Home LiteratureArticle Details
PMID: 12177431 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 99 ·No. 17 ·2002-08-20 ·Pages 11049-54

Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD

Abstract

Understanding biological systems and the roles of their constituents is facilitated by the ability to make quantitative, sensitive, and comprehensive measurements of how their proteome changes, e.g., in response to environmental perturbations. To this end, we have developed a high-throughput methodology to characterize an organism's dynamic proteome based on the combination of global enzymatic digestion, high-resolution liquid chromatographic separations, and analysis by Fourier transform ion cyclotron resonance mass spectrometry. The peptides produced serve as accurate mass tags for the proteins and have been used to identify with high confidence >61% of the predicted proteome for the ionizing radiation-resistant bacterium Deinococcus radiodurans. This fraction represents the broadest proteome coverage for any organism to date and includes 715 proteins previously annotated as either hypothetical or conserved hypothetical.

MeSH Terms
Bacteria/enzymology,genetics Bacterial Proteins/genetics Capillary Action Chromosome Mapping DNA-Directed RNA Polymerases/genetics Kinetics Proteome Rec A Recombinases/genetics Trypsin
Chemicals
Bacterial Proteins Proteome Rec A Recombinases DNA-Directed RNA Polymerases Trypsin
Authors & Affiliations
22 authors, click to expand affiliations / ORCID
Lipton Mary S
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99352, USA.
Pasa-Tolic' Ljiljana
Anderson Gordon A
Anderson David J
Auberry Deanna L
Battista John R
Daly Michael J
Fredrickson Jim
Hixson Kim K
Kostandarithes Heather
Masselon Christophe
Markillie Lye Meng
Moore Ronald J
Romine Margaret F
Shen Yufeng
Stritmatter Eric
Tolic' Nikola
Udseth Harold R
Venkateswaran Amudhan
Wong Kwong-Kwok
Zhao Rui
Smith Richard D
References (42)
42 references, click to expand
  1. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
    Nucleic Acids Res. 1987 Feb 11;15(3):1281-95 PMID: 3547335
  2. Physiologic determinants of radiation resistance in Deinococcus radiodurans.
    Appl Environ Microbiol. 2000 Jun;66(6):2620-6 PMID: 10831446
  3. Expression of recA in Deinococcus radiodurans.
    J Bacteriol. 1996 Jan;178(1):130-5 PMID: 8550406
  4. High-throughput peptide identification from protein digests using data-dependent multiplexed tandem FTICR mass spectrometry coupled with capillary liquid chromatography.
    Anal Chem. 2001 Jul 15;73(14):3312-22 PMID: 11476231
  5. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry.
    Nature. 1996 Feb 1;379(6564):466-9 PMID: 8559255
  6. High-throughput proteomics using high-efficiency multiple-capillary liquid chromatography with on-line high-performance ESI FTICR mass spectrometry.
    Anal Chem. 2001 Jul 1;73(13):3011-21 PMID: 11467548
  7. Engineering radiation-resistant bacteria for environmental biotechnology.
    Curr Opin Biotechnol. 2000 Jun;11(3):280-5 PMID: 10851141
  8. Prokaryotic DNA polymerase I: evolution, structure, and "base flipping" mechanism for nucleotide selection.
    J Mol Biol. 2001 May 18;308(5):823-37 PMID: 11352575
  9. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels.
    Anal Chem. 1996 Mar 1;68(5):850-8 PMID: 8779443
  10. Protection of Escherichia coli cells against the lethal effects of ultraviolet and x irradiation by prior x irradiation: a genetic and physiological study.
    Photochem Photobiol. 1976 Dec;24(6):515-23 PMID: 798210
  11. Utility of accurate mass tags for proteome-wide protein identification.
    Anal Chem. 2000 Jul 15;72(14):3349-54 PMID: 10939410
  12. Fourier transform ion cyclotron resonance mass spectrometry: a primer.
    Mass Spectrom Rev. 1998 Jan-Feb;17(1):1-35 PMID: 9768511
  13. In vivo damage and recA-dependent repair of plasmid and chromosomal DNA in the radiation-resistant bacterium Deinococcus radiodurans.
    J Bacteriol. 1994 Jun;176(12):3508-17 PMID: 8206827
  14. Genetic characterization of forty ionizing radiation-sensitive strains of Deinococcus radiodurans: linkage information from transformation.
    J Bacteriol. 1995 Sep;177(18):5232-7 PMID: 7665511
  15. ESI-FTICR mass spectrometry employing data-dependent external ion selection and accumulation.
    J Am Soc Mass Spectrom. 2002 Feb;13(2):144-54 PMID: 11838018
  16. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.
    Science. 1999 Nov 19;286(5444):1571-7 PMID: 10567266
  17. Measuring gene expression by quantitative proteome analysis.
    Curr Opin Biotechnol. 2000 Aug;11(4):396-401 PMID: 10975460
  18. An accurate mass tag strategy for quantitative and high-throughput proteome measurements.
    Proteomics. 2002 May;2(5):513-23 PMID: 11987125
  19. Mechanism for radiation lethality in M. radiodurans.
    Int J Radiat Biol Relat Stud Phys Chem Med. 1971;19(1):13-9 PMID: 5316586
  20. Engineering a recombinant Deinococcus radiodurans for organopollutant degradation in radioactive mixed waste environments.
    Nat Biotechnol. 1998 Oct;16(10):929-33 PMID: 9788348
  21. The release of a deoxyribonucleic acid fragment after x-irradiation of Micrococcus radiodurans.
    Int J Radiat Biol Relat Stud Phys Chem Med. 1974 Apr;25(4):329-37 PMID: 4545834
  22. Probing proteomes using capillary isoelectric focusing-electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.
    Anal Chem. 1999 Jun 1;71(11):2076-84 PMID: 10366890
  23. Controlled ion fragmentation in a 2-D quadrupole ion trap for external ion accumulation in ESI FTICR mass spectrometry.
    J Am Soc Mass Spectrom. 2001 Dec;12(12):1312-9 PMID: 11766758
  24. Radioresistance of Deinococcus radiodurans: functions necessary to survive ionizing radiation are also necessary to survive prolonged desiccation.
    J Bacteriol. 1996 Feb;178(3):633-7 PMID: 8550493
  25. The Nudix hydrolases of Deinococcus radiodurans.
    Mol Microbiol. 2001 Jan;39(2):286-90 PMID: 11136450
  26. A model for repair of radiation-induced DNA double-strand breaks in the extreme radiophile Deinococcus radiodurans.
    Bioessays. 1995 May;17(5):457-64 PMID: 7786292
  27. Reduction of Fe(III), Cr(VI), U(VI), and Tc(VII) by Deinococcus radiodurans R1.
    Appl Environ Microbiol. 2000 May;66(5):2006-11 PMID: 10788374
  28. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics.
    Microbiol Mol Biol Rev. 2001 Mar;65(1):44-79 PMID: 11238985
  29. Isolation and properties of strains of Micrococcus (Deinococcus) radiodurans unable to excise ultraviolet light-induced pyrimidine dimers from DNA: evidence for two excision pathways.
    J Gen Microbiol. 1983 Aug;129(8):2437-45 PMID: 6415229
  30. Repair of oxidized bases in the extremely radiation-resistant bacterium Deinococcus radiodurans.
    J Bacteriol. 1999 Jan;181(1):262-9 PMID: 9864339
  31. Against all odds: the survival strategies of Deinococcus radiodurans.
    Annu Rev Microbiol. 1997;51:203-24 PMID: 9343349
  32. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.
    Nat Biotechnol. 1999 Oct;17(10):994-9 PMID: 10504701
  33. Packed capillary reversed-phase liquid chromatography with high-performance electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for proteomics.
    Anal Chem. 2001 Apr 15;73(8):1766-75 PMID: 11338590
  34. The sequence of the human genome.
    Science. 2001 Feb 16;291(5507):1304-51 PMID: 11181995
  35. DNA repair in the extremely radioresistant bacterium Deinococcus radiodurans.
    Mol Microbiol. 1994 Jul;13(1):9-15 PMID: 7984097
  36. Predicted highly expressed genes of diverse prokaryotic genomes.
    J Bacteriol. 2000 Sep;182(18):5238-50 PMID: 10960111
  37. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.
    J Am Soc Mass Spectrom. 1994 Nov;5(11):976-89 PMID: 24226387
  38. Obtaining more accurate Fourier transform ion cyclotron resonance mass measurements without internal standards using multiply charged ions.
    J Am Soc Mass Spectrom. 2000 May;11(5):416-21 PMID: 10790845
  39. Targeted mutagenesis by duplication insertion in the radioresistant bacterium Deinococcus radiodurans: radiation sensitivities of catalase (katA) and superoxide dismutase (sodA) mutants.
    J Bacteriol. 1999 Jan;181(2):666-9 PMID: 9882685
  40. Dynamic range expansion applied to mass spectrometry based on data-dependent selective ion ejection in capillary liquid chromatography fourier transform ion cyclotron resonance for enhanced proteome characterization.
    Anal Chem. 2001 Nov 1;73(21):5052-60 PMID: 11721899
  41. Manganese(II) induces cell division and increases in superoxide dismutase and catalase activities in an aging deinococcal culture.
    J Bacteriol. 1990 Apr;172(4):2029-35 PMID: 2318808
  42. Glutamyl-tRNA(Gln) amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis.
    Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):12838-43 PMID: 9789001
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.172170199
Published
2002-08-20
Epub
2002-00-12
Pages
11049-54
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC129300
Subset
IM
Corrections
CommentIn
PMID: 12177454
External Links
PubMed source DOI: 10.1073/pnas.172170199 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2