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PubMed2001

Analysis of the replicon region and identification of an rRNA operon on pBM400 of Bacillus megaterium QM B1551.

An 18 633 bp region containing the replicon from the approximately 53 kb pBM400 plasmid of Bacillus megaterium QM B1551 has been sequenced and characterized. This region contained a complete rRNA operon plus 10 other potential open reading frames (ORFs). The replicon consisted of an upstream promoter and three contiguous genes (repM400, orfB and orfC) that could encode putative proteins of 428, 251 and 289 amino acids respectively. A 1.6 kb minimal replicon was defined and contained most of repM400. OrfB was shown to be required for stability. Three 12 bp identical tandem repeats were located within the coding region of repM400, and their presence on another plasmid caused incompatibility with their own cognate replicon. Nonsense, frameshift and deletion mutations in repM400 prevented replication, but each mutation could be complemented in trans. RepM400 had no significant similarity to sequences in the GenBank database, whereas five other ORFs had some similarity to gene products from other plasmids and the Bacillus genome. An rRNA operon was located upstream of the replication region and is the first rRNA operon to be sequenced from B. megaterium. Its unusual location on non-essential plasmid DNA has implications for systematics and evolutionary biology.

Adaptation, Physiological↗

PubMed1998

Growth rate-dependent accumulation of RNA from plasmid-borne rRNA operons in Escherichia coli.

Inadequate regulation of the expression of additional plasmid-borne rRNA operons in Escherichia coli was exaggerated at slow growth rates, resulting in increases of approximately 100% for RNA concentration and 33% for doubling time. These observations are consistent with the hypothesis that multiple rRNA operons constitute a metabolic burden at slow growth rates.

Escherichia coli↗

PubMed2000

Computer analysis of potential stem structures of rRNA operons in various procaryote genomes.

The processing of 16S rRNA and 23S rRNA by RNase III in E.coli is known to involve stem structures formed by both ends of the rRNA. Indeed, complementary nucleotide sequences are usually found at both ends of 16S rRNA and 23S rRNA. However, whether or not this phenomenon exists in various other bacteria has not yet been adequately studied. We have conducted computer analyses of potential stem structures of rRNA operons in 12 bacterial and 3 archaeal genomes, and compared characteristics of the stem structures among these species. We systematically computed free energy values by exhaustively 'annealing' sequences around the 5' end and sequences around the 3' end of both 16S rRNA and 23S rRNA genes, in order to predict potential stem structures. The results suggest that rRNAs in most species form stem structures at both ends. Some species, such as A.aeolicus, seem to form unusually stable stem structures. On the other hand, some rRNAs, such as rRNAs of D.radiodurans, seem not to form solid stem structures. This suggests that rRNA processing in those species must employ a reliable targeting mechanism other than recognizing stem structures by RNase III.

Bacteria↗

PubMed1990

Exchange of spacer regions between rRNA operons in Escherichia coli.

The Escherichia coli rRNA operons each have one of two types of spacer separating the 16S and 23S coding regions. The spacers of four operons encode tRNA(Glu2) and the other three encode both tRNA(Ile) and tRNA(Ala1B). We have prepared a series of mutants in which the spacer region of a particular rrn operon has been replaced by the opposite type. Included among these were a mutant retaining only a single copy of the tRNA(Glu2) spacer (at rrnG) and another retaining only a single copy of the tRNA(Ile)-tRNA(Ala1B) spacer (at rrnA). While both mutants grew more slowly than controls, the mutant deficient in tRNA(Glu2) spacers was more severely affected. At a frequency of 6 X 10(-5), these mutants phenotypically reverted to faster growing types by increasing the copy number of the deficient spacer. In most of these phenotypic revertants, the deficient spacer type appeared in a rrn operon which previously contained the surplus type, bringing the ratio of spacer types closer to normal. In a few cases, these spacer changes were accompanied by an inversion of the chromosomal material between the donor and recipient rrn operons. Two examples of inversion of one-half of the E. coli chromosome between rrnG and rrnH were observed. The correlation of spacer change with inversion indicated that, in these particular cases, the change was due to an intrachromatid gene conversion event accompanied by a reciprocal crossover rather than reciprocal exchange between sister chromatids.

Base Sequence↗

PubMed1996

Major differences between the rrnA operons of two strains of Agrobacterium vitis.

The sequence of the rrnA operon and its flanking regions was determined for the Agrobacterium vitis type strain NCPPB3554. Compared to the earlier obtained rrnA sequence of A. vitis strain S4, several important differences were noted: the sequences diverged at the 5'-flanking region, within the 16S-23S intergenic region, and within the 23S rRNA sequence. The B8 stem-loop structure at the 5'-end of the 23S rRNA of strain NCPPB3554 was 142 nt shorter than that of strain S4. These findings have important consequences for the use of ribosomal RNA gene sequences in phylogenetic comparisons.

Base Sequence↗

PubMed1987

Transcription control elements of the Mycoplasma pneumoniae rRNA operon.

The single RNA operon of Mycoplasma pneumoniae was cloned into a lambda vector and subcloned into pBR322. This was carried out in order to enable the analysis of the transcription control regions of this operon. S1 nuclease mapping was used to locate the 5' ends of RNA transcripts synthesized from the operon. The 5' ends of the 23S, 16S, and a precursor RNA synthesized in vivo in M. pneumoniae were mapped on the DNA template. Preliminary in vitro transcription experiments using RNA polymerase of Escherichia coli led to the conclusion that E. coli recognizes one promoter in the 5' region of the M. pneumoniae rRNA operon. The startsite of the in vitro transcript seems to lie downstream from the 5' end of the M. pneumoniae precursor transcript. Preliminary sequencing of the 5' regions of the M. pneumoniae rRNA operon and of the M. capricolum rRNA B operon enabled their comparison to each other and to known sequences from other organisms.

DNA, Bacterial↗

PubMed1988

Instability of rRNA operons in Bacillus subtilis.

Many laboratory strains of Bacillus subtilis contain 9 rather than 10 rRNA operons due to deletions occurring within the rrnJ-rrnW or rrnI-rrnH-rrnG gene cluster. These operons are members of two sets of closely spaced clusters located in the cysA-aroI region. Analysis of rescued DNA from integrants with insertions into rrnG and rrnH indicated that these tandemly arranged operons allowed frequent deletions of an rrn operon equivalent. These events may arise spontaneously by intrachromosomal recombination or by simultaneous double crossovers with a multimeric integrative plasmid.

Bacillus subtilis↗

PubMed1993

Buchnera aphidicola (a prokaryotic endosymbiont of aphids) contains a putative 16S rRNA operon unlinked to the 23S rRNA-encoding gene: sequence determination, and promoter and terminator analysis.

The aphid Schizaphis graminum is dependent on an association with Buchnera aphidicola, an eubacterial endosymbiont located in specialized host cells. Past studies have indicated that Escherichia coli is the closest known relative of the endosymbiont which has many genetic attributes of free-living bacteria. In order to obtain information on the properties of highly expressed genes, we have chosen for study the single-copy rrs (gene encoding 16S rRNA) of B. aphidicola. A 4.4-kb DNA fragment was cloned into E. coli and the nucleotide (nt) sequence determined. Several ORFs were identified; the order of genes was argS-rrs-ORF1-rnh-dnaQ. ArgS, RNase H and DnaQ had 36-57% amino acid (aa) identity to the homologous proteins of E. coli. B. aphidicola rrs appears to be part of an operon consisting of a putative promoter, rrs and two inverted repeats resembling Rho-independent terminators. Comparisons of the sequences of argS-rrn DNA fragments from endosymbionts of six additional aphid species indicated conservation of sequences corresponding to a single -35 (TTGACA) and -10 (TGTAAT) promoter region, as well as boxA (sequence involved in antitermination) and boxC. The B. aphidicola argS-rrn DNA fragments from endosymbionts from seven species of aphids had promoter activities in E. coli which ranged from 6 to 135% of that observed with a comparable DNA fragment of E. coli rrnB. Similarly, the putative B. aphidicola terminator was functional in E. coli. In most eubacteria, the rRNA-encoding genes are arranged in the order, 16S, 23S, 5S, and are part of a single operon.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed2006

Active transcription of rRNA operons is a driving force for the distribution of RNA polymerase in bacteria: effect of extrachromosomal copies of rrnB on the in vivo localization of RNA polymerase.

In contrast to eukaryotes, bacteria such as Escherichia coli contain only one form of RNA polymerase (RNAP), which is responsible for all cellular transcription. Using an RNAP-green fluorescent protein fusion protein, we showed previously that E. coli RNAP is partitioned exclusively in the nucleoid and that stable RNA synthesis, particularly rRNA transcription, is critical for concentrating a significant fraction of RNAP in transcription foci during exponential growth. The extent of focus formation varies under different physiological conditions, supporting the proposition that RNAP redistribution is an important element for global gene regulation. Here we show that extra, plasmid-borne copies of an rRNA operon recruit RNAP from the nucleoid into the cytoplasmic space and that this is accompanied by a reduction in the growth rate. Transcription of an intact rRNA operon is not necessary, although a minimal transcript length is required for this phenotype. Replacement of the ribosomal promoters with another strong promoter, Ptac, abolished the effect. These results demonstrate that active synthesis from rRNA promoters is a major driving force for the distribution of RNAP in bacteria. The implications of our results for the regulation of rRNA synthesis and cell growth are discussed.

Bacteria↗

PubMed2005

Polymorphism and gene conversion of the 16S rRNA genes in the multiple rRNA operons of Vibrio parahaemolyticus.

The genome sequence of a strain of Vibrio parahaemolyticus holds 11 copies of rRNA operons (rrn) with identical 16S rRNA genes (rrs). Conversely, the species type strain contains two rrs classes differing in 10 nucleotide sites within a short segment of 25 bp. Furthermore, we show here that the sequence of this particular segment largely differs between some strains of this species. We also show that of the eleven rrn operons in the species type strain, seven contain one rrs class and four the other, indicating gene conversion. Our results support the hypothesis that the rrs differences observed between strains of this species were caused by lateral transfer of an rrs segment and subsequent conversion.

Base Sequence↗

PubMed1979

In vivo transcription of rRNA operons in Escherichia coli initiates with purine nucleoside triphosphates at the first promoter and with CTP at the second promoter.

32P-labeled RNA was isolated from growing Escherichia coli and the 5' end nucleoside triphosphates of rRNA were analyzed after hybridization to various DNA fragments derived from one of the rRNA operons, rrnE. The results show that there are two transcription start sites for each rRNA operon in vivo, one initiating with ATP (or GTP), and the second initiating with CTP. Transcription from the first site was observed to be stronger than that from the second site. These two sites correspond to the two promoters identified in the previous in vitro studies, indicating that the two promoters are used in vivo. These results also demonstrate previously unrecognized transcription initiation with CTP in growing E. coli cells.

Cytidine Triphosphate↗

PubMedDate not supplied

[Mutual location of the rRNA operon and tuf gene in the Mycoplasma gallisepticum strain S6 genome].

The genomic library of Mycoplasma gallisepticum was constructed and two clones, selected by hybridization on E. coli 16S rRNA, were analyzed. The restriction map of the clones indicate that both clones belong to the same region of the M. gallisepticum genome. The results of Southern hybridization with either E. coli 16S rRNA, or E. coli 23S rRNA, or oligonucleotide synthesized as a part of M. gallisepticum 5S rRNA, led to the conclusion that the unspliced rRNA operon was cloned. The order of genes in the operon is common for eubacteria: 16S-23S-5S. The tuf gene of M. gallisepticum was mapped inside the cloned region 5 kb upstream of 16S gene by hydridization on E. coli tufA gene and oligonucleotide synthesized on the basis of M. gallisepticum tuf gene sequence. The direction of transcription of the gene and the expected direction of transcription of the rRNA operon coincide.

Bacteriophages↗

PubMed1990

Genes encoding the 7S RNA and tRNA(Ser) are linked to one of the two rRNA operons in the genome of the extremely thermophilic archaebacterium Methanothermus fervidus.

Analysis of gene structure in the extremely thermophilic archaebacterium, Methanothermus fervidus, has revealed the presence of a cluster of stable RNA-encoding genes arranged 5'-7S RNA-tRNA(Ser)-16S rRNA-tRNA(Ala)-23S rRNA-5S rRNA. The genome of M. fervidus contains two rRNA operons but only one operon has the closely linked 7S RNA-encoding gene. The sequences upstream from the two rRNA operons are identical for 206 bp but diverge at the 3' base of the tRNA(Ser) gene. The secondary structures predicted for the M. fervidus 7S, 16S rRNA, tRNA(Ala) and tRNA(Ser) have been compared with those of functionally homologous molecules from moderately thermophilic and mesophilic archaebacteria. A consensus secondary structure for archaebacterial 7S RNAs has been developed which incorporates bases and structural features also conserved in eukaryotic signal-recognition-particle RNAs and eubacterial 4.5S RNAs.

Archaea↗

PubMed1998

Molecular characterization and postsplicing fate of three introns within the single rRNA operon of the hyperthermophilic archaeon Aeropyrum pernix K1.

The single rRNA operon (arnS-arnL) of the hyperthermophilic archaeon Aeropyrum pernix K1 was sequenced. The DNA sequence data and detailed RNA analyses disclosed an unusual feature: the presence of three introns at hitherto undescribed insertion positions within the rRNA genes. The 699-nucleotide (nt) intron Ialpha was located at position 908 (Escherichia coli numbering [H. F. Noller, Annu. Rev. Biochem. 53:119-162, 1984]) of the 16S rRNA, while the 202-nt intron Ibeta and 575-nt intron Igamma were located at positions 1085 and 1927 (E. coli numbering), respectively, of the 23S rRNA. They were located within highly conserved sites which have been implicated as crucial for rRNA function in E. coli. All three introns were remarkably AT rich (41.5 to 43.1 mol% G+C) compared with the mature rRNAs (67.7 and 69.2 mol% G+C for 16S and 23S rRNAs, respectively). No obvious primary sequence similarities were detected among them. After splicing from rRNA transcripts in vivo, a large quantity of intronic RNAs were stably retained in the linear monomeric form, whereas a trace of topoisomeric RNA molecules also appeared, as characterized by their behavior in two-dimensional gel electrophoresis. Secondary structural models of the Ialpha-, Ibeta-, and Igamma-containing rRNA precursors agree with the bulge-helix-bulge motif. Two of the introns, Ialpha and Igamma, contained open reading frames whose protein translation exhibited no overall similarity with proteins reported so far. However, both share a LAGLI-DADG motif characteristic of homing endonucleases.

Amino Acid Sequence↗

PubMed1998

Implications of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256.

Sphingomonas sp. strain RB2256 is a representative of the dominant class of ultramicrobacteria that are present in marine oligotrophic waters. In this study we examined the rRNA copy number and ribosome content of RB2256 to identify factors that may be associated with the relatively low rate of growth exhibited by the organism. It was found that RB2256 contains a single copy of the rRNA operon, in contrast to Vibrio spp., which contain more than eight copies. The maximum number of ribosomes per cell was observed during mid-log phase; however, this maximum content was low compared to those of faster-growing, heterotrophic bacteria (approximately 8% of the maximum ribosome content of Escherichia coli with a growth rate of 1. 5 h-1). The low number of ribosomes per cell appears to correlate with the low rate of growth (0.16 to 0.18 h-1) and the presence of a single copy of the rRNA operon. However, on the basis of cell volume, RB2256 appears to have a higher concentration of ribosomes than E. coli (approximately double that of E. coli with a growth rate of 1.5 h-1). Ribosome numbers reached maximum levels during mid-log-phase growth but decreased rapidly to 10% of maximum during late log phase through 7 days of starvation. The cells in late log phase and at the onset of starvation displayed an immediate response to a sudden addition of excess glucose (3 mM). This result demonstrates that a ribosome content 10% of maximum is sufficient to allow cells to immediately respond to nutrient upshift and achieve maximum rates of growth. These data indicate that the bulk of the ribosome pool is not required for protein synthesis and that ribosomes are not the limiting factor contributing to a low rate of growth. Our findings show that the regulation of ribosome content, the number of ribosomes per cell, and growth rate responses in RB2256 are fundamentally different from those characteristics in fast-growing heterotrophs like E. coli and that they may be characteristics typical of oligotrophic ultramicrobacteria.

Alaska↗

PubMed1999

Investigation of an outbreak of Pseudomonas putida using antimicrobial susceptibility patterns, pulsed-field gel electrophoresis of genomic DNA and restriction fragment length polymorphism of PCR-amplified rRNA operons.

Seventeen Pseudomonas putida isolates were investigated which were collected from the urine specimens of 14 patients and one reflectrometer by comparing antimicrobial susceptibility patterns, pulsed-field gel electrophoresis (PFGE) of genomic DNA, and restriction fragment length polymorphism (RFLP) of PCR-amplified rRNA operons. Three susceptibility patterns were defined by testing 22 antimicrobial agents, with 14 isolates resistant to all agents. PFGE of XbaI-genomic DNA fragments divided the 17 isolates into 9 distinct types. One type, seen in 6 isolates showing identical patterns of approximately 35 fragments of 10 to 350 kb, was defined as the outbreak strain. Another 4 types, in a total of 6 isolates, were considered closely related to the outbreak strain; 2 types in 1 isolate each were possibly related to the outbreak strain; and 2 types in a total of 3 isolates were different from the outbreak strain. All 12 outbreak or closely related isolates were from patients in the surgical intensive care unit and a surgical ward, and were different from isolates in other wards, clearly indicating an outbreak of P. putida. Only two types were defined by the RFLP of 4.5 kb PCR-amplified rRNA operons; one type was seen in 15 isolates, while the other was seen in only 2 isolates. In conclusion, PFGE of genomic DNA is a highly discriminatory and reproducible method for epidemiological typing of P. putida.

DNA, Bacterial↗

PubMed1985

Alterations in the number of rRNA operons within the Bacillus subtilis genome.

Deletions and additions of rRNA gene sets in Bacillus subtilis were observed by Southern hybridizations using cloned radiolabeled rDNA sequences. Of the ten rRNA gene sets found in B. subtilis 168M or NCTC3610, one was deleted in strains possessing the leuB1, ilvC1, argA2 and pheA1 mutations. Among EcoRI restriction fragments of genomic DNA products, a 2.9-kb 23S rRNA homolog was missing. In HindIII digest, both 5.5- and 5.1-kb hybrid bands were lost with 16S and 23S probes, respectively. Similarly, genomic DNAs digested with SmaI showed the absence of both 2.1- and 2.0-kb fragments that hybridized to 16S and 5S sequences, respectively, in wild-type genomes. In contrast, B. subtilis strain 166 and its derivatives displayed a gain of a 3.3-kb HindIII fragment homologous to 16S rRNA. Transforming the ilvC1 and leuB1 mutations into new genetic backgrounds revealed in some clones the concomitant introduction of the ribosomal defect. Transformations with the slightly heterologous donor DNA from strain W23 yielded some Leu+ and Arg+ transformants with altered hybridization patterns when probed with cloned sequences. We propose that the deletion of the rRNA operon occurred in the ilv-leu gene cluster of the B. subtilis genome as a result of unequal recombination between redundant sequences.

Bacillus subtilis↗

PubMed1987

Analysis of rRNA operons in Ureaplasma urealyticum.

Physical maps of Ureaplasma urealyticum serotypes I and IV were obtained by differential hybridization of DNA restriction fragments to probes derived from the Escherichia coli rrnB operon. Each of the organisms contained two rRNA operons with genes linked in the typical order 5'-16S-23S-5S-3'. There was no BclI site in either of the operons, but there were several internal HindIII and EcoRI sites showing significant heterogeneity in their respective position in both of the serotypes.

DNA, Bacterial↗