In silico analysis of antibody triggering biofilm associated protein in Acinetobacter baumannii. (English) Zbl 1407.92104

Summary: Acinetobacter baumannii surface protein, commonly known as biofilm associated protein (Bap), is involved in biofilm formation. A high propensity among the clinical isolates to form biofilm and a significant association of biofilms with multiple drug resistance has been demonstrated. Production of antibodies can be used for inhibition of biofilm and control of the diseases caused by A. baumannii. Large molecular mass of Bap justifies an approach to identifying A. baumannii effective antigens. It has a core domain of seven repeat modules A-G. With the large number of available biofilm gene sequences, bioinformatic tools are needed to identify the genes encoding the antigens. Proteins containing these tandem repeats of Bap domains have high propensities to attach to each other to form biofilm. We hypothesized that conserved and functional domains of tandem repeat could be identified with a search and alignment of the repeats for evaluation of antigenic determinants. Here we demonstrate the results of bioinformatics screening and gene scan of the gene sequence database of homolog sequences to identify conserved domains. Higher scoring hits were found in repeat modules mostly D, B, C and A, respectively. Upon the analysis four regions of highly structural and functional conserved regions from Bap sequence of A. baumannii were selected. 3D structure, antigenicity and solubility predictions revealed that these regions were appropriate candidates for antibody production.


92D20 Protein sequences, DNA sequences
92C37 Cell biology
Full Text: DOI


[1] Altschul, S.F.; Madden, T.L.; Schäffer, A.A.; Zhang, J.; Zhang2, Z.; Miller, W.; Lipman, D.J., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic acids research, 25, 3389-3402, (1997)
[2] Andersen, P.H.; Nielsen, M.; Lund, O., Prediction of residues in discontinuous B-cell epitopes using protein 3D structures, Protein science, 15, 2558-2567, (2006)
[3] ARRIZUBIETA, #160, Jesus, M., TOLEDO-ARANA, Alejandro, AMORENA, Beatriz, PENADES, Jos, #233, R., LASA, and Inigo, 2004. Calcium inhibits bap-dependent multicellular behavior in Staphylococcus aureus. American Society for Microbiology, Washington, DC, ETATS-UNIS.
[4] Berezin, C.; Glaser, F.; Rosenberg, Y.; Paz, I.; Pupko, T.; Fariselli, P.; Casadio, R.; Ben-Tal, N., Conseq: the identification of functionally and structurally important residues in protein sequences, Bioinformatics, 20, 1322-1324, (2004)
[5] Bergogne-Berezin, E.; Towner, K.J., acinetobacter spp. as nosocomial pathogens: microbiological, clinical, and epidemiological features, Clinical microbiology reviews, 9, 148-165, (1996)
[6] Bhasin, M.; Garg, A.; Raghava, G.P., Pslpred: prediction of subcellular localization of bacterial proteins, Bioinformatics, 21, 2522-2524, (2005)
[7] Broek van den, P.J.; Arends, J.; Bernards, A.T.; De Brauwer, E.; Mascini, E.M.; van der Reijden, T.J.; Spanjaard, L.; Thewessen, E.A.; van der Zee, A.; van Zeijl, J.H.; Dijkshoorn, L., Epidemiology of multiple acinetobacter outbreaks in The Netherlands during the period 1999-2001, Clinical microbiology and infection, 12, 837-843, (2006)
[8] Bycroft, M.; Bateman, A.; Clarke, J.; Hamill, S.; Sandford, R.; Thomas, R.; Chothia, C., The structure of a PKD domain from polycystin—1: implications for polycystic kidney disease, EMBO journal, 18, 297-305, (1999)
[9] Centers for Disease Control and Prevention, 2004. Acinetobacter baumannii infections among patients at military medical facilities treating injured US service members, 2002-2004. Morbidity and Mortality Weekly Report 53, 1063-1066.
[10] Chang, H.C.; Wei, Y.F.; Dijkshoorn, L.; Vaneechoutte, M.; Tang, C.T.; Chang, T.C., Species-level identification of isolates of the acinetobacter calcoaceticus-acinetobacter baumannii complex by sequence analysis of the 16S-23S rrna gene spacer region, Journal of clinical microbiology, 43, 1632-1639, (2005)
[11] Charnot-Katsikas, A.; Dorafshar, A.H.; Aycock, J.K.; David, M.Z.; Weber, S.G.; Frank, K.M., Two cases of necrotizing fasciitis due to acinetobacter baumannii, Journal of clinical microbiology, 47, 258-263, (2009)
[12] Costerton, J.W.; Stewart, P.S.; Greenberg, E.P., Bacterial biofilms: a common cause of persistent infections, Science, 284, 1318-1322, (1999)
[13] Cucarella, C.; Solano, C.; Valle, J.; Amorena, B.; Lasa, I.; Penades, J.R., Bap, a staphylococcus aureus surface protein involved in biofilm formation, Journal of bacteriology, 183, 2888-2896, (2001)
[14] Davis, G.D.; Elisee, C.; Newham, D.M.; Harrison, R.G., New fusion protein systems designed to give soluble expression in Escherichia coli, Biotechnology and bioengineering, 65, 382-388, (1999)
[15] Delepelaire, P., Type I secretion in Gram-negative bacteria, Biochimica et biophysica acta (BBA)—molecular cell research, 1694, 149-161, (2004)
[16] Dijkshoorn, L.; Nemec, A.; Seifert, H., An increasing threat in hospitals: multidrug resistant acinetobacter baumannii, Nature reviews microbiology, 5, 939-951, (2007)
[17] Donlan, R.M.; Costerton, J.W., Biofilms: survival mechanisms of clinically relevant microorganisms, Clinical microbiology reviews, 15, 167-193, (2002)
[18] Edgar, R.C., MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic acids research, 32, (2004)
[19] Fournier, P.; Richet, H., The epidemiology and control of acinetobacter baumannii in health care facilities, Clinical infectious diseases, 42, 692-699, (2006)
[20] Garnier, J.; Gibrat, J.-F.; Robson, B., [32] GOR method for predicting protein secondary structure from amino acid sequence, (), 540-553
[21] Gasteiger, E.; Hoogland, C.; Gattiker, A.; Duvaud, S.; Wilkins, M.R.; Appel, R.D.; Bairoch, A., Protein identification and analysis tools on the expasy server, (), 571-607
[22] Harrison, R.G., Expression of soluble heterologous proteins via fusion with nusa protein, Innovations, 11, 4-7, (2000)
[23] Hinsa, S.M.; Espinosa-Urgel, M.; Ramos, J.L.; O’Toole, G.A., Transition from reversible to irreversible attachment during biofilm formation by pseudomonas fluorescens WCS365 requires an ABC transporter and a large secreted protein, Molecular microbiology, 49, 905-918, (2003)
[24] Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., Cuche, B., Castro, E.D., Lachaize, C., Langendijk-Genevaux, P.S., Sigrist, C.J.A.14., N.A.R.N., 2007. The 20 years of PROSITE. Nucleic Acids Research 36, 245-249.
[25] Jeong, S.H.; Bae, I.K.; Park, K.O.; An, Y.J.; Sohn, S.G.; Jang, S.J.; Sung, K.H.; Yang, K.S.; Lee, K.; Young, D.; Lee, S.H., Outbreaks of imipenem-resistant acinetobacter baumannii producing carbapenemases in Korea, Journal of microbiology, 44, (2006)
[26] Katsaragakis, S.; Markogiannakis, H.; Toutouzas, K.; Drimousis, P.; Larentzakis, A.; Theodoraki, E.M., Theodorou D: acinetobacter baumannii infections in a surgical intensive care unit: predictors of multi-drug resistance, World journal of surgery, 32, 1194-1202, (2008)
[27] Kelley, L.A.; Sternberg, M.J.E., Protein structure prediction on the web: a case study using the phyre server, Nature protocols, 4, 363-371, (2009)
[28] Kemp, D.J.; Coppel, R.L.; Anders, R.F., Repetitive proteins and genes of malaria, Annual review of microbiology, 41, (1987)
[29] Knoblauch, N.T.M.; Diger, S.R.; Nfeld, H.-J.S.; Driessen, A.J.M.; Schneider-Mergeneri, J.; Bukau, B., Substrate specificity of the secb chaperone, Journal of biological chemistry, 274, 34219-34225, (1999)
[30] Kolaskar, A.S.; Tongaonkar, P.C., A semi-empirical method for prediction of antigenic determinants on protein antigens, FEBS letters, 276, 172-174, (1990)
[31] Kuroda, A.; Rashid, M.H.; Sekiguchi, J., Molecular cloning and sequencing of the upstream region of the major bacillus subtilis autolysin gene: a modifier protein exhibiting sequence homology to the major autolysin and the spoiid product, Journal of general microbiology 138, 1067-1076, (1992)
[32] Larkin, M.A.; Blackshields, G.; Brown, N.P.; Chenna, R.; McGettigan, P.A.; McWilliam, H.; Valentin, F.; Wallace, I.M.; Wilm, A.; Lopez, R.; Thompson, J.D.; Gibson, T.J.; Higgins, D.G., Clustal W and clustal X version 2.0, Bioinformatics, 23, 2947-2948, (2007)
[33] Lasa, I.; Penadés, J.R., Bap: a family of surface proteins involved in biofilm formation, Research in microbiology, 157, 99-107, (2006)
[34] Latasa, C.; Solano, C.; Penadés, J.R.; Lasa, I., Biofilm-associated proteins, Comptes rendus—biologies, 329, 849-857, (2006)
[35] Latasa, C.; Roux, A.; Toledo-Arana, A.; Ghigo, J.M.; Gamazo, C.; Penadés, J.R.; Lasa, I., Bapa, a large secreted protein required for biofilm formation and host colonization of salmonella enterica serovar enteritidis, Molecular microbiology, 58, 1322-1339, (2005)
[36] Letunic, I.; Bork, P., Interactive tree of life (itol): an online tool for phylogenetic tree display and annotation, Bioinformatics, 23, 127-128, (2007)
[37] Loehfelm, T.W.; Luke, N.R.; Campagnari, A.A., Identification and characterization of an acinetobacter baumannii biofilm-associated protein, Journal of bacteriology, 190, 1036-1044, (2008)
[38] Lu, Z.; Szafron, D.; Greiner, R.; Lu, P.; Wishart, D.S.; Poulin, B.; Anvik, J.; Macdonell, C.; Eisner, R., Predicting subcellular localization of proteins using machine-learned classifiers, Bioinformatics, 20, 547-556, (2004)
[39] Marsden, R.L.; McGuffin, L.J.; Jones, D.T., Rapid protein domain assignment from amino acid sequence using predicted secondary structure, Protein science, 11, 2814-2824, (2002)
[40] O’Toole, G.A.; Kolter, R., Flagellar and twitching motility are necessary for pseudomonas aeruginosa biofilm development, Molecular cell, 30, 295-304, (1998)
[41] Ortiz, A.R.; Strauss, C.E.; Olmea, O., Mammoth (matching molecular models obtained from theory): an automated method for model comparison, Protein science, 11, 2606-2621, (2002)
[42] Perez, F.; Hujer, A.M.; Hujer, K.M.; Decker, B.K.; Rather, P.N.; Bonomo, R.A., Global challenge of multidrug-resistant acinetobacter baumannii, Antimicrobial agents and chemotherapy, 51, 3471-3484, (2007)
[43] Pertz, O.; Bozic, D.; Koch, A.W.; Fauser, C.; Brancaccio, A.; Engel, J., A new crystal structure, ca^{2+} dependence and mutational analysis reveal molecular details of E-cadherin homoassociation, EMBO journal, 18, 1738-1747, (1999)
[44] Petersen, B.; Petersen, T.N.; Andersen, P.; Nielsen, M.; Lundegaard, C., A generic method for assignment of reliability scores applied to solvent accessibility predictions, BMC structural biology, 9, (2009)
[45] Poirel, L.; Nordmann, P., Carbapenem resistance in acinetobacterbaumannii: mechanisms and epidemiology, Clinical microbiology and infection, 12, 826-836, (2006)
[46] Reeder, J.C.; Brown, G.V., Antigenic variation and immune evasion in plasmodium falciparum malaria, Immunology and cell biology, 74, 546-554, (1996)
[47] Saha, S.; Raghava, G.P.S., Bcepred: prediction of continuous B-cell epitopes in antigenic sequences using physico-chemical properties, Lecture notes in computer science, 3239, 197-204, (2004)
[48] Saha, S.; Raghava, G.P.S., Prediction of continuous B-cell epitopes in an antigen using recurrent neural network, Proteins, 65, 40-48, (2006)
[49] Sanz-Aparicio, J.; Hermoso, J.; Grangeiro, T.B.; Calvete, J.J.; Cavada, B.S., The crystal structure of canavalia brasiliensis lectin suggests a correlation between its quaternary conformation and its distinct biological properties from concanavalin A, FEBS letters, 405, 114-118, (1997)
[50] Shankar, V.; Baghdayan, A.S.; Huycke, M.M.; Lindahl, G.; Gilmore, M.S., Infection-derived enterococcus faecalis strains are enriched in esp, a gene encoding a novel surface protein, Infection and immunity, 67, 193-200, (1999)
[51] Shannon, C.E., The mathematical theory of communication, Bell system technical journal, 27, 379-423, (1948) · Zbl 1154.94303
[52] Skeiky, Y.A.; Benson, D.R.; Elwasila, M.; Badaro, R.; Burns, J.M.; Reed, S.G., Antigens shared by leishmania species and trypanosoma cruzi: immunological comparison of the acidic ribosomal P0 proteins, Infection and immunity, 62, 1643-1651, (1994)
[53] Soares, N.C.; Cabral, M.P.; Parreira, J.R.; Gayoso, C.; Barba, M.J.; Bou, G., 2-DE analysis indicates that acinetobacter baumannii displays a robust and versatile metabolism, Proteome science, 7, 37, (2009)
[54] Srinivasa, R.R.; Uma, K.R.; Singh, S.P.; Shashikala, P.; Kanungo, R.; Jayachandran, S.; Prashanth, K., Correlation between biofilm production and multiple drug resistance in imipenem resistant clinical isolates of acinetobacter baumannii, Indian journal of medical microbiology, 26, 333-337, (2008)
[55] Stoodley, P.; Sauer, K.; Davies, D.G.; Costerton, J.W., Biofilms as complex differentiated communities, Annual review of microbiology, 56, 187-209, (2002)
[56] Tolker-Nielsen, T.; Brinch, U.C.; Ragas, P.C.; Andersen, J.B.; Jacobsen, C.S.; Molin, S., Development and dynamics of pseudomonas sp. biofilms, Journal of bacteriology, 182, 6482-6489, (2000)
[57] Vidal, R.; Dominguez, M.; Urrutia, H.; Bello, H.; Garcia, A.; Gonzalez, G.; Zemelman, R., Effect of imipenem and sulbactam on sessile cells of acinetobacter baumannii growing in biofilm, Microbios, 91, 79-87, (1997)
[58] Vidal, R.M.; Dominguez, H.U.; Bello, H.; Gonzalez, G.; Garcia, A.; Zemelman, R., Biofilm formation by acinetobacter baumannii, Microbios, 86, 49-58, (1996)
[59] Villegas, M.V.; Hartstein, A.I., Acinetobacter outbreaks, 1977-2000, Infection control and hospital epidemiology, 24, 284-295, (2003)
[60] Waligora, A.J.; Hennequin, C.; Mullany, P.; Bourlioux, P.; Collignon, A.; Karjalainen, T., Characterization of a cell surface protein of clostridium difficile with adhesive properties, Infection and immunity, 69, 2144-2153, (2001)
[61] Wass, M.N.; Sternberg, M.J.E., Confunc—functional annotation in the twilight zone, Bioinformatics, 24, 798-806, (2008)
[62] Wass, M.N.; Sternberg, M.J., Prediction of ligand binding sites using homologous structures and conservation at CASP8, Proteins, 77, suppl. 9, 147-151, (2009)
[63] Wilkinson, D.L.; Harrison, R.G., Predicting the solubility of recombinant proteins in Escherichia coli, Nature biotechnology, 9, 443-448, (1991)
[64] Xiong, J.-P.; Stehle, T.; Zhang, R.; Joachimiak, A.; Frech, M.; Goodman, S.L.; Arnaout, M.A., Crystal structure of the extracellular segment of integrin alpha vbeta 3 in complex with an arg – gly – asp ligand, Science, 296, 151-155, (2002)
[65] Yu, C.S.; Chen, Y.C.; Lu, C.H.; Hwang, J.K., Prediction of protein subcellular localization, Proteins: structure, function, and bioinformatics, 64, 643-651, (2006)
[66] Zhang, Y.; Skolnick, J., TM-align: a protein structure alignment algorithm based on TM-score, Nucleic acids research, 33, 2302-2309, (2005)
[67] Zhou, Y.; Yang, W.; Kirberger, M.; Lee, H.-W.; Ayalasomayajula, G.; Yang, J.J., Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins, Proteins: structure, function, and bioinformatics, 65, 643-655, (2006)
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