RNase III cleavage is obligate for maturation but not for function of Escherichia coli pre-23S rRNA

RNase III participates in control of quorum sensing, pigmentation and oxidative stress resistance in Rhodobacter sphaeroides

RNase III is a dsRNA-specific endoribonuclease, highly conserved in bacteria and eukarya. In this study, we analysed the effects of inactivation of RNase III on the transcriptome and the phenotype of the facultative phototrophic α-proteobacterium Rhodobacter sphaeroides. RNA-seq revealed an unexpectedly high amount of genes with increased expression located directly downstream to the rRNA operons. Chromosomal insertion of additional transcription terminators restored wild type-like expression of the downstream genes, indicating that RNase III may modulate the rRNA transcription termination in R. sphaeroides. Furthermore, we identified RNase III as a major regulator of quorum-sensing autoinducer synthesis in R. sphaeroides. It negatively controls the expression of the autoinducer synthase CerI by reducing cerI mRNA stability. In addition, RNase III inactivation caused altered resistance against oxidative stress and impaired formation of photosynthetically active pigment-protein complexes. We also observed an increase in the CcsR small RNAs that were previously shown to promote resistance to oxidative stress. Taken together, our data present interesting insights into RNase III-mediated regulation and expand the knowledge on the function of this important enzyme in bacteria.

Maturation of the E. coli Glu2, Ile1 and Ala1B tRNAs utilizes a complex processing pathway

Despite significant progress in understanding the diversity of tRNA processing pathways in Escherichia coli, the mechanism for the maturation of tRNAs encoded within the rRNA operons has not received much attention. Here we show that the Glu2, Ile1 and Ala1B tRNAs, encoded by 10 genes located between the 16S and 23S rRNAs in the seven rRNA operons, are matured via a RNase E-independent processing pathway that utilizes at least six different enzymes. It has been shown that the Glu2 and Ile1-Ala1B pre-tRNAs released by initial RNase III cleavages of the 30S primary rRNA transcripts retain extended 5'-leader (35-139 nt) and 3'-trailer (166-185 nt) sequences. However, the 5' maturation of the tRNAs by RNase P is inhibited until the trailer sequences are shortened to 1-4 nucleotides, initially by a second RNase III cleavage at 31-42 nucleotides downstream of the CCA determinant followed by exonucleolytic trimming. The RNase III cleaved Glu2 and Ile1-Ala1B trailer fragments are degraded via PAP I- dependent exonucleolytic decay. Compared to the six previously characterized tRNA processing pathways, maturation of the Glu2, Ile1, and Ala1B tRNAs is considerably more complex and appears to be distinct from what occurs in Gram-positive bacteria.

Regulation of mRNA decay in E. coli

Detailed studies of the Gram-negative model bacterium, Escherichia coli, have demonstrated that post-transcriptional events exert important and possibly greater control over gene regulation than transcription initiation or effective translation. Thus, over the past 30 years, considerable effort has been invested in understanding the pathways of mRNA turnover in E. coli. Although it is assumed that most of the ribonucleases and accessory proteins involved in mRNA decay have been identified, our understanding of the regulation of mRNA decay is still incomplete. Furthermore, the vast majority of the studies on mRNA decay have been conducted on exponentially growing cells. Thus, the mechanism of mRNA decay as currently outlined may not accurately reflect what happens when cells find themselves under a variety of stress conditions, such as, nutrient starvation, changes in pH and temperature, as well as a host of others. While the cellular machinery for degradation is relatively constant over a wide range of conditions, intracellular levels of specific ribonucleases can vary depending on the growth conditions. Substrate competition will also modulate ribonucleolytic activity. Post-transcriptional modifications of transcripts by polyadenylating enzymes may favor a specific ribonuclease activity. Interactions with small regulatory RNAs and RNA binding proteins add additional complexities to mRNA functionality and stability. Since many of the ribonucleases are found at the inner membrane, the physical location of a transcript may help determine its half-life. Here we discuss the properties and role of the enzymes involved in mRNA decay as well as the multiple factors that may affect mRNA decay under various in vivo conditions.

RNase III, Ribosome Biogenesis and Beyond

The ribosome is the universal catalyst for protein synthesis. Despite extensive studies, the diversity of structures and functions of this ribonucleoprotein is yet to be fully understood. Deciphering the biogenesis of the ribosome in a step-by-step manner revealed that this complexity is achieved through a plethora of effectors involved in the maturation and assembly of ribosomal RNAs and proteins. Conserved from bacteria to eukaryotes, double-stranded specific RNase III enzymes play a large role in the regulation of gene expression and the processing of ribosomal RNAs. In this review, we describe the canonical role of RNase III in the biogenesis of the ribosome comparing conserved and unique features from bacteria to eukaryotes. Furthermore, we report additional roles in ribosome biogenesis re-enforcing the importance of RNase III.

A versatile cis-acting element reporter system to study the function, maturation and stability of ribosomal RNA mutants in archaea

General molecular principles of ribosome biogenesis have been well explored in bacteria and eukaryotes. Collectively, these studies have revealed important functional differences and few similarities between these processes. Phylogenetic studies suggest that the information processing machineries from archaea and eukaryotes are evolutionary more closely related than their bacterial counterparts. These observations raise the question of how ribosome synthesis in archaea may proceed in vivo. In this study, we describe a versatile plasmid-based cis-acting reporter system allowing to analyze in vivo the consequences of ribosomal RNA mutations in the model archaeon Haloferax volcanii. Applying this system, we provide evidence that the bulge-helix-bulge motif enclosed within the ribosomal RNA processing stems is required for the formation of archaeal-specific circular-pre-rRNA intermediates and mature rRNAs. In addition, we have collected evidences suggesting functional coordination of the early steps of ribosome synthesis in H. volcanii. Together our investigation describes a versatile platform allowing to generate and functionally analyze the fate of diverse rRNA variants, thereby paving the way to better understand the cis-acting molecular determinants necessary for archaeal ribosome synthesis, maturation, stability and function.

Maturation of atypical ribosomal RNA precursors in Helicobacter pylori

In most bacteria, ribosomal RNA is transcribed as a single polycistronic precursor that is first processed by RNase III. This double-stranded specific RNase cleaves two large stems flanking the 23S and 16S rRNA mature sequences, liberating three 16S, 23S and 5S rRNA precursors, which are further processed by other ribonucleases. Here, we investigate the rRNA maturation pathway of the human gastric pathogen Helicobacter pylori. This bacterium has an unusual arrangement of its rRNA genes, the 16S rRNA gene being separated from a 23S-5S rRNA cluster. We show that RNase III also initiates processing in this organism, by cleaving two typical stem structures encompassing 16S and 23S rRNAs and an atypical stem–loop located upstream of the 5S rRNA. Deletion of RNase III leads to the accumulation of a large 23S-5S precursor that is found in polysomes, suggesting that it can function in translation. Finally, we characterize a cis-encoded antisense RNA overlapping the leader of the 23S-5S rRNA precursor. We present evidence that this antisense RNA interacts with this precursor, forming an intermolecular complex that is cleaved by RNase III. This pairing induces additional specific cleavages of the rRNA precursor coupled with a rapid degradation of the antisense RNA.

Bacterial ribonucleases and their roles in RNA metabolism

Ribonucleases (RNases) are mediators in most reactions of RNA metabolism. In recent years, there has been a surge of new information about RNases and the roles they play in cell physiology. In this review, a detailed description of bacterial RNases is presented, focusing primarily on those from Escherichia coli and Bacillus subtilis, the model Gram-negative and Gram-positive organisms, from which most of our current knowledge has been derived. Information from other organisms is also included, where relevant. In an extensive catalog of the known bacterial RNases, their structure, mechanism of action, physiological roles, genetics, and possible regulation are described. The RNase complement of E. coli and B. subtilis is compared, emphasizing the similarities, but especially the differences, between the two. Included are figures showing the three major RNA metabolic pathways in E. coli and B. subtilis and highlighting specific steps in each of the pathways catalyzed by the different RNases. This compilation of the currently available knowledge about bacterial RNases will be a useful tool for workers in the RNA field and for others interested in learning about this area.

Doxycycline inhibits pre-rRNA processing and mature rRNA formation in E. coli

In bacteria, RNase III cleaves the initial long primary ribosomal RNA transcripts/precursors (pre-rRNAs), thereby releasing the pre-16S and pre-23S rRNAs for maturation. This cleavage is specified by the double-stranded secondary structures flanking the mature rRNAs, and not necessarily by the nucleotide sequences. Inhibition of this cleavage would lead to a build-up of pre-rRNA molecules. Doxycycline has earlier been shown to bind synthetic double-stranded RNAs and inhibit their cleavage by RNase III. Since bacterial rRNA processing is primarily dependent on RNase III cleavage (which is inhibited by doxycycline), doxycycline could therefore inhibit the normal processing of bacterial rRNA. In this study, the effect of doxycycline on bacterial rRNA processing was investigated by analyzing the amounts of various rRNAs in growing Escherichia coli cells treated with doxycycline. The results showed a doxycycline dose-dependent decrease in mature 16S and 23S rRNAs, concurrent with an accumulation of the initial rRNA transcripts and long precursors. Morphologically, treated cells were elongated at low drug concentrations, while nucleoid degeneration indicative of cell death occurred at higher drug concentrations. These observations suggest that doxycycline inhibits the cleavage and processing of bacterial rRNA transcripts/precursors, leading to impaired formation of mature rRNAs, and the consequent inhibition of protein synthesis for which the tetracycline group of antibiotics are renowned. Since rRNA structure and processing pathway is conserved among bacterial species, this mechanism may account for the broad spectrum of antibiotic activity and selective microbial protein synthesis inhibition of doxycycline and the tetracyclines.

RNase III Processing of rRNA in the Lyme Disease Spirochete Borrelia burgdorferi

The rRNA genes of Borrelia (Borreliella) burgdorferi are unusually organized; the spirochete has a single 16S rRNA gene that is more than 3 kb from a tandem pair of 23S-5S rRNA operons. We generated an rnc null mutant in B. burgdorferi that exhibits a pleiotropic phenotype, including decreased growth rate and increased cell length. Here, we demonstrate that endoribonuclease III (RNase III) is, as expected, involved in processing the 23S rRNA in B. burgdorferi The 5' and 3' ends of the three rRNAs were determined in the wild type and rncBb mutants; the results suggest that RNase III in B. burgdorferi is required for the full maturation of the 23S rRNA but not for the 5S rRNA nor, curiously, for the 16S rRNA.IMPORTANCE Lyme disease, the most common tick-borne zoonosis in the Northern Hemisphere, is caused by the bacterium Borrelia (Borreliella) burgdorferi, a member of the deeply branching spirochete phylum. B. burgdorferi carries a limited suite of ribonucleases, enzymes that cleave RNA during processing and degradation. Several ribonucleases, including RNase III, are involved in the production of ribosomes, which catalyze translation and are a major target of antibiotics. This is the first study to dissect the role of an RNase in any spirochete. We demonstrate that an RNase III mutant is viable but has altered processing of rRNA.

Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria

Gene expression in Gram-negative bacteria is regulated at many levels, including transcription initiation, RNA processing, RNA/RNA interactions, mRNA decay, and translational controls involving enzymes that alter translational efficiency. In this review, we discuss the various enzymes that control transcription, translation, and RNA stability through RNA processing and degradation. RNA processing is essential to generate functional RNAs, while degradation helps control the steady-state level of each individual transcript. For example, all the pre-tRNAs are transcribed with extra nucleotides at both their 5' and 3' termini, which are subsequently processed to produce mature tRNAs that can be aminoacylated. Similarly, rRNAs that are transcribed as part of a 30S polycistronic transcript are matured to individual 16S, 23S, and 5S rRNAs. Decay of mRNAs plays a key role in gene regulation through controlling the steady-state level of each transcript, which is essential for maintaining appropriate protein levels. In addition, degradation of both translated and nontranslated RNAs recycles nucleotides to facilitate new RNA synthesis. To carry out all these reactions, Gram-negative bacteria employ a large number of endonucleases, exonucleases, RNA helicases, and poly(A) polymerase, as well as proteins that regulate the catalytic activity of particular RNases. Under certain stress conditions, an additional group of specialized endonucleases facilitate the cell's ability to adapt and survive. Many of the enzymes, such as RNase E, RNase III, polynucleotide phosphorylase, RNase R, and poly(A) polymerase I, participate in multiple RNA processing and decay pathways.

Distinct and redundant functions of three homologs of RNase III in the cyanobacterium Synechococcus sp. strain PCC 7002

RNase III is a ribonuclease that recognizes and cleaves double-stranded RNA. Across bacteria, RNase III is involved in rRNA maturation, CRISPR RNA maturation, controlling gene expression, and turnover of messenger RNAs. Many organisms have only one RNase III while others have both a full-length RNase III and another version that lacks a double-stranded RNA binding domain (mini-III). The genome of the cyanobacterium Synechococcus sp. strain PCC 7002 (PCC 7002) encodes three homologs of RNase III, two full-length and one mini-III, that are not essential even when deleted in combination. To discern if each enzyme had distinct responsibilities, we collected and sequenced global RNA samples from the wild type strain, the single, double, and triple RNase III mutants. Approximately 20% of genes were differentially expressed in various mutants with some operons and regulons showing complex changes in expression levels between mutants. Two RNase III's had a role in 23S rRNA maturation and the third was involved in copy number regulation one of six native plasmids. In vitro, purified RNase III enzymes were capable of cleaving some of the known Escherichia coli RNase III target sequences, highlighting the remarkably conserved substrate specificity between organisms yet complex regulation of gene expression.

Comparison of preribosomal RNA processing pathways in yeast, plant and human cells - focus on coordinated action of endo- and exoribonucleases

Proper regulation of ribosome biosynthesis is mandatory for cellular adaptation, growth and proliferation. Ribosome biogenesis is the most energetically demanding cellular process, which requires tight control. Abnormalities in ribosome production have severe consequences, including developmental defects in plants and genetic diseases (ribosomopathies) in humans. One of the processes occurring during eukaryotic ribosome biogenesis is processing of the ribosomal RNA precursor molecule (pre-rRNA), synthesized by RNA polymerase I, into mature rRNAs. It must not only be accurate but must also be precisely coordinated with other phenomena leading to the synthesis of functional ribosomes: RNA modification, RNA folding, assembly with ribosomal proteins and nucleocytoplasmic RNP export. A multitude of ribosome biogenesis factors ensure that these events take place in a correct temporal order. Among them are endo- and exoribonucleases involved in pre-rRNA processing. Here, we thoroughly present a wide spectrum of ribonucleases participating in rRNA maturation, focusing on their biochemical properties, regulatory mechanisms and substrate specificity. We also discuss cooperation between various ribonucleolytic activities in particular stages of pre-rRNA processing, delineating major similarities and differences between three representative groups of eukaryotes: yeast, plants and humans.

Random pseuoduridylation in vivo reveals critical region of Escherichia coli 23S rRNA for ribosome assembly

Pseudouridine is the most common modified nucleoside in RNA, which is found in stable RNA species and in eukaryotic mRNAs. Functional analysis of pseudouridine is complicated by marginal effect of its absence. We demonstrate that excessive pseudouridines in rRNA inhibit ribosome assembly. Ten-fold increase of pseudouridines in the 16S and 23S rRNA made by a chimeric pseudouridine synthase leads to accumulation of the incompletely assembled large ribosome subunits. Hyper modified 23S rRNA is found in the r-protein assembly defective particles and are selected against in the 70S and polysome fractions showing modification interference. Eighteen positions of 23S rRNA were identified where isomerization of uridines interferes with ribosome assembly. Most of the interference sites are located in the conserved core of the large subunit, in the domain 0 of 23S rRNA, around the peptide exit tunnel. A plausible reason for pseudouridine-dependent inhibition of ribosome assembly is stabilization of rRNA structure, which leads to the folding traps of rRNA and to the retardation of the ribosome assembly.

RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA

Ribonucleases facilitate rapid turnover of RNA, providing cells with another mechanism to adjust transcript and protein levels in response to environmental conditions. While many examples have been documented, a comprehensive list of RNase targets is not available. To address this knowledge gap, we compared levels of RNA sequencing coverage of Escherichia coli and a corresponding RNase III mutant to expand the list of known RNase III targets. RNase III is a widespread endoribonuclease that binds and cleaves double-stranded RNA in many critical transcripts. RNase III cleavage at novel sites found in aceEF, proP, tnaC, dctA, pheM, sdhC, yhhQ, glpT, aceK, and gluQ accelerated RNA decay, consistent with previously described targets wherein RNase III cleavage initiates rapid degradation of secondary messages by other RNases. In contrast, cleavage at three novel sites in the ahpF, pflB, and yajQ transcripts led to stabilized secondary transcripts. Two other novel sites in hisL and pheM overlapped with transcriptional attenuators that likely serve to ensure turnover of these highly structured RNAs. Many of the new RNase III target sites are located on transcripts encoding metabolic enzymes. For instance, two novel RNase III sites are located within transcripts encoding enzymes near a key metabolic node connecting glycolysis and the tricarboxylic acid (TCA) cycle. Pyruvate dehydrogenase activity was increased in an rnc deletion mutant compared to the wild-type (WT) strain in early stationary phase, confirming the novel link between RNA turnover and regulation of pathway activity. Identification of these novel sites suggests that mRNA turnover may be an underappreciated mode of regulating metabolism.

The concerted action and overlapping functions of endoribonucleases, exoribonucleases, and RNA processing enzymes complicate the study of global RNA turnover and recycling of specific transcripts. More information about RNase specificity and activity is needed to make predictions of transcript half-life and to design synthetic transcripts with optimal stability. RNase III does not have a conserved target sequence but instead recognizes RNA secondary structure. Prior to this study, only a few RNase III target sites in E. coli were known, so we used RNA sequencing to provide a more comprehensive list of cleavage sites and to examine the impact of RNase III on transcript degradation. With this added information on how RNase III participates in transcript regulation and recycling, a more complete picture of RNA turnover can be developed for E. coli. Similar approaches could be used to augment our understanding of RNA turnover in other bacteria.

Regulation of mRNA Decay in Bacteria

Gram-negative and gram-positive bacteria use a variety of enzymatic pathways to degrade mRNAs. Although several recent reviews have outlined these pathways, much less attention has been paid to the regulation of mRNA decay. The functional half-life of a particular mRNA, which affects how much protein is synthesized from it, is determined by a combination of multiple factors. These include, but are not necessarily limited to, (a) stability elements at either the 5' or the 3' terminus, (b) posttranscriptional modifications, (c) ribosome density on individual mRNAs, (d) small regulatory RNA (sRNA) interactions with mRNAs, (e) regulatory proteins that alter ribonuclease binding affinities, (f) the presence or absence of endonucleolytic cleavage sites, (g) control of intracellular ribonuclease levels, and (h) physical location within the cell. Changes in physiological conditions associated with environmental alterations can significantly alter the impact of these factors in the decay of a particular mRNA.

RNase III mediated cleavage of the coding region of mraZ mRNA is required for efficient cell division in Corynebacterium glutamicum

The Corynebacterium glutamicum R cgR_1959 gene encodes an endoribonuclease of the RNase III family. Deletion mutant of cgR_1959 (Δrnc mutant) showed an elongated cell shape, and presence of several lines on the cell surface, indicating a required of RNase III for maintaining normal cell morphology in C. glutamicum. The level of mraZ mRNA was increased, whereas cgR_1596 mRNA encoding a putative cell wall hydrolase and ftsEX mRNA were decreased in the Δrnc mutant. The half-life of mraZ mRNA was significantly prolonged in the Δrnc and the Δpnp mutant strains. This indicated that the degradation of mraZ mRNA was performed by RNase III and the 3'-to-5' exoribonuclease, PNPase. Northern hybridization and primer extension analysis revealed that the cleavage site for mraZ mRNA by RNase III is in the coding region. Overproduction of MraZ resulted in an elongated cell shape. The expression of ftsEX decreased while that of cgR_1596 unchanged in an MraZ-overexpressing strain. An electrophoretic mobility shift assay and a transcriptional reporter assay indicate that MraZ is a transcriptional repressor of ftsEX in C. glutamicum. These results indicate that RNase III is required for efficient expression of MraZ-dependent ftsEX and MraZ-independent cgR_1596.

Exoribonucleases and Endoribonucleases

This review provides a description of the known Escherichia coli ribonucleases (RNases), focusing on their structures, catalytic properties, genes, physiological roles, and possible regulation. Currently, eight E. coli exoribonucleases are known. These are RNases II, R, D, T, PH, BN, polynucleotide phosphorylase (PNPase), and oligoribonuclease (ORNase). Based on sequence analysis and catalytic properties, the eight exoribonucleases have been grouped into four families. These are the RNR family, including RNase II and RNase R; the DEDD family, including RNase D, RNase T, and ORNase; the RBN family, consisting of RNase BN; and the PDX family, including PNPase and RNase PH. Seven well-characterized endoribonucleases are known in E. coli. These are RNases I, III, P, E, G, HI, and HII. Homologues to most of these enzymes are also present in Salmonella. Most of the endoribonucleases cleave RNA in the presence of divalent cations, producing fragments with 3'-hydroxyl and 5'-phosphate termini. RNase H selectively hydrolyzes the RNA strand of RNA?DNA hybrids. Members of the RNase H family are widely distributed among prokaryotic and eukaryotic organisms in three distinct lineages, RNases HI, HII, and HIII. It is likely that E. coli contains additional endoribonucleases that have not yet been characterized. First of all, endonucleolytic activities are needed for certain known processes that cannot be attributed to any of the known enzymes. Second, homologues of known endoribonucleases are present in E. coli. Third, endonucleolytic activities have been observed in cell extracts that have different properties from known enzymes.

Polyadenylation helps regulate functional tRNA levels in Escherichia coli

Here we demonstrate a new regulatory mechanism for tRNA processing in Escherichia coli whereby RNase T and RNase PH, the two primary 3' → 5' exonucleases involved in the final step of 3'-end maturation, compete with poly(A) polymerase I (PAP I) for tRNA precursors in wild-type cells. In the absence of both RNase T and RNase PH, there is a >30-fold increase of PAP I-dependent poly(A) tails that are ≤10 nt in length coupled with a 2.3- to 4.2-fold decrease in the level of aminoacylated tRNAs and a >2-fold decrease in growth rate. Only 7 out of 86 tRNAs are not regulated by this mechanism and are also not substrates for RNase T, RNase PH or PAP I. Surprisingly, neither PNPase nor RNase II has any effect on tRNA poly(A) tail length. Our data suggest that the polyadenylation of tRNAs by PAP I likely proceeds in a distributive fashion unlike what is observed with mRNAs.

RNase G participates in processing of the 5'-end of 23S ribosomal RNA

In Escherichia coli, primary rRNA transcripts must be processed by a complex process in which several ribonucleases are involved in order to generate mature 16S, 23S, and 5S rRNA molecules. While it is known that RNase G, a single-stranded RNA-specific endoribonuclease encoded by the rng gene, plays an active role in the maturation of the 5'-end of 16S rRNA, its involvement in the maturation of the 5'-end of 23S rRNA remains unclear. Here we show that E. coli cells deleted for the rng gene accumulate the 23S rRNA precursor containing an extra 77 nucleotides at its mature 5'-end. In vitro cleavage assays show that RNase G cleaves synthetic RNA containing a sequence encompassing the 5'-end to 77 nucleotides upstream of mature 23S rRNA at two sites present in single-stranded regions. Our results suggest the involvement of RNase G in the processing of the 5'-region of 23S rRNA precursors.

Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays

Tiling microarrays have proven to be a valuable tool for gaining insights into the transcriptomes of microbial organisms grown under various nutritional or stress conditions. Here, we describe the use of such an array, constructed at the level of 20 nt resolution for the Escherichia coli MG1655 genome, to observe genome-wide changes in the steady-state RNA levels in mutants defective in either RNase E or RNase III. The array data were validated by comparison to previously published results for a variety of specific transcripts as well as independent northern analysis of additional mRNAs and sRNAs. In the absence of RNase E, 60% of the annotated coding sequences showed either increases or decreases in their steady-state levels. In contrast, only 12% of the coding sequences were affected in the absence of RNase III. Unexpectedly, many coding sequences showed decreased abundance in the RNase E mutant, while more than half of the annotated sRNAs showed changes in abundance. Furthermore, the steady-state levels of many transcripts showed overlapping effects of both ribonucleases. Data are also presented demonstrating how the arrays were used to identify potential new genes, RNase III cleavage sites and the direct or indirect control of specific biological pathways.

Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing

The UPF0054 protein family is highly conserved with homologues present in nearly every sequenced bacterium. In some bacteria, the respective gene is essential, while in others its loss results in a highly pleiotropic phenotype. Despite detailed structural studies, a cellular role for this protein family has remained unknown. We report here that deletion of the Escherichia coli homologue, YbeY, causes striking defects that affect ribosome activity, translational fidelity and ribosome assembly. Mapping of 16S, 23S and 5S rRNA termini reveals that YbeY influences the maturation of all three rRNAs, with a particularly strong effect on maturation at both the 5'- and 3'-ends of 16S rRNA as well as maturation of the 5'-termini of 23S and 5S rRNAs. Furthermore, we demonstrate strong genetic interactions between ybeY and rnc (encoding RNase III), ybeY and rnr (encoding RNase R), and ybeY and pnp (encoding PNPase), further suggesting a role for YbeY in rRNA maturation. Mutation of highly conserved amino acids in YbeY, allowed the identification of two residues (H114, R59) that were found to have a significant effect in vivo. We discuss the implications of these findings for rRNA maturation and ribosome assembly in bacteria.

Maturation of 23S rRNA in Bacillus subtilis in the absence of Mini-III

23S rRNA maturation in Bacillus subtilis is catalyzed by the recently characterized enzyme Mini-RNase-III. Mini-III is dispensable, however, and 23S rRNA is matured by other ribonucleases in strains lacking this enzyme. Here we show that these RNases are the 5'-to-3' exoribonuclease RNase J1 and the 3'-to-5' exoribonucleases, principally RNase PH and YhaM.

Novel mutations in ribosomal proteins L4 and L22 that confer erythromycin resistance in Escherichia coli

L4 and L22, proteins of the large ribosomal subunit, contain globular surface domains and elongated ‘tentacles’ that reach into the core of the large subunit to form part of the lining of the peptide exit tunnel. Mutations in the tentacles of L4 and L22 confer macrolide resistance in a variety of pathogenic and non-pathogenic bacteria. In Escherichia coli, a Lys-to-Glu mutation in L4 and a three-amino-acid deletion in the L22 had been reported. To learn more about the roles of the tentacles in ribosome assembly and function, we isolated additional erythromycin-resistant E. coli mutants. Eight new mutations mapped in L4, all within the tentacle. Two new mutations were identified in L22; one mapped outside the tentacle. Insertion mutations were found in both genes. All of the mutants grew slower than the parent, and they all showed reduced in vivo rates of peptide-chain elongation and increased levels of precursor 23S rRNA. Large insertions in L4 and L22 resulted in very slow growth and accumulation of abnormal ribosomal subunits. Our results highlight the important role of L4 and L22 in ribosome function and assembly, and indicate that a variety of changes in these proteins can mediate macrolide resistance.

Ribosome biogenesis and the translation process in Escherichia coli

Translation, the decoding of mRNA into protein, is the third and final element of the central dogma. The ribosome, a nucleoprotein particle, is responsible and essential for this process. The bacterial ribosome consists of three rRNA molecules and approximately 55 proteins, components that are put together in an intricate and tightly regulated way. When finally matured, the quality of the particle, as well as the amount of active ribosomes, must be checked. The focus of this review is ribosome biogenesis in Escherichia coli and its cross-talk with the ongoing protein synthesis. We discuss how the ribosomal components are produced and how their synthesis is regulated according to growth rate and the nutritional contents of the medium. We also present the many accessory factors important for the correct assembly process, the list of which has grown substantially during the last few years, even though the precise mechanisms and roles of most of the proteins are not understood.

An ortholog of the Ro autoantigen functions in 23S rRNA maturation in D. radiodurans

In both animal cells and the eubacterium Deinococcus radiodurans, the Ro autoantigen, a ring-shaped RNA-binding protein, associates with small RNAs called Y RNAs. In vertebrates, Ro also binds the 3' ends of misfolded RNAs and is proposed to function in quality control. However, little is known about the function of Ro and the Y RNAs in vivo. Here, we report that the D. radiodurans ortholog Rsr (Ro sixty related) functions with exoribonucleases in 23S rRNA maturation. During normal growth, 23S rRNA maturation is inefficient, resulting in accumulation of precursors containing 5' and 3' extensions. During growth at elevated temperature, maturation is efficient and requires Rsr and the exoribonucleases RNase PH and RNase II. Consistent with the hypothesis that Y RNAs inhibit Ro activity, maturation is efficient at all temperatures in cells lacking the Y RNA. In the absence of Rsr, 23S rRNA maturation halts at positions of potential secondary structure. As Rsr exhibits genetic and biochemical interactions with the exoribonuclease polynucleotide phosphorylase, Rsr likely functions in an additional process with this nuclease. We propose that Rsr functions as a processivity factor to assist RNA maturation by exoribonucleases. This is the first demonstration of a role for Ro and a Y RNA in vivo.

Functional defects in transfer RNAs lead to the accumulation of ribosomal RNA precursors

Normal expression and function of transfer RNA (tRNA) are of paramount importance for translation. In this study, we show that tRNA defects are also associated with increased levels of immature ribosomal RNA (rRNA). This association was first shown in detail for a mutant strain that underproduces tRNA(Arg2) in which unprocessed 16S and 23S rRNA levels were increased several-fold. Ribosome profiles indicated that unprocessed 23S rRNA in the mutant strain accumulates in ribosomal fractions that sediment with altered mobility. Underproduction of tRNA(Arg2) also resulted in growth defects under standard laboratory growth conditions. Interestingly, the growth and rRNA processing defects were attenuated when cells were grown in minimal medium or at low temperatures, indicating that the requirement for tRNA(Arg2) may be reduced under conditions of slower growth. Other tRNA defects were also studied, including a defect in RNase P, an enzyme involved in tRNA processing; a mutation in tRNA(Trp) that results in its degradation at elevated temperatures; and the titration of the tRNA that recognizes rare AGA codons. In all cases, the levels of unprocessed 16S and 23S rRNA were enhanced. Thus, a range of tRNA defects can indirectly influence translation via effects on the biogenesis of the translation apparatus.

RNase III cleavage demonstrates a long range RNA: RNA duplex element flanking the hepatitis C virus internal ribosome entry site

Here, we show that Escherichia coli Ribonuclease III cleaves specifically the RNA genome of hepatitis C virus (HCV) within the first 570 nt with similar efficiency within two sequences which are ∼400 bases apart in the linear HCV map. Demonstrations include determination of the specificity of the cleavage sites at positions C²⁷ and U³³ in the first (5′) motif and G⁴³⁹ in the second (3′) motif, complete competition inhibition of 5′ and 3′ HCV RNA cleavages by added double-stranded RNA in a 1:6 to 1:8 weight ratio, respectively, 50% reverse competition inhibition of the RNase III T7 R1.1 mRNA substrate cleavage by HCV RNA at 1:1 molar ratio, and determination of the 5′ phosphate and 3′ hydroxyl end groups of the newly generated termini after cleavage. By comparing the activity and specificity of the commercial RNase III enzyme, used in this study, with the natural E.coli RNase III enzyme, on the natural bacteriophage T7 R1.1 mRNA substrate, we demonstrated that the HCV cuts fall into the category of specific, secondary RNase III cleavages. This reaction identifies regions of unusual RNA structure, and we further showed that blocking or deletion of one of the two RNase III-sensitive sequence motifs impeded cleavage at the other, providing direct evidence that both sequence motifs, besides being far apart in the linear RNA sequence, occur in a single RNA structural motif, which encloses the HCV internal ribosome entry site in a large RNA loop.

Importance of transient structures during post-transcriptional refolding of the pre-23S rRNA and ribosomal large subunit assembly

An important step of ribosome assembly is the folding of the rRNA into a functional structure. Despite knowledge of the folded state of rRNA in the ribosomal subunits, there is very little information on the rRNA folding pathway. We are interested in understanding how the functional structure of rRNA is formed and whether the rRNA folding intermediates have a role in ribosome assembly. To this end, transient secondary structures around both ends of pre-23S rRNA were analyzed by a chemical probing approach, using pre-23S rRNA transcripts. Metastable hairpin loop structures were found at both ends of 23S rRNA. The functional importance of the transient structures around the ends of 23S rRNA was tested by mutations that alter only the transient structure. The effect of mutations on 23S rRNA folding was tested in vitro and in vivo. It was found that both stabilization and destabilization of the transient structure around the 5' end of 23S rRNA inhibits post-transcriptional refolding in vitro and ribosome formation in vivo. The data suggest that the transient structure of rRNA has a function during 23S rRNA folding and thereby in ribosome assembly.

Functional interaction between RNase III and the Escherichia coli ribosome

BACKGROUND

RNase III is a dsRNA specific endoribonuclease which is involved in the primary processing of rRNA and several mRNA species in bacteria. Both primary structural elements and the secondary structure of the substrate RNA play a role in cleavage specificity.

RESULTS

We have analyzed RNase III cleavage sites around both ends of pre-23 S rRNA in the ribosome and in the protein-free pre-rRNA. It was found that in the protein-free pre-23 S rRNA the main cleavage site is at position (-7) in respect of the mature 5' end. When pre-23 S rRNA was in 70 S ribosomes or in 50 S subunits, the RNase III cleavage occurred at position (-3). We have demonstrated that RNase III interacts with both ribosomal subunits and with even higher affinity with 70 S ribosomes. Association of RNase III with 70 S ribosomes cannot be dissociated by poly(U) RNA indicating that the binding is specific.

CONCLUSIONS

In addition to the primary and secondary structural elements in RNA, protein binding to substrate RNA can be a determinant of the RNase III cleavage site.

RNA processing and degradation in Bacillus subtilis

This review focuses on the enzymes and pathways of RNA processing and degradation in Bacillus subtilis, and compares them to those of its gram-negative counterpart, Escherichia coli. A comparison of the genomes from the two organisms reveals that B. subtilis has a very different selection of RNases available for RNA maturation. Of 17 characterized ribonuclease activities thus far identified in E. coli and B. subtilis, only 6 are shared, 3 exoribonucleases and 3 endoribonucleases. Some enzymes essential for cell viability in E. coli, such as RNase E and oligoribonuclease, do not have homologs in B. subtilis, and of those enzymes in common, some combinations are essential in one organism but not in the other. The degradation pathways and transcript half-lives have been examined to various degrees for a dozen or so B. subtilis mRNAs. The determinants of mRNA stability have been characterized for a number of these and point to a fundamentally different process in the initiation of mRNA decay. While RNase E binds to the 5' end and catalyzes the rate-limiting cleavage of the majority of E. coli RNAs by looping to internal sites, the equivalent nuclease in B. subtilis, although not yet identified, is predicted to scan or track from the 5' end. RNase E can also access cleavage sites directly, albeit less efficiently, while the enzyme responsible for initiating the decay of B. subtilis mRNAs appears incapable of direct entry. Thus, unlike E. coli, RNAs possessing stable secondary structures or sites for protein or ribosome binding near the 5' end can have very long half-lives even if the RNA is not protected by translation.

The DEAD-box RNA helicase SrmB is involved in the assembly of 50S ribosomal subunits in Escherichia coli

Ribosome assembly in Escherichia coli involves 54 ribosomal proteins and three RNAs. Whereas functional subunits can be reconstituted in vitro from the isolated components, this process requires long incubation times and high temperatures compared with the in vivo situation, suggesting that non-ribosomal factors facilitate assembly in vivo. Here, we show that SrmB, a putative DEAD-box RNA helicase, is involved in ribosome assembly. The deletion of the srmB gene causes a slow-growth phenotype at low temperature. Polysome profile analyses of the corresponding cells reveal a deficit in free 50S ribosomal subunits and the accumulation of a new particle sedimenting around 40S. Analysis of the ribosomal RNA and protein contents of the 40S particle indicates that it represents a large subunit that is incompletely assembled. In particular, it lacks L13, one of the five ribosomal proteins that are essential for the early assembly step in vitro. Sucrose gradient fractionation also shows that, in wild-type cells, SrmB associates with a pre50S particle. From our results, we propose that SrmB is involved in an early step of 50S assembly that is necessary for the binding of L13. This step may consist of a structural rearrangement that, at low temperature, cannot occur without the assistance of this putative RNA helicase.

Ribonuclease III: new sense from nuisance

RNases play an important role in the processing of precursor RNAs, creating the mature, functional RNAs. The ribonuclease III family currently is one of the most interesting families of endoribonucleases. Surprisingly, RNase III is involved in the maturation of almost every class of prokaryotic and eukaryotic RNA. We present an overview of the various substrates and their processing. RNase III contains one of the most prominent protein domains used in RNA-protein recognition, the double-stranded RNA binding domain (dsRBD). Progress in the understanding of this domain is summarized. Furthermore, RNase III only recently emerged as a key player in the new exciting biological field of RNA silencing, or RNA interference. The eukaryotic RNase III homologues which are likely involved in this process are compared with the other members of the RNase III family.

Ribosome synthesis in Saccharomyces cerevisiae

The synthesis of ribosomes is one of the major metabolic pathways in all cells. In addition to around 75 individual ribosomal proteins and 4 ribosomal RNAs, synthesis of a functional eukaryotic ribosome requires a remarkable number of trans-acting factors. Here, we will discuss the recent, and often surprising, advances in our understanding of ribosome synthesis in the yeast Saccharomyces cerevisiae. These will underscore the unexpected complexity of eukaryotic ribosome synthesis.

A Streptomyces coelicolor antibiotic regulatory gene, absB, encodes an RNase III homolog

Streptomyces coelicolor produces four genetically and structurally distinct antibiotics in a growth-phase-dependent manner. S. coelicolor mutants globally deficient in antibiotic production (Abs(-) phenotype) have previously been isolated, and some of these were found to define the absB locus. In this study, we isolated absB-complementing DNA and show that it encodes the S. coelicolor homolog of RNase III (rnc). Several lines of evidence indicate that the absB mutant global defect in antibiotic synthesis is due to a deficiency in RNase III. In marker exchange experiments, the S. coelicolor rnc gene rescued absB mutants, restoring antibiotic production. Sequencing the DNA of absB mutants confirmed that the absB mutations lay in the rnc open reading frame. Constructed disruptions of rnc in both S. coelicolor 1501 and Streptomyces lividans 1326 caused an Abs(-) phenotype. An absB mutation caused accumulation of 30S rRNA precursors, as had previously been reported for E. coli rnc mutants. The absB gene is widely conserved in streptomycetes. We speculate on why an RNase III deficiency could globally affect the synthesis of antibiotics.

Accurate and high resolution in situ hybridization analysis of gene expression in secondary stem tissues

Accurate in situ hybridization analysis in secondary stem tissues of plants has been hindered by specific characteristics of these tissues. First, secondary cell walls non-specifically bind probes used for in situ hybridization thus preventing gene expression analysis in the lignified regions of the stem, such as the xylem. Second, the mRNA in the cambial meristem and its recent derivatives are prone to inadequate fixation when conventional techniques are used. Here we describe an in situ hybridization technique which uses fast freezing and freeze substitution to cryoimmobilize the mRNA followed by embedding in a methacrylate resin for high-resolution analysis of gene expression. By using a transgenic poplar line harbouring rolC:uidA, rolC:iaaM, the gene expression pattern could be compared with histochemical GUS staining. This in situ hybridization technique results in superior preservation of cellular contents, retention of mRNA in all cell types in the poplar stem, a significant reduction of non-specific binding to secondary cell walls and a resolution not previously possible in secondary tissues. This technique will be particularly valuable for the expression analysis of genes involved in xylogenesis and wood formation.

Yeast Rnt1p is required for cleavage of the pre-ribosomal RNA in the 3' ETS but not the 5' ETS

We have reexamined the role of yeast RNase III (Rnt1p) in ribosome synthesis. Analysis of pre-rRNA processing in a strain carrying a complete deletion of the RNT1 gene demonstrated that the absence of Rnt1p does not block cleavage at site A0 in the 5' external transcribed spacers (ETS), although the early pre-rRNA cleavages at sites A0, A1, and A2 are kinetically delayed. In contrast, cleavage in the 3' ETS is completely inhibited in the absence of Rnt1p, leading to the synthesis of a reduced level of a 3' extended form of the 25S rRNA. The 3' extended forms of the pre-rRNAs are consistent with the major termination at site T2 (+210). We conclude that Rnt1p is required for cleavage in the 3' ETS but not for cleavage at site A0. The sites of in vivo cleavage in the 3' ETS were mapped by primer extension. Two sites of Rnt1p-dependent cleavage were identified that lie on opposite sides of a predicted stem loop structure, at +14 and +49. These are in good agreement with the consensus Rnt1p cleavage site. Processing of the 3' end of the mature 25S rRNA sequence in wild-type cells was found to occur concomitantly with processing of the 5' end of the 5.8S rRNA, supporting previous proposals that processing in ITS1 and the 3' ETS is coupled.

Function, mechanism and regulation of bacterial ribonucleases

The maturation and degradation of RNA molecules are essential features of the mechanism of gene expression, and provide the two main points for post-transcriptional regulation. Cells employ a functionally diverse array of nucleases to carry out RNA maturation and turnover. Viruses also employ cellular ribonucleases, or even use their own in their reproductive cycles. Studies on bacterial ribonucleases, and in particular those from Escherichia coli, are providing insight into ribonuclease structure, mechanism, and regulation. Ongoing biochemical and genetic analyses are revealing that many ribonucleases are phylogenetically conserved, and exhibit overlapping functional roles and perhaps common catalytic mechanisms. This article reviews the salient features of bacterial ribonucleases, with a focus on those of E. coli, and in particular, ribonuclease III. RNase III participates in a number of RNA maturation and RNA decay pathways, and is regulated by phosphorylation in the T7 phage-infected cell. Plasmid and phage RNAs, in addition to cellular transcripts, are RNase III targets. RNase III orthologues occur in eukaryotic cells, and play key functional roles. As such, RNase III provides an important model with which to understand mechanisms of RNA maturation, RNA decay, and gene regulation.

Maturation of 23S ribosomal RNA requires the exoribonuclease RNase T

Ribosomal RNAs are generally synthesized as long, primary transcripts that must be extensively processed to generate the mature, functional species. In Escherichia coli, it is known that the initial 30S precursor is cleaved during its synthesis by the endonuclease RNase III to generate precursors to the 16S, 23S, and 5S rRNAs. However, despite extensive study, the processes by which these intermediate products are converted to their mature forms are poorly understood. In this article, we describe the maturation of 23S rRNA. Based on Northern analysis of RNA isolated from a variety of mutant strains lacking one or multiple ribonucleases, we show that maturation of the 3' terminus requires the action of RNase T, an enzyme previously implicated in the end turnover of tRNA and in the maturation of small, stable RNAs. Although other exoribonucleases can participate in shortening the 3' end of the initial RNase III cleavage product, RNase T is required for removal of the last few residues. In the absence of RNase T, 23S rRNA products with extra 3' residues accumulate and are incorporated into ribosomes, with only small effects on cell growth. Purified RNase T accurately and efficiently converts these immature ribosomes to their mature forms in vitro, whereas free RNA is processed relatively poorly. In vivo, the processing defect at the 3' end has no effect on 5' maturation, indicating that the latter process proceeds independently. We also find that a portion of the 23S rRNA that accumulates in many RNase T- cells becomes polyadenylated because of the action of poly(A) polymerase I. The requirement for RNase T in 23S rRNA maturation is discussed in relation to a model in which only this enzyme, among the eight exoribonucleases present in E. coli, is able to efficiently remove nucleotides close to the double-stranded stem generated by the pairing of the 5' and 3' termini of most stable RNAs.

Multiple functions of the transcribed spacers in ribosomal RNA operons

rRNA operons contain about 25% transcribed spacer sequences in addition to the 16S, 23S, 5S and tRNA genes. The spacer sequences are removed from the primary rRNA transcript by a series of co-ordinated nucleolytic events. Besides the role in rRNA processing, the spacer sequences are also involved in transcription and the ribosome assembly. In this study we analyze the spacer between tRNA and 23S rRNA genes. Based on computer modeling and chemical probing data, a model for the transient secondary structure of the intergenic spacer is proposed. Mutational analysis has shown that the transient secondary structure around the 5' end of 23S rRNA is involved in ribosome assembly. We propose that the transient structure at the 5' end of 23S rRNA directs 23S rRNA folding into the mature structure and facilitates ribosomal large subunit assembly.

The role of the 3' external transcribed spacer in yeast pre-rRNA processing

We have undertaken a deletion analysis of the 3' external transcribed spacer (3' ETS) in the pre-rRNA of Saccharomyces cerevisiae. A stem loop structure immediately 3' to the 25 S rRNA region is necessary and sufficient for processing of the 3' ETS. This is believed to be by cotranscriptional cleavage by Rnt1p, the yeast homologue of RNase III. In addition, this stem-loop is required for cleavage of site A3 by RNase MRP and for processing at site B1L, in the 3' region of ITS1. Processing at an upstream site in ITS1, site A2, and at sites in the 5' external transcribed spacer are not affected, even by complete deletion of the 3' ETS. We conclude that processing in the 3' ETS and in ITS1 is coupled. This would constitute a quality control that prevents synthesis of the 5. 8 S rRNA and 5' end maturation of the 25 S rRNA in transcripts which are incomplete due to premature transcription termination.

Base-pairing of 23 S rRNA ends is essential for ribosomal large subunit assembly

In ribosomal RNA precursors the spacer sequences bracketing mature 16 S and 23 S rRNA are base-paired to form long helices (processing stems). In pre-23 S rRNA, the processing stem is continued by eight base-pairs of mature 23 S rRNA known as helix 1. Recently, we have found that any part of 23 S rRNA between positions 40 and 2773 could be deleted without the loss of ribosome-like particle formation, while both end regions were indispensable. In this paper we have analyzed the role of the 5' and 3' end regions of 23 S rRNA during ribosomal 50 S assembly in vivo by using mutants of the 23 S rRNA gene. Deletions and substitutions in both strands of the helix 1 lead to the loss of plasmid derived 50 S formation. Compensatory mutations restoring helix 1 were assembled into functional 50 S subunits. We conclude that the helix 1 of 23 S rRNA is the main RNA determinant for ribosomal large-subunit assembly. Deletions in both the 5' and 3' strand of the processing stem reduced the ability of the 23 S rRNA to form ribosomal 50 S subunits. However, even the complete removal of either the 5' or the 3' strand of the processing stem did not abolish the 50 S assembly completely. Thus, processing stem facilitates, but is not essential for assembly.

RNase III deficient Salmonella typhimurium LT2 contains intervening sequences (IVSs) in its 23S rRNA

Salmonella typhimurium LT2 contains intervening sequences (IVSs) of 90-110 nt within all its 23S rRNA that are cleaved out by RNase III, resulting in rRNA fragmentation. In order to determine the functionality of 23S rRNA that contains unexcised IVSs, we constructed an S. typhimurium RNase III (rnc) deficient strain by transducing a mini-Tn10 (rnc-14::Tn10) from Escherichia coli K-12. The resulting strain of S. typhimurium was viable, contained IVSs within all of its 23S rRNA, and showed a growth reduction similar to that observed for the RNase III deficient strain of E. coli. These results indicate that ribosomes containing 23S rRNA in which IVSs are not excised are functional in translation, and make it unlikely that RNase III excision of IVSs from strain LT2 23S rRNA is dictated by a selective pressure to uphold the functional integrity of ribosomes.

RNA processing in prokaryotic cells

RNA processing in Escherichia coli and some of its phages is reviewed here, with primary emphasis on rRNA and tRNA processing. Three enzymes, RNase III, RNase E and RNase P are responsible for most of the primary endonucleolytic RNA processing events. The first two are proteins, while RNase P is a ribozyme. These three enzymes have unique functions and in their absence, the cleavage events they catalyze are not performed. On the other hand a relatively large number of exonucleases participate in the trimming of the 3' ends of tRNA precursor molecules and they can substitute for each other. Primary processing is the first event that happens to the nascent RNA molecule, while in secondary RNA processing, the substrate is a product of a primary processing event. Although most RNA processing occurs in RNP particles, it seems that only in secondary RNA processing is the RNP particle required for the reaction. Bacteria and especially bacteriophages contain self-splicing introns which in cases were probably acquired from other species.

A new rRNA processing mutant of Saccharomyces cerevisiae

We have identified from a collection of temperature sensitive yeast mutants strains which fail to process rRNA normally. Characterization of one such mutant is reported here. This strain accumulates increased amounts of the 35S primary transcript, '24S' molecules extending from the transcription start site to the 5.8S region, and two classes of 5.8S rRNA with 5' extensions of 7 and 149 bases, respectively. We show that this pleiotropic change in the rRNA processing pattern is due to a single mutation. Possible models for the function of the mutated gene are discussed.

Thermus thermophilus 16S rRNA is transcribed from an isolated transcription unit

A cloned 16S rRNA gene from the extreme thermophilic eubacterium Thermus thermophilus HB8 was used to characterize the in vivo expression of the 16S rRNA genes in this organism by nuclease S1 mapping. The gene represents an isolated transcription unit encoding solely 16S rRNA. Under exponential growth conditions, transcription was initiated at a single promoter, which represents the structural equivalent of Escherichia coli rrn P2 promoters. The promoter-leader region was very similar to the E. coli rrn P2 promoter-leader segment that is responsible for antitermination. The T. thermophilus leader region was approximately 85 nucleotides shorter than its E. coli P2 counterpart. Potential processing intermediates were correlated with a proposed secondary structure of T. thermophilus pre-16S rRNA.

Genetic analysis of the rnc operon of Escherichia coli

RNase III, an Escherichia coli double-stranded endoribonuclease, is known to be involved in maturation of rRNA and regulation of several bacteriophage and Escherichia coli genes. Clones of the region of the E. coli chromosome containing the gene for RNase III (rnc) were obtained by screening genomic libraries in lambda with DNA known to map near rnc. A phage clone with the rnc region was randomly mutagenized with a delta Tn10 element, and the insertions were recombined onto the chromosome, generating a series of strains with delta Tn10 insertions in the rnc region. Two insertions that had Rnc- phenotypes were located. One of them lay in the rnc gene, and one was in the rnc leader sequence. Polarity studies showed that rnc is in an operon with two other genes, era and recO. The sequence of the recO gene beyond era indicated it could encode a protein of approximately 26 kilodaltons and, like rnc and era, had codon usage consistent with a low level of expression. Experiments using antibiotic cassettes to disrupt the genes rnc, era, and recO showed that era is essential for E. coli growth but that rnc and recO are dispensable.

Processing pathway of Escherichia coli 16S precursor rRNA

Immediate precursors of 16S rRNA are processed by endonucleolytic cleavage at both 5' and 3' mature termini, with the concomitant release of precursor fragments which are further metabolized by both exo- and endonucleases. In wild-type cells rapid cleavages by RNase III in precursor-specific sequences precede the subsequent formation of the mature ends; mature termini can, however, be formed directly from pre-16S rRNA with no intermediate species. The direct maturation is most evident in a strain deficient in RNase III, and the results in whole cells are consistent with results from maturation reactions in vitro. Thus, maturation does not require cleavages within the double-stranded stems that enclose mature rRNA sequences in the pre-16S rRNA.