Quantification of the proteins of the bacterial ribosome using QconCAT technology

Journal of Proteome Research

Volumn 13, Issue 3, 2014, Pages 1211-1222

  Al Majdoub, Zubida M ^a,b   Carroll, Kathleen M ^a   Gaskell, Simon J ^c   Barber, Jill ^a,b  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

^c QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Bacterial ribosome; ribosome complexes; signature peptides; stoichiometry

Indexed keywords

BACTERIAL PROTEIN; GENTAMICIN; METALLOPROTEINASE; PEPTIDE; RIBOSOME PROTEIN; TRYPSIN;

ARTICLE; BIOTECHNOLOGY; COMPLEX FORMATION; CONTROLLED STUDY; ESCHERICHIA COLI; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN SYNTHESIS; QUANTITATIVE ANALYSIS; RIBOSOME; RIBOSOME SUBUNIT;

AMINO ACID SEQUENCE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION; GENETIC VECTORS; GENTAMICINS; METALLOENDOPEPTIDASES; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEIN BIOSYNTHESIS; PROTEIN ENGINEERING; PROTEIN SYNTHESIS INHIBITORS; RECOMBINANT FUSION PROTEINS; RIBOSOMAL PROTEINS; RIBOSOMES; TRYPSIN;

EID: 84896773198     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr400667h     Document Type: Article

References (30)

1. Wilson, D. N.; Nierhaus, K. H. The Weird and Wonderful World of Bacterial Ribosome Regulation Crit. Rev. Biochem. Mol. Biol 2007, 42, 187-219
2. Poehlsgaard, J.; Douthwaite, S. The Bacterial Ribosome as a Target for Antibiotics Nat. Rev. Microbiol 2005, 3, 870-881
3. Wimberley, B. T.; Brodersen, D. E.; Clemons, W. M., Jr.; Morgan-Warren, R. J.; Carter, A. P.; Vonrhein, C.; Hartsch, T.; Ramakrishnan, V. Structure of the 30S Ribosomal Subunit Nature 2000, 407, 327-339
4. Ban, N.; Nissen, P.; Hansen, J.; Moore, P. B.; Steitz, T. A. The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution Science 2000, 289, 905-920
5. Schleunzen, F.; Tocilj, A.; Zarivach, R.; Harms, J.; Gluehmann, M.; Janell, D.; Bashan, A.; Bartels, H.; Agmon, I.; Franceschi, F.; Yonath, A. Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Angstroms Resolution Cell 2000, 102, 615-623
6. Usary, J.; Champney, W. S. Erythromycin Inhibition of 50S Ribosomal Subunit Formation in Escherichia coli Cells Mol. Microbiol. 2001, 40, 951-962
7. Mehta, R.; Champney, W. S. 30S Ribosomal Subunit Assembly Is a Target for Inhibition by Aminoglycosides in Escherichia coli Antimicrob. Agents Chemother. 2002, 46, 1546-1549
8. Ong, S. E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; Mann, M. Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics Mol. Cell. Proteomics 2002, 1, 376-386
9. Multiplex Protein Quantitation using iTRAQ® Reagents-8plex. http://tools.lifetechnologies.com/content/sfs/manuals/cms-049786.pdf (accessed October 13, 2009).
10. Kirkpatrick, D. S.; Gerber, S. A.; Gygi, S. P. The Absolute Quantification Strategy: A General Procedure for the Quantification of Proteins and Post-Translational Modifications Methods 2005, 35, 265-273
11. Beynon, R. J.; Doherty, R. J.; Pratt, J. M.; Gaskell, S. J. Multiplexed Absolute Quantification in Proteomics Using Artificial QCAT Proteins of Concatenated Signature Peptides Nat. Methods 2005, 2, 587-589
12. Protein Prospector; University of California at San Francisco: San Francisco, CA; http://prospector.ucsf.edu/prospector/mshome.htm.
13. Wierenga, S. K.; Zocher, M. J.; Mirus, M. M.; Conrads, T. P.; Goshe, M. B.; Veenstra, T. D. A Method to Evaluate Tryptic Digestion Efficiency for High-Throughput Proteome Analyses Rapid Commun. Mass Spectrom. 2002, 16, 1404-1408
14. Mann, M. In solution digest for mass spectrometry (MS) analysis; RUBICON Protocols Database.
15. Nierhaus, K. H. Reconstitution of Ribosomes. In Ribosomes and Protein Synthesis: A Practical Approach; Spedding, G., Ed.; Oxford University Press: New York, 1990; Chapter 8.
16. Carroll, K. M.; Simpson, D. M.; Eyers, C. E.; Knight, C. G.; Brownridge, P.; Dunn, W. B.; Winder, C. L.; Lanthaler, K.; Pir, P.; Malys, N.; Kell, D.b.; Oliver, S. G.; Gaskell, S. J.; Beynon, R. J. Absolute Quantification of the Glycolytic Pathway in Yeast: Deployment of a Complete QconCAT Approach Mol. Cell. Proteomics 2011, 10, M111.007633-1-M111.007633-15
17. Swainston, N.; Jameson, D.; Carroll, K. A QconCAT Informatics Pipeline for the Analysis, Visualization and Sharing of Absolute Quantitative Proteomics Data Proteomics 2011, 11, 329-333
18. Savitzky, A.; Golay, M. J. E. Smoothing and Differentiation of Data by Simplified Least Squares Procedures Anal. Chem. 1964, 36, 1627-1639
19. Al-Majdoub, Z. M. Quantification of Ribosomal Proteins by Mass Spectrometry: An Approach to Drug Target Identification. Ph.D. Thesis, The University of Manchester, May 2013, pp 93-104.
20. Washburn, M. P.; Wolters, D.; Yates, J. R., III Large-Scale Analysis of the Yeast Proteome by Multidimensional Protein Identification Technology Nat. Biotechnol. 2001, 19, 242-247
21. Eyers, C. E.; Simpson, D. M.; Wong, S. C.; Beynon, R. J.; Gaskell, S. J. QCAL-a Novel Standard for Assessing Instrument Conditions for Proteome Analysis J. Am. Soc. Mass Spectrom. 2008, 19, 1275-1280
22. Warwood, S.; Mohammed, S.; Cristea, I. M.; Evans, C.; Whetton, A. D.; Gaskell, S. J. Guanidination Chemistry for Qualitative and Quantitative Proteomics Rapid Commun. Mass Spectrom. 2006, 20, 3245-3256
23. Beardsley, R. L.; Reilly, J. P. Optimization of Guanidination Procedure for MALDI Mass Mapping Anal. Chem. 2002, 74, 1884-1890
24. Al-Majdoub, Z. M.; Owenseni, A.; Gaskell, S. J.; Barber, J. Effects of Gentamicin on the Proteomes of Aerobic and Oxygen-Limited Escherichia coli J. Med. Chem. 2013, 56, 2904-2910
25. Van Knippenberg, P. H.; Hooykaas, P. J.; Van Duin, J. The Stoichiometry of E. coli Ribosomal Protein S1 on in Vivo and in Vitro Polyribosomes FEBS Lett. 1974, 41, 323-326
26. Volkmer, B.; Heinemann, M. Condition-dependent cell volume and concentration of Escherichia coli to facilitate data conversion for systems biology modelling PLoS ONE 2011, 6, e23126-1-e23126-6
27. Chen, S. S.; Williamson, J. R. Characterization of the Ribosome Biogenesis Landscape in E. coli using Quantitative Mass Spectrometry J. Mol. Biol. 2013, 425, 767-779
28. Gerber, S. A.; Rush, J.; Stemman, O.; Kirschner, M. W.; Gygi, S. P. Absolute Quantification of Proteins and Phosphoproteins from Cell Lysates by Tandem MS Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 6940-6945
29. British Society for Cell Biology Ribosome Page. http://www.bscb.org/?url= softcell/ribo (accessed December 6, 2013).
30. Russell, M. R.; Achour, B.; McKenzie, E. A.; Lopez, R.; Harwood, M. D.; Rostami-Hodjegan, A.; Barber, J. Alternative fusion protein strategies to express recalcitrant QconCAT proteins for quantitative proteomics of human drug metabolizing enzymes and transporters J. Proteome Res. 2013, 12, 5934-5942