Fig. 3
From: Global mRNA decay and 23S rRNA fragmentation in Gluconobacter oxydans 621H
mRNA half-lives versus FPKM expression values and ORF lengths. a Linear regression analysis showed a statistically significant slightly negative correlation (R = −0.24) between the abundance of transcripts and their half-lives. Plots are related to the half-life data obtained for 2500 transcripts (
) with R2 > 0.7 based on the 4 or 3 sampling times as described. Transcripts of the molecular chaperones GroES (GOX1901) and GroEL (GOX1901) exhibited high expression values as well as long half-lives (
). The operons of the F1Fo-type ATP synthase encoded by atpBEFF’ (GOX1110–13) and atpHAGDC (GOX1310–14) (
) belong to the operons/genes with the shortest mRNA half-lives in G. oxydans. In comparison, the transcripts of the second F1Fo-type ATP synthase encoded by GOX2167–75 (
) exhibited almost 2-fold longer half-lives and approximately 80-fold lower expression values. Among the genes of the incomplete TCA cycle (
) the transcript of aconitase of (acn, GOX1335) was the most stable, while the transcripts of malate:quinone oxidoreductase (mqo, GOX2070), dihydrolipoamide succinyl transferase (E2) of 2-oxoglutarate dehydrogenase (odhB, GOX1073), and dihydrolipoamide dehydrogenase (lpd, GOX2292) exhibited the shortest mRNA half-lives. FPKM values were obtained with cells grown on mannitol. b The mRNA half-lives and ORF lengths of 2500 transcripts (
) did not correlate (R = − 0.06)