The Large Subunit of the Mammalian Mitochondrial Ribosome

Koc, Emine C.; Burkhart, William; Blackburn, Kevin; Moyer, Mary B.; Schlatzer, Daniela; Moseley, Arthur; Spremulli, Linda L.

doi:10.1074/jbc.m106510200

Cited by 243 publications

(105 citation statements)

References 45 publications

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“…Here, we characterize one cisplatin-inducible gene, MRP S11, whose product, MRP S11, is a component of the ribosomal small subunit and binds to 12S rRNA. 12 MRP S11 appears to have RNA binding but not DNA binding activity. We have isolated the promoter region of MRP S11 in order to identify its transcriptional activators.…”

mentioning

confidence: 90%

ZNF143 activates gene expression in response to DNA damage and binds to cisplatin‐modified DNA

Ishiguchi

Izumi

Torigoe

et al. 2004

Intl Journal of Cancer

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We have identified a cisplatin-inducible gene, the mitochondrial ribosomal protein S11 (MRP S11) gene, by means of mRNA differential display. Functional analysis of the MRP S11 promoter showed that a Staf binding site in the promoter is required for both basal promoter activity and cisplatin-inducible activity. We also found that Cisplatin is a widely used anticancer agent, and DNA damage is believed to be the main basis of the antitumor effect of cisplatin. Since cisplatin resistance is a major obstacle to the treatment of solid tumors, understanding the molecular basis of the DNA damage response and of cisplatin resistance is important for clinical protocols. Cisplatin resistance is thought to involve several mechanisms, including increased drug efflux, the presence of cellular thiols, increased nucleotide excision repair activity and decreased mismatch repair activity. [1][2][3][4] In addition, several mechanisms are thought to contribute to the DNA damage response associated with cisplatin resistance. To understand fully these molecular mechanisms, it is desirable to identify and characterize all the transcription factors that are activated by DNA damage. We have previously shown that transcription factors such as Y-box binding protein (YB-1) and the CCAAT-binding transcription factor 2 (CTF2) are overexpressed in human cancer cell lines resistant to cisplatin. 5,6 YB-1 has been shown to bind preferentially to cisplatin-modified DNA 5 and is activated by nuclear translocation and by transcriptional mechanisms. Oct1 participates in the cellular response to DNA damage, 7,8 and its induction involves posttranscriptional mechanisms. Both c-Myc and AP-1 are also activated and involved in cellular responses to cisplatin. 8 One cisplatininducible cDNA clone has been shown to encode the vacuolar H ϩ -ATPase subunit c (ATP6L), 9,10 and analysis of its expression revealed that both Sp1 and Oct1 are critical for its activation by anticancer agents. 11 In order to identify novel mechanisms involved in the DNA damage response, we have used differential display to compare gene expression between control and cisplatin-treated cells. Here, we characterize one cisplatin-inducible gene, MRP S11, whose product, MRP S11, is a component of the ribosomal small subunit and binds to 12S rRNA. 12 MRP S11 appears to have RNA binding but not DNA binding activity. We have isolated the promoter region of MRP S11 in order to identify its transcriptional activators. Functional analysis revealed a critical Staf binding site in the core of the promoter. The zinc finger transcription factor, Staf, originally identified in the frog, is involved in transcriptional regulation of snRNA type and mRNA promoters transcribed either by RNA polymerase II or III. 13 Two human homologues of Staf, ZNF 76 and ZNF 143, have been isolated. 14 Here we show that activation of the transcriptional activator ZNF 143 upregulates the transcription of MRP S11. We present evidence that ZNF 143, but not ZNF 76, is induced by DNA damage. We further demonstrate that ZN...

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mentioning

confidence: 90%

ZNF143 activates gene expression in response to DNA damage and binds to cisplatin‐modified DNA

Ishiguchi

Izumi

Torigoe

et al. 2004

Intl Journal of Cancer

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“…Despite advances in software and instrumentation that have enabled rapid acquisition of very large data sets, the extreme complexity of proteomic samples typically leads to peptides being introduced into the mass spectrometer at a rate far exceeding that of MS/MS data acquisition [14,15]. This results in an under sampling of the proteome at least at the peptide level, and most often also at the protein level.…”

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confidence: 99%

“…Proteins synthesized in mammalian mitochondria are incorporated into complexes that are responsible for oxidative phosphorylation and the synthesis of the majority of the ATP in these organisms. The human 39S subunit has been reported to contain at least 48 distinct proteins, with over half of these being homologous to ribosomal proteins from other species [15]. The application of complementary ionization techniques in the analysis of a tryptic digest of the bovine 39S subunit has led to the identification of 51 ribosomal proteins.…”

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confidence: 99%

Exploiting the complementary nature of LC/MALDI/MS/MS and LC/ESI/MS/MS for increased proteome coverage

Bodnar

Blackburn

Krise

et al. 2003

J. Am. Soc. Mass Spectrom.

175

127

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The goal of this work was to evaluate the improvement in proteome coverage of complex protein mixtures gained by analyzing samples using both LC/ESI/MS/MS and LC/MALDI/ MS/MS. Parallel analyses of a single sample were accomplished by interfacing a Probot fractionation system with a nanoscale LC system. The Probot was configured to perform a post-column split such that a fraction (20%) of the column effluent was sent for on-line LC/ESI/MS/MS data acquisition, and the majority of the sample (80%) was mixed with a matrix solution and deposited onto the MALDI target plate. The split-flow approach takes advantage of the concentration sensitive nature of ESI and provides sufficient quantity of sample for MALDI/MS/MS. Hybrid quadrupole time-of-flight mass spectrometers were used to acquire LC/ESI/MS/MS data and LC/MALDI/MS/MS data from a tryptic digest of a preparation of mammalian mitochondrial ribosomes. The mass spectrometers were configured to operate in a data dependent acquisition mode in which precursor ions observed in MS survey scans are automatically selected for interrogation by MS/MS. This type of acquisition scheme maximizes the number of peptide fragmentation spectra obtained and is commonly referred to as shotgun analysis. While a significant degree of overlap (63%) was observed between the proteins identified in the LC/ESI/MS/MS and LC/MALDI/MS/MS data sets, both unique peptides and unique proteins were observed by each method. These results demonstrate that improved proteome coverage can be obtained using a combination of these ionization techniques. (J Am Soc Mass Spectrom 2003, 14, 971-979)

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“…or corresponded to ESTs. Sufficient MS/MS data was acquired for the identification of the full complement of the expected bovine 28S MRPs [23,[27][28][29], based on either sequence homology to known MRPs from other species, or the in-silico assembly of the full length protein sequence from overlapping ESTs.…”

Section: Variable Flow Nanoscale Lc/ms/ms Analysis Of Mitochondrial Rmentioning

confidence: 99%

A novel Interface for variable flow nanoscale LC/MS/MS for improved proteome coverage

Vissers¹,

Blackburn

Moseley

2002

J. Am. Soc. Mass Spectrom.

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A variable flow "peak trapping" liquid chromatography (LC) interface has been developed for the coupling of nanoscale LC to electrospray ionization mass spectrometry (ESI-MS). The presented peak trapping LC interface allows for the extended analysis time of co-eluting compounds and has been employed for the identification of proteins via tandem mass spectrometry (MS/MS). The variable flow process can be controlled either manually or in a completely automated manner where the mass spectrometer status determines the status of the variable flow interface. When the mass spectrometer operates in MS survey mode, the interface is operated in a so-called "high-flow" mode. Alternatively, the interface is operated in a "low-flow" mode during MS/MS analysis. In the "high-flow" mode of the variable flow process the column flow rate is typically around 200 nL/min, whereas in the "low-flow" mode the column effluent is introduced into the source of the mass spectrometer at 25 nL/min. In addition to the flow reduction during MS/MS analysis, the gradient is paused to preserve the peptide separation on the analytical nanoscale LC column. T he field of protein mass spectrometry has undergone a major paradigm shift over the past several years, moving from the analysis of individual proteins to the analysis of total digests of complex protein mixtures (also know as shotgun proteomics). The development of shotgun proteomics by Yates [1-3] couples nanoscale LC for peptide analysis [4,5], automated MS to MS/MS data acquisition software and hardware on modern tandem mass spectrometers [6], along with automated database searching software of modern search engines [7,8]. Shotgun proteomics has significantly increased the information content of protein mass spectrometry experiments, while at the same time significantly reducing the total analysis time required to analyze a complex protein mixture. Improvements in sample sensitivity and proteome coverage have been observed with this approach, compared to the "traditional" approach of using 2-D gels to separate the proteins, followed by in-gel digestion and analysis of the resulting peptides by mass spectrometry [3]. The shift in approach from the MS and MS/MS analysis of individual proteins to the analysis of complex mixtures of proteins has lead to the most significant figure of merit in proteomic analysis becoming the extent of proteome coverage obtained. Analytical methods that increase the coverage of the proteins in a sample will increase the impact of proteomics on biology.For a typical 50 kD protein, one would expect to have on the order of 40 -50 tryptic peptides. Characterization of the complex mixture of peptides resulting from a total digest of a complex protein mixture requires the mass spectrometric analysis of hundreds to many thousands of peptides. Clearly, the MS and MS/MS analysis of a sample comprised of hundreds to thousands of proteins is challenging. Modern mass spectrometers with data dependent scanning software are capable of acquiring MS and MS/MS data from many hund...

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The Large Subunit of the Mammalian Mitochondrial Ribosome

Cited by 243 publications

References 45 publications

ZNF143 activates gene expression in response to DNA damage and binds to cisplatin‐modified DNA

ZNF143 activates gene expression in response to DNA damage and binds to cisplatin‐modified DNA

Exploiting the complementary nature of LC/MALDI/MS/MS and LC/ESI/MS/MS for increased proteome coverage

A novel Interface for variable flow nanoscale LC/MS/MS for improved proteome coverage

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