Extensive reshaping of bacterial operons by programmed mRNA decay

Abstract

Bacterial operons synchronize the expression of multiple genes by placing them under the control of a shared promoter. It was previously shown that polycistronic transcripts can undergo differential RNA decay, leaving some genes within the polycistron more stable than others, but the extent of regulation by differential mRNA decay or its evolutionary conservation remains unknown. Here, we find that a substantial fraction of E. coli genes display non-uniform mRNA stoichiometries despite being coded from the same operon. We further show that these altered operon stoichiometries are shaped post-transcriptionally by differential mRNA decay, which is regulated by RNA structures that protect specific regions in the transcript from degradation. These protective RNA structures are generally coded within the protein-coding regions of the regulated genes and are frequently evolutionarily conserved. Furthermore, we provide evidence that differences in ribosome densities across polycistronic transcript segments, together with the conserved structural RNA elements, play a major role in the differential decay process. Our results highlight a major role for differential mRNA decay in shaping bacterial transcriptomes.

Exploring prokaryotic transcription, operon structures, rRNA maturation and modifications using Nanopore-based native RNA sequencing

“…c , Length of 3’ UTRs is based on the prediction of transcription termination sites (TTS) and the comparison to annotated gene ends. Distribution of lengths is shown for Nanopore data sets (purple) and compared to a Term-Seq E. coli Illumina data set (light-green) 108 . d , MEME analysis 45 of extracted sequences upstream of Nanopore-predicted TSS reveals bacterial (position −10) and archaeal-specific promoter elements (BRE: B-recognition element, recognized by transcription factor B, TATA: TATA-box bound by the TATA-binding protein TBP), therefore validating the positions of predicted TSS.…”

Loss of function from widely distributed, synonymous mutations at single codons

“…This is in contrast with other, previous studies that have used T7 RNA polymerase based assays, where the mRNA levels may be mis-estimated as the elongation rate of this polymerase is different from that of E.coli RNA polymerase (24). Moderate increase in the ccdAB mRNA levels relative to WT in most inactive mutants is likely a consequence of de-repression of the operon due to decrease in the CcdA: CcdB ratio (19), rather than being the primary cause for differential protein levels (27). This is in contrast to other studies which demonstrate mRNA levels to be directly correlated with protein levels (24).…”

Phosphate transporter PstSCAB of Campylobacter jejuni is essential for lactate-dependent growth and colonization in chickens

“…Differential stability within a polycistronic mRNA can be controlled through a conserved internal RNA hairpin that protects the transcript from RNA decay (14). The protective RNA structure is often present in the open reading frame of the downstream gene to protect the essential upstream gene from decay (14). Consistent with such a mechanism acting on the pstSCAB operon, we identified a thermodynamically stable hairpin loop structure (ΔG=-27.70) within the protein coding region of pstC gene ( Fig.…”