Fig 1.
Fermentation of L. buchneri CD034 grown under aerobic and anaerobic conditions.
The fermentation was separated in three phases: phase 1 represents aerobic, phase 2 anaerobic and phase 3 again aerobic conditions with respect to the oxygen concentration of the gas inlet (O2,in). (A) Gas phase composition during fermentation as described by oxygen and carbon dioxide concentrations in the gas inlet (O2,in, CO2,in) and in the gas outlet (O2,out, CO2,out). (B) pH, dissolved oxygen concentration in the medium (dO2) and optical density (OD). (C) Concentration of carbohydrates glucose, xylose and arabinose and (D) concentration of organic acids lactate and acetate. Fermentations were performed in duplicates. Arrows indicate sampling time points for RNA-Seq. Parameters shown originate from fermenter 1. For fermenter 2 see S1 Fig.
Table 1.
Overview on the sequencing of transcripts (mRNA) isolated from L. buchneri CD034 grown in two replicate fermenter systems under anaerobic vs. aerobic conditions.
Table 2.
The 25 most abundantly transcribed genes of L. buchneri CD034 cultivated under aerobic vs. anaerobic conditions.
Fig 2.
Volcano plot representing transcriptional levels for L. buchneri CD034 genes under aerobic vs. anaerobic conditions.
For each protein encoding gene the −log2(p-value) is plotted against its log2(fold change). Genes up-regulated (p < 0.01) under aerobic conditions are colored blue while down-regulated genes are colored red. Genes found to be located between bacteriophagous attachment sites are colored in yellow (ΦLbu-1) and orange (ΦLbu-2) irrespective of their relative transcriptional levels. For genes with gene names that were found to be highly up- (see Table 3) or down- (see Table 4) regulated the gene name is given. Abbreviations represent gene names: pox2, -3: pyruvate oxidase; lctO: lactate oxidase; hsp1, -2: molecular chaperones; oppA3: oligopeptide transport system, substrate binding protein; arcC3: carbamate kinase; aguA1: agmatine deiminase; pctA: putrescine carbamoyltransferase; gntP: H+/gluconate symporter; gntR: gluconate operon transcriptional regulator; gntK1: gluconokinase; pyrG: CTP synthetase; rihB: ribosylpyrimidine nucleosidase; pgd: 6-phosphogluconate dehydrogenase; adhA: alcohol dehydrogenase; hisD: histidinol dehydrogenase; tagG: teichoic acid permease; tagB, teichoic acid biosynthesis protein; argH: argininosuccinate lyase; nupC: pyrimidine specific nucleoside symporter. For genes lacking gene names the index numbers of their respective locus tags (LBUCD034_XXXX) are given.
Fig 3.
Metabolic pathway chart of gene products encoded by L. buchneri CD034 and metabolites that play a role in heterolactic fermentation.
Genes are represented by their locus tag and the gene name, if applicable. Locus tags and gene names with highlighted background indicate genes that were found to be up-regulated (blue) or down-regulated (red) under aerobic vs. anaerobic conditions. Locus tags and gene names printed in pink indicate genes that were found to be highly transcribed. Pathway end products (yellow) and intermediates (gray) are also highlighted.
Table 3.
Genes of L. buchneri CD034 found to be highly1 up-regulated under aerobic vs. anaerobic conditions.
Table 4.
Genes of L. buchneri CD034 found to be highly1 down-regulated under aerobic vs. anaerobic conditions.