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.
Highlights
There are only rare cases for highly conserved gene clusters throughout bacterial genomes due to evolutionary dynamics
The sRNA UpsM was described as the most abundant orphan sRNA of R. sphaeroides, which is encoded in the intergenic region (IGR) upstream of mraZ, the first gene of the dcw gene cluster
The terminator of UpsM has to allow read-throughs in order to guarantee transcription of mraZ. This has several consequences: 1.) mraZ or the dcw gene cluster have an uncommonly long 5’ UTR of 268 nt in length, which has not been reported for other bacterial dcw clusters, which show high conservation among rod shaped and gram negative bacteria. 2.) UpsM is not an sRNA derived from an IGR, but rather an sRNA which is generated by transcription termination within the 5’
Summary
There are only rare cases for highly conserved gene clusters throughout bacterial genomes due to evolutionary dynamics. Examples for such clusters are genes for ribosomal proteins, the atp operon or the dcw (division and cell wall) gene cluster [1]. Conservation of dcw genes, their regulation and especially their arrangement within the cluster are outstandingly conserved within bacterial groups of similar taxon and cell shape [2]. Besides regulatory mechanisms the conserved order of the genes may ensure an efficient coordination of growth and PLOS ONE | DOI:10.1371/journal.pone.0165694. The Dcw Gene Cluster of R. sphaeroides Features an Extended 5’ Leader (LW). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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