Identification and Characterization of the Genes for Mitochondrial Ribosomal Proteins of <i>Saccharomyces Cerevisiae</i>

Kitakawa, Madoka; Graack, Hanns‐Rüdiger; Grohmann, Lutz; Goldschmidt-Reisin, Sabine; Herfurth, Elke; Wittmann‐Liebold, Brigitte; Nishimura, Takehiro; Isono, Katsumi

doi:10.1111/j.1432-1033.1997.t01-2-00449.x

Cited by 39 publications

(52 citation statements)

References 34 publications

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“…Most of the identified small subunit ribosomal proteins were highly basic (pI > 9), as are their homologs in other sources, reflecting their interactions with the ribosomal RNA [32][33][34][35]. Mitochondrial ribosomal proteins, as a rule, are significantly longer than their eubacterial counterparts [31][32][33][34][35][36][37][38].…”

Section: Homologs Of Small Subunit Ribosomal Proteinsmentioning

confidence: 99%

“…Mitochondrial ribosomal proteins, as a rule, are significantly longer than their eubacterial counterparts [31][32][33][34][35][36][37][38]. This difference is due to the presence of N-or C-terminal extensions which were proposed to serve structural and/or functional compensation for the missing stemloop structures of the ribosomal RNAs [36], although this idea was not supported by the cryo-EM analysis of bovine mitoribosomes [31].…”

Section: Homologs Of Small Subunit Ribosomal Proteinsmentioning

confidence: 99%

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Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae

Maslov

Spremulli

Sharma

et al. 2007

Molecular and Biochemical Parasitology

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A novel type of ribonucleoprotein (RNP) complex has been described from the kinetoplastmitochondria of Leishmania tarentolae. The complex, termed the 45S SSU*, contains the 9S small subunit rRNA but does not contain the 12S large subunit rRNA. This complex is the most stable and abundant mitochondrial RNP complex present in Leishmania. As shown by tandem mass spectrometry, the complex contains at least 39 polypeptides with a combined molecular mass of almost 2.1 MDa. These components include several homologs of small subunit ribosomal proteins (S5, S6, S8 S9, S11, S15, S16, S17, S18, MRPS29); however, most of the polypeptides present are unique. Only a few of them show recognizable motifs, such as protein-protein (coiled-coil, Rhodanese) or protein-RNA (pentatricopeptide repeat) interaction domains. A cryo-electron microscopy examination of the 45S SSU* fraction reveals that 27% of particles represent SSU homodimers arranged in a head-to-tail orientation, while the majority of particles are clearly different and show an asymmetric bilobed morphology. Multiple classes of two-dimensional averages were derived for the asymmetrical particles, probably reflecting random orientations of the particles and difficulties in correlating these views with the known projections of ribosomal complexes. One class of the two-dimensional averages shows an SSU moiety attached to a protein mass or masses in a monosome-like appearance. The combined mass spectrometry and electron microscopy data thus indicate that the majority 45S SSU* particles represents a heterodimeric complex in which the SSU Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access

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Section: Homologs Of Small Subunit Ribosomal Proteinsmentioning

confidence: 99%

Section: Homologs Of Small Subunit Ribosomal Proteinsmentioning

confidence: 99%

Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae

Maslov

Spremulli

Sharma

et al. 2007

Molecular and Biochemical Parasitology

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“…49 Mrpl17p and Mrpl19p are mitochondrial ribosomal proteins of the large ribosomal subunit. 50 YDR116C has similarity to prokaryotic ribosomal protein L1 and is a probable component of mitochondrial ribosomes, as its mRNA abundance in DNA microarray analysis shows the same change patterns to a variety of drug treatments and mutations, as do many mitochondrial proteins. 51 The pro®le relationship between J0544 and these four mitochondrial ORFs suggests that J0544 may be involved in mitochondrial processes, perhaps as an activator or some other type of component.…”

Section: New Suggested Relationshipmentioning

confidence: 99%

Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions

Qian

Dolled‐Filhart

Lin

et al. 2001

Journal of Molecular Biology

171

146

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The complexity of biological systems provides for a great diversity of relationships between genes. The current analysis of whole-genome expression data focuses on relationships based on global correlation over a whole time-course, identifying clusters of genes whose expression levels simultaneously rise and fall. There are, of course, other potential relationships between genes, which are missed by such global clustering. These include activation, where one expects a time-delay between related expression pro®les, and inhibition, where one expects an inverted relationship. Here, we propose a new method, which we call local clustering, for identifying these time-delayed and inverted relationships. It is related to conventional gene-expression clustering in a fashion analogous to the way local sequence alignment (the Smith-Waterman algorithm) is derived from global alignment (Needleman-Wunsch). An integral part of our method is the use of random score distributions to assess the statistical signi®cance of each cluster. We applied our method to the yeast cellcycle expression dataset and were able to detect a considerable number of additional biological relationships between genes, beyond those resulting from conventional correlation. We related these new relationships between genes to their similarity in function (as determined from the MIPS scheme) or their having known protein-protein interactions (as determined from the large-scale two-hybrid experiment); we found that genes strongly related by local clustering were considerably more likely than random to have a known interaction or a similar cellular role. This suggests that local clustering may be useful in functional annotation of uncharacterized genes. We examined many of the new relationships in detail. Some of them were already well-documented examples of inhibition or activation, which provide corroboration for our results. For instance, we found an inverted expression pro®le relationship between genes YME1 and YNT20, where the latter has been experimentally documented as a bypass suppressor of the former. We also found new relationships involving uncharacterized yeast genes and were able to suggest functions for many of them. In particular, we found a timedelayed expression relationship between J0544 (which has not yet been functionally characterized) and four genes associated with the mitochondria. This suggests that J0544 may be involved in the control or activation of mitochondrial genes. We have also looked at other, less extensive datasets than the yeast cell-cycle and found further interesting relationships. Our clustering program and a detailed website of clustering results is available at

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“…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).…”

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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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Identification and Characterization of the Genes for Mitochondrial Ribosomal Proteins of Saccharomyces Cerevisiae

Cited by 39 publications

References 34 publications

Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae

Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae

Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions

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

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