Proteomic Analysis of the Mammalian Mitochondrial Ribosome

Suzuki, Tsutomu; Terasaki, Maki; Takemoto-Hori, Chie; Hanada, Takao; Ueda, Takuya; Wada, Akira; Watanabe, Kimitsuna

doi:10.1074/jbc.m103236200

Cited by 137 publications

(41 citation statements)

References 66 publications

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“…We have not observed any peptides from this small protein in 28 S or 39 S subunit preparations. This group has further reported that a subunit (CI-B14) of NADH-ubiquinone oxidoreductase (Complex I) is present in preparations of 55 S ribosomes (36). However, we have not observed peptides from this protein in either 28 S or 39 S subunit preparations.…”

Section: The New Classes Of Ribosomal Proteins With Homologs In Yeastcontrasting

confidence: 41%

The Large Subunit of the Mammalian Mitochondrial Ribosome

Koc¹,

Burkhart²,

Blackburn³

et al. 2001

Journal of Biological Chemistry

245

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Identification of all the protein components of the large subunit (39 S) of the mammalian mitochondrial ribosome has been achieved by carrying out proteolytic digestions of whole 39 S subunits followed by analysis of the resultant peptides by liquid chromatography and mass spectrometry. Peptide sequence information was used to search the human EST data bases and complete coding sequences were assembled. The human mitochondrial 39 S subunit has 48 distinct proteins. Twenty eight of these are homologs of the Escherichia coli 50 S ribosomal proteins L1, L2, L3 , L4, L7/L12, L9, L10, L11, L13, L14, L15, L16, L17, L18, L19, L20, L21, L22, L23, L24, L27, L28, L30, L32, L33, Mammalian mitochondria are responsible for the synthesis of 13 proteins localized in the inner membrane. These proteins are components of the oligomeric complexes essential for oxidative phosphorylation and, hence, for the synthesis of about 90% of the ATP in eukaryotic organisms. The 55 S mammalian mitochondrial ribosomes consists of small (28 S) and large (39 S) subunits (1). In contrast to bacterial ribosomes which are about 65% RNA, mammalian mitochondrial ribosomes are only 33% RNA. The low percentage of RNA in these ribosomes reflects a reduction in the size of the rRNA and a compensating increase in the number of ribosomal proteins. For example, the small subunit of the mammalian mitochondrial ribosome contains a 12 S rRNA (about 950 nucleotides) and an estimated 29 proteins (2). In contrast, the Escherichia coli 30 S subunit has a 16 S rRNA (1542 nucleotides in length) and 21 proteins (3). The large subunit of the mammalian mitochondrial ribosome contains a 16 S rRNA (about 1560 nucleotides) and about 50 proteins (4, 5).The identification of proteins in mammalian mitochondrial ribosomes has been challenging due to their low abundance. Recently 60 mammalian mitochondrial ribosomal proteins, 31 proteins from the large subunit and 29 proteins from the small subunit, have been characterized by different laboratories (2, 6 -14). The identification of these proteins used two approaches. The traditional approach was to separate the proteins on two-dimensional gels or high performance liquid chromatography followed by sequence analysis using Edman chemistry or mass spectrometry (MS). More recently, proteins present in the 28 S subunit have been characterized by proteolytic digestion of whole subunits. Sequence information on the peptides present in this complex mixture was obtained by liquid chromatography coupled to tandem mass spectrometry (LC/MS/MS).1 This strategy allowed the identification of 28 proteins of the small subunit including 14 proteins that had not previously been identified (2). In the present study, we have extended this approach to the 39 S subunit. In addition to direct analysis of 39 S digests by LC/MS, aliquots of the total digest were fractionated prior to reversed-phase LC/MS analysis to maximize the number of peptides sequenced. In the first approach, a portion of the total digest was fractionated by affinity selection ...

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Section: The New Classes Of Ribosomal Proteins With Homologs In Yeastcontrasting

confidence: 41%

The Large Subunit of the Mammalian Mitochondrial Ribosome

Koc¹,

Burkhart²,

Blackburn³

et al. 2001

Journal of Biological Chemistry

245

View full text Add to dashboard Cite

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“…An intramitochondrial pool of DAP3 apparently operates as a subunit of the mitochondrial ribosome, presumably involved in the translation of mitochondria genome-derived transcripts (23)(24)(25), whereas an extramitochondrial pool of DAP3 participates in apoptosis signaling within the extrinsic pathway (5-7). Unlike cytochrome c, however, there is no evidence thus far that DAP3 must be released from mitochondria to perform its cell death function (10).…”

Section: Discussionmentioning

confidence: 99%

Functional Role of Death-associated Protein 3 (DAP3) in Anoikis

Miyazaki

Shen

Fujikura

et al. 2004

Journal of Biological Chemistry

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“…In human mitochondria, only 42 of 54 E. coli r-protein orthologues and also many mitochondria-specific r-proteins are detected (O'Brien, 2003). Such mitochondria-specific rproteins appear to be involved in ribosome-specific functions besides translation, such as the involvement of DAP3 in apoptosis (Suzuki et al, 2001a).…”

Section: Review 2002mentioning

confidence: 99%

Proteomic study of the Bacillus subtilis ribosome: Finding of zinc-dependent replacement for ribosomal protein L31 paralogues

Nanamiya

Kawamura

Kosono

2006

J. Gen. Appl. Microbiol.

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The ribosome is a universal molecular machinery of translation comprising three kinds of ribosomal RNA (rRNA) and many ribosomal proteins (r-proteins). The functional domains of the ribosome, which are involved in the decoding of genetic information in messenger RNA and formation of peptide bonds, consist entirely of rRNAs (reviewed in Ramakrishnan, 2002). As rRNAs are subjected to strong selective pressure and are highly conserved, they have been used as a reference molecule in phylogeny. In contrast, r-proteins show more diversity in their sequences and composition, compared to rRNAs.Recent development of genomics and proteomics has enabled an examination of r-protein genes in prokaryotic, eukaryotic and organelle genomes. A recent comprehensive study of ribosomal genes in completed genomes revealed 57 r-protein families in the bacterial domain, 68 in the archaeal domain and 78 in the eukaryotic domain (Lecompte et al., 2002 Recent advanced studies of genomics and proteomics have revealed the variation and diversity of ribosomal proteins (r-proteins) in different organisms and organelles. Radical free and highly reducing (RFHR) two-dimensional (2-D) electrophoresis is known to be powerful for separating ribosomal proteins that are usually small and basic, and not separated well by standard 2-D electrophoresis. Using the RFHR method, we investigated the protein profile of the Bacillus subtilis ribosomes by a proteomic approach. We found that two L31 paralogue proteins (RpmE and YtiA) showed different temporal expression patterns in the ribosomes. The RpmE protein, which is an L31 variant with a Zn-binding motif, binds one zinc ion at the motif, which is required for stabilization of the protein in the cell. On the other hand, the expression of the ytiA gene, which encodes another L31 variant (YtiA) without the Zn-binding motif, is negatively controlled by the zinc-specific transcriptional repressor Zur and is likely induced by zinc starvation. This article reviews the recent findings that replacement of two types of L31 proteins in the ribosome is controlled by the intracellular zinc concentration.

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Proteomic Analysis of the Mammalian Mitochondrial Ribosome

Cited by 137 publications

References 66 publications

The Large Subunit of the Mammalian Mitochondrial Ribosome

The Large Subunit of the Mammalian Mitochondrial Ribosome

Functional Role of Death-associated Protein 3 (DAP3) in Anoikis

Proteomic study of the Bacillus subtilis ribosome: Finding of zinc-dependent replacement for ribosomal protein L31 paralogues

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