The Conserved Dcw Gene Cluster of R. sphaeroides Is Preceded by an Uncommonly Extended 5’ Leader Featuring the sRNA UpsM

Abstract

Cell division and cell wall synthesis mechanisms are similarly conserved among bacteria. Consequently some bacterial species have comparable sets of genes organized in the dcw (division and cell wall) gene cluster. Dcw genes, their regulation and their relative order within the cluster are outstandingly conserved among rod shaped and gram negative bacteria to ensure an efficient coordination of growth and division. A well studied representative is the dcw gene cluster of E. coli. The first promoter of the gene cluster (mraZ1p) gives rise to polycistronic transcripts containing a 38 nt long 5’ UTR followed by the first gene mraZ. Despite reported conservation we present evidence for a much longer 5’ UTR in the gram negative and rod shaped bacterium Rhodobacter sphaeroides and in the family of Rhodobacteraceae. This extended 268 nt long 5’ UTR comprises a Rho independent terminator, which in case of termination gives rise to a non-coding RNA (UpsM). This sRNA is conditionally cleaved by RNase E under stress conditions in an Hfq- and very likely target mRNA-dependent manner, implying its function in trans. These results raise the question for the regulatory function of this extended 5’ UTR. It might represent the rarely described case of a trans acting sRNA derived from a riboswitch with exclusive presence in the family of Rhodobacteraceae.

PcrX, an sRNA derived from the 3′‐ UTR of the Rhodobacter sphaeroides puf operon modulates expression of puf genes encoding proteins of the bacterial photosynthetic apparatus

“…In a global RNAseq analysis we tested the effect of the endoribonuclease RNase E on the transcriptome of R. sphaeroides (GEO Series accession number GSE104278). We compared RNA 5′ends in the wild‐type to the 5′ends in a mutant, which has the endogenous rne gene replaced by a temperature‐sensitive rne from Escherichia coli (Weber et al ., ). Identical growth behavior of the two strains at 32°C indicates that the E. coli enzyme can functionally replace the R. sphaeroides RNase E under these conditions (unpublished data).…”

“…PcrX targets pufX . A. PcrX‐ pufX duplex structure, predicted using the IntaRNA web tool (Mann et al ., ; Wright et al ., ; Busch et al ., ). B.…”

“…The RNAseq data also indicate that RNase E‐dependent cleavage at this site is already impaired at 32°C in the mutant. This observation was also made for the processing of the sRNA UpsM (Weber et al ., ) and is most likely due to the fact that E. coli RNase E cannot completely replace the endogenous RNase E, e.g. in regard to assembly of the degradosome.…”

“…Chao et al ., ). In R. sphaeroides the sRNA SorX was shown to be processed from the 3′ UTR of the RSP_0847 transcript (encoding an OmpR like regulator) (Peng et al ., ), while UpsM is generated from the 5′ UTR of the cell division gene cluster (Weber et al ., ). Both sRNAs are involved in the oxidative stress response of R. sphaeroides and RNase E has an essential role in their maturation.…”

Genome-wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA

“…Based on these matches, we annotated 19 sRNAs with predicted functions ( Tables 2 and S1). There were six riboswitches (including those binding thiamine pyrophosphate and cobalamin), three segments of transfer-mRNA (tmRNA), three segments of the catalytic RNA of ribonuclease P (RNase P RNA), the signal recognition particle (SRP) RNA (ffs), 6S RNA, an α-operon ribosome binding site, the cspA thermoregulator, the upstream sRNA of mraZ (UpsM) 18 and an sRNA homologous to a validated Rhodobacter sphaeroides sRNA (RSs1386). 19 Several sRNAs corresponding to fragments of the tmRNA and the RNase P RNA were predicted due to differences in read depth coverage across the full length of these transcripts.…”