Genomes and Genes
Summary: Genetic loci which direct transcription of ribosomal RNA in bacterial operons. They are designated rrnB, rrnC, rrnD, etc. according to the structural position of the transcription unit in the DNA sequence.
- Nanamiya H, Sato M, Masuda K, Sato M, Wada T, Suzuki S, et al. Bacillus subtilis mutants harbouring a single copy of the rRNA operon exhibit severe defects in growth and sporulation. Microbiology. 2010;156:2944-52 pubmed publisher..It is difficult to determine the functional significance of the heterogeneity of each rRNA operon fully due to the existence of multiple rRNA operons and because the sequence heterogeneity among the rRNA genes ..
- Candela M, Vitali B, Matteuzzi D, Brigidi P. Evaluation of the rrn operon copy number in Bifidobacterium using real-time PCR. Lett Appl Microbiol. 2004;38:229-32 pubmedA real-time PCR-based method was developed to evaluate the Bifidobacterium rRNA operon copy number. As a result of their repetitive nature, rRNA operons are very suitable targets for chromosomal integration of heterologous genes...
- Ma L, Martin D. Single-nucleotide polymorphisms in the rRNA operon and variable numbers of tandem repeats in the lipoprotein gene among Mycoplasma genitalium strains from clinical specimens. J Clin Microbiol. 2004;42:4876-8 pubmedWe characterized the single-nucleotide polymorphisms in the rRNA operon and variable numbers of tandem repeats in the lipoprotein gene MG309 among Mycoplasma genitalium strains from clinical specimens by PCR and sequencing...
- Ross W, Gosink K, Salomon J, Igarashi K, Zou C, Ishihama A, et al. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science. 1993;262:1407-13 pubmed..Since the same alpha mutations also block activation by some transcription factors, mechanisms of promoter stimulation by upstream DNA elements and positive control by certain transcription factors may be related. ..
- Hashimoto J, Stevenson B, Schmidt T. Rates and consequences of recombination between rRNA operons. J Bacteriol. 2003;185:966-72 pubmed..coli. These findings are discussed in the context of a conceptual model describing the presence of sequence heterogeneity in coevolving rRNA genes. ..
- de Vries M, Siezen R, Wijman J, Zhao Y, Kleerebezem M, de Vos W, et al. Comparative and functional analysis of the rRNA-operons and their tRNA gene complement in different lactic acid bacteria. Syst Appl Microbiol. 2006;29:358-67 pubmed..An active promoter was also identified within the Lb. plantarum rrnC operon preceding a cluster of 17 tRNA genes. ..
- Stewart F, Cavanaugh C. Intragenomic variation and evolution of the internal transcribed spacer of the rRNA operon in bacteria. J Mol Evol. 2007;65:44-67 pubmed..This study underscores the potential contribution of interoperon ITS variation to bacterial microdiversity studies, as well as unequivocally demonstrates the pervasiveness of concerted evolution in the rrn gene family. ..
- Kothapalli S, Nair S, Alokam S, Pang T, Khakhria R, Woodward D, et al. Diversity of genome structure in Salmonella enterica serovar Typhi populations. J Bacteriol. 2005;187:2638-50 pubmed..The phage types were determined, and the origins of the phage types appeared to be independent of the origins of the genome types. ..
- Dennis P, Ehrenberg M, Bremer H. Control of rRNA synthesis in Escherichia coli: a systems biology approach. Microbiol Mol Biol Rev. 2004;68:639-68 pubmed..This control of rrn P1 promoter strength forms part of a larger feedback loop that adjusts the synthesis of ribosomes to the availability of amino acids via amino acid-dependent control of ppGpp accumulation. ..
- Hirvonen C, Ross W, Wozniak C, Marasco E, Anthony J, Aiyar S, et al. Contributions of UP elements and the transcription factor FIS to expression from the seven rrn P1 promoters in Escherichia coli. J Bacteriol. 2001;183:6305-14 pubmed..These studies have implications for the control of gene expression of unlinked multigene families. ..
- Wang Y, Zhang Z, Ramanan N. The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J Bacteriol. 1997;179:3270-6 pubmed..Both types of 16S rRNA genes are transcribed and processed as determined by Northern (RNA) hybridization and reverse transcriptase-mediated PCR. ..
- Echeita M, Usera M. Chromosomal rearrangements in Salmonella enterica serotype typhi affecting molecular typing in outbreak investigations. J Clin Microbiol. 1998;36:2123-6 pubmed..We conclude that genetic rearrangements can occur during the emergence of an outbreak. ..
- Barker M, Gaal T, Josaitis C, Gourse R. Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J Mol Biol. 2001;305:673-88 pubmed..The accompanying paper evaluates potential models for positive control of amino acid promoters by ppGpp that might explain the requirement of ppGpp for amino acid prototrophy. ..
- Zacharias M, Göringer H, Wagner R. Analysis of the Fis-dependent and Fis-independent transcription activation mechanisms of the Escherichia coli ribosomal RNA P1 promoter. Biochemistry. 1992;31:2621-8 pubmed..In addition, the study demonstrates that both the helical geometry and the absolute distance of the UAS region relative to the promoter are crucial for transcription activation. ..
- Menéndez M, Rebollo M, Núñez M, Cox R, Garcia M. Analysis of the precursor rRNA fractions of rapidly growing mycobacteria: quantification by methods that include the use of a promoter (rrnA P1) as a novel standard. J Bacteriol. 2005;187:534-43 pubmed..fortuitum infected macrophages. It was shown that this bacterium actively synthesizes rRNA during the course of infection and that one of its rrn operons is preferentially used under such conditions...
- Matthews T, Rabsch W, Maloy S. Chromosomal rearrangements in Salmonella enterica serovar Typhi strains isolated from asymptomatic human carriers. MBio. 2011;2:e00060-11 pubmed publisher..Our results support the hypothesis that the restricted lifestyle of host-specific Salmonella is responsible for the frequent chromosomal rearrangements in these serovars. ..
- Jensen S, Duperron S, Birkeland N, Hovland M. Intracellular Oceanospirillales bacteria inhabit gills of Acesta bivalves. FEMS Microbiol Ecol. 2010;74:523-33 pubmed publisher..excavata from a rock-wall in the Trondheimsfjord. Purified gill DNA contained one dominant bacterial rRNA operon as indicated from analysis of broad range bacterial PCR amplicons in denaturant gradient gels, in clone ..
- Briant D, Hankins J, Cook M, Mackie G. The quaternary structure of RNase G from Escherichia coli. Mol Microbiol. 2003;50:1381-90 pubmed..We propose that many of the cysteines in RNase G lie on its surface and define, in part, the subunit-subunit interface. ..
- Macbeth M, Wool I. The phenotype of mutations of G2655 in the sarcin/ricin domain of 23 S ribosomal RNA. J Mol Biol. 1999;285:965-75 pubmed..Ribosomes with G2655Delta, G2655C, or G2655U mutations in 23 S rRNA are not active in protein synthesis, whereas those with the G2655A transition mutation suffer decreased activity. ..
- Murray H, Appleman J, Gourse R. Regulation of the Escherichia coli rrnB P2 promoter. J Bacteriol. 2003;185:28-34 pubmed..The rrnB P2 core promoter sequence (-37 to +7) is sufficient to serve as the target for growth rate-dependent regulation. ..
- Sander P, Belova L, Kidan Y, Pfister P, Mankin A, Bottger E. Ribosomal and non-ribosomal resistance to oxazolidinones: species-specific idiosyncrasy of ribosomal alterations. Mol Microbiol. 2002;46:1295-304 pubmed..In agreement with the results of the in vitro assay, class II mutants show a wild-type sequence of the complete rRNA operon. The lack of cross-resistance of the class II mutants to other antibiotics suggests a resistance mechanism ..
- Hill C. Large genomic sequence repetitions in bacteria: lessons from rRNA operons and Rhs elements. Res Microbiol. 1999;150:665-74 pubmed..Genomic sequencing of different species as well as comparative sequencing of independent isolates is providing provocative insights into previously obscure issues. ..
- Gonzalez Escalona N, Romero J, Guzman C, Espejo R. Variation in the 16S-23S rRNA intergenic spacer regions in Vibrio parahaemolyticus strains are due to indels nearby their tRNAGlu. FEMS Microbiol Lett. 2006;256:38-43 pubmed..Comparison of the nucleotide sequence between spacer classes suggests that intragenomic nonreciprocal recombination causes the size variations observed in the spacer regions of V. parahaemolyticus strains. ..
- Tu D, Blaha G, Moore P, Steitz T. Gene replacement in Haloarcula marismortui: construction of a strain with two of its three chromosomal rRNA operons deleted. Extremophiles. 2005;9:427-35 pubmed..The structural consequences of these and other such mutations can be determined with unusual accuracy because crystals of the large ribosomal subunit of H. marismortui diffract to atomic resolution...
- Boubakri H, de Septenville A, Viguera E, Michel B. The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo. EMBO J. 2010;29:145-57 pubmed publisher..Finally, Rep and UvrD also act at inverted sequences other than rrn, and promote replication through highly transcribed regions in wild-type E. coli. ..
- Marin B. Nested in the Chlorellales or independent class? Phylogeny and classification of the Pedinophyceae (Viridiplantae) revealed by molecular phylogenetic analyses of complete nuclear and plastid-encoded rRNA operons. Protist. 2012;163:778-805 pubmed publisher..For the present study, complete nuclear and plastid-encoded rRNA operon sequences have been determined for 37 taxa of green algae including 6 members of the Pedinophyceae, providing ..
- Yano K, Wada T, Suzuki S, Tagami K, Matsumoto T, Shiwa Y, et al. Multiple rRNA operons are essential for efficient cell growth and sporulation as well as outgrowth in Bacillus subtilis. Microbiology. 2013;159:2225-36 pubmed publisher..The results suggested that the copy number of the rrn operon has a major influence on cellular processes such as growth rate and sporulation frequency. ..
- Pabbaraju K, Miller W, Sanderson K. Distribution of intervening sequences in the genes for 23S rRNA and rRNA fragmentation among strains of the Salmonella reference collection B (SARB) and SARC sets. J Bacteriol. 2000;182:1923-9 pubmed
- Zhi H, Wang X, Cabrera J, Johnson R, Jin D. Fis stabilizes the interaction between RNA polymerase and the ribosomal promoter rrnB P1, leading to transcriptional activation. J Biol Chem. 2003;278:47340-9 pubmed..coli cells are emerging from a growth-arrested phase to a rapid growth phase. Thus, our results resolve an apparent paradox of the role of Fis in vitro and in vivo in the field. ..
- Davies K, Lewis P. Localization of rRNA synthesis in Bacillus subtilis: characterization of loci involved in transcription focus formation. J Bacteriol. 2003;185:2346-53 pubmed..This suggests that transcription foci comprise only the seven origin-proximal operons rrnO, rrnA, rrnJ, rrnW, rrnI, rrnH, and rrnG. These results have important implications for our understanding of microbial chromosome structure. ..
- Broccoli S, Rallu F, Sanscartier P, Cerritelli S, Crouch R, Drolet M. Effects of RNA polymerase modifications on transcription-induced negative supercoiling and associated R-loop formation. Mol Microbiol. 2004;52:1769-79 pubmed
- Itoh T, Suzuki K, Nakase T. Occurrence of introns in the 16S rRNA genes of members of the genus Thermoproteus. Arch Microbiol. 1998;170:155-61 pubmed..Occurrence of introns at the same insertion sites in the three strains would allow tracing of the evolutionary movements of these introns...
- Moissenet D, Bidet P, Garbarg Chenon A, Arlet G, Vu Thien H. Ralstonia paucula (Formerly CDC group IV c-2): unsuccessful strain differentiation with PCR-based methods, study of the 16S-23S spacer of the rRNA operon, and comparison with other Ralstonia species (R. eutropha, R. pickettii, R. gilardii, and R. sol. J Clin Microbiol. 2001;39:381-4 pubmed..The 16S-23S rDNA intergenic spacer of R. paucula contains the tRNA(Ile) and tRNA(Ala) genes, which are identical to genes described for R. pickettii and R. solanacearum. ..
- Kofoed C, Vester B. Interaction of avilamycin with ribosomes and resistance caused by mutations in 23S rRNA. Antimicrob Agents Chemother. 2002;46:3339-42 pubmed..It is inferred that avilamycin interacts with the ribosomes at the ribosomal A-site interfering with initiation factor IF2 and tRNA binding in a manner similar to evernimicin. ..
- Stjepandic D, Weinel C, Hilbert H, Koo H, Diehl F, Nelson K, et al. The genome structure of Pseudomonas putida: high-resolution mapping and microarray analysis. Environ Microbiol. 2002;4:819-23 pubmed..A tiling path of clones was selected, from the shotgun clones used for sequencing, for the production of DNA microarrays that represent the entire genome including its non-coding portions. ..
- Osorio C, Collins M, Romalde J, Toranzo A. Variation in 16S-23S rRNA intergenic spacer regions in Photobacterium damselae: a mosaic-like structure. Appl Environ Microbiol. 2005;71:636-45 pubmed..The main source of variation between ITS variants was due to different combinations of DNA sequence blocks, constituting a mosaic-like structure...
- Cabrera J, Jin D. 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. J Bacteriol. 2006;188:4007-14 pubmed..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 ..
- Cummings N, Connerton I. The Bacillus subtilis 168 chromosome from sspE to katA. Microbiology. 1997;143 ( Pt 6):1855-9 pubmed
- Chelo I, Zé Zé L, Chambel L, Tenreiro R. Physical and genetic map of the Weissella paramesenteroides DSMZ 20288T chromosome and characterization of different rrn operons by ITS analysis. Microbiology. 2004;150:4075-84 pubmed..paramesenteroides chromosome. The transcription direction of rrn loci was determined and three different rrn clusters were recognized regarding the presence/absence of tRNA genes in ITS regions. ..
- Xu W, Pagel F, Murgola E. Mutations in the GTPase center of Escherichia coli 23S rRNA indicate release factor 2-interactive sites. J Bacteriol. 2002;184:1200-3 pubmed
- Pérez Luz S, Fernandez J, Rodriguez Valera F, Pascual L, Moreno C, Amo A, et al. Sequence diversity of the internal transcribed spacer (ITS) region of the rRNA operons among different serogroups of Legionella pneumophila isolates. Syst Appl Microbiol. 2002;25:212-9 pubmed..Two of the 16S-23S rRNA ITS presented a tRNA Ala and the third one a tRNA Ile. Nevertheless, the variability expected in this region of the operon was not found and the rest of the ITS contained only punctual mutations. ..
- Todo K, Goto T, Honda A, Tamura M, Miyamoto K, Fujita S, et al. Comparative analysis of the four rRNA operons in Finegoldia magna ATCC29328. Syst Appl Microbiol. 2004;27:18-26 pubmed..In light of previous reports, we also assessed the correlation between intercistronic rRNA sequence differences and distances between the operons, but no positive correlation was seen in this strain...
- Clark M, Baumann L, Thao M, Moran N, Baumann P. Degenerative minimalism in the genome of a psyllid endosymbiont. J Bacteriol. 2001;183:1853-61 pubmed..These observations suggest that the C. ruddii genome is not subject to constraints that limit the evolution of other known eubacteria. ..
- Yang J, Zhang W, Yuan T, Zhou J. Genotypic characteristics of the rrn operon and genome of indigenous soybean Bradyrhizobia in cropping zones of China. Can J Microbiol. 2006;52:968-76 pubmed..liaoningense. Strains in Group III, mainly isolated from Central and East China, were closely related to the reference strains of B. japonicum. Strains in Group IV belonged to B. elkanii. ..
- Suzuki J, Sriraman P, Svab Z, Maliga P. Unique architecture of the plastid ribosomal RNA operon promoter recognized by the multisubunit RNA polymerase in tobacco and other higher plants. Plant Cell. 2003;15:195-205 pubmedExpression of the plastid rRNA operon (rrn) during development is highly regulated at the level of transcription...
- Afflerbach H, Schroder O, Wagner R. Effects of the Escherichia coli DNA-binding protein H-NS on rRNA synthesis in vivo. Mol Microbiol. 1998;28:641-53 pubmed..Determination of the cellular ppGpp concentrations revealed that H-NS does not mediate its function via alterations in the synthesis of the global effector ppGpp. ..
- Everett K, Thao M, Horn M, Dyszynski G, Baumann P. Novel chlamydiae in whiteflies and scale insects: endosymbionts 'Candidatus Fritschea bemisiae' strain Falk and 'Candidatus Fritschea eriococci' strain Elm. Int J Syst Evol Microbiol. 2005;55:1581-7 pubmed..We concluded that it was appropriate to propose 'Candidatus Fritschea bemisiae' strain Falk and 'Candidatus Fritschea eriococci' strain Elm as members of the family Simkaniaceae in the Chlamydiales...
- Kolmsee T, Delic D, Agyenim T, Calles C, Wagner R. Differential stringent control of Escherichia coli rRNA promoters: effects of ppGpp, DksA and the initiating nucleotides. Microbiology. 2011;157:2871-9 pubmed publisher..Our results support the notion that the seven rRNA operons are differentially regulated and underline the importance of a concerted activity between ppGpp, DksA and an adequate concentration of the respective iNTP. ..
- Srivastava A, Schlessinger D. Structure and organization of ribosomal DNA. Biochimie. 1991;73:631-8 pubmed
- Dingman D. Characterization of Paenibacillus popilliae rRNA operons. Can J Microbiol. 2004;50:779-91 pubmed..Comparative analysis of the nucleotides on the 3' end of the 16S rRNA gene suggests that translation of P. popilliae mRNA may occur in Bacillus subtilis and Escherichia coli...
- Kerkhof L, Speck M. Ribosomal RNA gene dosage in marine bacteria. Mol Mar Biol Biotechnol. 1997;6:260-7 pubmed..This report presents important preliminary data for developing quantitative molecular methods to address population dynamics of marine based of 16S rRNA sequences. ..
- Pagel F, Zhao S, Hijazi K, Murgola E. Phenotypic heterogeneity of mutational changes at a conserved nucleotide in 16 S ribosomal RNA. J Mol Biol. 1997;267:1113-23 pubmed..Finally, the association of a variety of phenotypes with different changes at the same nucleotide may eventually shed light on speculations about the coevolution of parts of ribosomal RNA with other translational macromolecules. ..