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Rivas M, Fox GE. Ancestry of RNA/RNA interaction regions within segmented ribosomes. RNA (NEW YORK, N.Y.) 2023; 29:1388-1399. [PMID: 37263782 PMCID: PMC10573304 DOI: 10.1261/rna.079654.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/14/2023] [Indexed: 06/03/2023]
Abstract
The ribosome is the universally conserved ribozyme that translates DNA coded instructions into proteins with the assistance of other RNA molecules, including transfer and messenger RNAs. Of particular interest is the segmentation phenomena, which is found in trypanosomatids and other protists. In these organisms, the large subunit ribosomal RNA is assembled from multiple smaller RNAs. This phenomenon posits several challenges to the folding and stabilization of such ribosomes to retain functionality and efficiency. In earlier studies, RNA/protein interactions were suggested to fully compensate for the fragmentation. Recently, several conserved RNA/RNA interaction regions were described in the cryo-EM structures of segmented ribosomes from trypanosomatids. These regions also seemed to aid in the folding and stabilization of such ribosomes, even before the ribosomal proteins start their association. In the present study, the existence of conserved RNA/RNA interaction regions shared between trypanosomatid and Euglena gracilis segmented ribosomes was confirmed, despite differences in segmentation patterns. Analysis of the crystallographic structures of unsegmented ribosomes from other Eukaryotes, Bacteria, and Archaea allowed us to estimate the relative age of highly conserved RNA/RNA interaction regions. These results strongly suggest that common interaction regions likely date far back into the ribosomes of the last common ancestor. Results also revealed that single hydrogen bonds are overwhelmingly facilitated by the 2'OH, a distinctive RNA feature. This supports the notion that RNA predates DNA and places some constraints on alternative nucleic acids proposals.
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Affiliation(s)
- Mario Rivas
- 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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2
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Rivas M, Fox GE. Nonstandard RNA/RNA interactions likely enhance folding and stability of segmented ribosomes. RNA (NEW YORK, N.Y.) 2022; 28:340-352. [PMID: 34876487 PMCID: PMC8848935 DOI: 10.1261/rna.079006.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/26/2021] [Indexed: 05/21/2023]
Abstract
The ribosome is the molecular factory that catalyzes all coded protein synthesis in extant organisms. Eukaryotic ribosomes are typically assembled out of four rRNAs; namely, 5S, 5.8S, 18S, and 28S. However, the 28S rRNA of some trypanosomatid organisms has been found to be segmented into six independent rRNAs of different sizes. The two largest segments have multiple sites where they jointly form stems comprised of standard base pairs that can hold them together. However, such regions of interaction are not observed among the four smaller RNAs. Early reports suggested that trypanosomatid segmented ribosome assembly was essentially achieved thanks to their association with rProteins. However, examination of cryo-EM ribosomal structures from Trypanosoma brucei, Leishmania donovani, and Trypanosoma cruzi reveals several long-range nonstandard RNA/RNA interactions. Most of these interactions are clusters of individual hydrogen bonds and so are not readily predictable. However, taken as a whole, they represent significant stabilizing energy that likely facilitates rRNA assembly and the overall stability of the segmented ribosomes. In the context of origin of life studies, the current results provide a better understanding of the true nature of RNA sequence space and what might be possible without an RNA replicase.
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Affiliation(s)
- Mario Rivas
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
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3
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Hernández R, Cevallos AM. Ribosomal RNA gene transcription in trypanosomes. Parasitol Res 2014; 113:2415-24. [PMID: 24828347 DOI: 10.1007/s00436-014-3940-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/01/2014] [Indexed: 11/30/2022]
Abstract
Leishmania major, Trypanosoma cruzi and Trypanosoma brucei are pathogenic species from the order Kinetoplastida. The molecular and cellular studies of parasites, such as of the biosynthesis of essential macromolecules, are important in designing successful strategies for control. A major stage in ribosome biogenesis is the transcription of genes encoding ribosomal (r)RNA. These genes are transcribed in trypanosome cells by RNA polymerase I, similar to what occurs in all eukaryotes analysed to date. In addition, and most remarkably, the African species, T. brucei, transcribe their major cell surface protein genes using this class of polymerase. Since its discovery, the research interest in this phenomenon has been overwhelming; therefore, analysis of the canonical, yet essential, transcription of rRNA has been comparatively neglected. In this work, a review of rRNA gene transcription and data on gene promoter structures, transcription machineries and epigenetic conditions is presented for trypanosomatids. Because species-specific molecules represent potential targets for chemotherapy, their existence within trypanosomes is highlighted.
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Affiliation(s)
- Roberto Hernández
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apartado Postal 70228, Ciudad Universitaria, 04510, México, D.F., Mexico,
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4
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Martínez-Calvillo S, Sunkin SM, Yan S, Fox M, Stuart K, Myler PJ. Genomic organization and functional characterization of the Leishmania major Friedlin ribosomal RNA gene locus. Mol Biochem Parasitol 2001; 116:147-57. [PMID: 11522348 DOI: 10.1016/s0166-6851(01)00310-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sequence and gene organization of the ribosomal RNA (rRNA) genes of Leishmania major Friedlin (LmjF) were determined. Interestingly, the rDNA repeat unit contained a duplicated 526 bp fragment at the 3' end of the unit with two copies of the LSUepsilon rRNA gene. Our results suggested the presence of only approximately 24 copies of the rRNA unit per diploid genome in LmjF. Repetitive elements (IGSRE) of 63 bp occurred in the intergenic spacer (IGS) between the LSUepsilon and the SSU rRNA genes. Among the different rDNA units, the region containing the IGSRE fluctuated in length from approximately 1.3 to approximately 18 kb. The transcription initiation site (TIS) of the rRNA unit was localized by primer extension to 1043 bp upstream of the SSU gene and 184 bp downstream of the IGSRE. Sequence comparison among several species of Leishmania showed a high degree of conservation around the TIS. Moreover, the IGSRE also showed considerable similarity between Leishmania species. In transient transfection assays, a fragment containing the TIS directed a 164- to 178-fold increase in luciferase activity over the no-insert control, indicating the presence of a promoter within this 391 bp fragment. The LmjF promoter region was also functional in other species of Leishmania. Nuclear run-on analyses demonstrated that only the rRNA-coding strand is transcribed, downstream of this RNA polymerase I (pol I) promoter. These experiments also suggested that transcription terminates upstream of the IGSRE.
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Affiliation(s)
- S Martínez-Calvillo
- Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle, WA 98109-1651, USA
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5
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Yan S, Lodes MJ, Fox M, Myler PJ, Stuart K. Characterization of the Leishmania donovani ribosomal RNA promoter. Mol Biochem Parasitol 1999; 103:197-210. [PMID: 10551363 DOI: 10.1016/s0166-6851(99)00126-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The rRNA genes of Leishmania donovani are organized on chromosome 27 as tandem repeats of approximately 12.5-kb units that each contain a promoter, the subunit rRNAs, and approximately 39 copies of a 64-bp species-specific sequence. The transcription initiation site was mapped to 1020 bp upstream of the 18S rRNA gene by RNase protection and primer extension. A 349-bp sequence between the 64-bp repeats and the 18S rRNA gene appears to contain a promoter, since it directs a 60-fold increase in luciferase expression over the no-insert control in transient transfection assays. Stepwise deletion and 10-bp replacement studies identified three domains that affect promoter activity. In strain LSB-51.1, a naturally occurring gene conversion with a portion of the LD1 sequence from chromosome 35 replaced the rRNA genes within one repeat unit, from downstream of the promoter to within the 64-bp repeats. Northern blot analysis of RNA from LSB-51.1 showed large transcripts from the external spacer regions that are not normally transcribed. These results imply that the gene conversion eliminated sequences at or near the 5' terminus of the 64-bp repeats which normally function in transcription termination.
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MESH Headings
- Animals
- Base Sequence
- Kinetoplastida/genetics
- Leishmania donovani/genetics
- Molecular Sequence Data
- Promoter Regions, Genetic
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 28S/genetics
- Repetitive Sequences, Nucleic Acid
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Terminator Regions, Genetic
- Transcription, Genetic
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Affiliation(s)
- S Yan
- Seattle Biomedical Research Institute, WA 98109-1651, USA
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6
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Abstract
The nucleotide (nt) sequence (2106 bp) of a cloned rDNA (encoding ribosomal RNA) spacer region from Trypanosoma cruzi was determined and a putative transcription start point (tsp) was mapped. The assigned length for the transcribed spacer is 1768 bp and its tsp is present 270-bp upstream from an alternative tsp published for the equivalent gene from another T. cruzi strain [Dietrich et al., Gene 125 (1993) 103-107]. Sequence comparisons of the nt flanking both T. cruzi tsp with the homologous regions from both other trypanosomatids, and other eukaryotes, indicate that these sequences are poorly conserved within the family Trypanosomatidae. This finding reinforces the proposal that the speciation of trypanosomatids may have occurred early in evolution.
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MESH Headings
- Animals
- Base Sequence
- Conserved Sequence
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, Protozoan/genetics
- Molecular Sequence Data
- Promoter Regions, Genetic/genetics
- RNA Processing, Post-Transcriptional
- RNA, Protozoan/analysis
- RNA, Ribosomal/analysis
- Sequence Alignment
- Sequence Analysis, DNA
- Transcription, Genetic
- Trypanosoma cruzi/genetics
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Affiliation(s)
- S Martínez-Calvillo
- Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Mexico D.F
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7
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Ghosh A, Ghosh T, Ghosh S, Das S, Adhya S. Interaction of small ribosomal and transfer RNAs with a protein from Leishmania donovani. Nucleic Acids Res 1994; 22:1663-9. [PMID: 8202369 PMCID: PMC308046 DOI: 10.1093/nar/22.9.1663] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Using synthetic antisense RNA from the 5'-untranslated region of the beta-tubulin gene as probe in gel retardation assays, a heat stable RNA-binding factor was identified in promastigotes of the kinetoplastid protozoan Leishmania donovani. The same or similar factors interact with several small ribosomal RNA (srRNA) species and, more weakly, with tRNA, as shown by binding and competition experiments. Deletion analysis indicated involvement of repeated purine-rich motifs on the antisense RNA, in the reaction. Related, conserved motifs occur on at least two of the srRNAs. By a modified Western blot assay, the RNA-binding species was identified as a single, small polypeptide. The activity is apparently specific for the promastigote stage of the parasite, being undetectable in amastigotes. The properties of this RNA-binding factor suggest that it is a novel, previously uncharacterized protein.
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Affiliation(s)
- A Ghosh
- Genetic Engineering Laboratory, Indian Institute of Chemical Biology, Calcutta
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8
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Hernández-Rivas R, Martínez-Calvillo S, Romero M, Hernández R. Trypanosoma cruzi 5S rRNA genes: molecular cloning, structure and chromosomal organization. FEMS Microbiol Lett 1992; 71:63-7. [PMID: 1624112 DOI: 10.1111/j.1574-6968.1992.tb05235.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
To further study the ribosomal RNA genetic system in Trypanosoma cruzi, the 5S rRNA gene family was characterized. We found that this gene family is reiterated about 1600 times per diploid nuclei and is mostly organized as a tandem repeat of 481 base pairs. These gene clusters were assigned to two chromosomes of about 1500 and 1400 kilobase pairs. We found that the 5S rRNA-coding region is comprised of 120 nucleotides, and contains the well-known internal control regions of eukaryotic RNA polymerase III. The two gene-spacer regions analysed exhibit a putative signal for transcription termination and six sites homologous to the consensus sequence for the binding of transcription factor Sp1.
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Affiliation(s)
- R Hernández-Rivas
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City
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9
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Galvan SC, Castro C, Segura E, Casas L, Castaneda M. Nucleotide sequences of the six very small molecules of Trypanosoma cruzi ribosomal RNA. Nucleic Acids Res 1991; 19:2496. [PMID: 2041786 PMCID: PMC329464 DOI: 10.1093/nar/19.9.2496] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- S C Galvan
- Departamento de Biologia del Desarrollo, Ciudad Universitaria, Mexico
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10
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Hernández R, Díaz-de Léon F, Castañeda M. Molecular cloning and partial characterization of ribosomal RNA genes from Trypanosoma cruzi. Mol Biochem Parasitol 1988; 27:275-9. [PMID: 3278230 DOI: 10.1016/0166-6851(88)90047-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
To further analyze the organization of the nuclear rDNA locus in Trypanosoma cruzi, genomic recombinant plasmid clones were constructed and isolated after hybridization with rRNA molecules as hybridization probes. Approximately 11 kilobase pairs from the cistron were cloned in three recombinant plasmids carrying adjacent genomic fragments. Restriction mapping and Southern hybridization experiments performed on these clones indicate the following relative arrangement of the mature rRNA coding sequences: 18S (2.46 kb), S3 (197 b), 24S alpha (2.02 kb), S1 (261 b), 24 beta (1.66 kb), S2 (217 b) and S6 (90 b). Neither S4 (141 b) nor S5 (110 b) sequences were found within these genomic clones. Nevertheless genomic Southerns suggest a linkage of S4 towards the 3' end of this genetic system.
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Affiliation(s)
- R Hernández
- Department of Developmental Biology, Universidad Nacional Autónoma de México, Mexico City
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11
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Spencer DF, Collings JC, Schnare MN, Gray MW. Multiple spacer sequences in the nuclear large subunit ribosomal RNA gene of Crithidia fasciculata. EMBO J 1987; 6:1063-71. [PMID: 16453755 PMCID: PMC553503 DOI: 10.1002/j.1460-2075.1987.tb04859.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
In Crithidia fasciculata, a trypanosomatid protozoan, the nuclear-encoded ;28S' rRNA is multiply fragmented, comprising two large (c and d) and four small (e, f, g and j) RNA species. We have determined that the coding sequences for these RNAs (and that of the 5.8S rRNA, species i) are separated from one another by spacer sequences ranging in size from 31 to 416 bp. Coding and spacer sequences are presumably co-transcribed, with excision of the latter during post-transcriptional processing generating a highly fragmented large subunit (LSU) rRNA. Secondary structure modelling indicates that the C. fasciculata LSU rRNA complex (seven segments, including 5.8S rRNA) is held together in part by long-range intermolecular base pairing interactions that are characteristic of intramolecular interactions in the covalently continuous LSU (23S) rRNA of Escherichia coli. At least one functionally critical region (encompassing the alpha-sarcin cleavage site) is contained in a small RNA species (f) rather than in one of the two large RNAs. Within a proposed secondary structure model of C. fasciculata LSU rRNA, discontinuities between the different segments (created by spacer excision) map to regions that are highly variable in structure in covalently continuous LSU rRNAs. We suggest that ;rRNA genes in pieces' and discontinuous rRNAs may represent an evolutionarily ancient pattern.
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Affiliation(s)
- D F Spencer
- Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
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12
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White TC, Rudenko G, Borst P. Three small RNAs within the 10 kb trypanosome rRNA transcription unit are analogous to domain VII of other eukaryotic 28S rRNAs. Nucleic Acids Res 1986; 14:9471-89. [PMID: 3797245 PMCID: PMC311971 DOI: 10.1093/nar/14.23.9471] [Citation(s) in RCA: 211] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We have localized the six ribosomal RNAs (rRNAs) which encode the 28S rRNA region of Trypanosoma brucei. These six rRNAs include two large rRNAs, 28S alpha (approx. 1840 nt) and 28S beta (approx. 1570 nt), and four small rRNAs of approximate sizes 220, 180, 140 and 70 nt. Three of these four small rRNAs (180, 70 and 140) are found at the 3' end of the 28S rRNAs region. Sequence analysis of this area shows that these three small rRNAs encode Domain VII, the last domain of secondary structure in the 28S rRNAs of eukaryotes. Hybridization of labeled nascent RNA to the cloned repeat unit and S1 nuclease protection analysis of putative precursors show that transcription initiates approximately 1.2 kb upstream of the 18S rRNA and terminates after the last small rRNA (140) at the 3' end of the 28S rRNA region. Analysis of three putative rRNA precursors suggests that the small rRNAs are not processed from the primary transcript until after the usual processing of the 5.8S rRNA region.
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13
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Albach RA, Prachayasittikul V, Heebner GM. Isolation and characterization of RNA of Entamoeba histolytica. Mol Biochem Parasitol 1984; 12:261-72. [PMID: 6090899 DOI: 10.1016/0166-6851(84)90083-5] [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: 01/18/2023]
Abstract
RNAs were isolated from Entamoeba histolytica with a high salt sodium dodecylsulfate-diethylpyrocarbonate technique. Majority species of 25 S, 17 S and 4 S RNAs were detected after sucrose gradient centrifugation. An additional 5 S RNA was detected by polyacrylamide gel electrophoresis. The molecular weights of these RNAs as determined by completely denaturing polyacrylamide gel electrophoresis were 1.31 X 10(6) (25 S), 0.803 X 10(6) (17 S), 4.0 X 10(4) (5 S) and 2.5 X 10(4) (4 S). The 25 S RNA was labile and dissociated under mild denaturing conditions (between 37 degrees C and 55 degrees C) into 17 S and 16 S RNAs with molecular weights of 0.700 X 10(6) and 0.614 X 10(6), respectively; under completely denaturing conditions an additional 5.8 S RNA with a molecular weight of 4.8 X 10(4) was detected. Evidence is presented which suggests that the lability of the 25 S RNA is the result of an in vivo cleavage rather than one which is generated during RNA isolation.
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14
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Hernández R, Castañeda M. An endonuclease restriction analysis of the ribosomal RNA genes of Trypanosoma cruzi. Mol Biochem Parasitol 1983; 8:305-15. [PMID: 6314136 DOI: 10.1016/0166-6851(83)90077-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The location of ribosomal RNA genes in total-nuclear-enriched DNA preparations of Trypanosoma cruzi was analyzed by using restriction endonucleases and the eight cytoplasmic ribosomal RNA species of this organism. Two contiguous SstI DNA fragments of about 9.88 and 1.7 kilobase pairs contained the three large-size ribosomal RNA species, 18 S, beta, and alpha, and three small-size ribosomal RNA species, s1, s2 and s3. The other two small-size ribosomal species, s4 and s5, were located outside the ribosomal RNA cistron and independently of each other. Spacers of a presumed large length, about 20 kilobase pairs or more, hampered the identification of putative adjacent ribosomal RNA cistrons.
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