Proteomic analysis of Escherichia coli detergent-resistant membranes (DRM)
Autoři:
José E. Guzmán-Flores aff001; Lidia Steinemann-Hernández aff001; Luis E. González de la Vara aff002; Marina Gavilanes-Ruiz aff003; Tony Romeo aff004; Adrián F. Alvarez aff001; Dimitris Georgellis aff001
Působiště autorů:
Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
aff001; Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Cinvestav-IPN, Irapuato, Gto, México
aff002; Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, México
aff003; Department of Microbiology and Cell Science, IFAS, University of Florida, Gainesville, Florida, United States of America
aff004
Vyšlo v časopise:
PLoS ONE 14(10)
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pone.0223794
Souhrn
Membrane microdomains or lipid rafts compartmentalize cellular processes by laterally organizing membrane components. Such sub-membrane structures were mainly described in eukaryotic cells, but, recently, also in bacteria. Here, the protein content of lipid rafts in Escherichia coli was explored by mass spectrometry analyses of Detergent Resistant Membranes (DRM). We report that at least three of the four E. coli flotillin homologous proteins were found to reside in DRM, along with 77 more proteins. Moreover, the proteomic data were validated by subcellular localization, using immunoblot assays and fluorescence microscopy of selected proteins. Our results confirm the existence of lipid raft-like microdomains in the inner membrane of E. coli and represent the first comprehensive profiling of proteins in these bacterial membrane platforms.
Klíčová slova:
Lipids – Cell membranes – Membrane proteins – Outer membrane proteins – Lipoproteins – Signal peptides – Integral membrane proteins – Transmembrane transport proteins
Zdroje
1. Astro V, de Curtis I. Plasma membrane-associated platforms: dynamic scaffolds that organize membrane-associated events. Sci Signal. 2015;8: re1. doi: 10.1126/scisignal.aaa3312 25759479
2. Lingwood D, Simons K. Lipid rafts as a membrane-organizing principle. Science. 2010;327: 46–50. doi: 10.1126/science.1174621 20044567
3. Browman DT, Hoegg MB, Robbins SM. The SPFH domain-containing proteins: more than lipid raft markers. Trends Cell Biol. 2007;17: 394–402. doi: 10.1016/j.tcb.2007.06.005 17766116
4. Langhorst MF, Reuter A, Stuermer CAO. Scaffolding microdomains and beyond: the function of reggie/flotillin proteins. Cell Mol Life Sci. 2005;62: 2228–2240. doi: 10.1007/s00018-005-5166-4 16091845
5. Morrow IC, Parton RG. Flotillins and the PHB domain protein family: rafts, worms and anaesthetics. Traffic. 2005;6: 725–740. doi: 10.1111/j.1600-0854.2005.00318.x 16101677
6. Kato N, Nakanishi M, Hirashima N. Flotillin-1 regulates IgE receptor-mediated signaling in rat basophilic leukemia (RBL-2H3) cells. J Immunol. 2006;177: 147–154. doi: 10.4049/jimmunol.177.1.147 16785509
7. Langhorst MF, Solis GP, Hannbeck S, Plattner H, Stuermer CAO. Linking membrane microdomains to the cytoskeleton: Regulation of the lateral mobility of reggie-1/flotillin-2 by interaction with actin. FEBS Lett. 2007;581: 4697–4703. doi: 10.1016/j.febslet.2007.08.074 17854803
8. Bach JN, Bramkamp M. Flotillins functionally organize the bacterial membrane. Mol Microbiol. 2013;88: 1205–1217. doi: 10.1111/mmi.12252 23651456
9. López D, Kolter R. Functional microdomains in bacterial membranes. Genes Dev. 2010;24: 1893–1902. doi: 10.1101/gad.1945010 20713508
10. Schneider J, Mielich-Süss B, Böhme R, Lopez D. In vivo characterization of the scaffold activity of flotillin on the membrane kinase KinC of Bacillus subtilis. Microbiology. 2015;161: 1871–1887. doi: 10.1099/mic.0.000137 26297017
11. Schneider J, Klein T, Mielich-Süss B, Koch G, Franke C, Kuipers OP, et al. Spatio-temporal Remodeling of Functional Membrane Microdomains Organizes the Signaling Networks of a Bacterium. Casadesús J, editor. PLOS Genet. 2015;11: e1005140. doi: 10.1371/journal.pgen.1005140 25909364
12. Feng X, Hu Y, Zheng Y, Zhu W, Li K, Huang C-H, et al. Structural and functional analysis of Bacillus subtilis YisP reveals a role of its product in biofilm production. Chem Biol. 2014;21: 1557–1563. doi: 10.1016/j.chembiol.2014.08.018 25308276
13. Mielich-Süss B, Wagner RM, Mietrach N, Hertlein T, Marincola G, Ohlsen K, et al. Flotillin scaffold activity contributes to type VII secretion system assembly in Staphylococcus aureus. PLOS Pathog. 2017;13: e1006728. doi: 10.1371/journal.ppat.1006728 29166667
14. Somani VK, Aggarwal S, Singh D, Prasad T, Bhatnagar R. Identification of novel raft marker protein, FlotP in Bacillus anthracis. Front Microbiol. 2016;7: 169. doi: 10.3389/fmicb.2016.00169 26925042
15. LaRocca TJ, Pathak P, Chiantia S, Toledo A, Silvius JR, Benach JL, et al. Proving lipid rafts exist: membrane domains in the prokaryote Borrelia burgdorferi have the same properties as eukaryotic lipid rafts. PLOS Pathog. 2013;9: e1003353. doi: 10.1371/journal.ppat.1003353 23696733
16. Hutton ML, D’Costa K, Rossiter AE, Wang L, Turner L, Steer DL, et al. A Helicobacter pylori homolog of eukaryotic flotillin is involved in cholesterol accumulation, epithelial cell responses and host colonization. Front Cell Infect Microbiol. 2017;7: 219. doi: 10.3389/fcimb.2017.00219 28634572
17. Guzmán-Flores JE, Alvarez AF, Poggio S, Gavilanes-Ruiz M, Georgellis D. Isolation of detergent-resistant membranes (DRMs) from Escherichia coli. Anal Biochem. 2017;518: 1–8. doi: 10.1016/j.ab.2016.10.025 27984012
18. Staneva G, Seigneuret M, Koumanov K, Trugnan G, Angelova MI. Detergents induce raft-like domains budding and fission from giant unilamellar heterogeneous vesicles: A direct microscopy observation. Chem Phys Lipids. 2005;136: 55–66. doi: 10.1016/j.chemphyslip.2005.03.007 15927174
19. Brown DA. Lipid rafts, detergent-resistant membranes, and raft targeting signals. Physiology (Bethesda). 2006;21: 430–439. doi: 10.1152/physiol.00032.2006 17119156
20. Yepes A, Schneider J, Mielich B, Koch G, García-Betancur J-C, Ramamurthi KS, et al. The biofilm formation defect of a Bacillus subtilis flotillin-defective mutant involves the protease FtsH. Mol Microbiol. 2012;86: 457–471. doi: 10.1111/j.1365-2958.2012.08205.x 22882210
21. Toledo A, Pérez A, Coleman JL, Benach JL. The lipid raft proteome of Borrelia burgdorferi. Proteomics. 2015;15: 3662–3675. doi: 10.1002/pmic.201500093 26256460
22. García-Fernández E, Koch G, Wagner RM, Fekete A, Stengel ST, Schneider J, et al. Membrane Microdomain Disassembly Inhibits MRSA Antibiotic Resistance. Cell. 2017; doi: 10.1016/j.cell.2017.10.012 29103614
23. Toledo A, Huang Z, Coleman JL, London E, Benach JL. Lipid rafts can form in the inner and outer membranes of Borrelia burgdorferi and have different properties and associated proteins. Mol Microbiol. 2018;108: 63–76. doi: 10.1111/mmi.13914 29377398
24. Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, et al. Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS. Proteomics. 2007;7: 484–493. doi: 10.1002/pmic.200600518 17309111
25. Bernsel A, Daley DO. Exploring the inner membrane proteome of Escherichia coli: which proteins are eluding detection and why? Trends Microbiol. 2009;17: 444–449. doi: 10.1016/j.tim.2009.07.005 19766000
26. Masuda T, Saito N, Tomita M, Ishihama Y. Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants. Mol Cell Proteomics. 2009;8: 2770–7. doi: 10.1074/mcp.M900240-MCP200 19767571
27. Papanastasiou M, Orfanoudaki G, Koukaki M, Kountourakis N, Sardis MF, Aivaliotis M, et al. The Escherichia coli peripheral inner membrane proteome. Mol Cell Proteomics. 2013;12: 599–610. doi: 10.1074/mcp.M112.024711 23230279
28. Lee H-L, Chiang I-C, Liang S-Y, Lee D-Y, Chang G-D, Wang K-Y, et al. Quantitative Proteomics Analysis Reveals the Min System of Escherichia coli Modulates Reversible Protein Association with the Inner Membrane. Mol Cell Proteomics. 2016;15: 1572–83. doi: 10.1074/mcp.M115.053603 26889046
29. Datsenko KA, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A. 2000;97: 6640–6645. doi: 10.1073/pnas.120163297 10829079
30. Uzzau S, Figueroa-Bossi N, Rubino S, Bossi L. Epitope tagging of chromosomal genes in Salmonella. Proc Natl Acad Sci U S A. 2001;98: 15264–15269. doi: 10.1073/pnas.261348198 11742086
31. Thanbichler M, Iniesta AA, Shapiro L. A comprehensive set of plasmids for vanillate- and xylose-inducible gene expression in Caulobacter crescentus. Nucleic Acids Res. 2007;35: e137. doi: 10.1093/nar/gkm818 17959646
32. Peña-Sandoval GR, Kwon O, Georgellis D. Requirement of the receiver and phosphotransfer domains of ArcB for efficient dephosphorylation of phosphorylated ArcA in vivo. J Bacteriol. 2005;187: 3267–3272. doi: 10.1128/JB.187.9.3267-3272.2005 15838055
33. Dykxhoorn DM, St Pierre R, Linn T. A set of compatible tac promoter expression vectors. Gene. 1996;177: 133–136. Available: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8921858 8921858
34. He L, Diedrich J, Chu YY, Yates JR. Extracting Accurate Precursor Information for Tandem Mass Spectra by RawConverter. Anal Chem. 2015;87: 11361–11367. doi: 10.1021/acs.analchem.5b02721 26499134
35. Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, et al. A guided tour of the Trans-Proteomic Pipeline [Internet]. Proteomics. WILEY-VCH Verlag; 2010. pp. 1150–1159.
36. Tsirigos KD, Peters C, Shu N, All L, Elofsson A. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Res. 2015;43. doi: 10.1093/nar/gkv485 25969446
37. Juncker AS, Willenbrock H, von Heijne G, Brunak S, Nielsen H, Krogh A. Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci. 2003;12: 1652–1662. doi: 10.1110/ps.0303703 12876315
38. Combet C, Blanchet C, Geourjon C, Deléage G. NPS@: Network protein sequence analysis. Trends Biochem Sci. 2000;25: 147–150. doi: 10.1016/s0968-0004(99)01540-6 10694887
39. Sambrook J, Russell DW. Molecular cloning: a Laboratory Manual. 3rd ed. NY: Cold Spring Harbor Laboratory: Cold Spring Harbor; 2001.
40. Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012;9: 671–675. doi: 10.1038/nmeth.2089 22930834
41. Lopez D, Koch G. Exploring functional membrane microdomains in bacteria: an overview. Curr Opin Microbiol. 2017;36: 76–84. doi: 10.1016/j.mib.2017.02.001 28237903
42. Thein M, Sauer G, Paramasivam N, Grin I, Linke D. Efficient subfractionation of gram-negative bacteria for proteomics studies. J Proteome Res. 2010;9: 6135–6147. doi: 10.1021/pr1002438 20932056
43. Emiola A, Andrews SS, Heller C, George J. Crosstalk between the lipopolysaccharide and phospholipid pathways during outer membrane biogenesis in Escherichia coli. Proc Natl Acad Sci. 2016;113: 3108–3113. doi: 10.1073/pnas.1521168113 26929331
44. Lai EC. Lipid rafts make for slippery platforms. J Cell Biol. 2003;162: 365–370. doi: 10.1083/jcb.200307087 12885764
45. Kenworthy AK, Nichols BJ, Remmert CL, Hendrix GM, Kumar M, Zimmerberg J, et al. Dynamics of putative raft-associated proteins at the cell surface. J Cell Biol. 2004;165: 735–746. doi: 10.1083/jcb.200312170 15173190
46. Klappe K, Hummel I, Hoekstra D, Kok JW. Lipid dependence of ABC transporter localization and function. Chem Phys Lipids. 2009;161: 57–64. doi: 10.1016/j.chemphyslip.2009.07.004 19651114
47. Zhou Z, White KA, Polissi A, Georgopoulos C, Raetz CRH. Function of Escherichia coli MsbA, an essential ABC family transporter, in lipid A and phospholipid biosynthesis. J Biol Chem. 1998;273: 12466–12475. doi: 10.1074/jbc.273.20.12466 9575204
48. Karow M, Georgopoulos C. The essential Escherichia coli msbA gene, a multicopy suppressor of null mutations in the htrB gene, is related to the universally conserved family of ATP-dependent translocators. Mol Microbiol. 1993;7: 69–79. doi: 10.1111/j.1365-2958.1993.tb01098.x 8094880
49. Yun UJ, Lee JH, Koo KH, Ye SK, Kim SY, Lee CH, et al. Lipid raft modulation by Rp1 reverses multidrug resistance via inactivating MDR-1 and Src inhibition. Biochem Pharmacol. 2013;85: 1441–1453. doi: 10.1016/j.bcp.2013.02.025 23473805
50. Allen JA, Halverson-Tamboli RA, Rasenick MM. Lipid raft microdomains and neurotransmitter signalling. Nat Rev Neurosci. 2007;8: 128–140. doi: 10.1038/nrn2059 17195035
51. Sáenz JP, Grosser D, Bradley AS, Lagny TJ, Lavrynenko O, Broda M, et al. Hopanoids as functional analogues of cholesterol in bacterial membranes. Proc Natl Acad Sci U S A. 2015;112: 11971–6. doi: 10.1073/pnas.1515607112 26351677
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