Curation, integration and visualization of bacterial virulence factors in PATRIC

Bioinformatics

Volumn 31, Issue 2, 2015, Pages 252-258

  Mao, Chunhong ^a   Abraham, David ^a   Wattam, Alice R ^a   Wilson, Meredith J C ^a   Shukla, Maulik ^a   Yoo, Hyun Seung ^a   Sobral, Bruno W ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); BARTONELLA; ESCHERICHIA; LISTERIA; MYCOBACTERIUM; SALMONELLA; SHIGELLA;

BACTERIAL PROTEIN; VIRULENCE FACTOR;

BACTERIAL GENOME; BACTERIAL INFECTION; BACTERIUM; CLASSIFICATION; COMPUTER GRAPHICS; FACTUAL DATABASE; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HUMAN; METABOLISM; MICROBIOLOGY; PATHOGENICITY; PROTEIN ANALYSIS; SYSTEM ANALYSIS; VIRULENCE;

BACTERIA; BACTERIAL INFECTIONS; BACTERIAL PROTEINS; COMPUTER GRAPHICS; DATABASES, FACTUAL; GENE EXPRESSION PROFILING; GENOME, BACTERIAL; GENOMICS; HUMANS; PROTEIN INTERACTION MAPPING; SYSTEMS INTEGRATION; VIRULENCE; VIRULENCE FACTORS;

EID: 84928993237     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu631     Document Type: Article

References (25)

1. Casadevall, A. and Pirofski, L.A. (2009) Virulence factors and their mechanisms of action: the view from a damage-response framework. J. Water Health, 7 (Suppl. 1), S2-S18.
2. Chen, L. et al. (2012) VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res., 40, D641-D645.
3. de Lorenzo, V. et al. (1986) Aerobactin biosynthesis and transport genes of plasmid ColV-K30 in Escherichia coli K-12. J. Bacteriol., 165, 570-578.
4. De Voss, J.J. et al. (2000) The salicylate-derived mycobactin siderophores of Mycobacterium tuberculosis are essential for growth in macrophages. Proc. Natl Acad. Sci. USA, 97, 1252-1257.
5. Driscoll, T. et al. (2011) Integration and visualization of host-pathogen data related to infectious diseases. Bioinformatics, 27, 2279-2287.
6. Gillespie, J.J. et al. (2011) PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect. Immun., 79, 4286-4298.
7. Kato, L. (1985) Absence of mycobactin in Mycobacterium leprae; probably a microbe dependent microorganism implications. Indian J. Lepr., 57, 58-70.
8. Keen, E.C. (2012) Paradigms of pathogenesis: targeting the mobile genetic elements of disease. Front. Cell Infect. Microbiol., 2, 161.
9. Maiden, M.C. (2006) Multilocus sequence typing of bacteria. Ann. Rev. Microbiol., 60, 561-588.
10. Meyer, F. et al. (2009) FIGfams: yet another set of protein families. Nucleic Acids Res., 37, 6643-6654.
11. Morrison, N.E. (1995) Mycobacterium leprae iron nutrition: bacterioferritin, myco-bactin, exochelin and intracellular growth. Int. J. Lepr. Other Mycobact. Dis., 63, 86-91.
12. Ngeleka, M. et al. (2002) Pathotypes of avian Escherichia coli as related to tsh-, pap-, pil-, iuc-DNA sequences, and antibiotic sensitivity of isolates from internal tissues and the cloacae of broilers. Avian Dis., 46, 143-152.
13. Ogata, H. et al. (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 27, 29-34.
14. Onderdonk, A.B. (1988) Host-microbe interactions: virulence mechanisms of bacterial pathogens. Science, 240, 1352-1360.
15. Overbeek, R. et al. (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res., 42, D206-D214.
16. Pierce, J.R. et al. (1983) Two fep genes are required for ferrienterochelin uptake in Escherichia coli K-12. J. Bacteriol., 155, 330-336.
17. Pruitt, K.D. et al. (2012) NCBI Reference sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
18. Quadri, L.E. et al. (1998) Identification of a Mycobacterium tuberculosis gene cluster encoding the biosynthetic enzymes for assembly of the virulence-conferring siderophore mycobactin. Chem. Biol., 5, 631-645.
19. Reddy, P.V. et al. (2013) Disruption of mycobactin biosynthesis leads to attenuation of Mycobacterium tuberculosis for growth and virulence. J. Infect. Dis., 208, 1255-1265.
20. Rodriguez, G.M. et al. (2002) ideR, An essential gene in mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism: oxidative stress response. Infect. Immun., 70, 3371-3381.
21. Tatusov, R.L. et al. (1997) A genomic perspective on protein families. Science, 278, 631-637.
22. UniProt, C. (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res., 39, D214-D219.
23. Wattam, A.R. et al. (2014) PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res., 42, D581-D591.
24. Wu, H.J. et al. (2008) Discovery of virulence factors of pathogenic bacteria. Curr. Opin. Chem. Biol., 12, 93-101.
25. Zhou, C.E. et al. (2007) MvirDB-A microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications. Nucleic Acids Res., 35, D391-D394.