Pre‐tRNA 3′‐Processing in <i>Saccharomyces cerevisiae</i>

Papadimitriou, Apollon; Groß, H.

doi:10.1111/j.1432-1033.1996.0747r.x

Cited by 27 publications

(30 citation statements)

References 44 publications

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“…They are consistent with the tRNA punctuation model, where endonucleolytic release of mature mt-tRNAs indicates the possibility that at least some mitochondrial tRNAs may undergo limited exonucleolytic 3 ′ -end processing; however, in agreement with previous reports, our study confirms that the major activity in mitochondria is provided by endonucleases (Chen and Martin 1988;Papadimitriou and Gross 1996). In S. cerevisiae, which contains only one long tRNase Z protein (ELAC2), it has to be targeted to both the nucleus and mitochondria.…”

Section: Discussionsupporting

confidence: 81%

“…However, CCA-less precursors in Bacillus subtilis are processed endonucleolytically by tRNase Z (Pellegrini et al 2003;Wen et al 2005). Conversely, the major pathway for eukaryotic tRNA 3 ′ -end processing is endonucleolytic, while trimming by exonucleases serves as an alternative (Garber and Gage 1979;Hagenbuchle et al 1979;Castaño et al 1985;Engelke et al 1985;Frendewey et al 1985;Manam and Van Tuyle 1987;Stange and Beier 1987;Furter et al 1992;Oommen et al 1992;Papadimitriou and Gross 1996;Han and Kang 1997;Nashimoto 1997;Mayer et al 2000;Schiffer et al 2002).…”

Section: Introductionmentioning

confidence: 99%

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tRNA 3′ processing in yeast involves tRNase Z, Rex1, and Rrp6

Skowronek

Grzechnik

Späth

et al. 2013

RNA

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Mature tRNA 3 ′ ends in the yeast Saccharomyces cerevisiae are generated by two pathways: endonucleolytic and exonucleolytic. Although two exonucleases, Rex1 and Rrp6, have been shown to be responsible for the exonucleolytic trimming, the identity of the endonuclease has been inferred from other systems but not confirmed in vivo. Here, we show that the yeast tRNA 3 ′ endonuclease tRNase Z, Trz1, is catalyzing endonucleolytic tRNA 3 ′ processing. The majority of analyzed tRNAs utilize both pathways, with a preference for the endonucleolytic one. However, 3′ -end processing of precursors with long 3 ′ trailers depends to a greater extent on Trz1. In addition to its function in the nucleus, Trz1 processes the 3 ′ ends of mitochondrial tRNAs, contributing to the general RNA metabolism in this organelle.

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Section: Discussionsupporting

confidence: 81%

Section: Introductionmentioning

confidence: 99%

tRNA 3′ processing in yeast involves tRNase Z, Rex1, and Rrp6

Skowronek

Grzechnik

Späth

et al. 2013

RNA

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“…The majority of nuclear and chloroplast 3Ј processing enzymes have been found to be endonucleases cleaving at the tRNA 3Ј end (5-10), although prokaryotic-like 3Ј maturation with exonucleases being involved has also been observed (11)(12)(13)(14). At present the general consensus appears to attribute a multistep processing pathway to prokaryotes, whereas in eukaryotes single-step reactions predominate.…”

Section: Introductionmentioning

confidence: 99%

5′ end maturation and RNA editing have to precede tRNA 3′ processing in plant mitochondria

Kunzmann

Brennicke

Marchfelder

1998

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

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We report the characterization and partial purification of potato mitochondrial RNase Z, an endonuclease that generates mature tRNA 3 ends. The enzyme consists of one (or more) protein(s) without RNA subunits. Products of the processing reaction are tRNA molecules with 3 terminal hydroxyl groups and 3 trailers with 5 terminal phosphates. The main processing sites are located immediately 3 to the discriminator and one nucleotide further downstream. This endonucleolytic processing at and close to the tRNA 3 end in potato mitochondria suggests a higher similarity to the eukaryotic than to the prokaryotic tRNA 3 processing pathway. Partial purification and separation of RNase Z from the 5 processing activity RNase P allowed us to determine biochemical characteristics of the enzyme. The activity is stable over broad pH and temperature ranges, with peak activity at pH 8 and 30°C. Optimal concentrations for MgCl 2 and KCl are 5 mM and 30 mM, respectively. The potato mitochondrial RNase Z accepts only tRNA precursors with mature 5 ends. The precursor for tRNA Phe requires RNA editing for efficient processing by RNase Z.In all genetic systems, mature functional tRNAs are generated by several processing reactions that include the removal of cotranscribed 5Ј and 3Ј extensions. Processing at the tRNA 5Ј end is catalyzed by the ubiquitous endoribonuclease RNase P (1, 2) well characterized in prokaryotes (3). Although the reaction at the tRNA 5Ј end is alike in bacteria, archaeas, and eukaryotes (nuclei and organelles), tRNA 3Ј end maturation seems to be more variable.In Escherichia coli an endonucleolytic cleavage several nucleotides downstream of the tRNA is followed by exonucleolytic removal of some of the residual nucleotides. Only after RNase P has then matured the 5Ј terminus of the tRNA are the remaining extra 3Ј residues removed. This step yields the mature tRNA molecule because the terminal CCA OH sequence is genomically encoded in E. coli (for review, see ref. 4).The majority of nuclear and chloroplast 3Ј processing enzymes have been found to be endonucleases cleaving at the tRNA 3Ј end (5-10), although prokaryotic-like 3Ј maturation with exonucleases being involved has also been observed (11)(12)(13)(14). At present the general consensus appears to attribute a multistep processing pathway to prokaryotes, whereas in eukaryotes single-step reactions predominate.Mitochondria may have retained a prokaryotic-like processing system because they are thought to be of prokaryotic origin according to the endosymbiont theory (15). On the other hand, they may have adapted the host nuclear enzymes for processing, precedence having been found with tRNA modifying enzymes in yeast mitochondria (16) and plant mitochondria (17). To clarify the nature and origin of the plant mitochondrial tRNA processing machinery, the enzymes involved have to be investigated and characterized in detail.A special feature of mitochondrial tRNA maturation in plant cells is the involvement of RNA editing (18)(19)(20)). Herein we demonstrate that...

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“…5C (left panel), in which the addition of 10 M UTP to the purified exonuclease had no effect on the degradation of the 6-U substrate RNA. Addition of a purified TUTase preparation 2 and UTP, on the other hand, produced 3Ј-extensions of the [G]6-U substrate RNA of up to several hundred Us (Fig. 5C, right panel).…”

Section: Us At the 3ј-end ([G]12-u) A Separate Assay Of Each Fractiomentioning

confidence: 99%

Isolation and Characterization of a U-specific 3′-5′-Exonuclease from Mitochondria of Leishmania tarentolae

Aphasizhev

Simpson

2001

Journal of Biological Chemistry

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We have purified a 3-5-exoribonuclease from mitochondrial extract of Leishmania tarentolae over 4000-fold through six column fractionations. This enzyme digested RNA in a distributive manner, showed a high level of specificity for 3-terminal Us, and was blocked by a terminal dU; there was slight exonucleolytic activity on a 3-terminal A or C but no activity on a 3-terminal G residue. The enzyme preferred single-stranded 3-oligo(U) overhangs and did not digest duplex RNA. Two other 3-5-exoribonuclease activities were also detected in the mitochondrial extract, one of which was stimulated by a 3-phosphate and the other of which degraded RNAs with a 3-OH to mononucleotides in a processive manner. The properties of the distributive U-specific 3-5-exoribonuclease suggest an involvement in the U-deletion RNA editing reaction that occurs in the mitochondrion of these cells.3Ј-5Ј-Exoribonucleases have been shown to play important roles in the maturation and degradation of RNAs, including the 3Ј-end maturation of the 5.8 S rRNA (1) and pre-tRNAs (2) and both deadenylation-dependent (3) and deadenylation-independent mRNA decay in eukaryotes (4). An exonuclease activity specific for removal of the post-transcriptionally added (5) 3Ј-oligo(U) tail of U6 small nuclear RNA has been partially purified and characterized (6). A number of 3Ј-5Ј-exoribonucleases have also been described in bacteria and shown to be involved in RNA processing. For example, RNase E from Escherichia coli is a site-specific endoribonuclease that also has a 3Ј-5Ј-exonuclease activity on poly(A) and poly(U) tails (7). There is conservation of some exoribonucleases between bacteria and eukaryotes. In yeast, four of the five components of the "exosome" complex required for the 3Ј-end processing of the 5.8 S rRNA are homologous to bacterial 3Ј-5Ј-exoribonucleases that have distributive, processive, and phosphorolytic activities (8). In addition, a conserved 3Ј-5Ј-exonuclease domain that is similar to the 3Ј-5Ј-proofreading domain of DNA polymerases has been identified by hidden Markov model and phylogenetic analysis (9).The presence of a U-specific 3Ј-5Ј-exoribonuclease in mitochondria of kinetoplastid protozoa was predicted by the enzyme cascade model of U-insertion/deletion RNA editing (10). This model involves an initial base-pairing interaction of specific guide RNAs with the pre-edited mRNAs just downstream of the first editing site, and a cleavage occurs at the first mismatched base of the mRNA. Then, in the case of U-deletion editing, a proposed U-specific 3Ј-5Ј-exonuclease removes non-base-paired Us from the 3Ј-end of the 5Ј-cleavage fragment, which is followed by ligation of the two mRNA cleavage fragments. Evidence from analysis of in vitro editing systems from the trypanosomatids Trypanosoma brucei (11-13) and Leishmania tarentolae (14, 15) has provided strong evidence for this model. All of the proposed enzymatic activities have been detected in mitochondrial extracts, including a U-specific 3Ј-5Ј-exoribonuclease activity (16). This activity has...

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Pre‐tRNA 3′‐Processing in Saccharomyces cerevisiae

Cited by 27 publications

References 44 publications

tRNA 3′ processing in yeast involves tRNase Z, Rex1, and Rrp6

tRNA 3′ processing in yeast involves tRNase Z, Rex1, and Rrp6

5′ end maturation and RNA editing have to precede tRNA 3′ processing in plant mitochondria

Isolation and Characterization of a U-specific 3′-5′-Exonuclease from Mitochondria of Leishmania tarentolae

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