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Akahori M, Miyazaki A, Koinuma H, Tokuda R, Iwabuchi N, Kitazawa Y, Maejima K, Namba S, Yamaji Y. Use of the 23S rRNA gene as a target template in the universal loop-mediated isothermal amplification (LAMP) of genomic DNA from phytoplasmas. Microbiol Spectr 2024; 12:e0010624. [PMID: 38534170 PMCID: PMC11064480 DOI: 10.1128/spectrum.00106-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
Plant-pathogenic bacteria cause numerous diseases in host plants and can result in serious damage. Timely and accurate diagnostic techniques are, therefore, crucial. While advances in molecular techniques have led to diagnostic systems able to distinguish known plant pathogens at the species or strain level, systems covering larger categories are mostly lacking. In this study, a specific and universal LAMP-based diagnostic system was developed for phytoplasmas, a large group of insect-borne plant-pathogenic bacteria that cause significant agricultural losses worldwide. Targeting the 23S rRNA gene of phytoplasma, the newly designed primer set CaPU23S-4 detected 31 'Candidatus Phytoplasma' tested within 30 min. This primer set also showed high specificity, without false-positive results for other bacteria (including close relatives of phytoplasmas) or healthy plants. The detection sensitivity was ~10,000 times higher than that of PCR methods for phytoplasma detection. A simple, rapid method of DNA extraction, by boiling phytoplasma-infected tissues, was developed as well. When used together with the universal LAMP assay, it enabled the prompt and accurate detection of phytoplasmas from plants and insects. The results demonstrate the potential of the 23S rRNA gene as a versatile target for the LAMP-based universal detection of bacteria at the genus level and provide a novel avenue for exploring this gene as molecular marker for phytoplasma presence detection.IMPORTANCEPhytoplasmas are associated with economically important diseases in crops worldwide, including lethal yellowing of coconut palm, "flavescence dorée" and "bois noir" of grapevine, X-disease in stone fruits, and white leaf and grassy shoot in sugarcane. Numerous LAMP-based diagnostic assays, mostly targeting the 16S rRNA gene, have been reported for phytoplasmas. However, these assays can only detect a limited number of 'Candidatus Phytoplasma' species, whereas the genus includes at least 50 of these species. In this study, a universal, specific, and rapid diagnostic system was developed that can detect all provisionally classified phytoplasmas within 1 h by combining the LAMP technique targeting the 23S rRNA gene with a simple method for DNA extraction. This diagnostic system will facilitate the on-site detection of phytoplasmas and may aid in the discovery of new phytoplasma-associated diseases and putative insect vectors, irrespective of the availability of infrastructure and experimental resources.
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Affiliation(s)
- Mako Akahori
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Akio Miyazaki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroaki Koinuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryosuke Tokuda
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Nozomu Iwabuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yugo Kitazawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Tsuchiya Y, Kaneda H, Kano Y, Koshino S. Detection of Beer Spoilage Organisms by Polymerase Chain Reaction Technology. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-50-0064] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Youichi Tsuchiya
- Brewing Research Laboratories, Sapporo Breweries, Ltd. 10, Okatohme, Yaizu-shi, Shizuoka, 425, Japan
| | - Hirotaka Kaneda
- Brewing Research Laboratories, Sapporo Breweries, Ltd. 10, Okatohme, Yaizu-shi, Shizuoka, 425, Japan
| | - Yukinobu Kano
- Brewing Research Laboratories, Sapporo Breweries, Ltd. 10, Okatohme, Yaizu-shi, Shizuoka, 425, Japan
| | - Shohei Koshino
- Brewing Research Laboratories, Sapporo Breweries, Ltd. 10, Okatohme, Yaizu-shi, Shizuoka, 425, Japan
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3
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Waminal NE, Ryu KB, Park BR, Kim HH. Phylogeny of Cucurbitaceae species in Korea based on 5S rDNA non-transcribed spacer. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0141-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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4
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Abstract
5S rRNA is an integral component of the ribosome of all living organisms. It is known that the ribosome without 5S rRNA is functionally inactive. However, the question about the specific role of this RNA in functioning of the translation apparatus is still open. This review presents a brief history of the discovery of 5S rRNA and studies of its origin and localization in the ribosome. The previously expressed hypotheses about the role of this RNA in the functioning of the ribosome are discussed considering the unique location of 5S rRNA in the ribosome and its intermolecular contacts. Based on analysis of the current data on ribosome structure and its functional complexes, the role of 5S rRNA as an intermediary between ribosome functional domains is discussed.
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Affiliation(s)
- G M Gongadze
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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5
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Globisch D, Pearson D, Hienzsch A, Brückl T, Wagner M, Thoma I, Thumbs P, Reiter V, Kneuttinger AC, Müller M, Sieber SA, Carell T. Systems-based analysis of modified tRNA bases. Angew Chem Int Ed Engl 2011; 50:9739-42. [PMID: 21882308 DOI: 10.1002/anie.201103229] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Indexed: 01/08/2023]
Affiliation(s)
- Daniel Globisch
- Center for Integrated Protein Science, Department of Chemistry, Ludwig Maximilian University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
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Globisch D, Pearson D, Hienzsch A, Brückl T, Wagner M, Thoma I, Thumbs P, Reiter V, Kneuttinger AC, Müller M, Sieber SA, Carell T. Systembasierte Analyse von modifizierten tRNA-Basen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103229] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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The Genus Magnetospirillum gen. nov. Description of Magnetospirillum gryphiswaldense sp. nov. and Transfer of Aquaspirillum magnetotacticum to Magnetospirillum magnetotacticum comb. nov. Syst Appl Microbiol 1991. [DOI: 10.1016/s0723-2020(11)80313-9] [Citation(s) in RCA: 216] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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8
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Nucleotide Sequence of the 16S Ribosomal RNA Gene from the Haloalkaliphilic Archaeon (Archaebacterium) Natronobacterium magadii, and the Phylogeny of Halobacteria. Syst Appl Microbiol 1991. [DOI: 10.1016/s0723-2020(11)80309-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Whiley RA, Fraser HY, Douglas CW, Hardie JM, Williams AM, Collins MD. Streptococcus parasanguis sp. nov., an atypical viridans Streptococcus from human clinical specimens. FEMS Microbiol Lett 1990; 56:115-21. [PMID: 1692001 DOI: 10.1111/j.1574-6968.1990.tb04133.x] [Citation(s) in RCA: 61] [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
Molecular taxonomic studies were performed on ten strains of an unusual 'viridans streptococcus' that were originally isolated from human throats, blood and urine. On the basis of DNA-DNA hybridization studies the strains formed a single homology group distinct from all recognized species of oral and viridans streptococci. 16S ribosomal RNA reverse transcriptase sequence studies confirmed the genealogical distinctiveness of the human strains. The results of the present study clearly demonstrate that the human strains represent a new species of the viridans group for which the name Streptococcus parasanguis sp. nov. is proposed. The type strain is ATCC 15912.
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Affiliation(s)
- R A Whiley
- Department of Oral Microbiology, London Hospital Medical College, U.K
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10
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Estrada-G IC, Colston M, Cox RA. Determination and evolutionary significance of nucleotide sequences near to the 3â²-end of 16S ribosomal RNA of mycobacteria. FEMS Microbiol Lett 1989. [DOI: 10.1111/j.1574-6968.1989.tb03638.x] [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] Open
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11
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Sneath P. Analysis and Interpretation of Sequence Data for Bacterial Systematics: The View of a Numerical Taxonomist. Syst Appl Microbiol 1989. [DOI: 10.1016/s0723-2020(89)80036-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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12
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Williams A, Farrow JA, Collins M. Reverse transcriptase sequencing of 16S ribosomal RNA from Streptococcus cecorum. Lett Appl Microbiol 1989. [DOI: 10.1111/j.1472-765x.1989.tb00244.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Embley MT, Smida J, Stackebrandt E. The Phylogeny of Mycolate-less Wall Chemotype IV Actinomycetes and Description of Pseudonocardiaceae fam. nov. Syst Appl Microbiol 1988. [DOI: 10.1016/s0723-2020(88)80047-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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14
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Zhou XQ, Liu WY, Wang MQ. Comparative study on the evolution of chloroplast ribosomal 5S RNA of a living fossil plant, Cycas revoluta Thumb. FEBS Lett 1988; 235:30-4. [PMID: 3136036 DOI: 10.1016/0014-5793(88)81228-6] [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: 01/04/2023]
Abstract
The complete nucleotide sequence of Cycas revoluta Thunb chloroplast 5 S rRNA was determined. It consists of 122 nucleotides. This is the only known 5 S rRNA sequence in Gymnospermae. It is highly homologous with chloroplast 5 S rRNA of higher plants (92-97%), but less homologous (about 54%) with those of lower plants. There is however 67% homology between Cycas and a procaryote a. nidulans. The chloroplast 5 S rRNAs of Angiospermae are nearly identical with each other (95-97%). S. oligorhize and L. minor have 100% homology among themselves. We have constructed a phylogenic tree of 5 S rRNA sequences from fifteen plant chloroplasts. The result suggests that the emergence of algae occurred at an early stage of plant chloroplast evolution and that green plants originated from green algae. This is in agreement with the classical view and other theories of molecular evolution. However there is no common ancestor in the case of Bryophyta and ferns. Among the Angiospermae, a precise evolutionary process cannot be deduced because the Knuc values among the species are very close to each other.
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Affiliation(s)
- X Q Zhou
- Shanghai Institute of Biochemistry, Academia Sinica, China
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15
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Witt D, Stackebrandt E. Disproving the hypothesis of a common ancestry for the Ochromonas danica chrysoplast and Heliobacterium chlorum. Arch Microbiol 1988. [DOI: 10.1007/bf00407787] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Stackebrandt E, Fischer A, Roggentin T, Wehmeyer U, Bomar D, Smida J. A phylogenetic survey of budding, and/or prosthecate, non-phototrophic eubacteria: membership of Hyphomicrobium, Hyphomonas, Pedomicrobium, Filomicrobium, Caulobacter and "dichotomicrobium" to the alpha-subdivision of purple non-sulfur bacteria. Arch Microbiol 1988; 149:547-56. [PMID: 2455491 DOI: 10.1007/bf00446759] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The phylogenetic position of various budding and/or or prosthecate Gram-negative eubacteria was determined by different methods. Members of the genera Hyphomicrobium, Filomicrobium, Pedomicrobium were investigated by 16S rRNA cataloguing, a 1373 nucleotide long portion of the 16S rRNA was sequenced from Hyphomicrobium vulgare and the 5S rRNAs were analyzed from two Hyphomicrobium strains, Hyphomonas polymorpha and Caulobacter crescentus. Comparison with published sequences indicated a membership of all of these organisms to the alpha subdivision of purple bacteria. While C. crescentus and Hyphomonas polymorpha constitute separate individual lines of descent, the position of a coherent cluster embracing Hyphomicrobium, Pedomicrobium and Filomicrobium is not yet settled. 16S rRNA cataloguing indicate the presence of a distinct line equivalent to other subgroups in its phylogenetic depth. 5S rRNA analysis, on the other hand, groups Hyphomicrobium vulgare and strain IFAM 1761 with members of subgroup alpha-2 (Rhodopseudomonas palustris, Nitrobacter winogradskyi and relatives). In contrast to the present classification, Pedomicrobium ferrugineum and Filimicrobium fusiforme are more closely related to certain Hyphomicrobium strains than these are related among each other. Budding mode of reproduction and prosthecate morphology are dominating morphological features of members of the alpha subdivision. These characteristics may gain diagnostic significance in a future formal description of this subdivision and its subgroups as a higher rank.
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Affiliation(s)
- E Stackebrandt
- Institut für Allgemeine Mikrobiologie, Christian Albrecht Universität, Kiel, Federal Republic of Germany
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17
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Satoh H, Nishida H, Isono K. Evidence for movement of the alpha-amylase gene into two phylogenetically distant Bacillus stearothermophilus strains. J Bacteriol 1988; 170:1034-40. [PMID: 3257753 PMCID: PMC210870 DOI: 10.1128/jb.170.3.1034-1040.1988] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The gene for an alpha-amylase cloned from strain DY-5 of Bacillus stearothermophilus was used to examine to what extent the corresponding genes are structurally similar in other B. stearothermophilus strains. The structure of the gene itself was almost identical in DY-5 and a group of strains represented by strain 799. The gene was not detected at all in strain DSM2334, which was phenotypically amylase deficient. Comparison of the structure of 5S rRNA and electrophoretic pattern of the ribosomal proteins indicates that strains DY-5 and DSM2334 are closely related to each other, whereas strain 799 is phylogenetically very distant from the two. We estimate that strain 799 separated from DY-5 and DSM2334 some 420 million years ago. Nucleotide sequencing of the region containing the amylase gene from strains DY-5 and 799 revealed the presence of a 3.4-kilobase stretch that was highly similar in the two strains. Furthermore, comparison of the restriction map surrounding the amylase gene of DY-5 with that of a corresponding region in DSM2334 indicated that the former strain contained an extra segment 5.5 kilobases in length, which included the 3.4-kilobase stretch mentioned above. This segment was missing in DSM2334. It thus appears that the alpha-amylase gene was brought into strains DY-5 and 799 from outside despite a large phylogenetic distance.
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Affiliation(s)
- H Satoh
- Department of Biology, Faculty of Science, Kobe University, Japan
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18
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10 The Application of 16S rRNA Cataloguing and 5S rRNA Sequencing in Bacterial Systematics. METHODS IN MICROBIOLOGY 1988. [DOI: 10.1016/s0580-9517(08)70416-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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19
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Manske CL, Chapman DJ. Nonuniformity of nucleotide substitution rates in molecular evolution: computer simulation and analysis of 5S ribosomal RNA sequences. J Mol Evol 1987; 26:226-51. [PMID: 3129569 DOI: 10.1007/bf02099855] [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: 01/04/2023]
Abstract
The effects of temporal (among different branches of a phylogeny) and spatial (among different nucleotide sites within a gene) nonuniformities of nucleotide substitution rates on the construction of phylogenetic trees from nucleotide sequences are addressed. Spatial nonuniformity may be estimated by using Shannon's (1948) entropy formula to measure the Relative Nucleotide Variability (RNV) at each nucleotide site in an aligned set of sequences; this is demonstrated by a comparative analysis of 5S rRNAs. New methods of constructing phylogenetic trees are proposed that augment the Unweighted Pair-Group Using Arithmetic Averages (UPGMA) algorithm by estimating and compensating for both spatial and temporal nonuniformity in substitution rates. These methods are evaluated by computer simulations of 5S rRNA evolution that include both kinds of nonuniformities. It was found that the proposed Reference Ratio Method improved both the ability to reconstruct the correct topology of a tree and also the estimation of branch lengths as compared to UPGMA. A previous method (Farris et al. 1970; Klotz et al. 1979; Li 1981) was found to be less successful in reconstructing topologies when there is high probability of multiple mutations at some sites. Phylogenetic analyses of 5S rRNA sequences support the endosymbiotic origins of both chloroplasts and mitochondria, even though the latter exhibit an accelerated rate of nucleotide substitution. Phylogenetic trees also reveal an adaptive radiation within the eubacteria and another within the eukaryotes for the origins of most major phyla within each group during the Precambrian era.
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Affiliation(s)
- C L Manske
- Department of Biology, University of California, Los Angeles 90024
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20
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Albrecht W, Fischer A, Smida J, Stackebrandt E. Verrucomicrobium spinosum, a Eubacterium Representing an Ancient Line of Descent. Syst Appl Microbiol 1987. [DOI: 10.1016/s0723-2020(87)80011-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Johnson AM, Murray PJ, Illana S, Baverstock PJ. Rapid nucleotide sequence analysis of the small subunit ribosomal RNA of Toxoplasma gondii: evolutionary implications for the Apicomplexa. Mol Biochem Parasitol 1987; 25:239-46. [PMID: 3320746 DOI: 10.1016/0166-6851(87)90087-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A method for obtaining a large proportion of the nucleotide sequence of the small subunit ribosomal RNA (srRNA) was applied to the obligate intracellular protozoon Toxoplasma gondii. The method uses reverse transcription of as little as 8 micrograms of total cellular RNA. This fast, efficient method has numerous advantages over traditional gene cloning methods when nucleotide sequences are required for evolutionary studies. A phylogenetic analysis of the srRNA sequence data showed that T. gondii is not especially closely related to any other organism for which srRNA sequences are available, including another member of the Apicomplexa.
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Affiliation(s)
- A M Johnson
- Unit of Clinical Microbiology, School of Medicine, Flinders University of South Australia, Bedford Park
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22
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Martens B, Spiegl H, Stackebrandt E. Sequence of a 16S Ribosomal RNA Gene of Ruminobacter amylophilus: The Relation Between Homology Values and Similarity Coefficients. Syst Appl Microbiol 1987. [DOI: 10.1016/s0723-2020(87)80026-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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Erdmann VA, Wolters J, Pieler T, Digweed M, Specht T, Ulbrich N. Evolution of organisms and organelles as studied by comparative computer and biochemical analyses of ribosomal 5S RNA structure. Ann N Y Acad Sci 1987; 503:103-24. [PMID: 3113313 DOI: 10.1111/j.1749-6632.1987.tb40602.x] [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: 01/04/2023]
Abstract
The results documented in this publication demonstrate that for evolutionary studies the ribosomal 5S rRNA is a suitable object for such an investigation and that as many methods as possible should be consulted. In this study the results of biochemical and chemical experiments were combined with those of computer sequence analyses, and they revealed that these methods complement each other nicely. We are currently at a state at which we are able to well define the secondary structures of the 5S rRNAs for eubacteria, organelles, archaebacteria, and eukaryotes and we are even able to propose a secondary structure for a Ur-5S rRNA. It is also clear that in the future the present studies should be continued and extended in such a way that the tertiary structures of these molecules will become known.
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24
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Mannella CA, Frank J, Delihas N. Interrelatedness of 5S RNA sequences investigated by correspondence analysis. J Mol Evol 1987; 24:228-35. [PMID: 3106638 DOI: 10.1007/bf02111236] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Correspondence analysis (a form of multivariate statistics) applied to 74 5S ribosomal RNA sequences indicates that the sequences are interrelated in a systematic, nonrandom fashion. Aligned sequences are represented as vectors in a 5N-dimensional space, where N is the number of base positions in the 5S RNA molecule. Mutually orthogonal directions (called factor axes) along which intersequence variance is greatest are defined in this hyperspace. Projection of the sequences onto planes defined by these factorial directions reveals clustering of species that is suggestive of phylogenetic relationships. For each factorial direction, correspondence analysis points to regions of "importance," i.e., those base positions at which the systematic changes occur that define that particular direction. In effect, the technique provides a rapid determination of group-specific signatures. In several instances, similarities between sequences are indicated that have only recently been inferred from visual base-to-base comparisons. These results suggest that correspondence analysis may provide a valuable starting point from which to uncover the patterns of change underlying the evolution of a macromolecule, such as 5S RNA.
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Erdmann VA, Pieler T, Wolters J, Digweed M, Vogel D, Hartmann R. Comparative Structural and Functional Studies on Small Ribosomal RNAs. SPRINGER SERIES IN MOLECULAR BIOLOGY 1986. [DOI: 10.1007/978-1-4612-4884-2_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Erdmann VA, Wolters J. Collection of published 5S, 5.8S and 4.5S ribosomal RNA sequences. Nucleic Acids Res 1986; 14 Suppl:r1-59. [PMID: 2422630 PMCID: PMC341310 DOI: 10.1093/nar/14.suppl.r1] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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27
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Rogers MJ, Simmons J, Walker RT, Weisburg WG, Woese CR, Tanner RS, Robinson IM, Stahl DA, Olsen G, Leach RH. Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data. Proc Natl Acad Sci U S A 1985; 82:1160-4. [PMID: 2579388 PMCID: PMC397214 DOI: 10.1073/pnas.82.4.1160] [Citation(s) in RCA: 124] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The 5S rRNA sequences of eubacteria and mycoplasmas have been analyzed and a phylogenetic tree constructed. We determined the sequences of 5S rRNA from Clostridium innocuum, Acholeplasma laidlawii, Acholeplasma modicum, Anaeroplasma bactoclasticum, Anaeroplasma abactoclasticum, Ureaplasma urealyticum, Mycoplasma mycoides mycoides, Mycoplasma pneumoniae, and Mycoplasma gallisepticum. Analysis of these and published sequences shows that mycoplasmas form a coherent phylogenetic group that, with C. innocuum, arose as a branch of the low G+C Gram-positive tree, near the lactobacilli and streptococci. The initial event in mycoplasma phylogeny was formation of the Acholeplasma branch; hence, loss of cell wall probably occurred at the time of genome reduction to approximately to 1000 MDa. A subsequent branch produced the Spiroplasma. This branch appears to have been the origin of sterol-requiring mycoplasmas. During development of the Spiroplasma branch there were several independent genome reductions, each to approximately 500 MDa, resulting in Mycoplasma and Ureaplasma species. Mycoplasmas, particularly species with the smallest genomes, have high mutation rates, suggesting that they are in a state of rapid evolution.
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28
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Delihas N, Andersen J, Singhal RP. Structure, function and evolution of 5-S ribosomal RNAs. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1984; 31:161-90. [PMID: 6397770 DOI: 10.1016/s0079-6603(08)60377-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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29
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Abstract
The nucleotide sequences of 5S rRNAs from three protozoa, Bresslaua vorax, Euplotes woodruffi and Chlamydomonas sp. have been determined and aligned together with the sequences of 12 protozoa species including unicellular green algae already reported by the authors and others. Using this alignment, a phylogenic tree of the 15 species of protozoa has been constructed. The tree suggests that the ancestor for protozoa evolved at an early time of eukaryotic evolution giving two major groups of organisms. One group, which shares a common ancestor with vascular plants, contains a unicellular green flagellate (Chlamydomonas) and unicellular green algae. The other group, which shares a common ancestor with the multicellular animals, includes various flagellated protozoa (including Euglena), ciliated protozoa and slime molds. Most of these protozoa appear to have separated from one another at a fairly early period of eukaryotic evolution.
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Huysmans E, Dams E, Vandenberghe A, De Wachter R. The nucleotide sequences of the 5S rRNAs of four mushrooms and their use in studying the phylogenetic position of basidiomycetes among the eukaryotes. Nucleic Acids Res 1983; 11:2871-80. [PMID: 6856478 PMCID: PMC325929 DOI: 10.1093/nar/11.9.2871] [Citation(s) in RCA: 72] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The nucleotide sequences of the 5 S ribosomal RNAs of the mushrooms Russula cyanoxantha, Pleurotus ostreatus, Agaricus edulis, and Auricularia auricula-judae were determined. The sequences fit in a universal five-helix secondary structure model for 5 S RNA. As in most other 5 S RNAs, some helical areas contain non-standard base pairs. A clustering method was used to reconstruct an evolutionary tree from 82 eukaryotic 5 S RNA sequences. It allows to make a choice between alternative systematic classifications for basidiomycetes and reveals that the fungal kingdom is highly polyphyletic.
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31
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Gojobori T, Li WH, Graur D. Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol 1982; 18:360-9. [PMID: 7120431 DOI: 10.1007/bf01733904] [Citation(s) in RCA: 245] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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32
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Fang BL, De Baere R, Vandenberghe A, De Wachter R. Sequences of three molluscan 5 S ribosomal RNAs confirm the validity of a dynamic secondary structure model. Nucleic Acids Res 1982; 10:4679-85. [PMID: 7133995 PMCID: PMC321121 DOI: 10.1093/nar/10.15.4679] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The collection of known 5 S rRNA primary structures is enriched with the sequences from three mollusca, the snails Helix pomatia and Arion rufus, and the mussel Mytilus edulis. The three sequences can be fitted in a five-helix secondary structure model previously shown (De Wachter et al. (1982) Biochimie 64, 311-329) to apply to all 5 S RNAs regardless of their origin. One of the helices in this model can undergo a bulge-internal loop transition. Within the metazoan kingdom, the dimensions of each helix and loop are rigidly conserved, except for one helix which can comprise either 6 or 7 base pairs.
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De Wachter R, Chen MW, Vandenberghe A. Conservation of secondary structure in 5 S ribosomal RNA: a uniform model for eukaryotic, eubacterial, archaebacterial and organelle sequences is energetically favourable. Biochimie 1982; 64:311-29. [PMID: 6809061 DOI: 10.1016/s0300-9084(82)80436-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The most commonly accepted secondary structure models for 5S RNA differ for molecules of eubacterial origin, where the four-helix model of Fox and Woese is generally cited, and those of eukaryotic origin, where a fifth helix is assumed to exist. We have carefully aligned all available sequences from eukaryotes, eubacteria, chloroplasts, archaebacteria and plant mitochondria. We could thus derive a unified secondary structure model applicable to all 5S RNA sequences known to-date. It contains the five helices already present in the eukaryotic model, extended by additional segments that were not previously assumed to be universally present. One of the helices can be written in two equilibrium forms, which could reflect the existence of a flexible, dynamic structure. For the derivation of the model and the estimation of the free energies we followed a set of rules optimized to predict the tRNA cloverleaf. The stability of the unified model is higher than that of nearly all previously proposed sequence-specific and general models.
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Spencer DF, Bonen L, Gray MW. Primary sequence of wheat mitochondrial 5S ribosomal ribonucleic acid: functional and evolutionary implications. Biochemistry 1981; 20:4022-9. [PMID: 7284306 DOI: 10.1021/bi00517a011] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Using the procedures of Donis-Keller et al. [Donis-Keller, H., Maxam, A. M., & Gilbert, W. (1977) Nucleic Acids Res. 4, 2527--2538 (1977)] and Peattie [Peattie, D. A. (1979) Proc. Natl. Acad. Sci. U.S.A. 76, 1760--1764], we have determined the nucleotide sequence of wheat mitochondrial 5S ribosomal ribonucleic acid (rRNA). This sequence [Formula: see text] is the first to be reported for a plant mitochondrial RNA. A highly conserved region (underlined) readily identifies the molecule as a structural homologue of other 5S rRNAs, as do potential base-paired regions which are characteristic of all known (prokaryotic, chloroplast, eukaryotic cytosol) 5S rRNA sequences. However, when assessed in terms of those structural features which distinguish prokaryotic from eukaryotic 5S rRNAs, wheat mitochondrial 5S rRNA cannot be classified readily as one or the other but instead displays characteristics of both types. In addition, the mitochondrial 5S rRNA has several unusual features, including (i) a variable number (two to three) of A residues at both the 5' and 3' ends, (ii) a unique sequence (CGACC, italic) in place of the prokaryotic sequence (CGAAC) which has been postulated to interact with aminoacyl-tRNA during translation, and (iii) a novel sequence, AUAUAUAU, immediately following the highly conserved sequence. In terms of overall primary sequence, wheat mitochondrial and cytosol 5S rRNAs seem to be slightly more divergent from each other than either is from Escherichia coli 5S rRNA, with which they are about equally homologous. From these observations, we propose that wheat mitochondrial 5S rRNA represents a distinct class of 5S rRNA. Our observations raise a number of questions about the evolutionary origin and functional role(s) of plant mitochondrial 5S rRNA.
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35
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Delihas N, Andersen J, Sprouse H, Kashdan M, Dudock B. The nucleotide sequence of spinach cytoplasmic 5 S ribosomal RNA. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)68992-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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36
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Jacq B. Sequence homologies between eukaryotic 5.8S rRNA and the 5' end of prokaryotic 23S rRNa: evidences for a common evolutionary origin. Nucleic Acids Res 1981; 9:2913-32. [PMID: 7024907 PMCID: PMC326902 DOI: 10.1093/nar/9.12.2913] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The question of the evolutionary origin of eukaryotic 5.8S rRNA was re-examined after the recent publication of the E. coli 23S rRNA sequence (26,40). A region of the 23S RNA located at its 5' end was found to be approximately 50% homologous to four different eukaryotic 5.8S rRNAs. A computer comparison analysis indicates that no other region of the E. coli ribosomal transcription unit (greater than 5 000 nucleotides in length) shares a comparable homology with 5.8S rRNA. Homology between the 5' end of e. coli 23S and four different eukaryotic 5.8S rRNAs falls within the same range as that between E. coli 5S RNA from the same four eukaryotic species. All these data strongly suggest that the 5' end of prokaryotic 23S rRNA and eukaryotic 5.8S RNA have a common evolutionary origin. Secondary structure models are proposed for the 5' region of E. coli 23S RNA.
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Studnicka GM, Eiserling FA, Lake JA. A unique secondary folding pattern for 5S RNA corresponds to the lowest energy homologous secondary structure in 17 different prokaryotes. Nucleic Acids Res 1981; 9:1885-904. [PMID: 6165963 PMCID: PMC326810 DOI: 10.1093/nar/9.8.1885] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A general secondary structure is proposed for the 5S RNA of prokaryotic ribosomes, based on helical energy filtering calculations. We have considered all secondary structures that are common to 17 different prokaryotic 5S RNAs and for each 5S sequence calculated the (global) minimum energy secondary structure (300,000 common structures are possible for each sequence). The 17 different minimum energy secondary structures all correspond, with minor differences, to a single, secondary structure model. This is strong evidence that this general 5S folding pattern corresponds to the secondary structure of the functional 5S rRNA. The general 5S secondary structure is forked and in analogy with the cloverleaf of tRNA is named the "wishbone" model. It constant 8 double helical regions; one in the stem, four in the first, or constant arm, and three in the second arm. Four of these double helical regions are present in a model earlier proposed (1) and four additional regions not proposed by them are presented here. In the minimum energy general structure, the four helices in the constant arm are exactly 15 nucleotide pairs long. These helices are stacked in the sequences from gram-positive bacteria and probably stacked in gram-negative sequences as well. In sequences from gram-positive bacteria the length of the constant arm is maintained at 15 stacked pairs by an unusual minimum energy interaction involving a C26-G57 base pair intercalated between two adjacent helical regions.
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Küntzel H, Heidrich M, Piechulla B. Phylogenetic tree derived from bacterial, cytosol and organelle 5S rRNA sequences. Nucleic Acids Res 1981; 9:1451-61. [PMID: 6785727 PMCID: PMC326769 DOI: 10.1093/nar/9.6.1451] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A phylogenetic tree was constructed by computer analysis of 47 completely determined 5S rRNA sequences. The wheat mitochondrial sequence is significantly more related to prokaryotic than to eukaryotic sequences, and its affinity to that of the thermophilic Gram-negative bacterium Thermus aquaticus is comparable to the affinity between Anacystis nidulans and chloroplastic sequences. This strongly supports the idea of an endosymbiotic origin of plant mitochondria. A comparison of the plant cytosol and chloroplast sub-trees suggests a similar rate of nucleotide substitution in nuclear genes and chloroplastic genes. Other features of the tree are a common precursor of protozoa and metazoa, which appears to be more related to the fungal than to the plant protosequence, and an early divergence of the archebacterial sequence (Halobacterium cutirubrum) from the prokaryotic branch.
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Vacek AT, Bourque DP. Mode of inheritance and evidence for cistron heterogeneity of chloroplast 16S ribosomal RNA genes in Nicotiana. Plasmid 1980; 4:205-14. [PMID: 6927814 DOI: 10.1016/0147-619x(80)90010-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Oligonucleotide maps (fingerprints) of T1 RNase digests of 125I-labeled 16 S chloroplast rRNA of Nicotiana tabacum and N. gossei revealed the presence of T1 oligonucleotide fragment 100 in the 16 S rRNA of N. gossei while N. tabacum 16 S rRNA had a unique T1 oligonucleotide (fragment 101) as well as some fragment 100. From the positions in the fingerprints and from fingerprints of secondary enzymatic digestion of the fragments, we conclude that fragments 100 and 101 are similar in sequence and size, but fragment 100 probably contains an extra uracil residue. This difference is shown to be maternally inherited, thus confirming the location of 16 S chloroplast rRNA genes on chloroplast DNA and ruling out the possibility of genetically active chloroplast rRNA genes in the nucleus. The presence of both fragments 100 and 101 in N. tabacum may indicate sequence heterogeneity between the two cistrons for 16 S chloroplast rRNA. These results demonstrate the feasibility of determining the inheritance of organelle genes by genetic analysis of their primary transcripts.
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40
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41
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Dyer TA, Bowman CM. Nucleotide sequences of chloroplast 5S ribosomal ribonucleic acid in flowering plants. Biochem J 1979; 183:595-604. [PMID: 540034 PMCID: PMC1161641 DOI: 10.1042/bj1830595] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Evidence for the sequence of duckweed (Lemna minor) chloroplast 5S rRNA was derived from the analysis of partial and complete enzymic digests of the 32P-labelled molecule. The possible sequence of the chloroplast 5S rRNA from three other flowering plants was deduced by complete digestion with T1 ribonuclease and comparison of the sequences of the oligonucleotide products with homologous sequences in the duckweed 5S rRNA. This analysis indicates that the chloroplast 5S rNA species differ appreciably from their cytosol counterparts but bear a strong resemblance to one another and to the 5S rRNA species of prokaryotes. Structural features apparently common to all 5S rRNA molecules are also discussed.
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42
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Kagawa H, Aizawa SI, Yamaguchi S, Ishizu JI. Isolation and characterization of bacterial flagellar hook proteins from salmonellae and Escherichia coli. J Bacteriol 1979; 138:235-40. [PMID: 108251 PMCID: PMC218261 DOI: 10.1128/jb.138.1.235-240.1979] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Flagellar hook proteins from Salmonella and Escherichia coli were dissociated in acid and purified by diethylamino-ethyl-cellulose column chromatography. These two proteins had the same electrophoretic mobility in sodium dodecyl sulfate-polyacrylamide gels. However, analytical electrofocusing patterns showed that these proteins had different isoelectric points (4.7 for Salmonella typhimurium and 4.4 for E. coli). Immunodiffusion and immuno-electron microscopy carried out with antisera prepared against purified hook proteins from S. typhimurium and E. coli showed that these antisera reacted with both hooks. Affinity chromatography allowed separation of antibodies specific for hook proteins from each bacterial species. These results indicate that the hook proteins share common antigenic determinants as well as specific antigens, although the specificity is not quantitatively resolved. From comparisons of the amino acid composition of the hook proteins and flagellins, it was concluded that the differences between flagellins from S. typhimurium and E. coli were larger than those between hook proteins from these species.
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43
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Hori H, Osawa S. Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species. Proc Natl Acad Sci U S A 1979; 76:381-5. [PMID: 284354 PMCID: PMC382943 DOI: 10.1073/pnas.76.1.381] [Citation(s) in RCA: 257] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Secondary structure models of 54 5S RNA species are constructed based on the comparative analyses of their primary structure. All 5S RNAs examined have essentially the same secondary structure. However, there are revealing characteristic differences between eukaryotic and prokaryotic types. The prokaryotic 5S RNAs may be further classified into two types, one having 120 nucleotides (120-N type) and another having 116 (116-N type). A possible mechanism for the conversion of the prokaryotic 116-N type to the 120-N type 5S RNAs (or vice versa) is discussed on the basis of their nucleotide alignments. Finally, by comparing the nucleotide alignments, we propose a phylogenic tree of the 54 5S RNA species.
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Abstract
The evolution of ribosomal proteins of about 70 bacterial strains belonging to the family Enterobacteriaceae has been studied by use of previously reported data (S. Osawa, T. Itoh, and E. Otaka, J. Bacteriol. 107:168-178, 1971) and those obtained in this paper. The proximity of the bacteria was quantified by co-chromatographing the differentially labeled ribosomal proteins from two strains on a column of carboxymethyl cellulose in various combinations. The were then classified into 12 groups (=species?) according to their ribosomal protein compositions and were placed in a phylogenic tree.
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45
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Mizutani H, Ponnamperuma C. The evolution of the protein synthesis system. I. A model of a primitive protein synthesis system. ORIGINS OF LIFE 1977; 8:183-219. [PMID: 600508 DOI: 10.1007/bf00930682] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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46
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Abstract
The rate of nucleotide substitution (k(nuc)) of 5s RNA was estimated to be (1.8 +/- 0.5) x 10(-10) per site per year by comparing the nucleotide sequences of human and Xenopus 5s RNA and using the geological time elapsed since the separation of mammals and amphibians. Similarly, k(nuc) of 5.8s rRNA was calculated to be 0.93 10(-1u) per site per year from the sequences of rat hepatoma cells and Saccbaromyces cerevisiae. For the comparison of these data with the amino acid substitution rate of known proteins, the k(nuc) values of 5s rRNA and 5.8s rRNA were converted to the rate of amino acid substitution (k(aa')). The k(aa') values in pauling units were 0.4 and 2 0.3, respectively. The average k(aa) of ribosomal proteins was also estimated to be 0.2 0.3 pauling from the N-terminal amino acid sequences of seventeen 30s ribosomal proteins of Bacillus stearothermopbilus and Eschericbia coli. Thus, the evolutionary rates of these ribosomal components studied here are similar to each other; they considerably slower than that of the known cellular proteins. Most, if not all, of the replacements in ribosomal proteins occurred between amino acids of a chemically similar nature.
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47
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Payne PI, Dyer TA. Evidence for the nucleotide sequence of 5-S rRNA from the flowering plant Secale cereale (Rye). EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 71:33-8. [PMID: 1009953 DOI: 10.1111/j.1432-1033.1976.tb11086.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Evidence for the sequence of rye 5-S rRNA was derived from the analysis of partial and complete enzymic digests of the 32P-labelled molecule. The probable sequence of 5-S rRNA from four other flowering plants was deduced by aligning, with the homologous sequences in the rye 5-S rRNA, oligonucleotides produced by T1 and pancreatic A ribonuclease digestion. The most dissimilar differed in only seven positions. From a comparison of the sequence of rye 5-S rRNA with those known for other types of organism, it was possible to distinguish some structural features of the molecule which are common to all of them. Also, information was obtained about the possible phylogenetic relationship of the flowering plants to other organisms whose 5-S rRNA has been sequenced.
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Abstract
Based on the comparative analyses of the primary structure of 5S RNAs from 19 organisms, a secondary structure model of 5S RNA is proposed. 5S RNA has essentially the same structure among all prokaryotic species. The same is true for eukaryotic 5S RNAs. Prokaryotic and eukaryotic 5S RNAs are also quite similar to each other, except for a difference in a specific region. By comparing the nucleotide alignment from the juxtaposed 5S RNA secondary structures, a phylogenic tree of nineteen organisms was constructed. The time of divergence between prokaryotes and eukaryotes was estimated to be 2.5 X 10(9) years ago (minimum estimate: 2.1 X 10(9).
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