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Orso C, Stefanello TB, Franceschi CH, Mann MB, Varela APM, Castro IMS, Frazzon J, Frazzon APG, Andretta I, Ribeiro AML. Changes in the ceca microbiota of broilers vaccinated for coccidiosis or supplemented with salinomycin. Poult Sci 2020; 100:100969. [PMID: 33684651 PMCID: PMC7938242 DOI: 10.1016/j.psj.2020.12.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 11/28/2020] [Accepted: 12/15/2020] [Indexed: 01/04/2023] Open
Abstract
The objective of this study was to characterize differences in the cecal microbiota of chickens vaccinated for coccidiosis or receiving salinomycin in the diet. In this study, 140 male 1-day-old broiler chickens were divided in 2 groups: vaccine group (live vaccine) vaccinated at the first day and salinomycin group (125 ppm/kg since the first day until 35 d of age). Each treatment was composed for 7 replicates of 10 birds per pen. At 28 d, the cecal content of one bird per replicate was collected for microbiota analysis. The genetic sequencing was conducted by the Miseq Illumina platform. Vaccine group showed lower body weight, weight gain, and poorer feed conversion in the total period (P < 0.05). Bacterial 16S rRNA genes were classified as 3 major phyla (Bacteroidetes, Firmicutes, and Proteobacteria), accounting for more than 98% of the total bacterial community. The microbiota complexity in the cecal was estimated based on the α-diversity indices. The vaccine did not reduce species richness and diversity (P > 0.05). The richness distribution in the salinomycin group was larger and more uniform than the vaccinated birds. Salinomycin group was related to the enrichment of Bacteroidetes, whereas Firmicutes and Proteobacteria phyla were in greater proportions in the vaccine group. The last phylum includes a wide variety of pathogenic bacteria. The vaccine did not decrease the species richness but decreased the percentage of Bacteroidetes, a phylum composed by genera that produce short-chain fatty acids improving intestinal health. Vaccine group also had higher Proteobacteria phylum, which may help explain its poorer performance.
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Affiliation(s)
- C Orso
- Department of Animal Science, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - T B Stefanello
- Department of Animal Science, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - C H Franceschi
- Department of Animal Science, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - M B Mann
- Department of Microbiology, Porto Alegre, Rio Grande do Sul, Brazil
| | - A P M Varela
- Department of Microbiology, Porto Alegre, Rio Grande do Sul, Brazil
| | - I M S Castro
- Universidade Federal de Ciências de Saúde de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - J Frazzon
- Institute of Food Science and Technology, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - A P G Frazzon
- Department of Microbiology, Porto Alegre, Rio Grande do Sul, Brazil
| | - I Andretta
- Department of Animal Science, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - A M L Ribeiro
- Department of Animal Science, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
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Biswas TK. Expression of the mitochondrial RNase P RNA subunit-encoding gene from a variant promoter sequence in Saccharomyces cerevisiae. Gene 1996; 170:23-30. [PMID: 8621084 DOI: 10.1016/0378-1119(95)00874-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Ribonuclease P (RNase P) is a common tRNA processing enzyme that removes the 5' leader sequence of precursor tRNAs. This activity is identified in yeast mitochondria as a separate enzyme from the nuclear RNase P. Like other RNase P enzymes, the mitochondrial (mt) RNase P is also a ribonucleoprotein composed of both RNA and protein subunits. The RNA subunit is encoded by a mt gene and the protein subunit is supplied by a nuclear gene. Earlier studies described one active promoter (FP1) located 5' to the mt tRNA(fMet)-RNase P RNA-tRNA(Pro) gene cluster, so that the mitochondrially encoded RNA subunit was thought to be co-transcribed with two of its substrate tRNAs. However, the results of in vitro transcription and primer extension experiments presented here demonstrate that the mt RNase P RNA subunit-encoding gene (RPM1) is transcribed from a new promoter (SP)which is located between the tRNA(fMet) and RPM1 genes. The sequence [5'-TATAAGAA(+1)] of the new promoter varies from the conserved promoter sequence [5'-TATAAGTA(+1)], but is one of the sequences that is active in the in vitro transcription assay to determine the consensus promoter sequence [5'-T A T/a A A/g/c G T/a/c N(+1)]. This result demonstrates that a naturally occurring variant promoter is used by RPM1. Identification of the novel SP promoter suggests that the synthesis of the mt RNase P RNA subunit might be uncoupled from the expression of upstream tRNA(fMet) gene, and that RPM1 might be independently transcribed in Saccharomyces cerevisiae.
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Affiliation(s)
- T K Biswas
- Department of Pathology, University of Chicago, IL 60637, USA.
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3
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Chapter 7 Mitochondrial tRNAs; Stricture, Modified Nucleosides and Codon Reading Patterns. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/s0301-4770(08)61493-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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Wolf K, Del Giudice L. The variable mitochondrial genome of ascomycetes: organization, mutational alterations, and expression. ADVANCES IN GENETICS 1988; 25:185-308. [PMID: 3057820 DOI: 10.1016/s0065-2660(08)60460-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- K Wolf
- Institut für Genetik und Mikrobiologie, Universität München, Munich, Federal Republic of Germany
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Mapping and sequencing of the wild-type and mutant (G116-40) alleles of the tyrosyl-tRNA mitochondrial gene in Saccharomyces cerevisiae. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)35745-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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6
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Wettstein-Edwards J, Ticho BS, Martin NC, Najarian D, Getz GS. In vitro transcription and promoter strength analysis of five mitochondrial tRNA promoters in yeast. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)35872-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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7
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de Zamaroczy M, Bernardi G. The primary structure of the mitochondrial genome of Saccharomyces cerevisiae--a review. Gene X 1986; 47:155-77. [PMID: 3549452 DOI: 10.1016/0378-1119(86)90060-0] [Citation(s) in RCA: 115] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We have collated and compiled all the available primary structure data on the mitochondrial genome of Saccharomyces cerevisiae. Data concern 78,500 bp, namely 92% of the 'long' genomes; they are derived from several laboratory strains. Interstrain differences belong to three classes: a small number of large deletions/additions, mainly concerning introns; a large number of small (10-150 bp) deletions/additions located in the intergenic sequences; 1-3 bp deletions/additions and point mutations; the interstrain sequence divergence due to the latter, is of the order of 2% for the strains compared; this low value is, however, an overestimate because of sequence mistakes.
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8
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Martin NC, Miller DL, Underbrink K, Ming X. Structure of a precursor to the yeast mitochondrial tRNAMetf. Implications for the function of the tRNA synthesis locus. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)89617-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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9
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Abstract
We have compiled the available primary structural data for the mitochondrial genome of Saccharomyces cerevisiae and have estimated the size of the remaining gaps, which represent 12-13% of the genome. The lengths of sequenced regions and of gaps lead to a new assessment of genome sizes; these range (in round figures) from 85 000 bp for the long genomes, to 78 000 bp for the short genomes, to 74 000 bp for the supershort genome of Saccharomyces carlsbergensis. These values are 8-11% higher than those previously estimated from restriction fragments. Interstrain differences concern not only facultative intervening sequences (introns) and mini-inserts, but also insertions/deletions in intergenic sequences. The primary structure appears to be extremely conserved in genes and ori sequences, and highly conserved in intergenic sequences. Since coding sequences represent at most 33-35% of the genome, at least two thirds of the genome are formed by noncoding and yet highly conserved sequences. The G + C level of genes or exon is 25%, and that of intronic open reading frames (ORFs) 22%; increasingly lower values are shown by intronic closed reading frames (CRFs), 20%, ori sequences, 19%, intergenic ORFs, 17.5% and intergenic sequences, 15%.
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10
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Christianson T, Rabinowitz M. Identification of multiple transcriptional initiation sites on the yeast mitochondrial genome by in vitro capping with guanylyltransferase. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44019-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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11
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Miller DL, Martin NC. Characterization of the yeast mitochondrial locus necessary for tRNA biosynthesis: DNA sequence analysis and identification of a new transcript. Cell 1983; 34:911-7. [PMID: 6313214 DOI: 10.1016/0092-8674(83)90548-2] [Citation(s) in RCA: 102] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Most components necessary for the biosynthesis of mitochondrial tRNAs are coded by nuclear genes, but one mitochondrial locus other than the tRNA genes themselves is required to make functional tRNAs in the yeast Saccharomyces cerevisiae. DNA sequence analysis of this yeast mitochondrial tRNA synthesis locus is reported here. This region of mitochondrial DNA is almost exclusively A+T-rich DNA with one G+C-rich element. Despite the unusual structure of the DNA in this region, we have demonstrated that it codes for a heretofore unidentified mitochondrial transcript about 450 bases in length. Since this RNA is the only RNA encoded by the tRNA synthesis locus, it must be the active agent of the locus. This RNA could either act autonomously through RNA-RNA interactions or as part of an RNA-protein complex to effect tRNA biosynthesis.
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Miller DL, Folse JR, Benson PJ, Martin NC. Identification and consequences of a guanosine-15 to adenosine-15 change in the yeast mitochondrial tRNASerUCX gene. Biochemistry 1983; 22:1709-14. [PMID: 6342666 DOI: 10.1021/bi00276a029] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have characterized a mutation affecting the yeast mitochondrial tRNASerUCX. The mutation is a single nucleotide substitution located within the structural portion of the tRNASerUCX gene which causes the strain to be respiratory deficient. The substitution is a G leads to A transition located in the dihydrouridine arm. The tRNASerUCX transcripts from the mutant gene are present in the same amount and are the same size as transcripts from the wild-type gene. The mutant tRNASerUCX can be charged in vitro with mitochondrial aminoacyl-tRNA synthetase. Mitochondrial protein synthesis does occur in the mutant, but the amount of cytochrome oxidase subunit I is significantly decreased relative to other mitochondrial translation products.
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13
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Underbrink-Lyon K, Miller DL, Ross NA, Fukuhara H, Martin NC. Characterization of a yeast mitochondrial locus necessary for tRNA biosynthesis. Deletion mapping and restriction mapping studies. MOLECULAR & GENERAL GENETICS : MGG 1983; 191:512-8. [PMID: 6355772 DOI: 10.1007/bf00425771] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Yeast mitochondrial DNA codes for a complete set of tRNAs. Although most components necessary for the biosynthesis of mitochondrial tRNA are coded by nuclear genes, there is one genetic locus on mitochondrial DNA necessary for the synthesis of mitochondrial tRNAs other than the mitochondrial tRNA genes themselves. Characterization of mutants by deletion mapping and restriction enzyme mapping studies has provided a precise location of this yeast mitochondrial tRNA synthesis locus. Deletion mutants retaining various segments of mitochondrial DNA were examined for their ability to synthesize tRNAs from the genes they retain. A subset of these strains was also tested for the ability to provide the tRNA synthesis function in complementation tests with deletion mutants unable to synthesize mature mitochondrial tRNAs. By correlating the tRNA synthetic ability with the presence or absence of certain wild-type restriction fragments, we have confined the locus to within 780 base pairs of DNA located between the tRNAMetf gene and tRNAPro gene, at 29 units on the wild-type map. Heretofore, no genetic function or gene product had been localized in this area of the yeast mitochondrial genome.
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15
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16
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Martin R, Sibler AP, Dirheimer G. The primary structures of three yeast mitochondrial serine tRNA isoacceptors. Biochimie 1982; 64:1073-9. [PMID: 6819004 DOI: 10.1016/s0300-9084(82)80389-1] [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: 01/22/2023]
Abstract
Yeast mitochondria contain several isoaccepting species of serine-tRNA. The relative amount of these isoacceptors varies according to the conditions used to grow the yeast cells. In order to gain insight into the structural differences among these isoacceptors, the three mitochondrial tRNAsSer, which are present in derepressed yeast cells, have been sequenced. The primary structure of tRNASer1 differs considerably from that of tRNASer2; these two isoacceptors have only 39 nucleotides in common. In contrast, tRNASer3 differs from tRNASer2 by only one post-transcriptional modification: the psi residue in position 28 of tRNASer2 is replaced by a normal U in tRNASer3. Unlike tRNASer2 and tRNASer3, the primary sequence of tRNASer1 shows two unusual structural features: it has a D in position 14 instead of the "universal" A14 of the standard tRNA cloverleaf and it contains two G residues between the D-stem and the anticodon-stem. Considering their respective anticodons, tRNASer1 should recognize the two serine codons A-G-C and A-G-U, whereas both tRNASer2 and tRNASer3 should recognize all four serine codons of the U-C-N series.
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17
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18
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Miller DL, Martin NC. Organization and expression of a tRNA gene cluster in Saccharomyces cerevisiae mitochondrial DNA. Curr Genet 1981; 4:135-43. [DOI: 10.1007/bf00365692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/1981] [Indexed: 10/26/2022]
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19
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A mutation in the tRNAAsp gene from yeast mitochondria. Effects on RNA and protein synthesis. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)68687-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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21
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Keyhani E. The locked-cell hypothesis: on the origin of mitochondria and the transition from prokaryotic to eukaryotic cells. Ann N Y Acad Sci 1981; 361:376-96. [PMID: 6941731 DOI: 10.1111/j.1749-6632.1981.tb46533.x] [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: 01/22/2023]
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22
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Sealy L, Hartley J, Donelson J, Chalkley R, Hutchison N, Hamkalo B. Characterization of a highly repetitive sequence DNA family in rat. J Mol Biol 1981; 145:291-318. [PMID: 6167723 DOI: 10.1016/0022-2836(81)90207-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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23
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Cedergren RJ, Sankoff D, LaRue B, Grosjean H. The evolving tRNA molecule. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1981; 11:35-104. [PMID: 7030617 DOI: 10.3109/10409238109108699] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The study of tRNA molecular evolution is crucial to understanding the origin and establishment of the genetic code as well as the differentiation and refinement of the machinery of protein synthesis in prokaryotes, eukaryotes, organelles, and phage systems. The small size of the molecule and its critical involvement in a multiplicity of roles distinguish its study from classical protein molecular evolution with respect to goals and methods. Here, the authors assess available and missing data, existing and needed methodology, and the impact of tRNA studies on current theories both of genetic code evolution and of the evolution of species. They analyze mutational "hot spots", the role of base modification, synthetase recognition, codon-anticodon interactions and the status of organelle tRNA.
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24
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Assembly of the mitochondrial membrane system. Organization of yeast mitochondrial DNA in the Oli1 region. Curr Genet 1980; 2:149-57. [DOI: 10.1007/bf00420627] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/1980] [Indexed: 10/26/2022]
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25
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MboI, ThaI and HinfI endonuclease cleavage maps of the yeast mitochondrial DNA. Curr Genet 1980; 2:121-9. [DOI: 10.1007/bf00420624] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/1980] [Indexed: 10/26/2022]
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26
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27
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Nobrega FG, Tzagoloff A. Assembly of the mitochondrial membrane system. Structure and location of the mitochondrial glutamic tRNA gene in Saccharomyces cerevisiae. FEBS Lett 1980; 113:52-4. [PMID: 6247202 DOI: 10.1016/0014-5793(80)80492-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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28
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Berlani RE, Pentella C, Macino G, Tzagoloff A. Assembly of the mitochondrial membrane system: isolation of mitochondrial transfer ribonucleic acid mutants and characterization of transfer ribonucleic acid genes of Saccharomyces cerevisiae. J Bacteriol 1980; 141:1086-97. [PMID: 6245059 PMCID: PMC293786 DOI: 10.1128/jb.141.3.1086-1097.1980] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A method is described for isolating cytoplasmic mutants of Saccharomyces cerevisiae with lesions in mitochondrial transfer ribonucleic acids (tRNA's). The mutants were selected for slow growth on glycerol and for restoration of wild-type growth by cytoplasmic "petite" testers that contain regions of mitochondrial deoxyribonucleic acid (DNA) with tRNA genes. The aminoacylated mitochondrial tRNA's of several presumptive tRNA mutants were analyzed by reverse-phase chromatography on RPC-5. Two mutant strains, G76-26 and G76-35, were determined to carry mutations in the cysteine and histidine tRNA genes, respectively. The cysteine tRNA mutant was used to isolate cytoplasmic petite mutants whose retained segments of mitochondrial DNA contain the cysteine tRNA gene. The segment of one such mutant (DS504) was sequenced and shown to have the cysteine, histidine, and threonine tRNA genes. The structures of the three mitochondrial tRNA's were deduced from the DNA sequence.
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Martin NC, Miller D, Hartley J, Moynihan P, Donelson JE. The tRNAAGYSer and tRNACGYArg genes from a gene cluster in yeast mitochondrial DNA. Cell 1980; 19:339-43. [PMID: 6244104 DOI: 10.1016/0092-8674(80)90508-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Yeast mitochondrial DNA-pBR322 recombinant DNA molecules screened for rRNA genes were used as a source of DNA for mitochondrial tRNA gene sequence analysis. We report here the sequences of yeast mitochondrial tRNA genes coding for a tRNAAGYSer and a tRNACGYArg. The tRNAAGYSer sequence deduced from the gene is the first reported sequence of a yeast tRNAAGYSer. It is also the second yeast mitochondrial tRNASer gene to be sequenced, and demonstrates unequivocally the presence of mitochondrial encoded serine tRNA isoacceptors. The tRNACGYArg sequence deduced from the gene is the most AT-rich (82%) tRNA sequence ever reported. Whereas all the mitochondrial genes sequenced to date exist singly on the genome and are separated by long stretches of AT-rich DNA, the tRNAACYSer and tRNAcgyarg genes exist in tandem, separated by only 3 bp. This gene arrangement strongly suggests that mitochondrial tRNA genes may be transcribed into multicistronic precursors.
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30
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Donelson JE, Majiwa PA, Williams RO. Kinetoplast DNA minicircles of Trypanosoma brucei share regions of sequence homology. Plasmid 1979; 2:572-88. [PMID: 231269 DOI: 10.1016/0147-619x(79)90055-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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