1
|
Sacconi S, Salviati L, Nishigaki Y, Walker WF, Hernandez-Rosa E, Trevisson E, Delplace S, Desnuelle C, Shanske S, Hirano M, Schon EA, Bonilla E, De Vivo DC, DiMauro S, Davidson MM. A functionally dominant mitochondrial DNA mutation. Hum Mol Genet 2008; 17:1814-20. [PMID: 18337306 PMCID: PMC2900892 DOI: 10.1093/hmg/ddn073] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mutations in mitochondrial DNA (mtDNA) tRNA genes can be considered functionally recessive because they result in a clinical or biochemical phenotype only when the percentage of mutant molecules exceeds a critical threshold value, in the range of 70-90%. We report a novel mtDNA mutation that contradicts this rule, since it caused a severe multisystem disorder and respiratory chain (RC) deficiency even at low levels of heteroplasmy. We studied a 13-year-old boy with clinical, radiological and biochemical evidence of a mitochondrial disorder. We detected a novel heteroplasmic C>T mutation at nucleotide 5545 of mtDNA, which was present at unusually low levels (<25%) in affected tissues. The pathogenic threshold for the mutation in cybrids was between 4 and 8%, implying a dominant mechanism of action. The mutation affects the central base of the anticodon triplet of tRNA(Trp) and it may alter the codon specificity of the affected tRNA. These findings introduce the concept of dominance in mitochondrial genetics and pose new diagnostic challenges, because such mutations may easily escape detection. Moreover, similar mutations arising stochastically and accumulating in a minority of mtDNA molecules during the aging process may severely impair RC function in cells.
Collapse
Affiliation(s)
- Sabrina Sacconi
- Féderation des maladies neuromusculaires, CHU de Nice and INSERM U638, Nice, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
Collapse
Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
| |
Collapse
|
3
|
Kim S, Lee Y. Function of the repeated sequence in the 3' flanking region of the Escherichia coli rnpB gene on transcription termination and RNA processing. FEBS Lett 1997; 407:353-6. [PMID: 9175883 DOI: 10.1016/s0014-5793(97)00377-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The 3' flanking region of the Escherichia coli rnpB gene-encoding M1 RNA, the RNA component of RNase P, contains a 113 bp repeated sequence. This sequence, successively reiterating 3.5 times, includes the region for intrinsic termination. In vivo termination of transcription occurs mostly at the first terminator (T1). Analysis of deletions at the 3' flanking region revealed that the second terminator (T2) and third (T3) are functional in vivo and that the sequences preceding the region coding for an RNA-terminator hairpin and U-rich 3' tail are essential for efficient termination. Transcripts terminating at T2 and T3 were also processed at the 3' end in a manner similar to those terminating at T1.
Collapse
Affiliation(s)
- S Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Taejon
| | | |
Collapse
|
4
|
Vianney A, Muller MM, Clavel T, Lazzaroni JC, Portalier R, Webster RE. Characterization of the tol-pal region of Escherichia coli K-12: translational control of tolR expression by TolQ and identification of a new open reading frame downstream of pal encoding a periplasmic protein. J Bacteriol 1996; 178:4031-8. [PMID: 8763928 PMCID: PMC178157 DOI: 10.1128/jb.178.14.4031-4038.1996] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The TolQ, TolR, TolA, TolB, and Pal proteins appear to function in maintaining the integrity of the outer membrane, as well as facilitating the uptake of the group A colicins and the DNA of the infecting filamentous bacteriophages. Sequence data showed that these genes are clustered in a 6-kb segment of DNA with the gene order orf1 tolQ tolR tolA tolB pal orf2 (a newly identified open reading frame encoding a 29-kD9 protein). Like those containing orf1, bacteria containing an insertion mutation in this gene showed no obvious phenotype. Analysis of beta-galactosidase activity from fusion constructs in which the lac operon was fused to various genes in the cluster showed that the genes in this region constitute two separate operons: orf1 tolQRA and tolB pal orf2. In the orf1 tolQRA operon, translation of MR was dependent on translation of the upstream tolQ region. Consistent with this result, no functional ribosome-binding site for TolR synthesis was detected.
Collapse
Affiliation(s)
- A Vianney
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon I, France
| | | | | | | | | | | |
Collapse
|
5
|
Gockel G, Hachtel W, Baier S, Fliss C, Henke M. Genes for components of the chloroplast translational apparatus are conserved in the reduced 73-kb plastid DNA of the nonphotosynthetic euglenoid flagellate Astasia longa. Curr Genet 1994; 26:256-62. [PMID: 7859309 DOI: 10.1007/bf00309557] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The colourless, nonphotosynthetic protist Astasia longa is phylogenetically related to Euglena gracilis. The 73-kb plastid DNA (ptDNA) of A. longa is about half the size of most chloroplast DNAs (cpDNAs). More than 38 kb of the Astasia ptDNA sequence has been determined. No genes for photosynthetic function have been found except for rbcL. Identified genes include rpoB, tufA, and genes coding for three rRNAs, 17 tRNAs, and 13 ribosomal proteins. Not only is the nucleotide sequence of these genes highly conserved between A. longa and E. gracilis, but a number of these genes are clustered in a similar fashion and have introns in the same positions in both species. The results further support the idea that photosynthetic genes normally encoded in cpDNA have been preferentially lost in Astasia, but that the chloroplast genes coding for components of the plastid translational apparatus have been maintained. This apparatus might be needed for the expression of rbcL and also for that of still unidentified nonphotosynthetic genes of Astasia ptDNA.
Collapse
Affiliation(s)
- G Gockel
- Botanisches Institut, Universität Bonn, Germany
| | | | | | | | | |
Collapse
|
6
|
Tsuchihashi Z, Brown PO. Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA(Lys) and an AAG lysine codon. Genes Dev 1992; 6:511-9. [PMID: 1547945 DOI: 10.1101/gad.6.3.511] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Synthesis of the gamma-subunit of DNA polymerase III holoenzyme depends on precise and efficient translational frameshifting to the -1 frame at a specific site in the dnaX gene of Escherichia coli. In vitro mutagenesis of this frameshift site demonstrated the importance of an A AAA AAG heptanucleotide sequence, which allows two adjacent tRNAs to retain a stable interaction with mRNA after they slip to the -1 position. The AAG lysine codon present in the 3' half of this heptanucleotide was a key element for highly efficient frameshifting. A tRNA(Lys) with a CUU anticodon, which has a strong affinity for AAG lysine codons, is present in eukaryotic cells but absent in E. coli. Expression in E. coli of a mutant tRNA(Lys) with a CUU anticodon specifically inhibited the frameshifting at the AAG codon, suggesting that the absence of this tRNA in E. coli contributes to the efficiency of the dnaX frameshift.
Collapse
Affiliation(s)
- Z Tsuchihashi
- Howard Hughes Medical Institute, Stanford University Medical Center, California 94305
| | | |
Collapse
|
7
|
Abstract
The tyrT operon of E. coli and several other tRNA operons of E. coli show striking structural features: they contain repeated sequence units including a 19bp motif resembling the 3' end of the corresponding mature tRNA. A novel RNA, encoded by the repeated sequence of the tyrT operon, was identified. The RNA, characterized by primer extension and Nuclease-S1 analysis, contained 171 nucleotides and terminated with the 19bp motif of the CCA-end of tRNA(1Tyr). The RNA, designated as rtT RNA, is probably released from the primary transcript of tyrT during tRNA processing, it includes the coding capacity for the arginine rich peptide Tpr. Predictions of secondary folding resulted a rather stable RNA structure with a free energy of -44.3kcal/mol. A weak ribosome binding site was found, preceding the second possible AUG initiator codon for Tpr. The comparison of rtT RNA with putative transcripts from the repeated sequences associated with related tRNA genes showed common features with respect to primary structure, arrangement and secondary folding. In E. coli cultures the lag-phase during growth, caused by transient glycine or by isoleucine limitation, was found to be overcome or markedly shortened in the presence of rtT RNA. These and previously reported results suggest a modulatory effect of rtT RNA on stringent response.
Collapse
Affiliation(s)
- M Bösl
- Institut für Biochemie, Medizinischen Fakultät, Universität Erlangen-Nürnberg, FRG
| | | |
Collapse
|
8
|
Sprinzl M, Dank N, Nock S, Schön A. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 1991; 19 Suppl:2127-71. [PMID: 2041802 PMCID: PMC331350 DOI: 10.1093/nar/19.suppl.2127] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- M Sprinzl
- Laboratorium für Biochemie, Universität Bayreuth, FRG
| | | | | | | |
Collapse
|
9
|
Brun YV, Breton R, Lanouette P, Lapointe J. Precise mapping and comparison of two evolutionarily related regions of the Escherichia coli K-12 chromosome. Evolution of valU and lysT from an ancestral tRNA operon. J Mol Biol 1990; 214:825-43. [PMID: 2201776 DOI: 10.1016/0022-2836(90)90339-n] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Two tRNA operons have been found near the gltX gene encoding the glutamyl-tRNA synthetase of Escherichia coli K-12. The alaW operon previously undetected from genetic data and containing two identical tRNA(GGCAla) genes is 800 base-pairs downstream from the gltX terminator and is transcribed from the same strand. The valU operon containing genes for three identical tRNA(UACVal) and one tRNA(UUULys) (the wild-type allele of supN), is adjacent to gltX and is transcribed from the opposite strand. Five open reading frames were also found in this region encoding putative polypeptides of 62, 105, 130, 167 and 294 amino acid residues. ORF294 is a new member of the lysR family of bacterial transcriptional activators. The possibility that this is the xapR gene is discussed. Comparison of the physical and linkage maps of the E. coli chromosome in the 52 minute region has permitted precise mapping of most of the 18 genes in this region with the order nupC-glk- less than (alaW beta-ala W alpha)-1 kb- less than gltX-0.3 kb-(valU alpha-valU beta-valU gamma-lysV = supN) greater than xapR-xapA- less than lig-1 kb-cysK greater than -0.4 kb-ptsH greater than -0.05 kb-pstI greater than -0.05 kb-crr greater than -cysM-cysA in the clockwise order (greater than and less than indicate the direction of transcription; kb, 10(3) bases). The last two genes of valU (52 min) and lysT (16.5 min) are arranged in a similar fashion and a highly conserved region has been found in both operons. This suggests that the valU and lysT operons probably arose by a duplication of an ancestral tRNA operon. This is the first example of what may be two different tRNA operons from the same organism evolving from an ancestral tRNA gene. Comparison of the 16 and 52 minute regions of the E. coli K-12 chromosome suggests that these two regions could share a common ancestor.
Collapse
Affiliation(s)
- Y V Brun
- Département de Biochimie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
| | | | | | | |
Collapse
|
10
|
Nakahigashi K, Inokuchi H, Ozeki H. Functional expression of the mutants of the chloroplast tRNA(Lys) gene from the liverwort, Marchantia polymorpha, in Escherichia coli. FEBS Lett 1990; 265:59-62. [PMID: 2194832 DOI: 10.1016/0014-5793(90)80883-k] [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: 12/30/2022]
Abstract
The anticodon of the tRNA(Lys) gene (trnK) in the liverwort, Marchantia polymorpha, was artificially converted to an amber anticodon. This mutant tRNA(Lys) (CTA) gene carrying either the intron of the C27-C43 mismatch at the anticodon-stem is not functional in Escherichia coli, but without both of them, it does work as a tRNA(Lys) amber suppressor.
Collapse
Affiliation(s)
- K Nakahigashi
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
| | | | | |
Collapse
|
11
|
Komine Y, Adachi T, Inokuchi H, Ozeki H. Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12. J Mol Biol 1990; 212:579-98. [PMID: 2184240 DOI: 10.1016/0022-2836(90)90224-a] [Citation(s) in RCA: 229] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
By using a set of 476 ordered DNA clones (in lambda phage vector) that covers the entire chromosome of Escherichia coli K12, we have made an exhaustive survey of tRNA genes in the E. coli genome. Ultraviolet-irradiated bacteria were separately infected with each of the 476 clones and the RNA molecules produced upon infection were labeled with 32P. The labeled tRNAs were separated by gel electrophoresis and then characterized by fingerprinting analysis. Fifty-nine of the 476 clones produced tRNAs, including adjacent overlapping ones that share the same tRNA genes. The products of all the previously mapped tRNA genes (about 60, to date) were detected according to their expected positions, and 19 more tRNA genes were newly elucidated. These new tRNA genes were identified by sequencing the DNA from relevant regions of the clones; the DNA sequences were scanned for the stretches that could be folded into the familiar cloverleaf structure and the transcription units were deduced by predicting the promoters and terminators. The total complement of the tRNA genes in E. coli K12 was 78 for 45 tRNA (or 41 anticodon) species, distributed in 40 different transcription units throughout the chromosome. In addition, a gene for selenocysteine tRNA was detected by hybridization and mapped to a specific DNA segment. A comprehensive tRNA gene map of E. coli was constructed, including the selenocysteine tRNA gene. All the tRNA genes encode the 3' CCA, and in several cases the terminal 19 nucleotides (including the 3' CCA) of a tRNA gene is repeated several times. Finally, in the present study the sites for a long inversion (approx. 800 x 10(3) base-pairs, around the oriC region) in Kohara's library was determined to be within the 23 S-5 S regions in rrnD and rrnE, revealing the exchange of combinations of spacer and distal tRNA genes between these two ribosomal RNA operons.
Collapse
Affiliation(s)
- Y Komine
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
| | | | | | | |
Collapse
|
12
|
Kleina LG, Miller JH. Genetic studies of the lac repressor. XIII. Extensive amino acid replacements generated by the use of natural and synthetic nonsense suppressors. J Mol Biol 1990; 212:295-318. [PMID: 2157024 DOI: 10.1016/0022-2836(90)90126-7] [Citation(s) in RCA: 143] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have altered the amino acid sequence of the lac repressor one residue at a time by utilizing a collection of nonsense suppressors that permit the insertion of 13 different amino acids in response to the amber (UAG) codon, as well as an additional amino acid in response to the UGA codon. We used this collection to suppress nonsense mutations at 141 positions in the lacI gene, which encodes the 360 amino acid long lac repressor, including 53 new nonsense mutations which we constructed by oligonucleotide-directed mutagenesis. This method has generated over 1600 single amino acid substitutions in the lac repressor. We have cataloged the effects of these replacements and have interpreted the results with the objective of gaining a better understanding of lac repressor structure, and protein structure in general. The DNA binding domain of the repressor, involving the amino-terminal 59 amino acids, is extremely sensitive to substitution, with 70% of the replacements resulting in the I- phenotype. However, the remaining 301 amino acid core of the repressor is strikingly tolerant of substitutions, with only 30% of the amino acids introduced causing the I- phenotype. This analysis reveals the location of sites in the protein involved in inducer binding, tighter binding to operator and thermal stability, and permits a virtual genetic image reconstruction of the lac repressor protein.
Collapse
Affiliation(s)
- L G Kleina
- Molecular Biology Institute, University of California, Los Angeles 90024
| | | |
Collapse
|
13
|
Hughes D, Thompson S, O'Connor M, Tuohy T, Nichols BP, Atkins JF. Genetic characterization of frameshift suppressors with new decoding properties. J Bacteriol 1989; 171:1028-34. [PMID: 2644219 PMCID: PMC209697 DOI: 10.1128/jb.171.2.1028-1034.1989] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Suppressor mutants that cause ribosomes to shift reading frame at specific and new sequences are described. Suppressors for trpE91, the only known suppressible -1 frameshift mutant, have been isolated in Escherichia coli and in Salmonella typhimurium. E. coli hopR acts on trpE91 within the 9-base-pair sequence GGA GUG UGA, is dominant, and is located at min 52 on the chromosome. Its Salmonella homolog maps at an equivalent position and arises as a rarer class in that organism as compared with E. coli. The Salmonella suppressor, hopE, believed to be in a duplicate copy of the same gene, maps at min 17. The +1 suppressor, sufT, acts at the nonmonotonous sequence CCGU, is dominant, and maps at min 59 on the Salmonella chromosome.
Collapse
Affiliation(s)
- D Hughes
- Department of Genetics, Trinity College, Dublin, Ireland
| | | | | | | | | | | |
Collapse
|
14
|
Mutants of translational components that alter reading frame by two steps forward or one step back. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)81328-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
15
|
Eggertsson G, Söll D. Transfer ribonucleic acid-mediated suppression of termination codons in Escherichia coli. Microbiol Rev 1988; 52:354-74. [PMID: 3054467 PMCID: PMC373150 DOI: 10.1128/mr.52.3.354-374.1988] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
16
|
Khan AS, Roe BA. Aminoacylation of synthetic DNAs corresponding to Escherichia coli phenylalanine and lysine tRNAs. Science 1988; 241:74-9. [PMID: 2455342 DOI: 10.1126/science.2455342] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Synthetic DNA oligomers (tDNAs) corresponding to Escherichia coli tRNA(Phe) or tRNA(Lys) have been synthesized with either deoxythymidine (dT) or deoxyuridine (dU) substituted in the positions occupied by ribouridine or its derivatives. The tDNAs inhibited the aminoacylation of their respective tRNAs with their cognate amino acids, but not the aminoacylation of tRNA(Leu) with Leu. In the presence of aminoacyl-tRNA synthetase, species of both a tDNA(Phe) synthesized with a 3' terminal riboadenosine and a tDNA(Lys) containing only deoxynucleotides could be aminoacylated with the appropriate amino acids, although the Michaelis constant Km and observed maximal rate Vmax values for aminoacylation were increased by three- to fourfold and decreased by two- to threefold, respectively. The aminoacylation of synthetic tDNAs demonstrates that the ribose backbone of a tRNA is not absolutely required for tRNA aminoacylation.
Collapse
Affiliation(s)
- A S Khan
- Department of Chemistry, University of Oklahoma, Norman 73019
| | | |
Collapse
|
17
|
López-Revilla R, Martínez HG, Santos-Díaz MS. Isolation and characterization of mammalian cell lines carrying suppressible mutations. MOLECULAR & GENERAL GENETICS : MGG 1988; 213:105-11. [PMID: 3221837 DOI: 10.1007/bf00333405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
To obtain animal cell lines carrying nonsense mutations and the corresponding suppressors, we used a "supersuppressor" selection strategy on the CHO cell line. The wild-type strain is resistant to the aminopterin present in HAT medium (i.e., it is HATr) because it contains the enzymes hypoxanthine-guanine phosphoribosyl transferase (HPRT) and thymidine kinase (TK), whereas both HPRT- mutants - selected by their resistance to 6-thioguanine (TGr) - and TK- mutants - selected by their resistance to 5-bromodeoxyuridine (BrdUrdr) - are HATs. Therefore, from HPRT- TK- double nonsense mutants, whose phenotype would be TGr BrdUrdr (HATs), simultaneous HPRT+ TK+ double phenotypic revertants could be obtained by selecting HATr (TGs BrdUrds) variants carrying the corresponding nonsense supersuppressors. Through ethylmethane sulfonate (EMS) mutagenesis of the CHO cell line we obtained 65 TGr variants, 53 of which were HATs and the rest HATr. Among 36 TGr (HATs) variants tested, 23 did not revert to HATr, 4 reverted spontaneously and with EMS, and 9 reverted only with EMS. Some of the latter were probably HPRT- nonsense mutants because they were very stringent (had less than 2% of wild-type [3H]hypoxanthine incorporation and HPRT enzyme activity), and did not complement genetically. The introduction of a second marker (BrdUrdr) in 7 of these strains allowed us to isolate 29 TGr BrdUrdr (HATs) double drug-resistant lines. Through one-step mutagenesis and selection in HAT medium, from two double resistant strains we could isolate HATr (TGs BrdUrds) wild-type phenotypic revertants, each of which probably carries suppressible HPRT and TK nonsense (or missense) alleles and the corresponding supersuppressor. Our strategy could now be extended to obtain variants carrying suppressors in other cell lines.
Collapse
Affiliation(s)
- R López-Revilla
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México DF, Mexico
| | | | | |
Collapse
|
18
|
Manzara T, Hu JX, Price CA, Hallick RB. Characterization of the TrnD, TrnK, PsaA locus of Euglena gracilis chloroplast DNA. PLANT MOLECULAR BIOLOGY 1987; 8:327-336. [PMID: 24301195 DOI: 10.1007/bf00021312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/1985] [Revised: 01/05/1987] [Accepted: 01/12/1987] [Indexed: 06/02/2023]
Abstract
The EcoRI fragment Eco J' of Euglena gracilis chloroplast DNA has previously been identified as a tRNA coding locus. The nucleotide sequence of a 2.3-kb region of the Eco J' fragment known to contain the tRNA genes has been determined. This locus was found to contain two tRNA genes, trnD-GTC and trnK-TTT. Separated from the trnK locus by a 43-bp spacer is an open reading frame of 398 codons. The open reading frame is 73-75% homologous to the amino-terminal coding regions of the spinach and maize genes for the P700 chlorophyll a apoprotein of photosystem I. It has been identified as exon I of an intron-containing psaA gene. The exon is followed by an intron of at least 214 bp that has features characteristic of other Euglena chloroplast introns. Major chloroplast RNA transcripts of sizes 5.5, 4.7, and 2.3 kb hybridize to a psaA-specific probe. The gene for a second photosystem I P700 apoprotein, psaB, has been located on an adjacent EcoRI fragment, Eco C.
Collapse
Affiliation(s)
- T Manzara
- Department of Botany, University of California, 94720, Berkeley, CA, USA
| | | | | | | |
Collapse
|
19
|
Rasmussen OF, Frydenberg J, Chirtiansen C. Analysis of the leader and spacer regions of the two rRNA operons of Mycoplasma PG50: two tRNA genes are located upstream of rrnA. ACTA ACUST UNITED AC 1987. [DOI: 10.1007/bf00330417] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
20
|
Structure and organization of the transfer ribonucleic acid genes of Escherichia coli K-12. Microbiol Rev 1985; 49:379-97. [PMID: 2419743 PMCID: PMC373044 DOI: 10.1128/mr.49.4.379-397.1985] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
21
|
Uemura H, Thorbjarnardóttir S, Gamulin V, Yano J, Andrésson OS, Söll D, Eggertsson G. supN ochre suppressor gene in Escherichia coli codes for tRNALys. J Bacteriol 1985; 163:1288-9. [PMID: 3897192 PMCID: PMC219277 DOI: 10.1128/jb.163.3.1288-1289.1985] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We describe the cloning and nucleotide sequence of a new tRNALys gene, lysV, in Escherichia coli. An ochre suppressor allele of this gene, supN, codes for a tRNALys with anticodon UUA, presumably derived by a single base change from a wild-type UUU anticodon. The sequence of the supN tRNALys is identical to the sequence of ochre suppressor tRNAs encoded by mutant alleles at the lysT locus. This locus, which contains the two previously known tRNALys genes of E. coli, is located far from the lysV locus on the chromosome.
Collapse
|
22
|
Caillet J, Plumbridge JA, Springer M. Evidence that pheV, a gene for tRNAPhe of E. coli is transcribed from tandem promoters. Nucleic Acids Res 1985; 13:3699-710. [PMID: 3892481 PMCID: PMC341267 DOI: 10.1093/nar/13.10.3699] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A DNA fragment of 487 bp containing a gene for tRNAPhe has been sequenced. Although the tRNAPhe sequence is identical to that of pheU (which maps at 94.5 min) the surrounding sequences are quite different. This sequence is thus that of a second gene for tRNAPhe (which we shall call pheV). In vitro transcription experiments and S1 mapping in vivo show the existence of two promoters separated by about 60 nucleotides. The second transcript starts only 3 nucleotides 5' from the tRNAPhe structural sequence. A DNA sequence characteristic of a rho-independent terminator is located 30 nucleotides 3' of the end of the structural gene and is shown to function efficiently in vitro.
Collapse
|
23
|
Yoshimura M, Inokuchi H, Ozeki H. Identification of transfer RNA suppressors in Escherichia coli. IV. Amber suppressor Su+6 a double mutant of a new species of leucine tRNA. J Mol Biol 1984; 177:627-44. [PMID: 6207302 DOI: 10.1016/0022-2836(84)90041-x] [Citation(s) in RCA: 24] [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
An Escherichia coli DNA fragment containing an Su+6 amber suppressor gene (supP) was cloned into a lambda gt lambda Ch vector by the shotgun method, selecting a Su+6 transducing phage lambda pSu+6. Through prophage integration followed by induction occurring at the transducing region of the lambda pSu+6 in Su- E. coli, a counterpart transducing phage carrying the wild-type allele (Su degrees 6) was isolated (lambda pSu degrees 6). The fingerprint of a tRNA encoded by lambda pSu degrees 6 was identical to that of an unidentified tRNAE previously reported (Ikemura & Ozeki, 1977). The cloverleaf structure of this tRNA was determined by combining the results of tRNA analysis and DNA sequencing of the gene. Judging from the anticodon of 5'-CAA-3', Su degrees 6 tRNA was identified as a new type of leucine isoacceptor in E. coli. Unlike other suppressors analyzed, Su+6 tRNA differed by two nucleotides from Su degrees 6 tRNA; one at the anticodon (CAA to CUA) and the other at the junction of D- and anticodon-stem (A27 to G27). DNA sequence analysis revealed that a single stretch of tRNA is flanked by the putative sequences of promoter and terminator. Thus a single copy of the Su degrees 6 tRNA gene constitutes a solitary tRNA transcription unit. Southern blotting showed only one copy of Su degrees 6 tRNA gene per haploid genome of E. coli. Since this single gene can mutate to the Su+6 suppressor, the Su degrees 6 leucine tRNA may be accounted as a dispensable species among the leucine isoacceptor tRNAs. Two possible open reading frames are found immediately following the Su degrees 6 tRNA gene.
Collapse
MESH Headings
- Bacteriophage lambda/genetics
- Bacteriophage lambda/isolation & purification
- Base Sequence
- Cloning, Molecular
- DNA, Bacterial
- Electrophoresis, Agar Gel
- Escherichia coli/genetics
- Genes, Bacterial
- Mutation
- RNA, Bacterial/genetics
- RNA, Transfer/genetics
- RNA, Transfer, Amino Acyl/genetics
- Suppression, Genetic
- Transduction, Genetic
Collapse
|