Abstract:
Parageobacillus thermoglucosidasius is a metabolically versatile, facultatively anaerobic
thermophile belonging to the family Bacillaceae. Previous studies have shown that this bacterium
harbours co-localised genes coding for a carbon monoxide (CO) dehydrogenase (CODH) and Ni-Fe
hydrogenase (Phc) complex and oxidises CO and produces hydrogen (H2) gas via the water-gas shift
(WGS) reaction. To elucidate the genetic events culminating in the WGS reaction, P. thermoglucosidasius
DSM 6285 was cultivated under an initial gas atmosphere of 50% CO and 50% air and total RNA
was extracted at ~8 (aerobic phase), 20 (anaerobic phase), 27 and 44 (early and late hydrogenogenic
phases) hours post inoculation. The rRNA-depleted fraction was sequenced using Illumina NextSeq,
v2.5, 1x75bp chemistry. Di erential expression revealed that at 8 vs. 20, 20 vs. 27 and 27 vs. 44 h
post inoculation, 2190, 2118 and 231 transcripts were di erentially (FDR < 0.05) expressed. Cluster
analysis revealed 26 distinct gene expression trajectories across the four time points. Of these, two
similar clusters, showing overexpression at 20 relative to 8 h and depletion at 27 and 44 h, harboured
the CODH and Phc transcripts, suggesting possible regulation by O2. The transition between aerobic
respiration and anaerobic growth was marked by initial metabolic deterioration, as reflected by
up-regulation of transcripts linked to sporulation and down-regulation of transcripts linked to
flagellar assembly and metabolism. However, the transcriptome and growth profiles revealed the
reversal of this trend during the hydrogenogenic phase.
Description:
Additional file 1: Table S1: Overview of RNA-seq read metrics of P. thermoglucosidasius DSM 6285. Culture were cultivated in two biological replicates in stoppered serum bottles with an initial gas atmosphere composition of 50% CO and 50% air over four time points. Table S2: Gene ontology (GO) enrichment of differentially. Figure S1: MDS plot showing pattern of transcripts expression in four RNA-seq samples of P. thermoglucosidasius DSM 6285 cultivated in two biological replicates (indicated by ‘_replicate number’) in stoppered serum bottles with an initial gas atmosphere composition of 50% CO and 50% air over four time points. Figure S2: DP_GP_cluster analysis of differentially expressed transcripts of P. thermoglucosidasius DSM 6285 cultivated in stoppered serum bottles with an initial gas atmosphere composition of 50%COand 50% air and samples over four time points. Figure S3. Trajectories of transcripts in the carbon monoxide dehydrogenase (CODH), uptake hydrogenase (Pha and Phb) and H2-evolving hydrogenase (Phc) loci.
Additional file 2: Table S2: Gene ontology (GO) enrichment of differentially expressed genes of P. thermoglucosidasius DSM 6285 at 20 vs. 8 h (P1), 27 vs. 20 h (P2) and 44 vs. 27 h (P3). The organism was grown with an initial gas atmosphere composition of 50% CO and 50% air genes at 20 vs. 8 h (P1), 27 vs. 20 h (P2) and 44 vs. 27 h (P3).
