A strategy for identifying gel-separated proteins in sequence databases by MS alone

Shevchenko, A.R.; Wilm, Matthias; Vorm, Ole; Jensen, O.N.; Podtelejnikov, Alexandre V.; Neubauer, Gitte; Shevchenko, Al.; Mortensen, Poul Erik; Mann, Matthias

doi:10.1042/bst0240893

Cited by 226 publications

(158 citation statements)

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“…Proteins were separated on a 4-15% gradient polyacrylamide gel (Bio-Rad, Hercules, CA), and bands were excised and processed for peptide mass fingerprinting as described (51). Samples were analyzed by MALDI-TOF MS using a Perseptive Voyager-DE (Stanford Protein and Nucleic Acid Facility, Stanford, CA).…”

Section: Msmentioning

confidence: 99%

Proteomic identification of tmRNA substrates

Hong

Lessner

Mahen

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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The tmRNA-SmpB system releases ribosomes stalled on truncated mRNAs and tags the nascent polypeptides to target them for proteolysis. In many species, mutations that disrupt tmRNA activity cause defects in growth or development. In Caulobacter crescentus cells lacking tmRNA activity there is a delay in the initiation of DNA replication, which disrupts the cell cycle. To understand the molecular basis for this phenotype, 73 C. crescentus proteins were identified that are tagged by tmRNA under normal growth conditions. Among these substrates, proteins involved in DNA replication, recombination, and repair were overrepresented, suggesting that misregulation of these factors in the absence of tmRNA activity might be responsible for the delay in initiation of DNA replication. Analysis of the tagging sites within these substrates revealed a conserved nucleotide motif 5 of the tagging site, which is required for wild-type tmRNA tagging.bacterial cell cycle ͉ proteolysis ͉ trans-translation

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Section: Msmentioning

confidence: 99%

Proteomic identification of tmRNA substrates

Hong

Lessner

Mahen

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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“…Tom5 was prepared for mass spectrometry by in-gel digestion according to procedures described previously (25)(26)(27). Peptides were dried and stored at Ϫ20°C.…”

Section: Strains and Growthmentioning

confidence: 99%

Role of Tom5 in Maintaining the Structural Stability of the TOM Complex of Mitochondria

Schmitt

Ahting²,

Eichacker

et al. 2005

Journal of Biological Chemistry

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Transport of nuclear encoded proteins into mitochondria is mediated by multisubunit translocation machineries in the outer and inner membranes of mitochondria. The TOM complex contains receptor and pore components that facilitate the recognition of preproteins and their transfer through the outer membrane. In addition, the complex contains a set of small proteins. Tom7 and Tom6 have been found in Neurospora and yeast, Tom5 has been found so far only in the latter organism. In the present study, we identified Neurospora Tom5 and analyzed its function in comparison to yeast Tom5, which has been proposed to play a role as a receptor-like component. Neurospora Tom5 crosses the outer membrane with its carboxyl terminus facing the intermembrane space like the other small Tom components. The temperature-sensitive growth phenotype of the yeast TOM5 deletion was rescued by overexpression of Neurospora Tom5. On the other hand, Neurospora cells deficient in tom5 did not exhibit any defect in growth. The structural stability of TOM complexes from cells devoid of Tom5 was significantly altered in yeast but not in Neurospora. The efficiency of protein import in Neurospora mitochondria was not affected by deletion of tom5, whereas in yeast it was reduced as compared with wild type. We conclude that the main role of Tom5, rather than being a receptor, is maintaining the structural integrity of the TOM complex.

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“…Samples were S-alkylated with 20 mM iodoacetamide at 25°C in the dark for 30 min and vacuum dried. In-gel digestion of excised bands with trypsin (sequencing grade, Promega) and extraction of peptides were done according to Shevchenko et al (44).…”

Section: Fig 1 Induction Of Mnsod Gene Transcription After Treatmenmentioning

confidence: 99%

Identification of Nucleophosmin as an NF-κB Co-activator for the Induction of the Human SOD2 Gene

Dhar

Lynn

Daosukho

et al. 2004

Journal of Biological Chemistry

100

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A strategy for identifying gel-separated proteins in sequence databases by MS alone

Cited by 226 publications

References 1 publication

Proteomic identification of tmRNA substrates

Proteomic identification of tmRNA substrates

Role of Tom5 in Maintaining the Structural Stability of the TOM Complex of Mitochondria

Identification of Nucleophosmin as an NF-κB Co-activator for the Induction of the Human SOD2 Gene

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