C) List of tracks for the circular representation of C. autoethanogenum's genome, from outside to inside: chromosomes/contigs; CDS, forward strand; CDS, reverse strand; RNAs; GC content, line plot; GC skew, line plot (left). General features of RNA-sequencing data as visualized in the IGV genome for the bifunctional acetaldehyde/alcohol dehydrogenase (AdhE; RS18395) and the primary acetaldehyde:ferredoxin oxidoreductase (AOR; RS00440) browser for the high-biomass condition (right). Gray shows a wiggle plot of the sequence read coverage at 3,000 reads for RS00440 and 30 reads for RS Lower pane shows the mapping of align reads where pink indicates (+) and blue (−) strand at 1,000 and 30 reads. See also Table S2.
Gene IDs are preceded with CAETHG_.
Cell Systems 2017 4, e5DOI: ( /j.cels )
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5. Figure 3
Central Metabolism Flux and Transcript Levels in Steady-State Syngas-Fermenting C. autoethanogenum Chemostats
See dashed inset for bar chart and heatmap details. Flux data for low- (blue bar) and high- (green) biomass concentrations are represented as the average ± average absolute deviation between two biological replicates, while data for medium (red) is from a single experiment. Arrows show the direction of calculated fluxes; red denotes uptake or secretion. Gene IDs next to heatmaps are preceded with CAETHG_RS. Transcripts forming a protein complex are highlighted with orange borders; FdhA (13,725) forms a complex with HytA–E (13,745–13,770) for direct CO2 reduction with H2. Median RPKM (reads per kilobase of transcript per million mapped reads) are shown for the Rnf and ATPase protein complexes. Refer to Figure S2 for the cofactors of the reactions used in the model. (a) Methylene-THF reductase flux is shown. (b) Transcript abundances for the bifunctional acetaldehyde/alcohol dehydrogenase (acetyl-CoA→ethanol). See Tables S3 and S4 for all flux data (SIM1-5) and Table S2 for all transcript abundances.
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6. Figure 4
Intracellular Metabolite Concentrations in Steady-State Syngas-Fermenting C. autoethanogenum Chemostats
(A) Intracellular redox state with increasing carbon flux into reduced by-products. Refer to Figure 1D for the relation between the biomass concentration and carbon flow into by-products.
(B) Decline of the intracellular acetyl-CoA (AcCoA) pool with increasing flux into AcCoA and biomass concentrations. Data are represented as the average ± average absolute deviation between two biological replicates for flux into AcCoA at two biomass levels. Range of right axis selected to highlight variation.
(C) Distribution of metabolite concentrations among the four studied biomass levels (see Figure 1A). Data are represented as the average ± SD between biological replicates.
Refer to Table S6 for metabolite abbreviations. See also Figure S3 and Table S5.
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7. Figure 5
Regulation of Carbon Distribution and ATP Metabolism through Extracellular Acetate Levels during Autotrophic Growth of C. autoethanogenum
Thickness of arrows and size of circles illustrate the relative difference of the magnitude of fluxes and metabolite pools, respectively, between high- and low-biomass conditions. Purple numbered squares: (1) higher biomass leads to higher levels of extracellular acetic acid; (2) increased uncoupling of the PMF by higher diffusion of acetic acid means higher cellular maintenance costs which demand higher ATP production; (3) ethanol synthesis is increased as ATP production through acetate synthesis needs to increase but its secretion would be detrimental; (4) CO oxidation and dissipation as CO2 is increased to meet the increased demands for Fdred for ATP and ethanol production; (5) the latter leads to less carbon being available for biomass synthesis, i.e., lower biomass yield; (6) increased ATP production through acetate synthesis surpasses the supply of acetyl-CoA from the WLP and depletes the acetyl-CoA pool (see also Figure 4B).
See also Figure S4.
Cell Systems 2017 4, e5DOI: ( /j.cels )
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