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2015, Number 4

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Rev Mex Patol Clin Med Lab 2015; 62 (4)

Genome-scale analysis of protein functions and evolution from acute diarrheal disease-causing bacteria

Moya-Salazar JJ, Ubidia-Incio RA

Language: Spanish
References: 42
Page: 206-219
PDF size: 480.69 Kb.


ABSTRACT

An analytical-correlational cross section study was designed to analyze the genomes of acute diarrheal disease (ADD) causing bacteria and functional relations were established between protein functions based on the analysis performed by COGs database and TaxPlot tools. We counted the percentages of COGs for every category for each species, and determined the percentages based on the total number of COGs for each species. We made an interproteic comparative analysis for each species using TaxPlot and a phylogenetic classification for the proteins codified in complete genomes using the UPGMA algorithm. A total of 15 microorganisms were included (9 AAD-causing bacteria and 6 saprophytic bacteria). Eleven of these 15 bacteria had higher COGs in the categories J –12.25%– (6 ADD-causing bacteria and 5 saprophytic bacteria). The metabolic functional categories were uniform, and the functional categories Y (0.00%), Z (0.03%), B (0.01%) and A (0.05%) had the smallest quantities. COGs can be extrapolated into exact data that describe the protein profile of these pathogenic agents. The TaxPlot phylogenetic method reduces analysis time and represents an holistic approximation for the study of the phylogenetic relations at a proteomic level.


REFERENCES

  1. MINSA. Plan de comunicaciones. Prevención de enfermedades diarreicas agudas (EDA) y cólera 2014. Versión preliminar. Disponible en: http://www.minsa.gob.pe/portada/Especiales/2014/ lavadomanos/archivo/Plan_de_comunic aciones-prevencion_de_ enfermedades_diarreicas_y_colera.pdf

  2. World Health Organization. The world health report: making a difference. Geneva: World Health Organization; 1999.

  3. Moya SJ, Pio DL, Terán VA, Olivo LJ. Yield diagnosis of blood agar with filter against karmali agar for isolation of Campylobacter in stool culture. J Microbiol Meth. 2015; [en prensa].

  4. Winn W, Allen S, Janda W, Koneman E, Procop G, Schreckenberger P et al. Koneman’s color atlas and textbook of diagnostic microbiology. 6th ed. Philadelphia: Lippincott Williams & Wilkins; 2006.

  5. Murga H, Huicho L, Guevara G. Acute diarrhoea and Campylobacter in Peruvian children: a clinical and epidemiologic approach. J Trop Pediatr. 1993; 39 (6): 338-341.

  6. Seas C, Alarcón M, Aragón JC, Beneit S, Quiñonez M, Guerra H et al. Surveillance of bacterial pathogens associated with acute diarrhea in Lima. Int Infect Dis. 2000; 4 (2): 96-99.

  7. Cama RI, Parashar UD, Taylor DN, Hickey T, Figueroa D, Ortega YR et al. Enteropathogens and other factors associated with severe disease in children with acute watery diarrhea in Lima, Peru. J Infect Dis. 1999; 179 (5): 1139-144.

  8. Roman LT, Michael YG, Darren AN, Eugene VK. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000; 28 (1): 33-36.

  9. Thorat SS, Thakare VP. Analysis of Staphylococcus using comparative genomics. IJSER. 2013; 4 (12): 1775-1779.

  10. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Church DM et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2005; 33 (Database issue): D39-D45.

  11. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science. 1997; 278 (5338): 631-637.

  12. Roman LT, Michael YG, Darren AN, Eugene VK. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000; 28 (1): 33-36.

  13. Wheeler D, Benson D, Rapp B. Using TaxPlot to compare genomes. Bethesda: NCBI News; 2001: p. 1-2.

  14. Makarova SK, Wolf IY, Koonin VE. Archaeal clusters of orthologous genes (arCOGs): an update and application for analysis of shared features between thermococcales, methanococcales and methanobacteriales. Life. 2015; 5: 818-840.

  15. Neupane S, Finlay RD, Alström S, Goodwin L, Kyrpides NC, Lucas S et al. Complete genome sequence of Serratia plymuthica strain AS12. Stand Genomic Sci. 2012; 6: 165-173.

  16. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ et al. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature. 2000; 406 (6795): 477-483.

  17. Bhagwat AA, Bhagwat M. Methods and tools for comparative genomics of food borne pathogens. Foodborne Pathog Dis. 2008; 5 (4): 487-497.

  18. Siddaramappa SS. Comparative and functional genomic studies of Histophilus somni (Haemophilus somnus) [Thesis]. Blacksburg: Virginia Polytechnic Institute and State University; 2007.

  19. Montiel AF. Flora bacteriana habitual. Boletín Escuela de Medicina U.C. Pontificia Universidad Católica de Chile. 1997; 26: 133-139.

  20. Kuske RC, Ticknor LO, Miller ME, Dunbar JM, Davis JA, Barns SM et al. Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. Appl Environ Microbiol. 2002; 68 (4): 1854-1863.

  21. Moran AN, Russell JA, Koga R, Fukatsu T. Evolutionary relationships of three new species of Enterobacteriaceae living as symbionts of aphids and other insects. Appl Environ Microbiol. 2005; 71 (6): 3302-3310.

  22. Chieh-Hua L, Chun-Yi L, Chao AH, Feng-Chi C. Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes. BMC Bioinformatics. 2011; 12 (Suppl 9): S19.

  23. Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J et al. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature. 2001; 413 (6858): 848-852.

  24. Salvucci E. Selfishness, warfare, and economics; or integration, cooperation, and biology. Cell Infect Microbiol. 2012; 54 (2): 1-12.

  25. Huddleston RJ. Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes. Infect Drug Resist. 2014; 7: 167-176.

  26. Petty NK, Bulgin R, Crepin VF, Cerdeño-Tárraga AM, Schroeder GN, Quail MA et al. The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli. J Bacteriol. 2010; 192 (2): 525-538.

  27. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M et al. The complete genome sequence of Escherichia coli K-12. Science. 1997; 277 (5331): 1453-1462.

  28. Perna NT, Plunkett G 3rd, Burland V, Mau B, Glasner JD, Rose DJ et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature. 2001; 409 (6819): 529-533.

  29. Barabote RD, Saier MH Jr. Comparative genomic analyses of the bacterial phosphotransferase system. Microbiol Mol Biol Rev. 2005; 69: 608-634.

  30. Bell KS, Sebaihia M, Pritchard L, Holden MTG, Hyman LJ, Holeva MC et al. Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc Natl Acad Sci USA. 2004; 101: 11105-11110.

  31. Götz A, Eylert E, Eisenreich W, Goebe W. Carbon metabolism of enterobacterial human pathogens growing in epithelial colorectal adenocarcinoma (Caco-2) cells. PLoS One. 2010; 5 (5): 1-14.

  32. Emerson AE. Dynamic homeostasis: a unifying principle in organic, social and ethical evolution. Zygon. 1968; 3 (2): 129-168.

  33. Alteri CJ, Mobley HLT. Escherichia coli physiology and metabolism dictates adaptation to diverse host microenvironments. Curr Opin Microbiol. 2012; 15 (1): 3-9.

  34. Luchi S, Weiner L. Cellular and molecular physiology of Escherichia coli in the adaptation to aerobic environments. J Biochem. 1996; 120: 1055-1063.

  35. Barkay T, Smets BF. Horizontal gene flow in microbial communities. ASM News. 2005; 71: 412-419.

  36. Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol. 2005; 3: 722-732.

  37. Sabbagh SC, Forest CG, Lepage C, Leclerc JM, Daigle F. So similar, yet so different: uncovering distinctive features in the genomes of Salmonella enterica serovars typhimurium and Typhi. FEMS Microbiol Lett. 2010; 305 (1): 1-13.

  38. Welch AR, Burland V, Plunkett G, Redford P, Roesch P, Rasko D et al. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA. 2002; 99 (26): 17020-17024.

  39. Ghosh A, Paul K, Chowdhury R. Role of the histone-like nucleoid structuring protein in colonization, motility and bile dependant repression of virulence gene expression in Vibrio cholerae. Infect Immun. 2006; 74 (5): 3060-3064.

  40. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science. 2006; 311 (5765): 1283-1287.

  41. Stecher B, Denzler R, Maier L, Bernet F, Sanders MJ, Pickard DJ, et al. Gut inflammation can boost horizontal gene transfer between pathogenic and comensal Enterobacteriaceae. PNAS. 2012; 109 (4): 1269-1274.

  42. Akortha EE, Filgona J. Transfer of gentamicin resistance genes among Enterobacteriaceae isolated from the out patents with urinary tract infections attending 3 hospitals in Mubi, Adamawa State. Sci Res Essays. 2009; 4 (8): 745-752.




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