Regulation of Ribosomal Protein Synthesis in Vibrio cholerae

Abstract

We have investigated the regulation of the S10 and spc ribosomal protein (r-protein) operons in Vibrio cholerae. Both operons are under autogenous control; they are mediated by r-proteins L4 and S8, respectively. Our results suggest that Escherichia coli-like strategies for regulating r-protein synthesis extend beyond the enteric members of the gamma subdivision of proteobacteria.In organisms as diverse as eubacteria, archaea, protist cyanelles, chloroplasts, and mitochondria, clusters of ribosomal protein (r-protein) genes are remarkably similar in organization (10,23,24). In spite of this striking degree of conservation, the mechanisms behind the expression of these genes are clearly diverse, since the positions of promoters and terminators are not well conserved. For example, in Escherichia coli, 28 r-protein genes in the S10-spc-alpha cluster are organized into three transcription units (12), but the corresponding genes in Bacillus subtilis are organized into a single transcription unit (8,11,21).In E. coli, most of the r-proteins are under autogenous control. That is, for a given r-protein operon, a specific rprotein has evolved to function not only as a component of the ribosome, but also as a regulatory protein responsible for coordinating expression of its operon with the availability of rRNA and other r-proteins (28). The 11-gene S10 operon of E. coli is regulated by r-protein L4, a component of the large ribosomal subunit, and encoded by the third gene of the operon. Unlike other autogenously controlled r-protein operons, which are regulated at the level of translation, the S10 operon is subject to both transcriptional and translational regulation (30). The two control mechanisms require partially overlapping but distinct determinants within the 172-base nontranslated region of the S10 mRNA (3,19).Previous studies have suggested that L4 proteins from species as divergent from E. coli as Bacillus stearothermophilus have maintained the determinants required for autogenous control of the S10 operon in E. coli (11,31). However, the autogenous control mechanism itself appears not to be so well conserved. For example, examination of potential secondary structures of RNA upstream of the S10 gene in other eubacterial species suggests that only a subset of species, confined to some members of the gamma branch of proteobacteria, have the structural determinants in the S10 leader that are necessary for L4-mediated autogenous control in E. coli (reference 1 and unpublished data). Moreover, when heterologous S10 leaders which can form those critical secondary structures are introduced into E. coli, they function as regulatory targets for L4, while those that do not have the potential to form the structures found in the E. coli S10 leader do not function as regulatory elements (1, 11).To directly address the mechanism for regulating r-protein synthesis within other eubacteria, we characterized the regulation of the S10 and spc operons in Vibrio cholerae, the most divergent of the gamma proteobacteria we suspected of...

Organization of a partial S10 operon and its transcriptional analysis inFlavobacterium hibernumstrain W22

“…The sequence exhibited a G1C content of 35.7% and consisted of five ORFs (Fig. To form a typical ribosomal protein operon in proteobacteria, the intergenic regions should be larger than 100 bp (Allen et al, 2004). The first ORF encoded a protein of 101 amino acids with homology to the 30S ribosomal protein rpsJ from different gram-positive and gram-negative bacteria (up to 97% identity with F. johnsoniae).…”

“…In spite of this striking similarity, the transcriptional organization of the S10 ribosomal protein genes varies substantially among different bacterial genera. In fact, the organization of many ribosomal protein operons does not follow the 'promoter-structural gene-terminator' paradigm (Allen et al, 2004). This E. coli-type mechanism of S10 operon expression is widespread among the gamma subdivision of the proteobacteria (Allen et al, 1999).…”

“…The bacterial ribosome is comprised of three rRNAs with sedimentation coefficients of 23S, 16S, and 5S and c. 52 ribosomal proteins (r-proteins) that are encoded by genes organized into 19 different operons (Allen et al, 2004). The genes encoding several ribosomal proteins constitute the contiguous transcription units termed the S10, spc (spectinomycin), and alpha operons (Watanabe et al, 1997).…”

Regulation of the rplY gene encoding 5S rRNA binding protein L25 in Escherichia coli and related bacteria

“…This regulatory strategy has been previously demonstrated for many r-protein operons from E. coli and, in some cases, from other bacterial species (Zengel and Lindahl 1994;Allen et al 1999Allen et al , 2004Boni et al 2001;Tchufistova et al 2003;Guillier et al 2005;Aseev et al 2008Aseev et al , 2009Fu et al 2013Fu et al , 2014. However, the overall picture remains incomplete, as information is available only for a half of E. coli r-protein operons.…”

A new regulatory circuit in ribosomal protein operons: S2-mediated control of the rpsB-tsf expression in vivo

“…Given that the hypothetical t44 gene appears to share the promoter with rpsB and, in addition, does not possess any reminiscent of transcription terminator, it seems very likely that the reported conservation actually reflects not the presence of a gene for sRNA with still-unknown functions, but the conservation of the rpsB 59-UTR structure involved in the S2 autoregulation (the rpsB operator). Phylogenetic conservation among g-proteobacteria of the hairpin structures implicated in autogenous control is typical for r-protein mRNAs (Allen et al 1999(Allen et al , 2004Boni et al 2001;Tchufistova et al 2003;Guillier et al 2005), and the rpsB mRNA represents one more prominent example (Fig. 3).…”