An integrated structural proteomics approach along the druggable genome of Corynebacterium pseudotuberculosis species for putative druggable targets

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• 作者：Leandro G Radusky ; Syed Shah Hassan ; Esteban Lanzarotti ; Sandeep Tiwari…
• 关键词：Corynebacterium pseudotuberculosis (Cp) ; Druggable genome ; Structural proteomics approach ; Putative globally/conserved druggable/bindable targets ; Caseous lymphadenitis
• 刊名：BMC Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：5-supp
• 全文大小：664 KB
• 参考文献：1.Hassan SS, Schneider MP, Ramos RT, Carneiro AR, Ranieri A, Guimaraes LC, et al: Whole-genome sequence of Corynebacterium pseudotuberculosis strain Cp162, isolated from camel. J Bacteriol. 2012, 194 (20): 5718-5719. 10.1128/JB.01373-12.PubMedCentral CrossRef PubMed
  2.Dorella FA, Pacheco LG, Oliveira SC, Miyoshi A, Azevedo V: Corynebacterium pseudotuberculosis: microbiology, biochemical properties, pathogenesis and molecular studies of virulence. Vet Res. 2006, 37 (2): 201-218. 10.1051/vetres:2005056.CrossRef PubMed
  3.Soares SC, Trost E, Ramos RT, Carneiro AR, Santos AR, Pinto AC, et al: Genome sequence of Corynebacterium pseudotuberculosis biovar equi strain 258 and prediction of antigenic targets to improve biotechnological vaccine production. J Biotechnol. 2013, 167 (2): 135-141. 10.1016/j.jbiotec.2012.11.003.CrossRef PubMed
  4.Khamis A, Raoult D, La Scola B: Comparison between rpoB and 16S rRNA gene sequencing for molecular identification of 168 clinical isolates of Corynebacterium. J Clin Microbiol. 2005, 43 (4): 1934-1936. 10.1128/JCM.43.4.1934-1936.2005.PubMedCentral CrossRef PubMed
  5.Luis MA, Lunetta AC: [Alcohol and drugs: preliminary survey of Brazilian nursing research]. Rev Lat Am Enfermagem. 2005, 1219-1230. 13 Spec No
  6.Peel MM, Palmer GG, Stacpoole AM, Kerr TG: Human lymphadenitis due to Corynebacterium pseudotuberculosis: report of ten cases from Australia and review. Clin Infect Dis. 1997, 24 (2): 185-191. 10.1093/clinids/24.2.185.CrossRef PubMed
  7.Williamson LH: Caseous lymphadenitis in small ruminants. Vet Clin North Am Food Anim Pract. 2001, 17 (2): 359-371. viiPubMed
  8.Kinnings SL, Xie L, Fung KH, Jackson RM, Xie L, Bourne PE: The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol. 2010, 6 (11): e1000976-10.1371/journal.pcbi.1000976.PubMedCentral CrossRef PubMed
  9.Anand P, Sankaran S, Mukherjee S, Yeturu K, Laskowski R, Bhardwaj A, et al: Structural annotation of Mycobacterium tuberculosis proteome. PLoS One. 2011, 6 (10): e27044-10.1371/journal.pone.0027044.PubMedCentral CrossRef PubMed
  10.Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A: Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct. 2000, 29: 291-325. 10.1146/annurev.biophys.29.1.291.CrossRef PubMed
  11.Radusky L, Defelipe LA, Lanzarotti E, Luque J, Barril X, Marti MA, Turjanski AG: TuberQ: a Mycobacterium tuberculosis protein druggability database. Database (Oxford). 2014, 2014 (0): bau035-10.1093/database/bau035.CrossRef
  12.Ruiz JC, D'Afonseca V, Silva A, Ali A, Pinto AC, Santos AR, et al: Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains. PLoS One. 2011, 6 (4): e18551-10.1371/journal.pone.0018551.PubMedCentral CrossRef PubMed
  13.Bilofsky HS, Burks C: The GenBank genetic sequence data bank. Nucleic Acids Res. 1988, 16 (5): 1861-1863. 10.1093/nar/16.5.1861.PubMedCentral CrossRef PubMed
  14.Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, et al: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2011, 39 (Database issue): D38-D51.PubMedCentral CrossRef PubMed
  15.Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25 (17): 3389-3402. 10.1093/nar/25.17.3389.PubMedCentral CrossRef PubMed
  16.Li W, Jaroszewski L, Godzik A: Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics. 2001, 17 (3): 282-283. 10.1093/bioinformatics/17.3.282.CrossRef PubMed
  17.Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A: Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci. Edited by: John E Coligan [et al]. 2007, Chapter 2 (Unit 2.9):
  18.Sali A, Blundell TL: Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993, 234 (3): 779-815. 10.1006/jmbi.1993.1626.CrossRef PubMed
  19.Melo F, Feytmans E: Assessing protein structures with a non-local atomic interaction energy. J Mol Biol. 1998, 277 (5): 1141-1152. 10.1006/jmbi.1998.1665.CrossRef PubMed
  20.Melo F, Sali A: Fold assessment for comparative protein structure modeling. Protein Sci. 2007, 16 (11): 2412-2426. 10.1110/ps.072895107.PubMedCentral CrossRef PubMed
  21.Benkert P, Kunzli M, Schwede T: QMEAN server for protein model quality estimation. Nucleic Acids Res. 2009, 37 (Web Server issue): W510-W514.PubMedCentral CrossRef PubMed
  22.Melo F, Sanchez R, Sali A: Statistical potentials for fold assessment. Protein Sci. 2002, 11 (2): 430-448.PubMedCentral CrossRef PubMed
  23.Velec HF, Gohlke H, Klebe G: DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. Journal of medicinal chemistry. 2005, 48 (20): 6296-6303. 10.1021/jm050436v.CrossRef PubMed
  24.Soares SC, Abreu VA, Ramos RT, Cerdeira L, Silva A, Baumbach J, et al: PIPS: pathogenicity island prediction software. PLoS One. 2012, 7 (2): e30848-10.1371/journal.pone.0030848.PubMedCentral CrossRef PubMed
  25.Barh D, Gupta K, Jain N, Khatri G, Leon-Sicairos N, Canizalez-Roman A, et al: Conserved host-pathogen PPIs. Globally conserved inter-species bacterial PPIs based conserved host-pathogen interactome derived novel target in C. pseudotuberculosis, C. diphtheriae, M. tuberculosis, C. ulcerans, Y. pestis, and E. coli targeted by Piper betel compounds. Integr Biol (Camb). 2013, 5 (3): 495-509. 10.1039/c2ib20206a.CrossRef
  26.Barh D, Jain N, Tiwari S, Parida BP, D'Afonseca V, Li L, et al: A novel comparative genomics analysis for common drug and vaccine targets in Corynebacterium pseudotuberculosis and other CMN group of human pathogens. Chem Biol Drug Des. 2011, 78 (1): 73-84. 10.1111/j.1747-0285.2011.01118.x.CrossRef PubMed
  27.Zhang R, Ou HY, Zhang CT: DEG: a database of essential genes. Nucleic Acids Res. 2004, 32 (Database issue): D271-D272.PubMedCentral CrossRef PubMed
  28.Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28 (1): 27-30. 10.1093/nar/28.1.27.PubMedCentral CrossRef PubMed
  29.Yoon SH, Park YK, Lee S, Choi D, Oh TK, Hur CG, Kim JF: Towards pathogenomics: a web-based resource for pathogenicity islands. Nucleic Acids Res. 2007, 35 (Database issue): D395-D400.PubMedCentral CrossRef PubMed
  30.Magrane M, Consortium U: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011, 2011: bar009-CrossRef
  31.Yu CS, Lin CJ, Hwang JK: Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci. 2004, 13 (5): 1402-1406. 10.1110/ps.03479604.PubMedCentral CrossRef PubMed
  32.Garg SK, Alam MS, Kishan KV, Agrawal P: Expression and characterization of alpha-(1,4)-glucan branching enzyme Rv1326c of Mycobacterium tuberculosis H37Rv. Protein Expr Purif. 2007, 51 (2): 198-208. 10.1016/j.pep.2006.08.005.CrossRef PubMed
  33.Sanchez-Martinez M, Marcos E, Tauler R, Field M, Crehuet R: Conformational compression and barrier height heterogeneity in the N-acetylglutamate kinase. J Phys Chem B. 2013, 117 (46): 14261-14272. 10.1021/jp407016v.CrossRef PubMed
  34.Anishetty S, Pulimi M, Pennathur G: Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysis. Comput Biol Chem. 2005, 29 (5): 368-378. 10.1016/j.compbiolchem.2005.07.001.CrossRef PubMed
  35.Mathieu M, Debousker G, Vincent S, Viviani F, Bamas-Jacques N, Mikol V: Escherichia coli FolC structure reveals an unexpected dihydrofolate binding site providing an attractive target for anti-microbial therapy. J Biol Chem. 2005, 280 (19): 18916-18922. 10.1074/jbc.M413799200.CrossRef PubMed
  36.Pillai B, Cherney MM, Diaper CM, Sutherland A, Blanchard JS, Vederas JC, James MNG: Structural insights into stereochemical inversion by diaminopimelate epimerase: An antibacterial drug target. Proc Natl Acad Sci U S A. 2006, 103 (23): 8668-8673. 10.1073/pnas.0602537103.PubMedCentral CrossRef PubMed
  37.Jia DF: [Novel targets for antibiotics discovery: riboswitches]. Yao Xue Xue Bao. 2013, 48 (9): 1361-1368.PubMed
  38.Hassan SS, Tiwari S, Guimarães LC, Jamal SB, Folador E, Sharma NB, et al: Proteome Scale Comparative Modeling for Conserved Drug and Vaccine Targets Identification in Corynebacterium pseudotuberculosis. BMC Genomics. 2014, 15 (Suppl 7): S3-PubMedCentral PubMed
  
• 作者单位：Leandro G Radusky (1)
  Syed Shah Hassan (3)
  Esteban Lanzarotti (1)
  Sandeep Tiwari (3)
  Syed Babar Jamal (3)
  Javed Ali (4)
  Amjad Ali (5)
  Rafaela Salgado Ferreira (6)
  Debmalya Barh (7)
  Artur Silva (8)
  Adrián G Turjanski (1) (2)
  Vasco AC Azevedo (3)
  
  1. Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Buenos Aires, C1428EHA, Argentina
  3. PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
  4. Department of Chemistry, Kohat University of Science and Technology (KUST), KPK, Pakistan
  5. Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences & Technology (NUST), Islamabad, Pakistan
  6. Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
  7. Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, India
  8. Institute of Biological Sciences, Federal University of Pará, Belém, Para, Brazil
  2. INQUIMAE/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Buenos Aires, C1428EHA, Argentina
  
• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background The bacterium Corynebacterium pseudotuberculosis (Cp) causes caseous lymphadenitis (CLA), mastitis, ulcerative lymphangitis, and oedema in a number of hosts, comprising ruminants, thereby intimidating economic and dairy industries worldwide. So far there is no effective drug or vaccine available against Cp. Previously, a pan-genomic analysis was performed for both biovar equi and biovar ovis and a Pathogenicity Islands (PAIS) analysis within the strains highlighted a large set of proteins that could be relevant therapeutic targets for controlling the onset of CLA. In the present work, a structural druggability analysis pipeline was accomplished along 15 previously sequenced Cp strains from both biovar equi and biovar ovis.