Functional Interactions between Yeast Mitochondrial Ribosomes and mRNA 5′ Untranslated Leaders

Green-Willms, Noelle S.; Fox, Thomas D.; Costanzo, Maria C.

doi:10.1128/mcb.18.4.1826

Cited by 61 publications

(41 citation statements)

References 72 publications

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“…RMD9 was the gene isolated in transformants of CAB76 bearing a cDNA inserted into pFL61 (Minet et al 1992). RMD9 was also isolated from a library of genomic fragments in YEP24 (Green-Willms et al 1998). Chromosomal mutations were identified by PCR amplification of mutant genes from genomic DNA and sequence analysis of the total amplification products.…”

Section: Methodsmentioning

confidence: 99%

Translation Initiation inSaccharomyces cerevisiaeMitochondria: Functional Interactions Among Mitochondrial Ribosomal Protein Rsm28p, Initiation Factor 2, Methionyl-tRNA-Formyltransferase and Novel Protein Rmd9p

et al. 2007

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Rsm28p is a dispensable component of the mitochondrial ribosomal small subunit in Saccharomyces cerevisiae that is not related to known proteins found in bacteria. It was identified as a dominant suppressor of certain mitochondrial mutations that reduced translation of the COX2 mRNA. To explore further the function of Rsm28p, we isolated mutations in other genes that caused a synthetic respiratory defective phenotype together with rsm28D. These mutations identified three nuclear genes: IFM1, which encodes the mitochondrial translation initiation factor 2 (IF2); FMT1, which encodes the methionyl-tRNA-formyltransferase; and RMD9, a gene of unknown function. The observed genetic interactions strongly suggest that the ribosomal protein Rsm28p and Ifm1p (IF2) have similar and partially overlapping functions in yeast mitochondrial translation initiation. Rmd9p, bearing a TAP-tag, was localized to mitochondria and exhibited roughly equal distribution in soluble and membrane-bound fractions. A small fraction of the Rmd9-TAP sedimented together with presumed monosomes, but not with either individual ribosomal subunit. Thus, Rmd9 is not a ribosomal protein, but may be a novel factor associated with initiating monosomes. The poorly respiring rsm28D, rmd9-V363I double mutant did not have a strong translationdefective phenotype, suggesting that Rmd9p may function upstream of translation initiation, perhaps at the level of localization of mitochondrially coded mRNAs.

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Section: Methodsmentioning

confidence: 99%

Translation Initiation inSaccharomyces cerevisiaeMitochondria: Functional Interactions Among Mitochondrial Ribosomal Protein Rsm28p, Initiation Factor 2, Methionyl-tRNA-Formyltransferase and Novel Protein Rmd9p

et al. 2007

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“…The degradosome is a protein complex with both the 3Ј-5Ј exoribonuclease Dss1p and the RNA helicase Suv3p Dziembowski et al 1998Dziembowski et al , 2003. RNA maturation and turnover are also controlled by several RNA-stabilizing proteins and translation activator proteins that bind to the 5Ј-UTL of mitochondrial RNAs (Wiesenberger et al 1995;Wiesenberger and Fox 1997;Green-Willms et al 1998;Chen et al 1999;Islas-Osuna et al 2002, 2003. Likewise, the 55-kDa RNA dodecamer sequence-binding protein (DBP) recognizes a dodecamer sequence in 3Ј-UTRs (Li and Zassenhaus 1999).…”

Section: Introductionmentioning

confidence: 99%

Transcription and RNA-processing in fission yeast mitochondria

Schäfer¹,

Hansen²,

Lang³

2005

RNA

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We systematically examined transcription and RNA-processing in mitochondria of the petite-negative fission yeast Schizosaccharomyces pombe. Two presumptive transcription initiation sites at opposite positions on the circular-mapping mtDNA were confirmed by in vitro capping of primary transcripts with guanylyl-transferase. The major promoter (P ma ) is located adjacent to the 5-end of the rnl gene, and a second, minor promoter (P mi ) upstream from cox3. The primary 5-termini of the mature rnl and cox3 transcripts remain unmodified. A third predicted accessory transcription initiation site is within the group IIA1 intron of the cob gene (cobI1). The consensus promoter motif of S. pombe closely resembles the nonanucleotide promoter motifs of various yeast mtDNAs. We further characterized all mRNAs and the two ribosomal RNAs by Northern hybridization, and precisely mapped their 5-and 3-ends. The mRNAs have leader sequences with a length of 38 up to 220 nt and, in most instances, are created by removal of tRNAs from large precursor RNAs. Like cox2 and rnl, cox1 and cox3 are not separated by tRNA genes; instead, transcription initiation from the promoters upstream from rnl and cox3 compensates for the lack of tRNA-mediated 5-processing. The 3-termini of mRNAs and of SSU rRNA are processed at distinct, C-rich motifs that are located at a variable distance (1-15 nt) downstream from mRNA and SSU-rRNA coding regions. The accuracy of RNAprocessing at these sites is sequence-dependent. Similar 3-RNA-processing motifs are present in species of the genus Schizosaccharomyces, but not in budding yeasts that have functionally analogous A+T-rich dodecamer processing signals.

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“…To date, these approaches have identified only a subset of the total number of mitochondrial ribosomal proteins. In yeast, the eukaryote in which most of the studies were performed, only 14 proteins of the small mitochondrial ribosomal subunit have been characterized experimentally (1,6).…”

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confidence: 99%

Identification of 12 New Yeast Mitochondrial Ribosomal Proteins Including 6 That Have No Prokaryotic Homologues

Saveanu¹,

Fromont‐Racine²,

Harington³

et al. 2001

Journal of Biological Chemistry

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Mitochondrial ribosomal proteins were studied best in yeast, where the small subunit was shown to contain about 35 proteins. Yet, genetic and biochemical studies identified only 14 proteins, half of which were predictable by sequence homology with prokaryotic ribosomal components of the small subunit. Using a recently described affinity purification technique and tagged versions of yeast Ykl155c and Mrp1, we isolated this mitochondrial ribosomal subunit and identified a total of 20 proteins, of which 12 are new. For a subset of the newly described ribosomal proteins, we showed that they are localized in mitochondria and are required for the respiratory competency of the yeast cells. This brings to 26 the total number of proteins described as components of the mitochondrial small ribosomal subunit. Remarkably, almost half of the previously and newly identified mitochondrial ribosomal components showed no similarity to any known ribosomal protein. Homologues could be found, however, in predicted protein sequences from Schizosaccharomyces pombe. In more distant species, putative homologues were detected for Ykl155c, which shares conserved motifs with uncharacterized proteins of higher eukaryotes including humans. Another newly identified ribosomal protein, Ygl129c, was previously shown to be a member of the DAP-3 family of mitochondrial apoptosis mediators.In yeast mitochondria, the majority of the characterized ribosomal proteins are essential for protein synthesis (for review see Ref. 1). Homologues of about 18 of the 21 prokaryotic small ribosomal subunit proteins can be identified by similarity searches in the yeast complete genomic sequence. However, the number of ribosomal proteins is larger in the small subunit of yeast mitochondria, estimated to be 33 or 36 (2, 3).Thus far, yeast mitochondrial ribosomal proteins have been identified either by the study of mutant strains with mitochondrial dysfunction (pet mutants; for review see Ref. 4) or by direct biochemical approaches involving isolation of mitochondria, purification of mitochondrial ribosomes, and protein separation followed by microsequencing (5). Mitochondrial ribosome purification has thus far been technically difficult, because the ribosomal proteins represent only 2-3% of the mitochondrial proteins (2). To date, these approaches have identified only a subset of the total number of mitochondrial ribosomal proteins. In yeast, the eukaryote in which most of the studies were performed, only 14 proteins of the small mitochondrial ribosomal subunit have been characterized experimentally (1, 6).We were originally interested in the study of the yeast YKL155C gene because it was found in a two-hybrid exhaustive screen to interact with the Prp11 splicing factor (7). To test whether this protein was associated with splicing factors under physiological conditions, we used the recently described tandem affinity purification technique (8) that allows the isolation of protein complexes by two successive affinity purification steps under mild conditions. Instea...

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Functional Interactions between Yeast Mitochondrial Ribosomes and mRNA 5′ Untranslated Leaders

Cited by 61 publications

References 72 publications

Translation Initiation inSaccharomyces cerevisiaeMitochondria: Functional Interactions Among Mitochondrial Ribosomal Protein Rsm28p, Initiation Factor 2, Methionyl-tRNA-Formyltransferase and Novel Protein Rmd9p

Translation Initiation inSaccharomyces cerevisiaeMitochondria: Functional Interactions Among Mitochondrial Ribosomal Protein Rsm28p, Initiation Factor 2, Methionyl-tRNA-Formyltransferase and Novel Protein Rmd9p

Transcription and RNA-processing in fission yeast mitochondria

Identification of 12 New Yeast Mitochondrial Ribosomal Proteins Including 6 That Have No Prokaryotic Homologues

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