Genes, variant genes and pseudogenes of the human tRNAVal gene family expression and pre-tRNA maturation in vitro

Thomann, Hans-Ulrich; Schmutzler, Cornelia; Hüdepohl, Uwe; Blow, Margret; Groß, H.

doi:10.1016/0022-2836(89)90590-1

Cited by 35 publications

(31 citation statements)

References 98 publications

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“…Nuclear-encoded tRNA Val consisting of a 73-nt canonical tRNA and a 14-nt 3Ј end trailer (Ref. 29; accession number X17514) was constructed using the same methods. Similarly, inserts consisting of the EcoRI site, T7 promoterstrong start, hybridization box-hammerhead ribozyme, 69-nt tRNA Ser -(UCN), 19-nt 3Ј end trailer, hepatitis delta virus ribozyme, and HindIII runoff site were designed to produce an 88-nt pre-tRNA after ribozyme cleavage (27).…”

Section: Baculovirus Expression Of Human Trnase Zmentioning

confidence: 99%

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Naturally Occurring Mutations in Human Mitochondrial Pre-tRNASer(UCN) Can Affect the Transfer Ribonuclease Z Cleavage Site, Processing Kinetics, and Substrate Secondary Structure

Yan¹,

Zareen²,

Levinger

2006

Journal of Biological Chemistry

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tRNAs are transcribed as precursors with a 5 end leader and a 3 end trailer. The 5 end leader is processed by RNase P, and in most organisms in all three kingdoms, transfer ribonuclease (tRNase) Z can endonucleolytically remove the 3 end trailer. Long ( L ) and short ( S ) forms of the tRNase Z gene are present in the human genome. tRNase Z L processes a nuclear-encoded pre-tRNA ϳ1600-fold more efficiently than tRNase Z S and is predicted to have a strong mitochondrial transport signal. tRNase Z L could, thus, process both nuclear-and mitochondrially encoded pre-tRNAs. More than 150 pathogenesis-associated mutations have been found in the mitochondrial genome, most of them in the 22 mitochondrially encoded tRNAs. All the mutations investigated in human mitochondrial tRNA Ser(UCN) affect processing efficiency, and some affect the cleavage site and secondary structure. These changes could affect tRNase Z processing of mutant pre-tRNAs, perhaps contributing to mitochondrial disease.Mitochondria, the intracellular organelles responsible for most of a eukaryotic cell energy production, possess their own maternally inherited genome. The circular 16,568-base pair human mitochondrial genome (1) is bidirectionally transcribed into long polycistronic heavy (H) 4 -and light (L)-strand precursor RNAs. Two rRNAs and 11 mRNAs encoding 13 polypeptides (all of them subunits of complexes in the respiratory transport chain) are punctuated by 22 tRNAs (1 tRNA for each of 18 amino acids and 2 each for leucine and serine with different anticodons) with very little intergenic RNA (2, 3). Several thousand additional polypeptides required for mitochondrial metabolism are nuclear-encoded, cytoplasmically translated and imported.Precursor tRNA transcripts have a 5Ј end leader and a 3Ј end trailer. Eukaryotic nuclear-encoded tRNAs are transcribed from RNA polymerase III promoters with short 5Ј end leaders and 3Ј end trailers ending with a U 3 tail. The characteristic length and sequence of mitochondrial pre-tRNA leaders and trailers, on the other hand, depend on the setting of individual tRNAs among the neighboring functional RNA units (other tRNAs, mRNAs, rRNAs) on the long polycistronic H-and L-strand transcripts (4).The 5Ј end leader is removed from pre-tRNAs by RNase P in a largely conserved, well characterized reaction (5). On the other hand, there are different paths to a mature tRNA 3Ј end (6). In the tRNAs of some prokaryotes, CCA is transcriptionally encoded, and the 3Ј end trailer is removed by the sequential activity of an endonuclease (RNase E) and exonucleases (7,8). In contrast, in most organisms in all three kingdoms and in extranuclear organelles, CCA is not transcriptionally encoded and can be added to the discriminator (the unpaired nucleotide after the 3Ј end of the acceptor stem, which is retained in mature tRNA) after precise endonucleolytic removal of the 3Ј end trailer by tRNase Z (9 -14).Intriguingly, CCA is a tRNase Z anti-determinant that prevents mature tRNA from recycling through tRNase Z, thus ensuring that ...

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Section: Baculovirus Expression Of Human Trnase Zmentioning

confidence: 99%

“…7B; Ref. 29, accession number X17514). Mitochondrial pre-tRNA Leu(UUR) has a length of 75 nt to the discriminator and was constructed with a 38-nt 3Ј end trailer ( Fig.…”

Section: Panel B Cf A)mentioning

confidence: 99%

Naturally Occurring Mutations in Human Mitochondrial Pre-tRNASer(UCN) Can Affect the Transfer Ribonuclease Z Cleavage Site, Processing Kinetics, and Substrate Secondary Structure

Yan¹,

Zareen²,

Levinger

2006

Journal of Biological Chemistry

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“…Most tRNAs are encoded by dispersed multigene families of 10 to 20 members in eukaryotes, including gene variants and pseudogenes. More than 10 members of the human valine tRNA (tRNA Val ) gene family have been cloned and characterized (11,52,56). One member of the human tRNA Val gene family, designated clone pHtV8, is highly expressed in HeLa cells and human placenta (48).…”

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confidence: 99%

“…1) for tRNA Val cannot distinguish family members. However, the family member used for DNA repair studies (clone pHtV8) is highly expressed in HeLa cells and human placenta and is also strongly transcribed in vitro (48,56). For the genomic footprinting analysis we used primers which correspond to the sequence of the tRNA Val gene of clone pHtV8 isolated from a human genomic library (56).…”

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confidence: 99%

Lack of Gene- and Strand-Specific DNA Repair in RNA Polymerase III-Transcribed Human tRNA Genes

Dammann

Pfeifer

1997

Molecular and Cellular Biology

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UV light induces DNA lesions which are removed by nucleotide excision repair. Genes transcribed by RNA polymerase II are repaired faster than the flanking chromatin, and the transcribed strand is repaired faster than the coding strand. Transcription-coupled repair is not seen in RNA polymerase I-transcribed human rRNA genes. Since repair of genes transcribed by RNA polymerase III has not been analyzed before, we investigated DNA repair of tRNA genes after irradiation of human fibroblasts with UVC. We studied the repair of UV-induced cyclobutane pyrimidine dimers at nucleotide resolution by ligation-mediated PCR. A single-copy gene encoding selenocysteine tRNA, a tRNA valine gene, and their flanking sequences were analyzed. Protein-DNA footprinting showed that both genes were occupied by regulatory factors in vivo, and Northern blotting and nuclear run-on analysis of the tRNA indicated that these genes were actively transcribed. We found that both genes were repaired slower than RNA polymerase II-transcribed genes. No major difference between repair of the transcribed and the coding DNA strands was detected. Transcribed sequences of the tRNA genes were not repaired faster than flanking sequences. Indeed, several sequence positions in the 5 flanking region of the tRNA Val gene were repaired more efficiently than the gene itself. These results indicate that unlike RNA polymerase II, RNA polymerase III has no stimulatory effect on DNA repair. Since tRNA genes are covered by the regulatory factor TFIIIC and RNA polymerase III, these proteins may actually inhibit the DNA's accessibility to repair enzymes.Irradiation of DNA with UV light induces mutagenic DNA lesions, and exposure to sunlight has been linked to the development of human skin cancer. UVB (280 to 320 nm) and UVC (200 to 280 nm) irradiation of DNA produces two major photoproducts: cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (for reviews, see references 6, 35, 44, and 61). CPDs are formed between two adjacent pyrimidines: 5Ј-TpT, 5Ј-TpC, 5Ј-CpT, or 5Ј-CpC. The rates of formation and repair of CPDs vary strongly due to structural features of chromatin and DNA sequence (53, 61). Since CPDs are repaired much more slowly than pyrimidine (6-4) pyrimidone photoproducts, CPDs are thought to be the most mutagenic UV lesions in mammalian cells (6, 44). Efficient DNA repair must occur before DNA replication to prevent the formation of stable transition mutations. C-to-T transitions are the major class of UV-induced mutations. UVinduced mutations were previously studied in RNA polymerase III-transcribed suppressor tRNA genes in Saccharomyces cerevisiae (1, 2) or tRNA marker genes propagated in human cells (7, 49). Intriguingly, there was a preference for UV-induced mutations to occur at sites where the dipyrimidine was on the RNA polymerase III-transcribed strand (1, 2). On the other hand, in genes transcribed by RNA polymerase II, mutations can be ascribed to dipyrimidine photoproducts on the nontranscribed strand (68). RNA poly...

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“…Even at elevated temperatures (600C) no difference was seen, indicating comparable stability of both wild-type and Y9 tRNAGlu (data not shown). However, as the base exchange may affect the rate of tRNA processing and the amounts of mature-size tRNAs (33,34), a mutation in the Y9 tRNAGlu gene would be consistent with the reduced abundance of the corresponding tRNA in Y9 chloroplasts.…”

Section: Methodsmentioning

confidence: 99%

A point mutation in Euglena gracilis chloroplast tRNA(Glu) uncouples protein and chlorophyll biosynthesis.

Stange-Thomann

Thomann

Lloyd

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

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The universal precursor of tetrapyrrole pigments (e.g., chlorophylls and hemes) is 5-aminolevulinic acid (ALA), which in Euglena gracilis chloroplasts is derived via the two-step C5 pathway from glutamate charged to tRNAGIW. The first enzyme in this pathway, Glu-tRNA reductase (GluTR) catalyzes the reduction of glutamyl-tRNAGu (Glu-tRNA) to glutamate 1-semialdehyde (GSA) with the release of the uncharged tRNAGIu. The second enzyme, GSA-2,1-aminomutase, converts GSA to ALA. tRNAGIu is a specific cofactor for the NADPH-dependent reduction by GluTR, an enzyme that recognizes the tRNA in a sequence-specific manner. This RNA is the normal tRNAGUI, a dual-function molecule participating both in protein and in ALA and, hence, chlorophyll biosynthesis. A chlorophyll-deficient mutant of E. gracilis (YgZNaIL)

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Genes, variant genes and pseudogenes of the human tRNAVal gene family expression and pre-tRNA maturation in vitro

Cited by 35 publications

References 98 publications

Naturally Occurring Mutations in Human Mitochondrial Pre-tRNASer(UCN) Can Affect the Transfer Ribonuclease Z Cleavage Site, Processing Kinetics, and Substrate Secondary Structure

Naturally Occurring Mutations in Human Mitochondrial Pre-tRNASer(UCN) Can Affect the Transfer Ribonuclease Z Cleavage Site, Processing Kinetics, and Substrate Secondary Structure

Lack of Gene- and Strand-Specific DNA Repair in RNA Polymerase III-Transcribed Human tRNA Genes

A point mutation in Euglena gracilis chloroplast tRNA(Glu) uncouples protein and chlorophyll biosynthesis.

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