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Chimeric RNA Design Principles for RNA-Mediated Gene Fusion. Cells 2022; 11:cells11061002. [PMID: 35326453 PMCID: PMC8947500 DOI: 10.3390/cells11061002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 12/02/2022] Open
Abstract
One common genetic alteration in cancer is gene fusion resulting from chromosomal translocations. The mechanisms that create such oncogenic fusion genes are not well understood. Previously, we provided the direct evidence that expression of a designed chimeric RNA can drive the formation of TMPRSS2-ERG gene fusion. Central to this RNA-mediated gene fusion mechanism is a proposed three-way junction formed by RNA/DNA hybrid and the intergenic DNA stem formed by target genes. In this study, we determined the important parameters for chimeric RNA-mediated gene fusion using TMPRSS2-ERG fusion gene as the model. Our results indicate that both the chimeric RNA lengths and the sizes of unpaired bulges play important roles in inducing TMPRSS2-ERG gene fusion. The optimal length of unpaired bulges was about 35 nt, while the optimal chimeric RNA length was about 50 nt for targeting. These observations were consistent regardless of the target locations within TMPRSS2 and ERG genes. These empirically determined parameters provide important insight for searching cellular RNAs that may initiate oncogenic fusion genes. The knowledge could also facilitate the development of useful genomic technology for manipulating mammalian genomes.
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2
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Stepanov VG, Fox GE. Expansion segments in bacterial and archaeal 5S ribosomal RNAs. RNA (NEW YORK, N.Y.) 2021; 27:133-150. [PMID: 33184227 PMCID: PMC7812874 DOI: 10.1261/rna.077123.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/09/2020] [Indexed: 05/10/2023]
Abstract
The large ribosomal RNAs of eukaryotes frequently contain expansion sequences that add to the size of the rRNAs but do not affect their overall structural layout and are compatible with major ribosomal function as an mRNA translation machine. The expansion of prokaryotic ribosomal RNAs is much less explored. In order to obtain more insight into the structural variability of these conserved molecules, we herein report the results of a comprehensive search for the expansion sequences in prokaryotic 5S rRNAs. Overall, 89 expanded 5S rRNAs of 15 structural types were identified in 15 archaeal and 36 bacterial genomes. Expansion segments ranging in length from 13 to 109 residues were found to be distributed among 17 insertion sites. The strains harboring the expanded 5S rRNAs belong to the bacterial orders Clostridiales, Halanaerobiales, Thermoanaerobacterales, and Alteromonadales as well as the archael order Halobacterales When several copies of a 5S rRNA gene are present in a genome, the expanded versions may coexist with normal 5S rRNA genes. The insertion sequences are typically capable of forming extended helices, which do not seemingly interfere with folding of the conserved core. The expanded 5S rRNAs have largely been overlooked in 5S rRNA databases.
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MESH Headings
- Alteromonadaceae/classification
- Alteromonadaceae/genetics
- Alteromonadaceae/metabolism
- Base Pairing
- Base Sequence
- Clostridiales/classification
- Clostridiales/genetics
- Clostridiales/metabolism
- Firmicutes/classification
- Firmicutes/genetics
- Firmicutes/metabolism
- Genome, Archaeal
- Genome, Bacterial
- Halobacteriales/classification
- Halobacteriales/genetics
- Halobacteriales/metabolism
- Nucleic Acid Conformation
- Phylogeny
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- Thermoanaerobacterium/classification
- Thermoanaerobacterium/genetics
- Thermoanaerobacterium/metabolism
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Affiliation(s)
- Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
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3
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Prillinger H, Deml G, Dörfler C, Laaser G, Lockau W. Ein Beitrag zur Systematik und Entwicklungsbiologie höherer Pilze: Hefe-Typen der Basidiomyceten. Teil II:Microbotryum-Typ. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1991.tb00188.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Wang Y, Hao B, Zhang Q, Tuo E, Sun G, Zhang R, Jin S, Zhu M, Wang Y, Hsiang T. Discovery of multiple IGS haplotypes within genotypes of Puccinia striiformis. Fungal Biol 2012; 116:522-8. [PMID: 22483050 DOI: 10.1016/j.funbio.2012.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 02/02/2012] [Accepted: 02/05/2012] [Indexed: 10/28/2022]
Abstract
In a search for specific molecular markers for population analysis of Puccinia striiformis f. sp. tritici, the ribosomal DNA (rDNA) intergenic spacer (IGS) 1 region (rDNA-IGS1, between the 28S and the 5S rDNA genes) was amplified, cloned, and sequenced. It was found to exhibit multiple bands and length polymorphism. Surprisingly, single isolates were found to possess between three to five different IGS1 haplotypes. Bands were cloned and sequenced, and two highly variable regions (α and β) were found between conserved regions, with repeat units interspersed in both types of regions. There were 14 different repeat units, and these were sometimes grouped further into four combinations of repeat units, with a few individual nucleotides (A or C) inserted between the repeats. Among three geographically dispersed isolates, the variable region α was divided into eight types, and the variable region β was divided into two types based on repeat units. Most of the 14 repeat units were shared by the variable and the conserved regions. Among the three isolates, there were a total of 12 IGS1 haplotypes, but some of these were shared between isolates such that there were only eight unique haplotypes. The occurrence of multiple haplotypes within single isolates may be useful for analyzing the population structure, tracking the origin of annual epidemics and providing insights into evolutionary biology of this pathogen.
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Affiliation(s)
- Yanchun Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, PR China
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5
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Abstract
Highly variable intergenic spacer and intron regions from nuclear and cytoplasmic DNA have been used for species identification. Noncoding internal transcribed spacers (ITSs) located in 18S-5.8S-26S, and 5S ribosomal RNA genes (rDNAs) represent suitable region for medicinal plant authentication. Noncoding regions from two cytoplasmic DNA, chloroplast DNA (trnT-F intergenic spacer region), and mitochondrial DNA (fourth intron region of nad7 gene) are also successfully applied for the proper identification of medicinal plants. Single-nucleotide polymorphism (SNP) sites obtained from the amplification of intergenic spacer and intron regions are properly utilized for the verification of medicinal plants in species level using multiplex PCR. Multiplex PCR as a variant of PCR technique used to amplify more than two loci simultaneously.
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Affiliation(s)
- Ok Ran Lee
- Department of Oriental Medicinal Materials and Processing, College of Life Science, Kyung Hee University, Suwon, South Korea
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6
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Zakhia F, de Lajudie P. [Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)]. Can J Microbiol 2006; 52:169-81. [PMID: 16604113 DOI: 10.1139/w05-092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.
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Affiliation(s)
- Frédéric Zakhia
- Laboratoire des symbioses tropicales et Méditerranéennes, Unité mixte de recherche (UMR) 113, Institut de recherche pour le développement, Université Montpellier II (UM-II), CEDEX, France
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7
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Pitchiaya S, Krishnan Y. First blueprint, now bricks: DNA as construction material on the nanoscale. Chem Soc Rev 2006; 35:1111-21. [PMID: 17057840 DOI: 10.1039/b602886c] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For the most part DNA was considered Nature's instruction manual for life leading to the popular description 'blueprint of life'. However, DNA is now taking on a new aspect where it is finding use as a construction element for architecture on the nanoscale. This tutorial review addresses the importance of building ordered structures with DNA on the nanoscale, the underlying principles and approaches to build such scaffolds, the current limitations and the anticipated trajectory of the area. This is would be of interest to the chemical biology, supramolecular and bioengineering communities in particular.
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8
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Abstract
Four novel small nucleolar RNAs (snoRNAs), h5sn1, h5sn2, h5sn3, and h5sn4, were successfully amplified from human total RNAs using RT-PCR. They exhibited the structural hallmarks of box H/ACA snoRNAs and formed sequence complementarity to 5S rRNA. The nucleotide sequences of the snoRNAs from different donors were highly conserved as evidenced by single-stranded conformational polymorphism and direct nucleotide sequence analysis. Although their host genes had no protein-coding potential, the expression of the snoRNAs was differentially displayed in different tissues. Noticeably, h5sn2 was highly expressed in normal brain, but its expression drastically decreased in meningioma. This opens the fascinating possibility of the relationship between the processing of snoRNAs and carcinogenesis.
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Affiliation(s)
- Long Sen Chang
- Institute of Biomedical Sciences, National Sun Yat-Sen University, 804, Kaohsiung, Taiwan.
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9
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Characterisation of a length polymorphism in the two intergenic spacers of ribosomal RNA in Puccinia striiformis f. sp. tritici, the causal agent of wheat yellow rust. ACTA ACUST UNITED AC 2002. [DOI: 10.1017/s0953756202006251] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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10
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Use of RFLP and SSCP analysis to differentiate the pine rusts Cronartium flaccidum and Peridermium pini. ACTA ACUST UNITED AC 1998. [DOI: 10.1017/s0953756297005467] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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11
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Chang LS, Lin SK, Wu PF. Differentially expressed snoRNAs in Bungarus multicinctus (Taiwan banded krait). Biochem Biophys Res Commun 1998; 245:397-402. [PMID: 9571162 DOI: 10.1006/bbrc.1998.8433] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Twenty novel snoRNAs forming extensive sequence complementarities to mature 5S rRNA were identified from Bungarus multicinctus by reverse transcription-polymerase chain reaction. It was found that the snoRNA species were differentially transcribed in different tissues as evidenced by single stranded conformational polymorphism analysis and direct nucleotide sequence analysis. Although the diversity in the sequences of snoRNAs is observed, comparison of these snoRNA genes reveals that the regions involved in binding to 5S rRNA are highly conserved and form two 12-nt-15-nt tracts of complementarity to phylogenetically invariant sequences in eukaryotic 5S rRNAs. Nevertheless, the lower conservation of box C/D or box H/ACA in these snoRNAs was observed. Likewise, the sequences in several fish and human genes forming perfect duplexes with 5S rRNA also did not highly retain these box elements. These results may infer that the box elements are dispensable for the function of snoRNA species identified in the present study. Moreover, the novel finding of the differentially expressed snoRNA variants in B. multicinctus suggests that the snoRNA genes are selectively processed in different tissues and are likely associated with tissue-specific regulation of their host gene transcripts.
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Affiliation(s)
- L S Chang
- Department of Biochemistry, Kaohsiung Medical College, Taiwan, Republic of China.
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12
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Diagnosis of Legionella infection by reverse transcription of 5S-ribosomal RNA and polymerase chain reaction. J Infect Chemother 1998. [DOI: 10.1007/bf02490058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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13
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Kwon-Chung KJ, Chang YC, Penoyer L. Species of the genus Filobasidielladiffer in the organization of their 5S rRNA genes. Mycologia 1997. [DOI: 10.1080/00275514.1997.12026777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- K. J. Kwon-Chung
- Molecular Microbiology Section, Laboratory of Clinical Investigation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
| | - Yun C. Chang
- Molecular Microbiology Section, Laboratory of Clinical Investigation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
| | - L. Penoyer
- Molecular Microbiology Section, Laboratory of Clinical Investigation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
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14
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Van de Peer Y, Chapelle S, De Wachter R. A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acids Res 1996; 24:3381-91. [PMID: 8811093 PMCID: PMC146102 DOI: 10.1093/nar/24.17.3381] [Citation(s) in RCA: 176] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A recently developed method for estimating the variability of nucleotide sites in a sequence alignment [Van de Peer, Y., Van der Auwera, G. and De Wachter, R. (1996) J. Mol. Evol. 42, 201-210] was applied to bacterial 16S, 5S and 23S rRNAs. In this method, the variability of each nucleotide site is defined as its evolutionary rate relative to the average evolutionary rate of all the nucleotide sites of the molecule. Spectra of evolutionary rates were calculated for each rRNA and show the fastest evolving sites substituting at rates more than 1000 times that of the slowest ones. Variability maps are presented for each rRNA, consisting of secondary structure models where the variability of each nucleotide site is indicated by means of a colored dot. The maps can be interpreted in terms of higher order structure, function and evolution of the molecules and facilitate the selection of areas suitable for the design of PCR primers and hybridization probes. Variability measurement is also important for the precise estimation of evolutionary distances and the inference of phylogenetic trees.
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MESH Headings
- Biological Evolution
- Databases, Factual
- Genetic Variation
- Models, Molecular
- Nucleic Acid Conformation
- Nucleotides/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/genetics
- Sequence Alignment/methods
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Affiliation(s)
- Y Van de Peer
- Departement Biochemie, Universiteit Antwerpen (UIA), Belgium
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15
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Cronn RC, Zhao X, Paterson AH, Wendel JF. Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. J Mol Evol 1996; 42:685-705. [PMID: 8662014 DOI: 10.1007/bf02338802] [Citation(s) in RCA: 169] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
5S RNA genes and their nontranscribed spacers are tandemly repeated in plant genomes at one or more chromosomal loci. To facilitate an understanding of the forces that govern 5S rDNA evolution, copy-number estimation and DNA sequencing were conducted for a phylogenetically well-characterized set of 16 diploid species of cotton (Gossypium) and 4 species representing allopolyploid derivatives of the diploids. Copy number varies over twentyfold in the genus, from approximately 1,000 to 20,000 copies/2C genome. When superimposed on the organismal phylogeny, these data reveal examples of both array expansion and contraction. Across species, a mean of 12% of nucleotide positions are polymorphic within individual arrays, for both gene and spacer sequences. This shows, in conjunction with phylogenetic evidence for ancestral polymorphisms that survive speciation events, that intralocus concerted evolutionary forces are relatively weak and that the rate of interrepeat homogenization is approximately equal to the rate of speciation. Evidence presented also shows that duplicated 5S rDNA arrays in allopolyploids have retained their subgenomic identity since polyploid formation, thereby indicating that interlocus concerted evolution has not been an important factor in the evolution of these arrays. A descriptive model, one which incorporates the opposing forces of mutation and homogenization within a selective framework, is outlined to account for the empirical data presented. Weak homogenizing forces allow equivalent levels of sequence polymorphism to accumulate in the 5S gene and spacer sequences, but fixation of mutations is nearly prohibited in the 5S gene. As a consequence, fixed interspecific differences are statistically underrepresented for 5S genes. This result explains the apparent paradox that despite similar levels of gene and spacer diversity, phylogenetic analysis of spacer sequences yields highly resolved trees, whereas analyses based on 5S gene sequences do not.
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MESH Headings
- Base Sequence
- DNA, Plant/genetics
- DNA, Ribosomal/genetics
- Diploidy
- Evolution, Molecular
- Genes, Plant
- Gossypium/genetics
- Molecular Sequence Data
- Phylogeny
- Polymorphism, Genetic
- Polyploidy
- RNA, Plant/genetics
- RNA, Ribosomal, 5S/genetics
- Repetitive Sequences, Nucleic Acid
- Sequence Alignment
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- R C Cronn
- Department of Botany, Iowa State University, Ames, IA 50011, USA
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16
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Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 1996; 60:407-38. [PMID: 8801440 PMCID: PMC239450 DOI: 10.1128/mr.60.2.407-438.1996] [Citation(s) in RCA: 354] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question.
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Affiliation(s)
- P Vandamme
- Laboratorium voor Microbiologie, Universiteit Gent, Belgium
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17
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Barciszewska MZ, Erdmann VA, Barciszewski J. Ribosomal 5S RNA: tertiary structure and interactions with proteins. Biol Rev Camb Philos Soc 1996; 71:1-25. [PMID: 8603119 DOI: 10.1111/j.1469-185x.1996.tb00740.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- M Z Barciszewska
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Poznań, Poland
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18
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Belkhiri A, Klassen GR. Diverged 5s rRNA sequences adjacent to 5s rRNA genes in the rDNA ofPythium pachycaule. Curr Genet 1996. [DOI: 10.1007/bf02221560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Zanke C, Borisjuk N, Ruoss B, Schilde-Rentschler L, Ninnemann H, Hemleben V. A specific oligonucleotide of the 5S rDNA spacer and species-specific elements identify symmetric somatic hybrids between Solanum tuberosum and S. pinnatisectum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 90:720-726. [PMID: 24174033 DOI: 10.1007/bf00222139] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/1994] [Accepted: 07/28/1994] [Indexed: 06/02/2023]
Abstract
The nucleotide sequences of the 5S rRNA genes (5S rDNA) of two Solanum tuberosum breeding lines (R1 and B15) and of the Mexican wild species S. pinnatisectum were determined and compared with each other and to the 5S rDNA of other Solanaceae species (Lycopersicon esculentum, Nicotiana rustica and Petunia hybrida). The 5S rDNA repeats of the Solanum species are 324-329 bp in length, and they exhibit 91-95% sequence identity. Sequence variability is mainly located in a short region of the spacer separating the 5S rRNA coding regions. A synthetic 28-mer oligonucleotide constructed according to this region can be used as a specific hybridization probe to distinguish symmetric somatic hybrids between S. tubersosum breeding line B15 and S. pinnatisectum produced by protoplast fusion. Interestingly, the two Solanum breeding lines R1 and B15 differ also in this spacer region.
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Affiliation(s)
- C Zanke
- Lehrstuhl für Allgemeine Genetik, Biologisches Institut, Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
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20
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Lane BG, Ofengand J, Gray MW. Pseudouridine and O2'-methylated nucleosides. Significance of their selective occurrence in rRNA domains that function in ribosome-catalyzed synthesis of the peptide bonds in proteins. Biochimie 1995; 77:7-15. [PMID: 7599278 DOI: 10.1016/0300-9084(96)88098-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pseudouridine (5-ribosyluracil, psi) was the first of a host of modified nucleoside constituents detected in cellular RNA and it remains the most abundant, being broadly distributed in the RNA of archaebacteria, eubacteria and eukaryotes. Like some other modifications, psi is particularly abundant in more complex organisms, reaching 2-3% of the total nucleoside constituents in tRNA, snRNA and rRNA of multicellular plants and animals. Like all other modified nucleosides, psi arises by site-specific, enzymically catalyzed modification of a nucleoside residue in an RNA molecule. Unlike all other modified nucleosides, psi arises by isomerisation (not substitution) of a classical nucleoside, uridine (1-ribosyluracil). There have been suggestions that key processes such as ribosome assembly and peptidyl transfer may rely, more than is generally appreciated, on RNA modifications such as O2'-methylation and pseudouridylation, respectively. However, a persuasive case for the view that secondary modifications are of primary importance in ribosome function has not been convincingly made. Accordingly, we think it is timely to broaden what is generally meant by the 'catalytic properties of rRNA', and to ask, to what extent do modifications contribute to in vivo rates of ribosome assembly and ribosomal peptide-bond synthesis? The first part of this article sets forth the evidence that there is a conspicuous association between modified nucleosides and cellular RNAs that participate in group-transfer reactions. The second part reviews evidence in support of the view that the functions of psi and other modified nucleosides are likely of central importance for understanding the dynamics and stereostructural modeling at functionally significant sites in the ribosome.
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Affiliation(s)
- B G Lane
- Biochemistry Department, University of Toronto, ON, Canada
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21
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The Phylogenetic Position of the Haloalkaliphilic Archaeon Natronobacterium magadii, determined from its 23S Ribosomal RNA Sequence. Syst Appl Microbiol 1994. [DOI: 10.1016/s0723-2020(11)80057-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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Gazumyan A, Schwartz JJ, Liveris D, Schwartz I. Sequence analysis of the ribosomal RNA operon of the Lyme disease spirochete, Borrelia burgdorferi. Gene 1994; 146:57-65. [PMID: 7520403 DOI: 10.1016/0378-1119(94)90833-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
An 11,955-bp region of the Borrelia burgdorferi chromosome containing all the genes encoding ribosomal RNA (rRNA) has been sequenced. The region contains a single gene encoding 16S rRNA and two genes encoding the 23S and 5S rRNAs. The sizes of the 16S, 23S and 5S rRNAs encoded by these genes are 1537, 2926 and 112 nucleotides, respectively. In addition, the genes encoding tRNA(Ala) and tRNA(Ile) are located in the intergenic spacer between the 16S and 23S rDNAs. The tDNAs do not encode the common CCA 3' end which presumably must be added posttranscriptionally. All the genes are present in the same orientation, except for that encoding tRNA(Ile), which is transcribed from the opposite strand. The latter implies that the rDNAs are not transcribed as a single unit. The location of putative promoters and termination signals in the sequence suggest that the 16S rRNA and tRNA(Ala) are transcribed as a single unit, tRNA(Ile) is produced as an individual transcript and the 23S and 5S rDNAs are co-transcribed. Several of the features of this rDNA organization are unique, not having been described previously in any other eubacteria.
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MESH Headings
- Base Sequence
- Borrelia burgdorferi
- Borrelia burgdorferi Group/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- Operon
- RNA, Bacterial
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S
- RNA, Ribosomal, 23S
- RNA, Ribosomal, 5S
- RNA, Transfer, Ala/genetics
- RNA, Transfer, Ile/genetics
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Affiliation(s)
- A Gazumyan
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla 10595
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23
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Keppen OI, Baulina OI, Kondratieva EN. Oscillochloris trichoides neotype strain DG-6. PHOTOSYNTHESIS RESEARCH 1994; 41:29-33. [PMID: 24310011 DOI: 10.1007/bf02184143] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/1993] [Accepted: 03/01/1994] [Indexed: 05/24/2023]
Abstract
The new strain of filamentous green bacterium strain DG-6 was isolated in pure culture from the spring of Caucuses. The study of this bacterium allows to suggest that it is a member of the familyChloroflexaceae and may be considered asOscillochloris trichoides neotype strain. The description of this green bacterium is given.
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Affiliation(s)
- O I Keppen
- Department of Microbiology of Moscow State University, 119898, Moscow, Russia
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24
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Thermohydrogenium kirishiense gen. nov. and sp. nov., a new anaerobic thermophilic bacterium. Arch Microbiol 1993. [DOI: 10.1007/bf00245311] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Kessler HH, Reinthaler FF, Pschaid A, Pierer K, Kleinhappl B, Eber E, Marth E. Rapid detection of Legionella species in bronchoalveolar lavage fluids with the EnviroAmp Legionella PCR amplification and detection kit. J Clin Microbiol 1993; 31:3325-8. [PMID: 8308130 PMCID: PMC266420 DOI: 10.1128/jcm.31.12.3325-3328.1993] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A molecular assay based on a rapid DNA extraction protocol and the EnviroAmp Legionella Kits was used to detect Legionella species in bronchoalveolar fluid specimens. All Legionella strains isolated from tap water in hospitals could be detected distinctly. Both sensitivity and specificity were tested. In a prospective study, bronchoalveolar lavage fluids obtained from patients with atypical pneumonia were investigated. Three positive samples were detected with the molecular techniques and were subsequently confirmed by culture. Application of the system described may lead to safe and early diagnosis of Legionnaires' disease in patients with atypical pneumonia.
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Affiliation(s)
- H H Kessler
- Institute of Hygiene, KF-University Graz, Austria
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26
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Palmer CJ, Tsai YL, Paszko-Kolva C, Mayer C, Sangermano LR. Detection of Legionella species in sewage and ocean water by polymerase chain reaction, direct fluorescent-antibody, and plate culture methods. Appl Environ Microbiol 1993; 59:3618-24. [PMID: 8285669 PMCID: PMC182507 DOI: 10.1128/aem.59.11.3618-3624.1993] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Legionella spp. are ubiquitous in most environmental water sources; however, sewage treatment plants have not been examined as potential environmental reservoirs for these bacteria. This study used polymerase chain reaction, direct fluorescent-antibody staining, and culture methods to examine raw and treated sewage, ocean-receiving waters, and nearshore coastal environments for the presence of Legionella pneumophila and other Legionella spp. The study concluded that Legionella spp. are present in all phases of sewage treatment and that population numbers do not significantly decline through the treatment process. Ocean-receiving waters located 5 miles offshore, where the treated sewage is discharged, were found to contain Legionella spp., but ocean water between the discharge site and coastal bathing beaches was negative. This suggests that the Legionella spp. from the ocean discharge site were not reaching the nearshore beach waters. A flood control channel and river that entered the ocean were found to contain Legionella spp., and a nearby beach swimming area was also found to be positive, suggesting that land runoff from the flood control channel and river were the source of the Legionella spp. in the beach water samples that tested positive.
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Affiliation(s)
- C J Palmer
- Environmental Sciences Laboratory, County Sanitation Districts of Orange County, Fountain Valley, California 92728-8127
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27
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Gaskins CJ, Smith JF, Ogilvie MK, Hanas JS. Comparison of the sequence and structure of transcription factor IIIA from Bufo americanus and Rana pipiens. Gene 1992; 120:197-206. [PMID: 1398134 DOI: 10.1016/0378-1119(92)90094-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Amino acid (aa) sequences of transcription factor IIIA (TFIIIA) from the toad, Bufo americanus, and the grass frog, Rana pipiens, were determined by cDNA cloning and DNA sequencing. The 3'-untranslated regions of the cDNAs reveal that the TFIIIA gene polyadenylation signal is ATTAAA, rather than the conventional AATAAA. The B. americanus and R. pipiens proteins share about 60% aa sequence homology with each other and with Xenopus laevis TFIIIA. Although these results indicate that TFIIIA has more sequence variation than other DNA-binding proteins, a number of conserved features are evident and of likely functional significance. These include potential guanine nucleotide-binding sites at arginines in zinc fingers (ZnF) II, V, and IX, acidic residues between metal-coordinating cysteines, and a basic region in the C-terminal tail possibly involved in transcription promotion. Sequence similarity also exists in an aa stretch bridging the ninth ZnF and C-terminal tail of both TFIIIA and the 5S RNA-binding protein, p43. DNase I protection analyses demonstrate that B. americanus and R. pipiens TFIIIA interact with the internal control region (ICR) of the Xenopus borealis 5S RNA-encoding gene (5S) in different manners: the B. americanus interaction is similar to X. laevis TFIIIA, protecting the entire 5S gene ICR (nt +96 to +43) from DNase I digestion, whereas the R. pipiens TFIIIA strongly protects the ICR from nt +96 up to +78 and less strongly from +78 to +43. Possibly accounting for the binding differences observed, R. pipiens and R. catesbeiana oocyte 5S RNAs (and by inference 5S genes) were found to contain a G or U at nt position 50 while B. americanus, X. laevis, and other eukaryotic 5S RNAs have an A in the analogous position (nt 53 in generalized eukaryotic structure).
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Affiliation(s)
- C J Gaskins
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City 73190
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28
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Fukuchi S, Otsuka J. Evolution of metabolic pathways by chance assembly of enzyme proteins generated from sense and antisense strands of pre-existing genes. J Theor Biol 1992; 158:271-91. [PMID: 1287363 DOI: 10.1016/s0022-5193(05)80734-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In order to get an insight into the evolutionary aspect of metabolic pathways, especially of the ubiquitous glycolytic pathway, we have carried out an extensive search of sense-sense and sense-antisense similarities for enzyme proteins in the glycolytic pathway, the pentose phosphate cycle, alcohol and lactate fermentation pathways and the TCA cycle. This investigation of amino acid sequences reveals a curious pattern of similarity relations; no similarity can be found between the enzyme proteins in a section of the glycolytic pathway where the glyceraldehyde-3-phosphate or even glycerol-3-phosphate is converted into the pyruvate while many examples of sense-sense and sense-antisense similarities are found even between enzyme proteins in distant blocks, e.g. between the proteins in the TCA cycle and those in the pentose phosphate cycle, as well as between the functionally associated proteins in each of these blocks. Complementary to this characteristic pattern of amino acid sequence similarity, the search for similarities of nucleotide sequences also finds that the similarities of glycolytic enzyme genes, some sense-sense and others sense-antisense similarities, are concentrated on the nucleotide sequences of prokaryotic 16S or eukaryotic 18S ribosomal RNA gene with its flanks, although some of the copy sequences are also found in transfer RNA genes as well as in 23S or 26S ribosomal RNA gene. These results strongly suggest that the metabolic pathways have been developed by the chance assembly of enzyme proteins generated from the sense and antisense strands of pre-existing genes, e.g. the fermentation pathways and pentose phosphate cycle by the proteins from the genes of enzymes in the glycolytic pathway and the TCA cycle from all these successively increased genes, ascribing the origin of metabolic enzyme genes to the close relation between the glycolytic enzyme protein genes and the RNA gene cluster.
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Affiliation(s)
- S Fukuchi
- Department of Applied Biological Science, Faculty of Science and Technology, Science University of Tokyo, Noda, Japan
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29
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Van Ryk DI, Nazar RN. Effect of sequence mutations on the higher order structure of the yeast 5 S rRNA. J Mol Biol 1992; 226:1027-35. [PMID: 1518042 DOI: 10.1016/0022-2836(92)91050-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mutant yeast ribosomal 5 S RNAs were probed by enzymatic cleavage and chemical reactivity to define further the higher order structure. Mutations that destabilized helix IV resulted in an altered tertiary structure in which a reduced reactivity to ethylnitrosourea at U90 and G91 could be correlated with greater enzymatic and Fe(II)-EDTA cleavages in helices II and V. The results provide direct evidence for, and a further definition of, a structural juxtaposition between helix II and the end of helix IV and indicate that, in contrast to earlier suggestions, the remaining tertiary structure is sufficiently stable to prevent "pseudoknot-like" interactions between helices III and IV. The data are fully consistent with the "lollipop" model of the tertiary structure.
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MESH Headings
- Base Sequence
- Edetic Acid/pharmacology
- Ethylnitrosourea/pharmacology
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis
- Nucleic Acid Conformation
- RNA, Fungal/chemistry
- RNA, Fungal/drug effects
- RNA, Fungal/genetics
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/drug effects
- RNA, Ribosomal, 5S/genetics
- Ribonucleases/pharmacology
- Saccharomyces cerevisiae/chemistry
- Saccharomyces cerevisiae/genetics
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Affiliation(s)
- D I Van Ryk
- Department of Molecular Biology and Genetics, University of Guelph, Ontario, Canada
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30
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Barciszewska M, Huang H, Marshall A, Erdmann V, Barciszewski J. Biochemical and NMR spectroscopy evidence for a new tertiary A-U base pair in lupin ribosomal 5 S RNA structure. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42057-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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31
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Kim WK, Zerucha T, Klassen GR. A region of heterogeneity adjacent to the 5s ribosomal RNA gene of cereal rusts. Curr Genet 1992; 22:101-5. [PMID: 1339324 DOI: 10.1007/bf00351468] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Total genomic DNA was isolated from three cereal stem rusts, Puccinia graminis f. sp. tritici, f. sp. secalis, f. sp. avenae, and two cereal leaf rusts, P. recondita f. sp. tritici and P. coronata f. sp. avenae, and analyzed for the presence of heterogeneity in the intergenic region of the ribosomal DNA repeat unit. A 1 kb region of the repeat unit between the 26s and the 5s rRNA genes (IGR-1) was amplified by PCR and was found to be heterogeneous within each isolate and variable in size between races and species. The PCR results were confirmed by Southern blot analysis of native DNA. In an isolate of race C36(48), heterogeneity appeared to be due to variable numbers of 0.1 kb subrepeats in IGR-1. Nine wheat stem rust strains representing nine different races produced a unique pattern of heterogeneity while two different isolates of one race were identical, as were five of another. This may provide a rapid method for race identification in wheat stem rust. Heterogeneity and polymorphism in rye stem rust, oat stem rust, wheat leaf rust, and oat crown rust, was less pronounced than in wheat stem rust. In the course of this work, the 5s rRNA gene was located and its position and orientation within the ribosomal repeat unit was established.
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Affiliation(s)
- W K Kim
- Agriculture Canada, Research Station, Winnipeg, Manitoba
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32
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Guédon G, Pébay M, Colmin C, Simonet JM, Decaris B. The 23S-5S spacer of two rRNA loci of Streptococcus salivarius subsp thermophilus includes a promoter. Biochimie 1992; 74:585-8. [PMID: 1381619 DOI: 10.1016/0300-9084(92)90159-c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The nucleotide sequence of the 3' part of a ribosomal and transfer RNA locus from Streptococcus salivarius subsp thermophilus NST1403 was determined. The sequenced DNA fragment includes the 3' end of a 23S rRNA gene, a 5S rRNA gene, a tRNA(asn) gene and a potential transcriptional terminator. The tRNA gene does not encode for the CCA 3'terminus of mature tRNA. We compared this sequence to a promoter-carrying DNA fragment sequence (P20) of Streptococcus salivarius subsp thermophilus A054 [1]. We found that the P20 sequence included the 3' end of a 23S rRNA gene, a 5S rRNA gene and the 5' part of a tRNA(val) gene. The two 23S-5S spacer sequences are identical and contain a promoter and a potential 23S rRNA processing site. Therefore, 5S rRNA and tRNA genes could be transcribed from a promoter located within the 23S-5S spacer of at least two of the six rRNA loci.
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Affiliation(s)
- G Guédon
- Laboratoire de Génétique et Microbiologie, Faculté des Sciences, Université de Nancy I, Vandoeuvre-lès-Nancy, France
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33
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Alvarez-Cohen L, McCarty PL, Boulygina E, Hanson RS, Brusseau GA, Tsien HC. Characterization of a methane-utilizing bacterium from a bacterial consortium that rapidly degrades trichloroethylene and chloroform. Appl Environ Microbiol 1992; 58:1886-93. [PMID: 1377902 PMCID: PMC195700 DOI: 10.1128/aem.58.6.1886-1893.1992] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A mixed culture of bacteria grown in a bioreactor with methane as a carbon and energy source rapidly oxidized trichloroethylene and chloroform. The most abundant organism was a crescent-shaped bacterium that bound the fluorescent oligonucleotide signature probes that specifically hybridize to serine pathway methylotrophs. The 5S rRNA from this bacterium was found to be 93.5% homologous to the Methylosinus trichosporium OB3b 5S RNA sequence. A type II methanotrophic bacterium, isolated in pure culture from the bioreactor, synthesized soluble methane monooxygenase during growth in a copper-limited medium and was also capable of rapid trichloroethylene oxidation. The bacterium contained the gene that encodes the soluble methane monooxygenase B component on an AseI restriction fragment identical in size to a restriction fragment present in AseI digests of DNA from bacteria in the mixed culture. The sequence of the 16S rRNA from the pure culture was found to be 92 and 94% homologous to the 16S rRNAs of M. trichosporium OB3b and M. sporium, respectively. Both the pure and mixed cultures oxidized naphthalene to naphthol, indicating the presence of soluble methane monooxygenase. The mixed culture also synthesized soluble methane monooxygenase, as evidenced by the presence of proteins that cross-reacted with antibodies prepared against purified soluble methane monooxygenase components from M. trichosporium OB3b on Western blots (immunoblots). It was concluded that a type II methanotrophic bacterium phylogenetically related to Methylosinus species synthesizes soluble methane monooxygenase and is responsible for trichloroethylene oxidation in the bioreactor.
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Affiliation(s)
- L Alvarez-Cohen
- Department of Civil Engineering, University of California, Berkeley 94720
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34
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Cox AV, Bennett MD, Dyer TA. Use of the polymerase chain reaction to detect spacer size heterogeneity in plant 5S-rRNA gene clusters and to locate such clusters in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1992; 83:684-690. [PMID: 24202741 DOI: 10.1007/bf00226685] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/1991] [Accepted: 08/08/1991] [Indexed: 06/02/2023]
Abstract
We have used the polymerase chain reaction to analyse variation in the size of individual 5S-ribosomal gene spacer sequences. This reaction can be used to demonstrate inter- and intraspecific variation in spacer size, and combined with DNA sequencing it may thus be a valuable taxonomic tool. Two sets of nested polymerase chain reaction primers were designed to amplify the nontranscribed spacer DNA between repeated 5S-rRNA genes. These "universal" primers were used to generate fragments from the genomic DNA from several unrelated monocotyledonous plants. Ribosomal RNA spacer sequences generated in these experiments could also be used to locate 5S-rRNA gene clusters on specific chromosomes in hexaploid wheat (Triticum aestivum). Three distinct spacer sizes were observed after amplification. These were assigned locations on chromosomes by analysing amplification products of genomic DNA from nullisomic/tetrasomic and ditelosomic wheat stocks. "Large" 508-bp 5S repeats are located on the short arm of chromosome 5B and "short" 416-bp and 425-bp repeat unit variants are located on the short arms of chromosomes 1B and 1D, respectively. No other loci were detected. The spacer fragments were cloned, sequenced, and shown to be homologous to wheat 5S-rRNA spacers previously identified. Spacers of uniform size but with some sequence heterogeneity were shown to be located at each locus.
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Affiliation(s)
- A V Cox
- Jodrell Laboratory, Royal Botanic Gardens, TW9 3DS, Surrey, Kew, Richmond, UK
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35
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Preparata RM, Beam CA, Himes M, Nanney DL, Meyer EB, Simon EM. Crypthecodinium and Tetrahymena: an exercise in comparative evolution. J Mol Evol 1992; 34:209-18. [PMID: 1588596 DOI: 10.1007/bf00162970] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nucleotide sequences have been determined for the highly variable D2 region of the large rRNA molecule for over 60 strains of dinoflagellates. These strains were selected from a worldwide collection that represents all the known sibling species (compatibility groups, Mendelian species) in the sibling swarm referred to as Crypthecodinium cohnii. A phylogenetic tree has been constructed from an analysis of the variations in a length of about 180 bases, using PHYLOGEN string analysis programs. The Crypthecodinium tree is compared with the previously published but here augmented tree constructed upon the same rRNA region for the sibling species of a worldwide collection of ciliated protozoa related to the genus Tetrahymena. The first reported sequence of Lambornella clarki, the parasite of tree-hole mosquitoes, is included. The dinoflagellate species complex is much more homogeneous with respect to ribosomal variation. The mean number of differences among sequences from different Crypthecodinium species is about 7, in comparison with 22 differences among the ciliate species examined. Moreover, all the diversity in the dinoflagellates can be explained by base substitutions, whereas insertions and deletions are common in the ciliates. The dinoflagellates are also much more uniform with respect to nutritional and genetic economies. The two complexes differ also in the relationship between molecular variations and breeding compatibility. All tetrahymenine sibling species thus far examined are monomorphic in the D2 region, but several dinoflagellate species are polymorphic. Several different dinoflagellate species, moreover, have identical D2 regions. This kind of ribosomal identity of incompatible strains is found in these ciliates only in one tight cluster of species--Group C. The tetrahymenine swarm is apparently much older than the Crypthecodinium swarm, and the dinoflagellate species produce incompatible progeny species much more readily than do the ciliates, perhaps by the acquisition of mutations that potentiate incompatibility in sympatric populations.
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Affiliation(s)
- R M Preparata
- Department of Ecology, Ethology and Evolution, University of Illinois, Urbana 61801
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36
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Somerville CC, Jouannic S, Loiseaux-de Goër S. Sequence, proposed secondary structure, and phylogenetic analysis of the chloroplast 5S rRNA gene of the brown alga Pylaiella littoralis (L.) Kjellm. J Mol Evol 1992; 34:246-53. [PMID: 1588597 DOI: 10.1007/bf00162973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The chloroplast 5S rRNA gene of the brown alga Pylaiella littoralis (L.) Kjellm has been cloned and sequenced. The gene is located 23 bp downstream from the 3' end of the 23S rRNA gene. The sequence of the gene is as follows: GGTCTTG GTGTTTAAAGGATAGTGGAACCACATTGAT CCATATCGAACTCAATGGTGAAACATTATT ACAGTAACAATACTTAAGGAGGAGTCCTTTGGGAAGATAGCTTATGCCTAAGAC. A secondary structure model is proposed, and compared to those for the chloroplast 5S rRNAs of spinach and the red alga Porphyra umbilicalis. Cladograms based on chloroplast and bacterial 5S rRNA and rRNA gene sequences were constructed using the MacClade program with a user-defined character transformation in which transitions and transversions were assigned unequal step values. The topology of the resulting cladogram indicates a polyphyletic origin for photosynthetic organelles.
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Affiliation(s)
- C C Somerville
- Centre d'Etudes Oceanologiques et de Biologie Marine, CNRS-UPR4601, Roscoff, France
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37
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Röder MS, Sorrells ME, Tanksley SD. 5S ribosomal gene clusters in wheat: pulsed field gel electrophoresis reveals a high degree of polymorphism. MOLECULAR & GENERAL GENETICS : MGG 1992; 232:215-20. [PMID: 1557028 DOI: 10.1007/bf00279999] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The long-range structure of 5S rRNA gene clusters has been investigated in wheat (Triticum aestivum L.) by means of pulsed field gel electrophoresis. Using aneuploid stocks, 5S rRNA gene clusters were assigned to sites on chromosomes 1B, 1D, 5B and 5D. Cluster sizes were evaluated and the copy number of 5S DNA repeats was estimated at 4700-5200 copies for the short repeating unit (410 bp) and about 3100 copies for the long repeat (500 bp) per haploid genome. A comparison of wheat cultivars revealed extremely high levels of polymorphism in the 5S rRNA gene clusters. With one restriction enzyme digest all varieties tested gave unique banding patterns and, on a per fragment basis, 21-fold more polymorphism was detected among cultivars for 5S DNA compared to standard restriction fragment length polymorphisms (RFLPs) detected with single copy clones. Experiments with aneuploid stocks suggest that the 5S rRNA gene clusters at several chromosomal sites contribute to this polymorphism. A number of previous reports have shown that wheat cultivars are not easily distinguished by isozymes or RFLPs. The high level of variation detected in 5S rRNA gene clusters therefore offers the possibility of a sensitive fingerprinting method for wheat. 5S DNA and other macro-satellite sequences may also serve as hypervariable Mendelian markers for genetic and breeding experiments in wheat.
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Affiliation(s)
- M S Röder
- Department of Plant Breeding and Biometry, Cornell University, Ithaca, NY 14853
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38
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Fink PS, Zhao Y, Prochaska LJ, Leffak M. Nucleotide sequence of a 23S and a 5S-like rRNA gene from the thermophilic Bacillus sp. strain PS3. Nucleic Acids Res 1991; 19:5437. [PMID: 1923830 PMCID: PMC328913 DOI: 10.1093/nar/19.19.5437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- P S Fink
- Department of Biological Sciences, Wright State University, Dayton, OH 45435
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39
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Venkateswarlu K, Lee SW, Nazar RN. Conserved upstream sequence elements in plant 5S ribosomal RNA-encoding genes. Gene 1991; 105:249-54. [PMID: 1937022 DOI: 10.1016/0378-1119(91)90158-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
As a basis for further comparative studies, nuclear 5S rRNA gene repeats from two plants of the Solanaceae family, tobacco (Nicotiana rustica) and tomato (Lycopersicon esculentum), were isolated and sequenced. The more abundant 5S rRNA gene repeat in tobacco is 430 bp long, while a second less common variant is 521 bp long. In contrast, the 5S rRNA gene repeat from tomato is only 355 bp long. The spacer sequences from these gene repeats, as well as from other published plant nuclear 5S rRNA genes, were compared for repeating or conserved sequence elements. The results indicate that often observed, but non-conserved, repeating sequence elements probably arise spontaneously by unequal crossover with no functional significance. However, three conserved sequence elements immediately upstream of the coding sequence; a C residue at -1, a G + C-rich element centered at -13, and an A + T-rich element centered at -26 resemble regulatory features which have been identified in other types of genes.
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Affiliation(s)
- K Venkateswarlu
- Department of Molecular Biology and Genetics, University of Guelph, Ontario, Canada
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40
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Brunel C, Romby P, Westhof E, Ehresmann C, Ehresmann B. Three-dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling. J Mol Biol 1991; 221:293-308. [PMID: 1717695 DOI: 10.1016/0022-2836(91)80220-o] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The conformation of Escherichia coli 5 S rRNA was investigated using chemical and enzymatic probes. The four bases were monitored at one of their Watson-Crick positions with dimethylsulfate (at C(N-3) and A(N-1], with a carbodiimide derivative (at G(N-1) and U(N-3] and with kethoxal (at G(N-1, N-2]. Position N-7 of purine was probed with diethylpyrocarbonate (at A(N-7] and dimethylsulfate (at G(N-7]. Double-stranded or stacked regions were tested with RNase V1 and unpaired guanine residues with RNase T1. We also used lead(II) that has a preferential affinity for interhelical and loop regions and a high sensitivity for flexible regions. Particular care was taken to use uniform conditions of salt, magnesium, pH and temperature for the different enzymatic chemical probes. Derived from these experimental data, a three dimensional model of the 5 S rRNA was built using computer modeling which integrates stereochemical constraints and phylogenetic data. The three domains of 5 S rRNA secondary structure fold into a Y-shaped structure that does not accommodate long-range tertiary interactions between domains. The three domains have distinct structural and dynamic features as revealed by the chemical reactivity and the lead(II)-induced hydrolysis: domain 2 (loop B/helix III/loop C) displays a rather weak structure and possesses dynamic properties while domain 3 (helix V/region E/helix IV/loop D) adopts a highly structured and overall helical conformation. Conserved nucleotides are not crucial for the tertiary folding but maintain an intrinsic structure in the loop regions, especially via non-canonical pairing (A.G, G.U, G.G, A.C, C.C), which can close the loops in a highly specific fashion. In particular, nucleotides in the large external loop C fold into an organized conformation leading to the formation of a five-membered loop motif. Finally, nucleotides at the hinge region of the Y-shape are involved in a precise array of hydrogen bonds based on a triple interaction between U14, G69 and G107 stabilizing the quasi-colinearity of helices II and V. The proposed tertiary model is consistent with the localization of the ribosomal protein binding sites and possesses strong analogy with the model proposed for Xenopus laevis 5 S rRNA, indicating that the Y-shape model can be generalized to all 5 S rRNAs.
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Affiliation(s)
- C Brunel
- Institut de Biologie Moléculaire et Cellulaire de CNRS, Strasbourg, France
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41
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Kitada K, Oka S, Kimura S, Shimada K, Serikawa T, Yamada J, Tsunoo H, Egawa K, Nakamura Y. Detection of Pneumocystis carinii sequences by polymerase chain reaction: animal models and clinical application to noninvasive specimens. J Clin Microbiol 1991; 29:1985-90. [PMID: 1774325 PMCID: PMC270246 DOI: 10.1128/jcm.29.9.1985-1990.1991] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Pneumocystis carinii is a eukaryotic microbe which causes fatal pneumonia in patients with AIDS. Oligonucleotide primers were used to amplify the 5S rDNA sequence of P. carinii by the polymerase chain reaction (PCR) in various clinical and animal samples. Of 35 independent lung specimens tested, PCR detected the P. carinii sequence in all 23 cases which were known to be P. carinii infected, i.e., 15 from mice, 1 from rat, 3 from human autopsy, and 4 from biopsy of AIDS patients by needle aspiration. The results were consistent with clinical and microscopic diagnosis. The detection was highly sensitive and specific. Direct sequencing of these amplified DNAs revealed homogeneity of 5S rDNA sequences of independent isolates from mice, rats, and humans. Preliminary trials manifested efficacy of the PCR method to detect P. carinii sequences in induced sputum or blood from AIDS patients, the latter case suggesting that P. carinii might enter peripheral blood via phagocytosis or direct intrusion. Development of less-invasive or noninvasive PCR diagnostic techniques to detect P. carinii infection would greatly facilitate therapeutic and prophylactic management of P. carinii pneumonia.
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MESH Headings
- Acquired Immunodeficiency Syndrome/complications
- Animals
- Base Sequence
- DNA, Fungal/genetics
- DNA, Fungal/isolation & purification
- Disease Models, Animal
- Evaluation Studies as Topic
- Humans
- Mice
- Mice, Nude
- Molecular Sequence Data
- Opportunistic Infections/complications
- Opportunistic Infections/diagnosis
- Opportunistic Infections/microbiology
- Pneumocystis/genetics
- Pneumocystis/isolation & purification
- Pneumonia, Pneumocystis/complications
- Pneumonia, Pneumocystis/diagnosis
- Pneumonia, Pneumocystis/microbiology
- Polymerase Chain Reaction/methods
- Polymerase Chain Reaction/statistics & numerical data
- RNA, Fungal/genetics
- RNA, Fungal/isolation & purification
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/isolation & purification
- Sensitivity and Specificity
- Sequence Homology, Nucleic Acid
- Species Specificity
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Affiliation(s)
- K Kitada
- Department of Tumor Biology, University of Tokyo, Japan
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42
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Gniadkowski M, Fiett J, Borsuk P, Hoffman-Zacharska D, Stepień PP, Bartnik E. Structure and evolution of 5S rRNA genes and pseudogenes in the genus Aspergillus. J Mol Evol 1991; 33:175-8. [PMID: 1920453 DOI: 10.1007/bf02193632] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have cloned and determined the nucleotide sequence of 18 DNA fragments hybridizing to 5S rRNA from two Aspergillus species--A. wentii and A. awamori. Four of the analyzed sequences were pseudogenes. The gene sequences of these two species were very similar and differed from Aspergillus nidulans at both constant and microheterogeneous sites.
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Affiliation(s)
- M Gniadkowski
- Department of Genetics, University of Warsaw, Poland
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43
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Specht T, Wolters J, Erdmann VA. Compilation of 5S rRNA and 5S rRNA gene sequences. Nucleic Acids Res 1991; 19 Suppl:2189-91. [PMID: 2041804 PMCID: PMC331352 DOI: 10.1093/nar/19.suppl.2189] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
This is an update for the 5S rRNA sequences of the BERLIN RNA DATABANK last published in 1990 (1). The new entry consists of 25 eubacterial and 2 eukaryotic 5S rRNA sequences and 10 plant 5S rRNA pseudogenes (Table 1). Thus the BERLIN RNA DATABANK contains as of February 1, 1991 the 5S rRNA sequences of 44 archaebacteria, 292 eubacteria, 20 plastids, 6 mitochondria, 321 eukaryotes and 21 eukaryotic pseudogenes. The BERLIN RNA DATABANK uses the format of the EMBL Nucleotide Sequence Data Library complemented by a Sequence Alignment (SA) field including secondary structure information.
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Affiliation(s)
- T Specht
- Institut für Biochemie, Freie Universität Berlin, FRG
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44
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Liesack W, Sela S, Bercovier H, Pitulle C, Stackebrandt E. Complete nucleotide sequence of the Mycobacterium leprae 23 S and 5 S rRNA genes plus flanking regions and their potential in designing diagnostic oligonucleotide probes. FEBS Lett 1991; 281:114-8. [PMID: 2015881 DOI: 10.1016/0014-5793(91)80372-a] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The complete nucleotide sequences of the Mycobacterium leprae 23 S and 5 S rRNA genes and their flanking regions are presented. As compared to other eubacterial homologous molecules the 23 S rDNA exhibits two insertions. A 16 nucleotide long insertion is almost unique to members of the genus Mycobacterium, while the second represents an extended version of helix 54. The potential of both insertions to serve as target for diagnostic oligonucleotide probes was proven by comparative sequence analysis of 23 S rRNA of several Mycobacterium species and by dot blot hybridization. In addition, a 19-mer oligonucleotide probe is described, which can be considered genus Mycobacterium-specific.
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Affiliation(s)
- W Liesack
- Department of Microbiology, University of Queensland, St. Lucia, Australia
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45
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Barns SM, Lane DJ, Sogin ML, Bibeau C, Weisburg WG. Evolutionary relationships among pathogenic Candida species and relatives. J Bacteriol 1991; 173:2250-5. [PMID: 2007550 PMCID: PMC207775 DOI: 10.1128/jb.173.7.2250-2255.1991] [Citation(s) in RCA: 185] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Small subunit rRNA sequences have been determined for 10 of the most clinically important pathogenic species of the yeast genus Candida (including Torulopsis [Candida] glabrata and Yarrowia [Candida] lipolytica) and for Hansenula polymorpha. Phylogenetic analyses of these sequences and those of Saccharomyces cerevisiae, Kluyveromyces marxianus var. lactis, and Aspergillus fumigatus indicate that Candida albicans, C. tropicalis, C. parapsilosis, and C. viswanathii form a subgroup within the genus. The remaining significant pathogen, T. glabrata, falls into a second, distinct subgroup and is specifically related to S. cerevisiae and more distantly related to C. kefyr (psuedotropicalis) and K. marxianus var. lactis. The 18S rRNA sequence of Y. lipolytica has evolved rapidly in relation to the other Candida sequences examined and appears to be only distantly related to them. As anticipated, species of several other genera appear to bear specific relationships to members of the genus Candida.
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Affiliation(s)
- S M Barns
- GENE-TRAK Systems, Framingham, Massachusetts 01701
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46
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Hartmann RK, Toschka HY, Erdmann VA. Processing and termination of 23S rRNA-5S rRNA-tRNA(Gly) primary transcripts in Thermus thermophilus HB8. J Bacteriol 1991; 173:2681-90. [PMID: 2013580 PMCID: PMC207837 DOI: 10.1128/jb.173.8.2681-2690.1991] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The two 23S rRNA-5S rRNA-tRNAGly operons from the extreme thermophilic eubacterium Thermus thermophilus HB8 were used to characterized the in vivo processing and termination of 23S rRNA-5S rRNA-tRNAGly primary transcripts in this organism by nuclease S1 mapping. A processing site in the pre-23S rRNA 3'-flanking region is located approximately 25 nucleotides upstream of 5S rRNA and precedes a putative 23S-5S rRNA spacer antitermination box A. Cleavage at this site and 5S rRNA 5' end formation were shown to be inseparable events. Termination of transcription at the uridine cluster following the termination-associated hairpin was shown to be efficient but leaky. Subsequent to the operon, a functional promoter was detected whose -35 box coincided with the uridine-rich termination region. The promoter directed synthesis of a beta-galactosidase fusion protein in Escherichia coli.
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MESH Headings
- Base Sequence
- Chromosome Mapping
- Cloning, Molecular
- Molecular Sequence Data
- Molecular Structure
- Operon
- Peptide Chain Termination, Translational
- Promoter Regions, Genetic
- RNA Probes
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/genetics
- RNA, Transfer, Gly/genetics
- Thermus/genetics
- Transcription, Genetic
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Affiliation(s)
- R K Hartmann
- Institut für Biochemie, Freie Universität Berlin, Federal Republic of Germany
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47
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Nanney DL, Mobley DO, Preparata RM, Meyer EB, Simon EM. Eukaryotic origins: string analysis of 5S ribosomal RNA sequences from some relevant organisms. J Mol Evol 1991; 32:316-27. [PMID: 1907666 DOI: 10.1007/bf02102190] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Using the PHYLOGEN tree-forming programs, we evaluate the published 5S rRNA sequences in certain of the files in the Berlin DataBank in an attempt to identify the connection between archaebacteria and the eukaryotic protists. These programs are based on methods of string analysis developed by Sankoff and others. Their discriminatory power is derived from their continuous realignment of sequences through repeated assessment of insertions and deletions as well as substitutions. The programs demonstrate that even these small molecules (ca. 120 bases) retain substantial records of evolutionary events that occurred over a billion years ago. The eukaryotes seem to have been derived from ancestors near the common origins of the halobacterial and Methanococcales groups. Identifying what might have been a primordial eukaryote is more difficult because several of the species considered as early derivatives from the common root are isolated species with large genetic differences from each other and from all other extant forms that have been sequenced. The ameboid, flagellated, and ciliated protists seem to have emerged nearly simultaneously from an ancient cluster, but the sarcodinid protozoa have preference as the group of most ancient origin. The euglenozoa and the ciliates are of later derivation. Our ability to tease plausible trees from such small molecules suggests that the mode of analysis rather than the size of the molecule is often a major limitation in the reconstruction of acceptable ancient phylogenics.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- D L Nanney
- Department of Ecology, Ethology, and Evolution, University of Illinois, Urbana 61801
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48
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Troitsky AV, Melekhovets YuF, Rakhimova GM, Bobrova VK, Valiejo-Roman KM, Antonov AS. Angiosperm origin and early stages of seed plant evolution deduced from rRNA sequence comparisons. J Mol Evol 1991; 32:253-61. [PMID: 1904502 DOI: 10.1007/bf02342748] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Complete or partial nucleotide sequences of five different rRNA species, coded by nuclear (18S, 5.8S, and 5S) or chloroplast genomes (5S, 4.5S) from a number of seed plants were determined. Based on the sequence data, the phylogenetic dendrograms were built by two methods, maximum parsimony and compatibility. The topologies of the trees for different rRNA species are not fully congruent, but they share some common features. It may be concluded that both gymnosperms and angiosperms are monophyletic groups. The data obtained suggest that the divergence of all the main groups of extant gymnosperms occurred after the branching off of the angiosperm lineage. As the time of divergence of at least some of these gymnosperm taxa is traceable back to the early Carboniferous, it may be concluded that the genealogical splitting of gymnosperm and angiosperm lineages occurred before this event, at least 360 million years ago, i.e., much earlier than the first angiosperm fossils were dated. Ancestral forms of angiosperms ought to be searched for among Progymnospermopsida. Genealogical relationships among gymnosperm taxa cannot be deduced unambiguously on the basis of rRNA data. The only inference may be that the taxon Gnetopsida is an artificial one, and Gnetum and Ephedra belong to quite different lineages of gymnosperms. As to the phylogenetic position of the two Angiospermae classes, extant monocotyledons seem to be a paraphyletic group located near the root of the angiosperm branch; it emerged at the earliest stages of angiosperm evolution. We may conclude that either monocotyledonous characters arose independently more than once in different groups of ancient Magnoliales or that monocotyledonous forms rather than dicotyledonous Magnoliales were the earliest angiosperms. Judging by the rRNA trees, Magnoliales are the most ancient group among dicotyledons. The most ancient lineage among monocotyledons leads to modern Liliaceae.
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Affiliation(s)
- A V Troitsky
- A.N. Belozersky Laboratory of Molecular Biology and Bioorganic Chemistry, Moscow State University, USSR
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49
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Barciszewska MZ, Lorenz S, Joachimiak A, Ulbrich N, Erdmann VA, Barciszewski J. New model of tertiary structure of plant 5S rRNA is confirmed by digestions with alpha-sarcin. FEBS Lett 1990; 269:83-5. [PMID: 2387418 DOI: 10.1016/0014-5793(90)81124-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The cytotoxin alpha-sarcin was employed to test the model of secondary and tertiary structures of plant 5S rRNAs, which we recently proposed [(1990) Int. J. Biol. Macromol. (in press)]. alpha-Sarcin is a novel ribonuclease that hydrolyzes phosphodiester bonds adjacent to purines in nucleic acids. The digestion pattern obtained for lupin and wheat germ 5S rRNAs strongly suggests the existence of tertiary interactions between residues C34, C35, C36, A37 and G85, G86, G87, U88 as previously proposed. The results on the secondary structure of plant 5S rRNA are in line with a previously proposed model.
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Affiliation(s)
- M Z Barciszewska
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Poznan
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50
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Abstract
5S rRNA sequences from six additional green algae lend strong molecular support for the major outlines of higher plant and green algae phylogeny that have been proposed under varying naming conventions by several authors. In particular, the molecular evidence now available unequivocally supports the existence of at least two well-separated divisions of the Chlorobionta: the Chlorophyta and the Streptophyta (i.e., charophytes) (according to the nomenclature of Bremer). The chlamydomonad 5S rRNAs are, however, sufficiently distinct from both clusters that it may ultimately prove preferable to establish a third taxon for them. In support of these conclusions 5S rRNA sequence data now exist for members of four diverse classes of chlorophytes. These sequences all exhibit considerably more phylogenetic affinity to one another than any of them show toward members of the other cluster, the Streptophyta, or the two Chlamydomonas strains. Among the Charophyceae, new 5S rRNA sequences are provided herein for three genera, Spirogyra, Klebsormidium, and Coleochaete. All of these sequences and the previously published Nitella sequence show greater resemblance among themselves and to the higher plants than they do to any of the other green algae examined to date. These results demonstrate that an appropriately named taxon that includes these green algae and the higher plants is strongly justified. The 5S rRNA data lack the resolution needed, however, to unequivocally determine which of several subdivisions of the charophytes is the sister group of the land plants. The evolutionary diversity of Chlamydomonas relative to the other green algae was recognized in earlier 5S rRNA studies but was unanticipated by ultrastructural work.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- R Devereux
- Department of Biology, University of Houston, Texas 77204-5500
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