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Lui LM, Nielsen TN, Arkin AP. A method for achieving complete microbial genomes and improving bins from metagenomics data. PLoS Comput Biol 2021; 17:e1008972. [PMID: 33961626 PMCID: PMC8172020 DOI: 10.1371/journal.pcbi.1008972] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 06/02/2021] [Accepted: 04/16/2021] [Indexed: 11/19/2022] Open
Abstract
Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app.
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Affiliation(s)
- Lauren M. Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Torben N. Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, CA, United States of America
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2
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Iost I, Chabas S, Darfeuille F. Maturation of atypical ribosomal RNA precursors in Helicobacter pylori. Nucleic Acids Res 2019; 47:5906-5921. [PMID: 31006803 PMCID: PMC6582327 DOI: 10.1093/nar/gkz258] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/28/2019] [Accepted: 04/18/2019] [Indexed: 01/01/2023] Open
Abstract
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.
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Affiliation(s)
- Isabelle Iost
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, France
| | - Sandrine Chabas
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, France
| | - Fabien Darfeuille
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, France
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3
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Wu CM, Wu H, Ning Y, Wang J, Du X, Shen J. Induction of macrolide resistance inMycoplasma gallisepticumin vitro and its resistance-related mutations within domain V of 23S rRNA. FEMS Microbiol Lett 2005; 247:199-205. [PMID: 15936901 DOI: 10.1016/j.femsle.2005.05.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2005] [Revised: 05/03/2005] [Accepted: 05/04/2005] [Indexed: 11/21/2022] Open
Abstract
Antibiotic-resistant mutants of Mycoplasma gallisepticum were selected in vitro from the susceptible strains S6 and BG44T by serial passages in stepwise concentrations of erythromycin, tylosin, or tilmicosin. High resistance to erythromycin or tilmicosin developed readily, whereas resistance to tylosin developed only after greater numbers of passages. Three mutants selected by each selector antibiotic were cloned and detected, and all cloned mutants exhibited cross-resistance to the three selector antibiotics as well as to lincomycin. Portions of the genes encoding domain V of 23S rRNA of the cloned mutants were amplified by PCR, and their nucleotide sequences were compared to those of the susceptible parent strains. Five of the six mutants selected by erythromycin harbored an A2058G (Escherichia coli numbering) mutation in one of the two 23S rRNA. One of the six mutants selected by erythromycin harbored a G2057A mutation and an A2059G mutation in the other 23S rRNA. In tilmicosin-selected mutants, two mutations, A2058G and A2503U, occurred in one of the two 23S rRNA. No mutation was detected in the two 23S rRNA of tylosin-selected mutants with low-level resistance. Mutations at homologous locations in the 23S rRNA of other macrolide-resistant bacteria indicate that the phenotype of macrolide resistance occurring in M. gallisepticum is strongly associated with point mutations in domain V of 23S rRNA.
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Affiliation(s)
- Cong-Ming Wu
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, China
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4
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Papazisi L, Gorton TS, Kutish G, Markham PF, Browning GF, Nguyen DK, Swartzell S, Madan A, Mahairas G, Geary SJ. The complete genome sequence of the avian pathogen Mycoplasma gallisepticum strain R(low). MICROBIOLOGY (READING, ENGLAND) 2003; 149:2307-2316. [PMID: 12949158 DOI: 10.1099/mic.0.26427-0] [Citation(s) in RCA: 181] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The complete genome of Mycoplasma gallisepticum strain R(low) has been sequenced. The genome is composed of 996,422 bp with an overall G+C content of 31 mol%. It contains 742 putative coding DNA sequences (CDSs), representing a 91 % coding density. Function has been assigned to 469 of the CDSs, while 150 encode conserved hypothetical proteins and 123 remain as unique hypothetical proteins. The genome contains two copies of the rRNA genes and 33 tRNA genes. The origin of replication has been localized based on sequence analysis in the region of the dnaA gene. The vlhA family (previously termed pMGA) contains 43 genes distributed among five loci containing 8, 2, 9, 12 and 12 genes. This family of genes constitutes 10.4% (103 kb) of the total genome. Two CDSs were identified immediately downstream of gapA and crmA encoding proteins that share homology to cytadhesins GapA and CrmA. Based on motif analysis it is predicted that 80 genes encode lipoproteins and 149 proteins contain multiple transmembrane domains. The authors have identified 75 proteins putatively involved in transport of biomolecules, 12 transposases, and a number of potential virulence factors. The completion of this sequence has spawned multiple projects directed at defining the biological basis of M. gallisepticum.
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Affiliation(s)
- Leka Papazisi
- Department of Pathobiology and Veterinary Science, The University of Connecticut, Storrs, CT 06269-3089, USA
- Center of Excellence for Vaccine Research, The University of Connecticut, Storrs, CT 06269-3089, USA
| | - Timothy S Gorton
- Department of Pathobiology and Veterinary Science, The University of Connecticut, Storrs, CT 06269-3089, USA
- Center of Excellence for Vaccine Research, The University of Connecticut, Storrs, CT 06269-3089, USA
| | - Gerald Kutish
- Plum Island Animal Disease Center, US Department of Agriculture, Greenport, NY 11944, USA
| | - Philip F Markham
- Department of Veterinary Science, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Glenn F Browning
- Department of Veterinary Science, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Di Kim Nguyen
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | | | - Anup Madan
- The Institute for Systems Biology, Seattle, WA 98103-8904, USA
| | | | - Steven J Geary
- Department of Pathobiology and Veterinary Science, The University of Connecticut, Storrs, CT 06269-3089, USA
- Center of Excellence for Vaccine Research, The University of Connecticut, Storrs, CT 06269-3089, USA
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5
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Massung RF, Lee K, Mauel M, Gusa A. Characterization of the rRNA genes of Ehrlichia chaffeensis and Anaplasma phagocytophila. DNA Cell Biol 2002; 21:587-96. [PMID: 12215262 DOI: 10.1089/104454902320308960] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The rRNA genes of Ehrlichia chaffeensis and Anaplasma phagocytophila have been analyzed. The 16S rRNA genes were previously characterized for both of these agents. Southern hybridization was used to show that there are single copies of both the 16S and 23S rRNA genes in the genomes of each organism, and that the 16S rRNA genes were upstream from the 23S rRNA genes by at least 16 and 11 Kb for E. chaffeensis and A. phagocytophila, respectively. PCR amplification and gene walking was used to sequence the 23S and 5S rRNA genes, and show that these genes are contiguous and are likely expressed as a single operon. The level of homology between the E. chaffeensis and A. phagocytophila 23S and 5S rRNA genes, and 23S-5S spacers, was 91.8, 81.5, and 40%, respectively. To confirm the hybridization data, genome walking was used to sequence downstream of the 16S rRNA genes, and although no tRNA genes were identified, open reading frames encoding homologues of the Escherichia coli succinate dehydrogenase, subunit C, were found in both E. chaffeensis and A. phagocytophila. Phylogenetic analysis using the 23S rRNA gene suggests that reorganization of the phylum Proteobacteria by division of the class Alphaproteobacteria into two separate subclasses, may be appropriate.
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Affiliation(s)
- Robert F Massung
- Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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6
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Skamrov A, Feoktistova E, Goldman M, Beabealashvilli R. Mycoplasma gallisepticum rpoA gene cluster. FEMS Microbiol Lett 2002; 208:281-5. [PMID: 11959450 DOI: 10.1111/j.1574-6968.2002.tb11095.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Two conservative gene clusters, the S10 ribosomal protein region and one (of the two) set of rRNA genes, were split in a genome crossover rearrangement event in Mycoplasma gallisepticum. As a result of the rearrangement the major part of the S10 ribosomal protein cluster is located upstream of genes for 23S-5S rRNA (rrn23-5), but the genes infA-rpl36-rps13-rpoA-rpl17 are located immediately downstream of the isolated gene for 16S rRNA (rrn16). A new ribosomal protein cluster infA-rpl36-rps13-rpoA-rpl17-rps16-trmD-rpl19 was formed. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis revealed that this ribosomal protein cluster is an operon.
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Affiliation(s)
- Andrei Skamrov
- National Cardiology Research Center, Ministry of Health of the Russian Federation, 3rd Cherepkovskaya str., 15A, 121552 Moscow, Russia.
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7
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Ho KC, Tsai CC, Chung TL. Organization of ribosomal RNA genes from a Loofah witches' broom phytoplasma. DNA Cell Biol 2001; 20:115-22. [PMID: 11244569 DOI: 10.1089/104454901750070328] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Using the technique of integrative mapping with three vectors carrying chromosomal rDNA sequences, one of two rRNA operons of loofah witches' broom (LfWB) phytoplasma was constructed. This is the first complete rRNA operon of a phytoplasma to be reported. The operon has a context of 5'-16S-23S-5S-3' with a tRNA(Ile) gene in the ITS and tRNA(Val) and tRNA(Asn) genes downstream from the 5S rRNA gene. Although the other operon has not been cloned, the DNA sequence of a PCR-amplified product shows that it has no tRNA(Ile) gene in the ITS region. The complete nucleotide sequences of 16S, 23S, and 5S rDNA are 1538, 2864, and 113 bp, respectively. Five -10-like sequences, but no -35 sequences, were found within a 494-bp leader region. There was a TG dinucleotide two nucleotides upstream from each -10-like sequence. The existence of a TG dinucleotide at this position has been reported to enhance the efficiency of a promoter without a -35 region. The regions immediately flanking the 5' and 3' ends of 16S and 23S rDNA can form long basepaired stems that contain sites for processing by RNase III. No obvious sequence for a rho-dependent or rho-independent termination site was found downstream from the tRNA(Asn) gene. The transcription may stop within a pyrimidine-rich region, as has been reported for several polypeptide-encoding genes and rRNA operons of archaeobacteria. The presence of the tRNA genes downstream from the 5S rRNA gene in the rRNA operon of LfWB phytoplasma further supports the hypothesis that phytoplasmas are phylogenetically closer to acholeplasmas than to mycoplasmas. The phylogenetic relatedness of LfWB phytoplasma to other phytoplasmas is discussed on the basis of the nucleotide sequence of rRNA genes and ITS.
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MESH Headings
- 3' Untranslated Regions/analysis
- 5' Untranslated Regions/analysis
- Amino Acid Sequence
- Base Sequence
- Cloning, Molecular
- DNA, Ribosomal Spacer/analysis
- Gene Dosage
- Gene Order
- Genes, Bacterial
- Molecular Sequence Data
- Mycoplasma/genetics
- Operon
- Plants/microbiology
- RNA, Bacterial/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/isolation & purification
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/isolation & purification
- Sequence Analysis, DNA
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Affiliation(s)
- K C Ho
- Department of Botany, National Taiwan University, Taipei, Taiwan
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8
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Vester B, Douthwaite S. Macrolide resistance conferred by base substitutions in 23S rRNA. Antimicrob Agents Chemother 2001; 45:1-12. [PMID: 11120937 PMCID: PMC90232 DOI: 10.1128/aac.45.1.1-12.2001] [Citation(s) in RCA: 380] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- B Vester
- Department of Molecular Biology, University of Copenhagen, DK-1307 Copenhagen K, Denmark.
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9
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Skamrov AV, Gol’dman MA, Feoktistova ES, Bibilashvili RS. Sequencing and analysis of aMycoplasma gallisepticum A5969 chromosome region containing the S10 andrrn23-5 operons. Mol Biol 2000. [DOI: 10.1007/bf02759662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Taylor DE, Ge Z, Purych D, Lo T, Hiratsuka K. Cloning and sequence analysis of two copies of a 23S rRNA gene from Helicobacter pylori and association of clarithromycin resistance with 23S rRNA mutations. Antimicrob Agents Chemother 1997; 41:2621-8. [PMID: 9420030 PMCID: PMC164180 DOI: 10.1128/aac.41.12.2621] [Citation(s) in RCA: 170] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In this study, two identical copies of a 23S-5S gene cluster, which are separately situated within the Helicobacter pylori UA802 chromosome, were cloned and sequenced. Comparison of the DNA sequence of the H. pylori 23S rRNA gene with known sequences of other bacterial 23S rRNA genes indicated that the H. pylori UA802 23S rRNA genes are closely related to those of Campylobacter spp. and therefore belong in the proposed Proteobacteria subdivision. The 5'-terminal nucleotide T or A of the 23S rRNA is close to a Pribnow box which could be a -10 region of the transcription promoter for the 23S rRNA gene, suggesting that a posttranscriptional process is likely not involved in the maturation of the H. pylori 23S rRNA. Clinical isolates of H. pylori resistant to clarithromycin were examined by using natural transformation and pulsed-field gel electrophoresis. Cross-resistance to clarithromycin and erythromycin, which was transferred by natural transformation from the Cla(r) Ery(r) donor strain H. pylori E to the Cla(s) Ery(s) recipient strain H. pylori UA802, was associated with an single A-to-G transition mutation at position 2142 of both copies of the 23S rRNA in UA802 Cla(r) Ery(r) mutants. The transformation frequency for Cla(r) and Ery(r) was found to be approximately 2 x 10(-6) transformants per viable cell, and the MICs of both clarithromycin and erythromycin for the Cla(r) Ery(r) mutants were equal to those for the donor isolate. Our results confirmed the previous findings that mutations at positions 2142 and 2143 of the H. pylori 23S rRNA gene are responsible for clarithromycin resistance and suggest that acquisition of clarithromycin resistance in H. pylori could also result from horizontal transfer.
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Affiliation(s)
- D E Taylor
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Canada.
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Woo TH, Smythe LD, Symonds ML, Norris MA, Dohnt MF, Patel BK. Rapid distinction between Leptonema and Leptospira by PCR amplification of 16S-23S ribosomal DNA spacer. FEMS Microbiol Lett 1996; 142:85-90. [PMID: 8759793 DOI: 10.1111/j.1574-6968.1996.tb08412.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The PCR amplification of the genomic DNA of Leptonema illini strain 3055 using primers directed against conserved regions of the rRNA operon provided evidence that the 16S and 23S rRNA genes were linked via an intergenic spacer region. The sequencing of the intergenic spacer region indicated that it was 435 nucleotides in length and sequence similarity searches revealed that it bore no homology to any known sequences including tRNA available in databases. Further investigations using Southern blot hybridization revealed that there were two copies of these linked genes in the genome. However, similar PCR studies on a representative strain from each of the 23 serogroups of Leptospira interrogans, which are pathogenic, and eight strains from the 6 serogroups of Leptospira biflexa, which are non-pathogenic, revealed that the 16S and 23S rRNA genes were not linked.
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Affiliation(s)
- T H Woo
- School of Biomolecular and Biomedical Sciences, Faculty of Science and Technology, Griffith University, Nathan, Australia
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12
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Abstract
The genome of Mycoplasma gallisepticum A5969 contains a truncated pseudogene for 16S rRNA in addition to a single unsplit rRNA-operon and a second discontinuous set of rRNA genes. Other M. gallisepticum strains tested do not possess the truncated gene. This gene is almost identical to full-size isolated 16S rRNA gene starting from at least 500 nucleotides upstream of the coding sequence and ending at the 977th nucleotide within the structural part of 16S rRNA.
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Affiliation(s)
- A Skamrov
- Cardiology Research Center, Russian Academy of Medical Science, Moscow
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13
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Rouhbakhsh D, Baumann P. Characterization of a putative 23S-5S rRNA operon of Buchnera aphidicola (endosymbiont of aphids) unlinked to the 16S rRNA-encoding gene. Gene 1995; 155:107-12. [PMID: 7535281 DOI: 10.1016/0378-1119(94)00910-k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Buchnera aphidicola (Ba) is an endosymbiont of the aphid Schizaphis graminum. In order to obtain information on highly expressed genes, we have chosen to study Ba genes coding for rRNAs. Previously, the single-copy rrs gene was cloned and sequenced [Munson et al., Gene 137 (1993) 171-178], and found to constitute a single transcription unit unlinked to rrl and rrf. In the present study, a 6.1-kb Ba DNA fragment containing rrl was cloned into Escherichia coli (Ec) and sequenced. Based on sequence similarity to Ec, the following genes were identified: aroE-tRNA(Glu)-rrl-rrf-cysS. AroE and CysS had 48 and 54% amino acid (aa) identity, respectively, to the corresponding Ec proteins; tRNA(Glu), rrl and rrf had 80-90% nucleotide (nt) identity with the corresponding genes of Ec rrnB. Ba tRNA(Glu)-rrl-rrs appears to be part of a single transcriptional unit; a putative promoter and a Rho-independent terminator were identified. Comparisons of sequences of aroE-rrl from endosymbionts of seven additional species of aphids indicated conservation of the -35 (TTGACT) and -10 (TGTAA/TT) promoter regions, and boxA, tRNA(Glu) and boxC. Secondary structure analysis indicated that the Ba tRNA(Glu)-rrl-rrf operon resembled the homologous region of Ec rrnB. The results of this and previous studies indicate that Ba differs from most bacteria in having the single-copy rRNA genes organized into two transcription units.
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Affiliation(s)
- D Rouhbakhsh
- Microbiology Section, University of California, Davis 95616-8665, USA
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14
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Gorton TS, Goh MS, Geary SJ. Physical mapping of the Mycoplasma gallisepticum S6 genome with localization of selected genes. J Bacteriol 1995; 177:259-63. [PMID: 7798142 PMCID: PMC176583 DOI: 10.1128/jb.177.1.259-263.1995] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We report the construction of a physical map of the Mycoplasma gallisepticum S6 genome by field-inversion gel electrophoresis of DNA fragments generated by digestion of genomic DNA with rare-cutting restriction endonucleases. The size of the M. gallisepticum S6 genome was calculated to be approximately 1,054 kb. The loci of several genes have been assigned to the map by Southern hybridization utilizing specific gene probes.
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Affiliation(s)
- T S Gorton
- Department of Pathobiology, University of Connecticut, Storrs 06269-3089
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15
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Rouhbakhsh D, Moran NA, Baumann L, Voegtlin DJ, Baumann P. Detection of Buchnera, the primary prokaryotic endosymbiont of aphids, using the polymerase chain reaction. INSECT MOLECULAR BIOLOGY 1994; 3:213-217. [PMID: 7535631 DOI: 10.1111/j.1365-2583.1994.tb00169.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Members of the genus Buchnera constitute a distinct prokaryotic lineage containing the primary endosymbionts of aphids (Homoptera: Aphidoidea). Using synthetic oligonucleotides in conjunction with the polymerase chain reaction, we propose three approaches for the identification of members of this genus. The first is based on unique sequences within rrs (gene coding for 16S ribosomal RNA). The second is based on a different and unique organization of the ribosomal RNA operons of Buchnera and the close proximity of aroE upstream of rrl (gene coding for 23S rRNA). The third is based on the linkage relationship of argS which is upstream of rrs. Validation of these three approaches requires their more extensive application.
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Affiliation(s)
- D Rouhbakhsh
- Microbiology Section, University of California, Davis 95616-8665
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16
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Konkel ME, Marconi RT, Mead DJ, Cieplak W. Identification and characterization of an intervening sequence within the 23S ribosomal RNA genes of Campylobacter jejuni. Mol Microbiol 1994; 14:235-41. [PMID: 7530317 DOI: 10.1111/j.1365-2958.1994.tb01284.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Campylobacter jejuni is a significant cause of bacterial enteritis in humans. Three of seven C. jejuni isolates examined were found to contain fragmented 23S rRNA. The occurrence of fragmented 23S rRNA correlated with the presence of an intervening sequence (IVS) within the 23S rRNA genes. The IVS is 157 nucleotides in length and replaces an eight nucleotide sequence in the 23S rRNA genes of C. jejuni isolates that contain intact 23S rRNA. The two ends of the IVS share 31 bases of complementarity that could form a stem-loop structure. Fragmentation of the 23S ribosomal RNA results from the excision of the IVS from the transcribed RNA; the 3' cleavage site maps within the putative stem-loop formed by the IVS. Southern hybridization analysis revealed that the IVS is not present in the genomes of isolates that contain intact 23S rRNA, suggesting that the IVS is not derived from Campylobacter chromosomal sequences. The C. jejuni IVS is located at a position analogous to that of the IVSs found in both Salmonella and Yersinia spp.
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MESH Headings
- Base Sequence
- Biological Evolution
- Blotting, Northern
- Blotting, Southern
- Campylobacter jejuni/genetics
- DNA Primers
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, Bacterial
- Introns
- Molecular Sequence Data
- Nucleic Acid Conformation
- Oligonucleotide Probes
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
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Affiliation(s)
- M E Konkel
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840
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17
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Abstract
A combined physical and genetic map of the Serpulina hyodysenteriae B78T genome was constructed by using pulsed-field gel electrophoresis and DNA blot hybridizations. The S. hyodysenteriae genome is a single circular chromosome about 3.2 Mb in size. The physical map of the chromosome was constructed with the restriction enzymes BssHII, EclXI, NotI, SalI, and SmaI. The physical map was used to constructed a linkage map for genes encoding rRNA, flagellum subunit proteins, DNA gyrase, NADH oxidase, and three distinct hemolysins. Several flaB2-related loci, encoding core flagellum subunit proteins, were detected and are dispersed around the chromosome. The rRNA gene organization in S. hyodysenteriae is unusual. S. hyodysenteriae has one gene each for 5S (rrf), 16S (rrs), and 23S (rrl) rRNAs. The rrf and rrl genes are closely linked (within 5 kb), while the rrs gene is about 860 kb from the other two rRNA genes. Using a probe for the S. hyodysenteriae gyrA gene, we identified a possible location for the chromosomal replication origin. The size and genetic organization of the S. hyodysenteriae chromosome are different from those of previously characterized spirochetes.
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Affiliation(s)
- R L Zuerner
- Leptospirosis and Mycobacteriosis Research Unit, U.S. Department of Agriculture, Ames, Iowa 50010
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18
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Munson MA, Baumann L, Baumann P. 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. Gene 1993; 137:171-8. [PMID: 7507875 DOI: 10.1016/0378-1119(93)90003-l] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
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)
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Affiliation(s)
- M A Munson
- Microbiology Section, University of California, Davis 95616-8665
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19
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Kim NW, Lombardi R, Bingham H, Hani E, Louie H, Ng D, Chan VL. Fine mapping of the three rRNA operons on the updated genomic map of Campylobacter jejuni TGH9011 (ATCC 43431). J Bacteriol 1993; 175:7468-70. [PMID: 8226692 PMCID: PMC206892 DOI: 10.1128/jb.175.22.7468-7470.1993] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The three rRNA gene loci of Campylobacter jejuni TGH9011 (ATCC 43431) were cloned. All three rRNA operons were shown to possess a contiguous 16S-23S structure and contain intercistronic tRNA(Ala) and tRNA(Ile). The three RNA operons and additional 14 genetic markers were mapped in the updated genomic map of C. jejuni TGH9011, which now has a total of 24 genetic markers.
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Affiliation(s)
- N W Kim
- Department of Microbiology, University of Toronto, Ontario, Canada
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20
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Townsend KM, Dawkins HJ. Field alternation gel electrophoresis--status quo. JOURNAL OF CHROMATOGRAPHY 1993; 618:223-49. [PMID: 8227258 DOI: 10.1016/0378-4347(93)80036-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Since the description of the original technique of field alternation gel electrophoresis (FAGE) about ten years ago there have been significant developments in the area. Between 1983 and early 1987 dramatic improvements in the technique and apparatus resulted in a 500- to 600-fold increase in the functional separation capacity of conventional agarose gel electrophoresis. Details of the improvements in technique and equipment was the subject of an earlier review [H. J. S. Dawkins, J. Chromatogr., 492 (1989) 615]. This review concentrates on the application of FAGE technology. The FAGE technique is no longer restricted to simply separating large DNA fragments. This method is presently being used for electrophoretic karyotyping, long-range genomic mapping, cloning of large DNA fragments into new vectors, the study of pathogenic chromosomal alterations and the structural analysis of chromosomes. The applications of FAGE in molecular biology and genetics is constantly expanding, with the full potential of this technique still to be realised.
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Affiliation(s)
- K M Townsend
- Department of Pathology, Queen Elizabeth II Medical Centre, Nedlands, Western Australia
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21
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Kim NW, Bingham H, Khawaja R, Louie H, Hani E, Neote K, Chan VL. Physical map of Campylobacter jejuni TGH9011 and localization of 10 genetic markers by use of pulsed-field gel electrophoresis. J Bacteriol 1992; 174:3494-8. [PMID: 1350583 PMCID: PMC206033 DOI: 10.1128/jb.174.11.3494-3498.1992] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The physical map of Campylobacter jejuni TGH9011 (ATCC 43430) was constructed by mapping the three restriction enzyme sites SacII (CCGCGG), SalI (GTCGAC), and SmaI (CCCGGG) on the genome of C. jejuni by using pulsed-field gel electrophoresis and Southern hybridization. A total of 25 restriction enzyme sites were mapped onto the C. jejuni chromosome. The size of the genome was reevaluated and was shown to be 1,812.5 kb. Ten C. jejuni genetic markers that have been isolated in our laboratory were mapped to specific restriction enzyme fragments. Furthermore, we have accurately mapped one of the three rRNA operons (rrnA) and have demonstrated a separation of the 16S and 23S rRNA-encoding sequences in one of the rRNA operons.
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Affiliation(s)
- N W Kim
- Department of Microbiology, University of Toronto, Ontario, Canada
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22
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Harasawa R, Uemori T, Asada K, Kato I, Shiragami N. 'boxA'-like sequence between the 16 S/23 S spacer in rRNA operon of mycoplasmas. FEBS Lett 1992; 297:209-11. [PMID: 1371968 DOI: 10.1016/0014-5793(92)80539-s] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We have found that a boxA-like sequence is conserved in the 16 S and 23 S rRNA intergenic spacer regions of mycoplasmas, and that it always locates on loop regions of the hypothetical secondary stem-loop structures. A nucleotide sequence similar to the '-10' box of prokaryotic promoters was identified at upstream sites of the boxA-like sequence in the 16 S/23 S spacer regions. These structures may represent an internal promoter between the 16 S and 23 S rRNA genes in mycoplasmas.
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Affiliation(s)
- R Harasawa
- Faculty of Medicine, University of Tokyo, Japan
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23
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Abstract
Little information concerning the genome of either Campylobacter jejuni or Campylobacter coli is available. Therefore, we constructed genomic maps of C. jejuni UA580 and C. coli UA417 by using pulsed-field gel electrophoresis. The genome sizes of C. jejuni and C. coli strains are approximately 1.7 Mb, as determined by SalI and SmaI digestion (N. Chang and D. E. Taylor, J. Bacteriol. 172:5211-5217, 1990). The genomes of both species are represented by single circular DNA molecules, and maps were constructed by partial restriction digestion and hybridization of DNA fragments extracted from low-melting-point agarose gels. Homologous DNA probes, encoding the flaAB and 16S rRNA genes, as well as heterologous DNA probes from Escherichia coli, Bacillus subtilis, and Haemophilus influenzae, were used to identify the locations of particular genes. C. jejuni and C. coli contain three copies of the 16S and 23S rRNA genes. However, they are not located together within an operon but show a distinct split in at least two of their three copies. The positions of various housekeeping genes in both C. jejuni UA580 and C. coli UA417 have been determined, and there appears to be some conservation of gene arrangement between the two species.
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Affiliation(s)
- D E Taylor
- Department of Medical Microbiology, University of Alberta, Edmonton, Canada
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24
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Fukunaga M, Sohnaka M. Tandem repeat of the 23S and 5S ribosomal RNA genes in Borrelia burgdorferi, the etiological agent of Lyme disease. Biochem Biophys Res Commun 1992; 183:952-7. [PMID: 1567408 DOI: 10.1016/s0006-291x(05)80282-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The DNA fragments containing the rrl and rrf genes were subcloned from a EMBL3 recombinant phage of Borrelia burgdorferi strain B31 into pUC18 and were characterized by restriction analysis and Southern hybridization. A fine restriction map of the fragments was constructed and the organization of the genes was determined. The genomic hybridization using the gene probes from B. burgdorferi showed that there are two sets of rrl/rrf genes in that genome. The results also revealed the important fact that the gene sets are repeated directly by 3.2-kb long. This is the first report of this remarkable feature in the organization of the eubacterial rRNA genes.
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Affiliation(s)
- M Fukunaga
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Fukuyama, Hiroshima, Japan
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25
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Fukunaga M, Okuzako N, Mifuchi I, Arimitsu Y, Seki M. Organization of the ribosomal RNA genes in Treponema phagedenis and Treponema pallidum. Microbiol Immunol 1992; 36:161-7. [PMID: 1374831 DOI: 10.1111/j.1348-0421.1992.tb01653.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The genomic DNA fragment which contains ribosomal RNA (rRNA) genes for Treponema phagedenis was cloned into bacteriophage vector lambda EMBL3. A restriction map of the fragment was constructed and the organization of the rRNA genes was determined. The fragment contained at least one copy of the 16S, 23S and 5S sequences and the genes are arranged in the order 16S-23S-5S. Southern hybridization using radiolabeled rRNA gene probes to genomic DNA from T. phagedenis strain Reiter and T. pallidum strain Nichols showed that these organisms have two radioactive fragments which hybridize to the probes in their genome. These results suggest that both pathogenic and non-pathogenic strains of Treponema may carry at least two sets of rRNA genes on their chromosomes.
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Affiliation(s)
- M Fukunaga
- Faculty of Pharmacy, University of Fukuyama, Hiroshima, Japan
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26
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Scamrov A, Beabealashvilli R. Mycoplasma gallisepticum strain S6 genome contains three regions hybridizing with 16 S rRNA and two regions hybridizing with 23 S and 5 S rRNA. FEBS Lett 1991; 291:71-4. [PMID: 1718781 DOI: 10.1016/0014-5793(91)81106-i] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Southern hybridization and cloning experiments revealed existence of 3 regions hybridizing with 16 S rRNA and 2 regions hybridizing with 23 S and 5 S rRNA in Mycoplasma Gallisepticum strain S6 genome thus forming 4 separate contiguous regions. One set of a putative rRNA genes is organized classically for eubacteria order 16 S-23 S-5 S. The other two 16 S rRNA and the other one 23 S-5 S rRNA hybridizing regions are separated from each other and from the complete rRNA operon for a distance of more than 6 kb.
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MESH Headings
- Base Sequence
- Blotting, Southern
- DNA, Bacterial
- Genome, Bacterial
- Molecular Sequence Data
- Mycoplasma/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/genetics
- Restriction Mapping
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Affiliation(s)
- A Scamrov
- National Cardiology Research Center, USSR Academy of Medical Science, Moscow
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27
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Abstract
Three trends are seen in the organization of ribosomal DNA genes during evolution: 1) gradual separation and separability of the regulation of transcription of 5S and larger subunit rRNAs; 2) retention of a transcription unit containing both large and small rRNAs; and 3) clustering of genes for both 5S and 18S-28S rDNAs, with the possible association of other 'non-rDNA' in the clusters of 18S-28S rDNA genes by the time mammals evolve.
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MESH Headings
- Animals
- Biological Evolution
- DNA, Ribosomal/genetics
- Escherichia coli/genetics
- Mammals/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 5S/genetics
- Transcription, Genetic
- Yeasts/genetics
- rRNA Operon/genetics
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Affiliation(s)
- A K Srivastava
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110
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28
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Menke MAOH, Liesack W, Stackebrandt E. Ribotyping of 16S and 23S rRNA genes and organization of rrn operons in members of the bacterial genera Gemmata, Planctomyces, Thermotoga, Thermus, and Verrucomicrobium. Arch Microbiol 1991. [DOI: 10.1007/bf00252210] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Abstract
Recent progress in studies on the bacterial chromosome is summarized. Although the greatest amount of information comes from studies on Escherichia coli, reports on studies of many other bacteria are also included. A compilation of the sizes of chromosomal DNAs as determined by pulsed-field electrophoresis is given, as well as a discussion of factors that affect gene dosage, including redundancy of chromosomes on the one hand and inactivation of chromosomes on the other hand. The distinction between a large plasmid and a second chromosome is discussed. Recent information on repeated sequences and chromosomal rearrangements is presented. The growing understanding of limitations on the rearrangements that can be tolerated by bacteria and those that cannot is summarized, and the sensitive region flanking the terminator loci is described. Sources and types of genetic variation in bacteria are listed, from simple single nucleotide mutations to intragenic and intergenic recombinations. A model depicting the dynamics of the evolution and genetic activity of the bacterial chromosome is described which entails acquisition by recombination of clonal segments within the chromosome. The model is consistent with the existence of only a few genetic types of E. coli worldwide. Finally, there is a summary of recent reports on lateral genetic exchange across great taxonomic distances, yet another source of genetic variation and innovation.
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Affiliation(s)
- S Krawiec
- Department of Biology, Lehigh University, Bethlehem, Pennsylvania 18015
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30
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Fukunaga M, Masuzawa T, Okuzako N, Mifuchi I, Yanagihara Y. Linkage of ribosomal RNA genes in Leptospira. Microbiol Immunol 1990; 34:565-73. [PMID: 2266880 DOI: 10.1111/j.1348-0421.1990.tb01033.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We determined the linkage of 16S, 23S, and 5S rRNA genes in several strains of Leptospira and Leptonema by DNA-DNA hybridization. Almost all the hybridizations in all leptospires used in these experiments gave two radioactive bands and the results strongly suggest that the number of the 16S and the 23S rRNA genes in those strains is two, respectively. In contrast with the larger rRNAs, the number of 5S rRNA gene was different. In the strains of leptospires, L. biflexa, which were non-parasitic, there are two genes for 5S rRNA, whereas only one gene for 5S rRNA is carried in L. interrogans, which were originally isolated as parasitic. Southern hybridization experiments suggest that those rRNA genes are interspersed on the leptospiral chromosome.
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Affiliation(s)
- M Fukunaga
- Faculty of Pharmacy and Pharmaceutical Science, University of Fukuyama, Hiroshima
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31
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Fukunaga M, Horie I, Mifuchi I. Isolation and characterization of the 5S rRNA gene of Leptospira interrogans. J Bacteriol 1990; 172:3264-8. [PMID: 2345145 PMCID: PMC209134 DOI: 10.1128/jb.172.6.3264-3268.1990] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The gene encoding the 5S rRNA for Leptospira interrogans serovar canicola strain Moulton was isolated and sequenced. The 5S rRNA gene occurs as a single copy within the genome and encodes a 117-nucleotide-long RNA molecule. The 5S rRNA gene is flanked at both the 5' and 3' ends by regions of A + T-rich sequences, and the 5'-flanking region contains a promoter sequence. L. interrogans has a unique and remarkable organization of the 5S rRNA gene. The 5S rRNA molecule exhibits a strong similarity to typical eubacterial 5S rRNA in terms of overall secondary structure, while the primary sequence is conserved to a lesser degree. Restriction analysis of the 5S rRNA gene indicated that the DNA sequence including the 5S rRNA gene is highly conserved in the genomes of parasitic leptospires.
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Affiliation(s)
- M Fukunaga
- Faculty of Pharmacy and Pharmaceutical Science, University of Fukuyama, Hiroshima, Japan
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