Split tRNA genes and their products: A paradigm for the study of cell function and evolution

Culbertson, Michael R.; Winey, Mark

doi:10.1002/yea.320050602

Cited by 52 publications

(26 citation statements)

References 86 publications

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“…Interestingly, the hBH type of splicing motif as described above has some resemblance to the splicing substrate consensus "hBh" present in most yeast pre-tRNAs harboring introns at 37/38 (for review, see Culbertson and Winey 1989;Trotta and Abelson 1999). In this latter case, the intronic helix h is the same anticodon stem as for archaeal pre-tRNAs.…”

Section: Only Helix H and One Of The Two Helices H Or H Are Major Detmentioning

confidence: 98%

Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications

Marck¹,

Grosjean²

2003

RNA

112

163

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Most introns of archaeal tRNA genes (tDNAs) are located in the anticodon loop, between nucleotides 37 and 38, the unique location of their eukaryotic counterparts. However, in several Archaea, mostly in Crenarchaeota, introns have been found at many other positions of the tDNAs. In the present work, we revisit and extend all previous findings concerning the identification, exact location, size, and possible fit to the proposed bulge-helix-bulge structural motif (BHB, now renamed hBHBh) of the sequences spanning intron-exon junctions in intron-containing tRNAs of 18 archaea. A total of 103 introns were found located at the usual position 37/38 and 33 introns at 14 other different positions, that is, in the anticodon stem and loop, in the D-and T-loops, in the V-arm, or in the amino acid arm. For introns located at 37/38 and elsewhere in the pre-tRNA, canonical hBHBh motifs were not always found. Instead, a relaxed hBH or HBh motif including the constant central 4-bp helix H flanked by one helix (h or h) on either side generating only one bulge could be disclosed. Also, for introns located elsewhere than at position 37/38, the hBHBh (or HBh) structure competes with the three-dimensional structure of the mature tRNA, attesting to important structural rearrangements during the complex multistep maturation-splicing processes. A homotetramer-type of splicing endonuclease (like in all Crenarchaeota) instead of a homodimeric-type of enzyme (as in most Euryarchaeota) appears to best fit the requirement for splicing introns at relaxed hBH or HBh motifs, and may represent the most primitive form of this enzyme.

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Section: Only Helix H and One Of The Two Helices H Or H Are Major Detmentioning

confidence: 98%

Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications

Marck¹,

Grosjean²

2003

RNA

112

163

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“…A number of genes that play a role in tRNA splicing have been identified. These include genes that encode or otherwise affect known enzyme activities, specifically SEN1 and SEN2, which are required for full endonuclease activity in vitro (40), and RLG1, which codes for the tRNA-splicing ligase (5). SEN2 encodes the 42-kDa subunit of the endonuclease (26), but antibodies directed against Sen1, which is a nuclear protein, do not recognize any of the catalytic subunits of the endonuclease (38), indicating that Sen1 is required in some other capacity for enzyme activity (7).…”

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confidence: 99%

The Yeast SEN3 Gene Encodes a Regulatory Subunit of the 26S Proteasome Complex Required for Ubiquitin-Dependent Protein Degradation In Vivo

DeMarini

Papa

Swaminathan

et al. 1995

Molecular and Cellular Biology

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The yeast Sen1 protein was discovered by virtue of its role in tRNA splicing in vitro. To help determine the role of Sen1 in vivo, we attempted to overexpress the protein in yeast cells. However, cells with a high-copy SEN1-bearing plasmid, although expressing elevated amounts of SEN1 mRNA, show little increase in the level of the encoded protein, indicating that a posttranscriptional mechanism limits SEN1 expression. This control depends on an amino-terminal element of Sen1. Using a genetic selection for mutants with increased expression of Sen1-derived fusion proteins, we identified mutations in a novel gene, designated SEN3. SEN3 is essential and encodes a 945-residue protein with sequence similarity to a subunit of an activator of the 20S proteasome from bovine erythrocytes, called PA700. Earlier work indicated that the 20S proteasome associates with a multisubunit regulatory factor, resulting in a 26S proteasome complex that degrades substrates of the ubiquitin system. Mutant sen3-1 cells have severe defects in the degradation of such substrates and accumulate ubiquitin-protein conjugates. Most importantly, we show biochemically that Sen3 is a subunit of the 26S proteasome. These data provide evidence for the involvement of the 26S proteasome in the degradation of ubiquitinated proteins in vivo and for a close relationship between PA700 and the regulatory complexes within the 26S proteasome, and they directly demonstrate that Sen3 is a component of the yeast 26S proteasome.In the yeast Saccharomyces cerevisiae, mature tRNAs are produced from primary transcripts through a series of nuclear RNA-processing events that sometimes include the removal of an intron adjacent to the anticodon loop. Intron excision and tRNA ligation require the activities of three known enzymes: a heterotrimeric endonuclease that catalyzes both 5Ј and 3Ј cleavages, a monomeric tRNA ligase, and an NAD-dependent phosphotransferase (22) that removes a 2Ј-phosphate from the splice junction to produce mature tRNA (reviewed in reference 5). A number of genes that play a role in tRNA splicing have been identified. These include genes that encode or otherwise affect known enzyme activities, specifically SEN1 and SEN2, which are required for full endonuclease activity in vitro (40), and RLG1, which codes for the tRNA-splicing ligase (5).

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“…The sen1-1 mutant confers temperature-sensitive growth and results in pre-tRNA accumulation in vivo and in vitro (48). Cloning and characterization of SENI show it to be essential for cellular viability and required for processing of all 10 families of intron-containing tRNAs (5). Mutant sen2-3 accumulates tRNA two-thirds molecules (5' half-molecule plus intron), which suggests that it may be defective in cleavage at the 5' splice site of the intervening sequence (12).…”

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confidence: 99%

SPL1-1, a Saccharomyces cerevisiae mutation affecting tRNA splicing

Kolman

Söll

1993

J Bacteriol

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A genetic approach was used to isolate and characterize Saccharomyces cerevisiae genes affecting tRNA processing. Three mutants were isolated which were able to process and utilize splicing-deficient transcripts from inactivated Schizosaccharomyces pombe suppressor tRNA genes. Extragenic recovery of suppressibility was verified by the suppression of nonsense mutations in LEU2, HIS4, and ADE1. One mutant, SPL1-1, was chosen for detailed analysis on the basis of its increased synthesis of mature suppressor tRNA over wild-type cell levels as determined by Northern (RNA) analysis. This mutant exhibited strong suppression exclusively with the defective tRNA gene used in the mutant selection. Genetic analysis revealed that a single, dominant, haplo-lethal mutation was responsible for the suppression phenotype. The mutation mapped on chromosome III to an essential 1.5-kb open reading frame (L. S. Symington and T. D. Petes, Mol. Cell. Biol. 8:595-604, 1988), recently named NFS1 (S. G. Oliver et al., Nature [London] 357:38-46, 1992), located adjacent (centromere proximal) to LEU2.

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Split tRNA genes and their products: A paradigm for the study of cell function and evolution

Cited by 52 publications

References 86 publications

Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications

Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications

The Yeast SEN3 Gene Encodes a Regulatory Subunit of the 26S Proteasome Complex Required for Ubiquitin-Dependent Protein Degradation In Vivo

SPL1-1, a Saccharomyces cerevisiae mutation affecting tRNA splicing

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