Abstract
Background: Most of the proteomic studies in Escherichia coli have focussed on pathogenic strains, while very few studies have studied the commensal strains. It is important to study the commensal strains because under the selective pressure of their habitat, commensal strains might serve as reservoirs of virulent and pathogenic strains.
Objective: In this study, we have performed a comparative proteomic analysis of commensal and pathogenic strains of E. coli isolated from a major river flowing through northern India.
Methods: Proteins were resolved by two dimensional gel electrophoresis and the differentially expressed proteins were identified using matrix-assisted laser desorption ionization-time of flight mass-spectrometry (MALDI-TOF MS).
Results: Many proteins of the commensal strain showed an increased expression compared to the pathogenic strain, of which seventeen proteins were identified by MALDI-TOF MS. Functional classification of these proteins revealed that they belonged to different functional pathways like energy metabolism, nucleotide and nucleoside conversions, translation, biosynthesis of amino acids and motility and energytaxis/chemotaxis.
Conclusion: As per the best of our knowledge, this is the first report on comparative proteomic analysis of E. coli commensal and pathogenic strains of aquatic origin. Our results suggest that the increased production of these proteins might play an important role in adaptation of E. coli to a commensal/pathogenic lifestyle. However, further experiments are required to understand the precise role of these proteins in regulating the pathogenicity/commensalism of E. coli.
Keywords: Escherichia coli, commensal, pathogenic, proteomics, two dimensional gel electrophoresis, adaptation.
Graphical Abstract
[1]
Méric, G.; Kemsley, E.K.; Falush, D.; Saggers, E.J.; Lucchini, S. Phylogenetic distribution of traits associated with plant colonization in Escherichia coli. Environ. Microbiol., 2013, 15(2), 487-501.[http://dx.doi.org/10.1111/j.1462-2920.2012.02852.x] [PMID: 22934605]
[2]
Dobrindt, U.; Agerer, F.; Michaelis, K.; Janka, A.; Buchrieser, C.; Samuelson, M.; Svanborg, C.; Gottschalk, G.; Karch, H.; Hacker, J. Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays. J. Bacteriol., 2003, 185(6), 1831-1840.[http://dx.doi.org/10.1128/JB.185.6.1831-1840.2003] [PMID: 12618447]
[3]
Leimbach, A.; Hacker, J.; Dobrindt, U. E. coli as an all-rounder: the thin line between commensalism and pathogenicity. Curr. Top. Microbiol. Immunol., 2013, 358, 3-32.[http://dx.doi.org/10.1007/82_2012_303] [PMID: 23340801]
[4]
Clermont, O.; Bonacorsi, S.; Bingen, E. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl. Environ. Microbiol., 2000, 66(10), 4555-4558.[http://dx.doi.org/10.1128/AEM.66.10.4555-4558.2000] [PMID: 11010916]
[5]
Walk, S.T.; Alm, E.W.; Calhoun, L.M.; Mladonicky, J.M.; Whittam, T.S. Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches. Environ. Microbiol., 2007, 9(9), 2274-2288.[http://dx.doi.org/10.1111/j.1462-2920.2007.01341.x] [PMID: 17686024]
[6]
Estrada-Garcia, T.; Lopez-Saucedo, C.; Thompson-Bonilla, R.; Abonce, M.; Lopez-Hernandez, D.; Santos, J.I.; Rosado, J.L.; DuPont, H.L.; Long, K.Z. Association of diarrheagenic Escherichia coli Pathotypes with infection and diarrhea among Mexican children and association of atypical Enteropathogenic E. coli with acute diarrhea. J. Clin. Microbiol., 2009, 47(1), 93-98.[http://dx.doi.org/10.1128/JCM.01166-08] [PMID: 19020055]
[7]
Figueira, V.; Serra, E.; Manaia, C.M. Differential patterns of antimicrobial resistance in population subsets of Escherichia coli isolated from waste- and surface waters. Sci. Total Environ., 2011, 409(6), 1017-1023.[http://dx.doi.org/10.1016/j.scitotenv.2010.12.011] [PMID: 21215425]
[8]
Arimizu, Y.; Kirino, Y.; Sato, M.P.; Uno, K.; Sato, T.; Gotoh, Y.; Auvray, F.; Brugere, H.; Oswald, E.; Mainil, J.G.; Anklam, K.S.; Döpfer, D.; Yoshino, S.; Ooka, T.; Tanizawa, Y.; Nakamura, Y.; Iguchi, A.; Morita-Ishihara, T.; Ohnishi, M.; Akashi, K.; Hayashi, T.; Ogura, Y. Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains. Genome Res., 2019, 29(9), 1495-1505.[http://dx.doi.org/10.1101/gr.249268.119] [PMID: 31439690]
[9]
Bajaj, P.; Singh, N.S.; Kanaujia, P.K.; Virdi, J.S. Distribution and molecular characterization of genes encoding CTX-M and AmpC β-lactamases in Escherichia coli isolated from an Indian urban aquatic environment. Sci. Total Environ., 2015, 505, 350-356.[http://dx.doi.org/10.1016/j.scitotenv.2014.09.084] [PMID: 25461036]
[10]
Bisht, D.; Singhal, N.; Sharma, P.; Venkatesan, K. An improved sample preparation method for analyzing mycobacterial proteins in two-dimensional gels. Biochemistry (Mosc.), 2007, 72(6), 672-674.[http://dx.doi.org/10.1134/S0006297907060119] [PMID: 17630913]
[11]
Bradford, M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem., 1976, 72, 248-254.[http://dx.doi.org/10.1016/0003-2697(76)90527-3] [PMID: 942051]
[12]
Sharma, P.; Kumar, B.; Singhal, N.; Katoch, V.M.; Venkatesan, K.; Chauhan, D.S.; Bisht, D. Streptomycin induced protein expression analysis in Mycobacterium tuberculosis by two-dimensional gel electrophoresis & mass spectrometry. Indian J. Med. Res., 2010, 132, 400-408.[PMID: 20966518]
[13]
Singhal, N.; Sharma, P.; Kumar, M.; Joshi, B.; Bisht, D. Analysis of intracellular expressed proteins of Mycobacterium tuberculosis clinical isolates. Proteome Sci., 2012, 10(1), 14.[http://dx.doi.org/10.1186/1477-5956-10-14] [PMID: 22375954]
[14]
Singhal, N.; Kumar, M.; Sharma, D.; Bisht, D. Comparative protein profiling of intraphagosomal expressed proteins of Mycobacterium bovis BCG. Protein Pept. Lett., 2016, 23(1), 51-54.[http://dx.doi.org/10.2174/0929866523666151106123121] [PMID: 26548863]
[15]
Keseler, I.M.; Mackie, A.; Santos-Zavaleta, A.; Billington, R.; Bonavides-Martínez, C.; Caspi, R.; Fulcher, C.; Gama-Castro, S.; Kothari, A.; Krummenacker, M.; Latendresse, M.; Muñiz-Rascado, L.; Ong, Q.; Paley, S.; Peralta-Gil, M.; Subhraveti, P.; Velázquez-Ramírez, D.A.; Weaver, D.; Collado-Vides, J.; Paulsen, I.; Karp, P.D. The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. Nucleic Acids Res., 2017, 45(D1), D543-D550.[http://dx.doi.org/10.1093/nar/gkw1003] [PMID: 27899573]
[16]
Schmidt, A.; Kochanowski, K.; Vedelaar, S.; Ahrné, E.; Volkmer, B.; Callipo, L.; Knoops, K.; Bauer, M.; Aebersold, R.; Heinemann, M. The quantitative and condition-dependent Escherichia coli proteome. Nat. Biotechnol., 2016, 34(1), 104-110.[http://dx.doi.org/10.1038/nbt.3418] [PMID: 26641532]
[17]
Li, H.; Zhang, D.F.; Lin, X.M.; Peng, X.X. Outer membrane proteomics of kanamycin-resistant Escherichia coli identified MipA as a novel antibiotic resistance-related protein. FEMS Microbiol. Lett., 2015, 362(11), fnv074.[http://dx.doi.org/10.1093/femsle/fnv074] [PMID: 25940639]
[18]
Wurpel, D.J.; Totsika, M.; Allsopp, L.P.; Webb, R.I.; Moriel, D.G.; Schembri, M.A. Comparative proteomics of uropathogenic Escherichia coli during growth in human urine identify UCA-like (UCL) fimbriae as an adherence factor involved in biofilm formation and binding to uroepithelial cells. J. Proteomics, 2016, 131, 177-189.[http://dx.doi.org/10.1016/j.jprot.2015.11.001] [PMID: 26546558]
[19]
Egea, L.; Aguilera, L.; Giménez, R.; Sorolla, M.A.; Aguilar, J.; Badía, J.; Baldoma, L. Role of secreted glyceraldehyde- 3-phosphate dehydrogenase in the infection mechanism of enterohemorrhagic and enteropathogenic Escherichia coli: Interaction of the extracellular enzyme with human plasminogen and fibrinogen. Int. J. Biochem. Cell Biol., 2007, 39(6), 1190-1203.[http://dx.doi.org/10.1016/j.biocel.2007.03.008] [PMID: 17449317]
[20]
Ferreira, E.; Giménez, R.; Cañas, M.A.; Aguilera, L.; Aguilar, J.; Badia, J.; Baldomà, L. Glyceraldehyde-3-phosphate dehydrogenase is required for efficient repair of cytotoxic DNA lesions in Escherichia coli. Int. J. Biochem. Cell Biol., 2015, 60, 202-212.[http://dx.doi.org/10.1016/j.biocel.2015.01.008] [PMID: 25603270]
[21]
Abdel-Hamid, A.M.; Attwood, M.M.; Guest, J.R. Pyruvate oxidase contributes to the aerobic growth efficiency of Escherichia coli. Microbiology, 2001, 147(Pt 6), 1483-1498.[http://dx.doi.org/10.1099/00221287-147-6-1483] [PMID: 11390679]
[22]
Vita, A.; Amici, A.; Cacciamani, T.; Lanciotti, M.; Magni, G. Uridine phosphorylase from Escherichia coli B. Enzymatic and molecular properties. Int. J. Biochem., 1986, 18(5), 431-435.[http://dx.doi.org/10.1016/0020-711X(86)90185-0] [PMID: 3519310]
[23]
Brodersen, D.E.; Nissen, P. The social life of ribosomal proteins. FEBS J., 2005, 272(9), 2098-2108.[http://dx.doi.org/10.1111/j.1742-4658.2005.04651.x] [PMID: 15853795]
[24]
Bryant, R.E.; Sypherd, P.S. Genetic analysis of cold-sensitive ribosome maturation mutants of Escherichia coli. J. Bacteriol., 1974, 117(3), 1082-1092.[http://dx.doi.org/10.1128/JB.117.3.1082-1092.1974] [PMID: 4591943]
[25]
Schulze, H.; Nierhaus, K.H. Minimal set of ribosomal components for reconstitution of the peptidyltransferase activity. EMBO J., 1982, 1(5), 609-613.[http://dx.doi.org/10.1002/j.1460-2075.1982.tb01216.x] [PMID: 6765232]
[26]
Peltz, S.W.; Hammell, A.B.; Cui, Y.; Yasenchak, J.; Puljanowski, L.; Dinman, J.D. Ribosomal protein L3 mutants alter translational fidelity and promote rapid loss of the yeast killer virus. Mol. Cell. Biol., 1999, 19(1), 384-391.[http://dx.doi.org/10.1128/MCB.19.1.384] [PMID: 9858562]
[27]
Hudak, K.A.; Dinman, J.D.; Tumer, N.E. Pokeweed antiviral protein accesses ribosomes by binding to L3. J. Biol. Chem., 1999, 274(6), 3859-3864.[http://dx.doi.org/10.1074/jbc.274.6.3859] [PMID: 9920941]
[28]
Meskauskas, A.; Harger, J.W.; Jacobs, K.L.M.; Dinman, J.D. Decreased peptidyltransferase activity correlates with increased programmed -1 ribosomal frameshifting and viral maintenance defects in the yeast Saccharomyces cerevisiae. RNA, 2003, 9(8), 982-992.[http://dx.doi.org/10.1261/rna.2165803] [PMID: 12869709]
[29]
Bøsling, J.; Poulsen, S.M.; Vester, B.; Long, K.S. Resistance to the peptidyl transferase inhibitor tiamulin caused by mutation of ribosomal protein l3. Antimicrob. Agents Chemother., 2003, 47(9), 2892-2896.[http://dx.doi.org/10.1128/AAC.47.9.2892-2896.2003] [PMID: 12936991]
[30]
Petrov, A.; Meskauskas, A.; Dinman, J.D. Ribosomal protein L3: influence on ribosome structure and function. RNA Biol., 2004, 1(1), 59-65.[http://dx.doi.org/10.4161/rna.1.1.957] [PMID: 17194937]
[31]
Jones, S.A.; Jorgensen, M.; Chowdhury, F.Z.; Rodgers, R.; Hartline, J.; Leatham, M.P.; Struve, C.; Krogfelt, K.A.; Cohen, P.S.; Conway, T. Glycogen and maltose utilization by Escherichia coli O157:H7 in the mouse intestine. Infect. Immun., 2008, 76(6), 2531-2540.[http://dx.doi.org/10.1128/IAI.00096-08] [PMID: 18347038]
[32]
Fabich, A.J.; Jones, S.A.; Chowdhury, F.Z.; Cernosek, A.; Anderson, A.; Smalley, D.; McHargue, J.W.; Hightower, G.A.; Smith, J.T.; Autieri, S.M.; Leatham, M.P.; Lins, J.J.; Allen, R.L.; Laux, D.C.; Cohen, P.S.; Conway, T. Comparison of carbon nutrition for pathogenic and commensal Escherichia coli strains in the mouse intestine. Infect. Immun., 2008, 76(3), 1143-1152.[http://dx.doi.org/10.1128/IAI.01386-07] [PMID: 18180286]
[33]
Pettersen, V.K.; Steinsland, H.; Wiker, H.G. Comparative proteomics of enterotoxigenic Escherichia coli reveals differences in surface protein production and similarities in metabolism. J. Proteome Res., 2018, 17(1), 325-336.[http://dx.doi.org/10.1021/acs.jproteome.7b00593] [PMID: 29185342]
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