Identification of protein partners in mycobacteria using a single-step affinity purification method

PLoS ONE

Volumn 9, Issue 3, 2014, Pages

  Płociński, Przemysław ^a   Laubitz, Daniel ^a   Cysewski, Dominik ^a   Stoduś, Krystian ^a   Kowalska, Katarzyna ^a   Dziembowski, Andrzej ^a,b  

^a INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

^b UNIVERSITY OF WARSAW   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; ENHANCED GREEN FLUORESCENT PROTEIN; HEMAGGLUTININ; PEPTIDE; PROTEIN A; RNA POLYMERASE; RNA POLYMERASE SUBUNIT A; UNCLASSIFIED DRUG;

AFFINITY PURIFICATION METHOD; ANALYTIC METHOD; ARTICLE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; HIGH THROUGHPUT SCREENING; MASS SPECTROMETRY; MOLECULAR DYNAMICS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PROTEIN BINDING; PROTEIN CROSS LINKING; PROTEIN DETERMINATION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; RADIATION INJURY; ULTRAVIOLET RADIATION; AFFINITY CHROMATOGRAPHY; CHEMISTRY; ISOLATION AND PURIFICATION; LIQUID CHROMATOGRAPHY; METABOLISM; MYCOBACTERIUM; PROCEDURES; PROTEIN ANALYSIS; TANDEM MASS SPECTROMETRY;

BACTERIAL PROTEINS; CHROMATOGRAPHY, AFFINITY; CHROMATOGRAPHY, LIQUID; MYCOBACTERIUM; PROTEIN INTERACTION MAPPING; TANDEM MASS SPECTROMETRY;

EID: 84899713549     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0091380     Document Type: Article

References (42)

1. Kelkar DS, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, et al. (2011) Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol Cell Proteomics 10: M111 011627.
2. Kuhner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, et al. (2009) Proteome organization in a genome-reduced bacterium. Science 326: 1235- 1240.
3. Rain JC, Selig L, De Reuse H, Battaglia V, Reverdy C, et al. (2001) The protein-protein interaction map of Helicobacter pylori. Nature 409: 211-215. (Pubitemid 32144288)
4. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98: 4569-4574. (Pubitemid 32295017)
5. Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322: 104-110.
6. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, et al. (2003) A protein interaction map of Drosophila melanogaster. Science 302: 1727-1736. (Pubitemid 37505730)
7. Wang Y, Cui T, Zhang C, Yang M, Huang Y, et al. (2010) Global protein-protein interaction network in the human pathogen Mycobacterium tuberculosis H37Rv. J Proteome Res 9: 6665-6677.
8. Zhou H, Wong L (2011) Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets. BMC Genomics 12 Suppl 3: S20.
9. Tharad M, Samuchiwal SK, Bhalla K, Ghosh A, Kumar K, et al. (2011) A three-hybrid system to probe in vivo protein-protein interactions: application to the essential proteins of the RD1 complex of M. tuberculosis. PLoS One 6: e27503.
10. Singh A, Mai D, Kumar A, Steyn AJ (2006) Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association. Proc Natl Acad Sci U S A 103: 11346-11351. (Pubitemid 44156520)
11. Dziedzic R, Kiran M, Plocinski P, Ziolkiewicz M, Brzostek A, et al. (2010) Mycobacterium tuberculosis ClpX interacts with FtsZ and interferes with FtsZ assembly. PLoS One 5: e11058.
12. Padiadpu J, Vashisht R, Chandra N (2010) Protein-protein interaction networks suggest different targets have different propensities for triggering drug resistance. Syst Synth Biol 4: 311-322.
13. Gingras AC, Gstaiger M, Raught B, Aebersold R (2007) Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol 8: 645-654. (Pubitemid 47106612)
14. Nesvizhskii AI (2012) Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics 12: 1639-1655.
15. Williams KJ, Joyce G, Robertson BD (2010) Improved mycobacterial tetracycline inducible vectors. Plasmid 64: 69-73.
16. Wepf A, Glatter T, Schmidt A, Aebersold R, Gstaiger M (2009) Quantitative interaction proteomics using mass spectrometry. Nat Methods 6: 203-205.
17. Li MZ, Elledge SJ (2007) Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods 4: 251-256. (Pubitemid 46358876)
18. Rothbauer U, Zolghadr K, Muyldermans S, Schepers A, Cardoso MC, et al. (2008) A versatile nanotrap for biochemical and functional studies with fluorescent fusion proteins. Mol Cell Proteomics 7: 282-289. (Pubitemid 351298442)
19. Tomecki R, Kristiansen MS, Lykke-Andersen S, Chlebowski A, Larsen KM, et al. (2010) The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L. EMBO J 29: 2342-2357.
20. Fabisiewicz A, Janion C (1998) DNA mutagenesis and repair in UV-irradiated E. coli K-12 under condition of mutation frequency decline. Mutat Res 402: 59-66.
21. Kirchhofer A, Helma J, Schmidthals K, Frauer C, Cui S, et al. (2010) Modulation of protein properties in living cells using nanobodies. Nat Struct Mol Biol 17: 133-138.
22. Yang B, Wu YJ, Zhu M, Fan SB, Lin J, et al. (2012) Identification of cross-linked peptides from complex samples. Nat Methods 9: 904-906.
23. Brizzard BL, Chubet RG, Vizard DL (1994) Immunoaffinity purification of FLAG epitope-tagged bacterial alkaline phosphatase using a novel monoclonal antibody and peptide elution. Biotechniques 16: 730-735. (Pubitemid 2067227)
24. Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, et al. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17: 1030-1032. (Pubitemid 29474865)
25. Puig O, Caspary F, Rigaut G, Rutz B, Bouveret E, et al. (2001) The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24: 218-229. (Pubitemid 32846428)
26. Murakami KS, Darst SA (2003) Bacterial RNA polymerases: the wholo story. Curr Opin Struct Biol 13: 31-39. (Pubitemid 36170252)
27. Tagami S, Sekine S, Kumarevel T, Hino N, Murayama Y, et al. (2010) Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein. Nature 468: 978-982.
28. Mostowy S, Cousins D, Brinkman J, Aranaz A, Behr MA (2002) Genomic deletions suggest a phylogeny for the Mycobacterium tuberculosis complex. J Infect Dis 186: 74-80. (Pubitemid 34666916)
29. Luo J, Fishburn J, Hahn S, Ranish J (2012) An integrated chemical cross-linking and mass spectrometry approach to study protein complex architecture and function. Mol Cell Proteomics 11: M111 008318.
30. Orren DK, Sancar A (1990) Formation and enzymatic properties of the UvrB.DNA complex. J Biol Chem 265: 15796-15803.
31. Van Houten B, Croteau DL, DellaVecchia MJ, Wang H, Kisker C (2005) 'Close-fitting sleeves': DNA damage recognition by the UvrABC nuclease system. Mutat Res 577: 92-117. (Pubitemid 41225491)
32. Hochuli E, Dobeli H, Schacher A (1987) New metal chelate adsorbent selective for proteins and peptides containing neighbouring histidine residues. J Chromatogr 411: 177-184.
33. Stofko-Hahn RE, Carr DW, Scott JD (1992) A single step purification for recombinant proteins. Characterization of a microtubule associated protein (MAP 2) fragment which associates with the type II cAMP-dependent protein kinase. FEBS Lett 302: 274-278.
34. Lichty JJ, Malecki JL, Agnew HD, Michelson-Horowitz DJ, Tan S (2005) Comparison of affinity tags for protein purification. Protein Expr Purif 41: 98-105. (Pubitemid 40406368)
35. Young CL, Britton ZT, Robinson AS (2012) Recombinant protein expression and purification: a comprehensive review of affinity tags and microbial applications. Biotechnol J 7: 620-634.
36. Wang H, Chong S (2003) Visualization of coupled protein folding and binding in bacteria and purification of the heterodimeric complex. Proc Natl Acad Sci U S A 100: 478-483. (Pubitemid 36126076)
37. Li Y, Franklin S, Zhang MJ, Vondriska TM (2011) Highly efficient purification of protein complexes from mammalian cells using a novel streptavidin-binding peptide and hexahistidine tandem tag system: application to Bruton's tyrosine kinase. Protein Sci 20: 140-149.
38. Huang F, He ZG (2012) Characterization of a conserved interaction between DNA glycosylase and ParA in Mycobacterium smegmatis and M. tuberculosis. PLoS One 7: e38276.
39. Opalka N, Brown J, Lane WJ, Twist KA, Landick R, et al. (2010) Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. PLoS Biol 8.
40. Schurig H, Beaucamp N, Ostendorp R, Jaenicke R, Adler E, et al. (1995) Phosphoglycerate kinase and triosephosphate isomerase from the hyperthermophilic bacterium Thermotoga maritima form a covalent bifunctional enzyme complex. EMBO J 14: 442-451.
41. Mao Y, Muller MT (2003) Down modulation of topoisomerase I affects DNA repair efficiency. DNA Repair (Amst) 2: 1115-1126. (Pubitemid 39662826)
42. Ahn B (2000) A physical interaction of UvrD with nucleotide excision repair protein UvrB. Mol Cells 10: 592-597.