Current Science

Open Access Open Access  Restricted Access Subscription Access

Mtb-HID:A Unified Database of Host–Pathogen Interaction for Various Mycobacterium tuberculosis Strains


Affiliations
1 Department of Biotechnology, Graphic Era Deemed to be University, Dehradun 248 002, India
 

Databases developed till now for studying human– Mycobacterium tuberculosis (MTB) host–pathogen interactions are scarce and pertain to specific strains of pathogen. Therefore, in the present study, a database (Mtb-HID) has been developed to serve as a unified host–pathogen interaction platform with information on interaction between various strains of MTB and humans. Mtb-HID is different from other databases since it houses information about multiple strains and is an extensive integrated repository of experimental host–pathogen protein–protein interaction (HP-PPIs) data imported from various public databases and derived from interolog-based HP-PPIs. Currently, Mtb-HID hosts records of interaction between five MTB strains and human host. It is freely accessible at http://www.pantlab.co.in/mtb-hid/.

Keywords

Database, Host–Pathogen Interaction, Humans, Mycobacterium tuberculosis.
User
Notifications
Font Size

  • WHO, Global tuberculosis report 2018, World Health Organization, Geneva, 2018.

  • Manabe, Y. C. et al., Different strains of Mycobacterium tuberculosis cause various spectrums of disease in the rabbit model of tuberculosis. Infect. Immunol., 2003, 71(10), 6004–6011.

  • Toossi, Z., The inflammatory response in Mycobacterium tuberculosis infection. In Inflammation (ed. Cronstein, B. N.), Springer, The Netherlands, 2001, pp. 139–151.

  • Koch, A., and Mizrahi, V., Mycobacterium tuberculosis. Trends Microbiol., 2018, 26(6), 555–556.

  • Farver, C. F. and Jagirdar, J., Mycobacterial diseases. In Pulmonary Pathology (ed. Tomashefski, J. F.), 2018, 2nd edn, pp. 201–216.

  • Cole, S. et al., Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature, 1998, 393(6685), 537.

  • Brown, T., Nikolayevskyy, V., Velji, P. and Drobniewski, F., Associations between Mycobacterium tuberculosis strains and phenotypes. Emerg. Infect. Dis., 2010, 16(2), 272.

  • Bouwman, A. S. et al., Genotype of a historic strain of Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA, 2012, 109(45), 18511–18516.

  • Stucki, D. et al., Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages. Nature Genet., 2016, 48(12), 1535.

  • Hershberg, R., Human host range of Mycobacterium tuberculosis. Nature Genet., 2016, 48(12), 1453.

  • Yimer, S. A. et al., Mycobacterium tuberculosis lineage 7 strains are associated with prolonged patient delay in pulmonary tuberculosis patients in Amhara region, Ethiopia. J. Clin. Microbiol., 2015, 53(4), 1301–1309.

  • Borrell, S. and Gagneux, S., Infectiousness, reproductive fitness and evolution of drugresistant Mycobacterium tuberculosis (state of the art). Int. J. Tuberc. Lung Dis., 2009, 13(12), 1456–1466.

  • Comas, I. et al., Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nature Genet., 2013, 45(10), 1176–1182.

  • Sen, R., Nayak, L. and De, R. K., A review on host–pathogen interactions: classification and prediction. Eur. J. Clin. Microbiol. Infect. Dis., 2016, 35(10), 1581–1599.

  • Rana, A., Ahmed, M., Rub, A. and Akhter, Y., A tug-of-war between the host and the pathogen generates strategic hotspots for the development of novel therapeutic interventions against infectious diseases. Virulence, 2015, 6(6), 566–580.

  • Bonetta, L., Protein–protein interactions: interactome under construction. Nature, 2010, 468(7325), 851.

  • Huo, T., Liu, W., Guo, Y., Yang, C., Lin, J. and Rao, Z., Prediction of host–pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs. BMC Bioinformat., 2015, 16(1), 100.

  • Winnenburg, R., Baldwin, T. K., Urban, M., Rawlings, C., Köhler, J. and Hammond-Kosack, K. E., PHI-base: a new database for pathogen host–interactions. Nucleic Acids Res. (suppl. 1), 2006, 34, D459–D464.

  • Xiang, Z., Tian, Y. and He, Y., PHIDIAS: a pathogen–host interaction data integration and analysis system. Genome. Biol., 2007, 8(7), R150.1–R150.15.

  • Wattam, A. R. et al., PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids. Res., 2013, 42(D1), D581–D591.

  • Rapanoel, H. A., Mazandu, G. K. and Mulder, N. J., Predicting and analyzing interactions between Mycobacterium tuberculosis and its human host. PLoS ONE, 2013, 8(7), e67472, 1–4.

  • Zhou, H., Gao, S., Nguyen, N. N., Fan, M., Jin, J., Liu, B. and Wong, L., Stringent homology-based prediction of H. sapiens–M. tuberculosis H37Rv protein–protein interactions. Biol. Direct, 2014, 9(1), 5, 1–30.

  • Chen, C., Huang, H. and Wu, C. H., Protein bioinformatics databases and resources. In Protein Bioinformatics, Humana Press, New York, USA, 2017, pp. 3–39.

  • Garcia-Garcia, J., Schleker, S., Klein-Seetharaman, J. and Oliva, B., BIPS: BIANA Interolog Prediction Server. A tool for protein– protein interaction inference. Nucleic Acids Res., 2012, 40(W1), W147–W151.

  • Powell, S. et al., eggNOG v3. 0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res., 2011, 40(D1), D284–D289.

  • Walhout, A. J. et al., Protein interaction mapping in C. elegans using proteins involved in vulval development. Science, 2000, 287(5450), 116–122.

  • UniProt Consortium, UniProt: the universal protein knowledgebase. Nucleic Acids Res., 2017, 45(D1), D158–D169.

  • Cohen, T., van Helden, P. D., Wilson, D., Colijn, C., McLaughlin, M. M., Abubakar, I. and Warren, R. M., Mixed-strain Mycobacterium tuberculosis infections and the implications for tuberculosis treatment and control. Clin. Microbiol. Rev., 2012, 25(4), 708– 719.


Abstract Views: 509

PDF Views: 120




  • Mtb-HID:A Unified Database of Host–Pathogen Interaction for Various Mycobacterium tuberculosis Strains

Abstract Views: 509  |  PDF Views: 120

Authors

Kumud Pant
Department of Biotechnology, Graphic Era Deemed to be University, Dehradun 248 002, India
Devvret
Department of Biotechnology, Graphic Era Deemed to be University, Dehradun 248 002, India
Neema Tufchi
Department of Biotechnology, Graphic Era Deemed to be University, Dehradun 248 002, India
Ajay Pandaya
Department of Biotechnology, Graphic Era Deemed to be University, Dehradun 248 002, India
Ashish Thapliyal
Department of Biotechnology, Graphic Era Deemed to be University, Dehradun 248 002, India

Abstract


Databases developed till now for studying human– Mycobacterium tuberculosis (MTB) host–pathogen interactions are scarce and pertain to specific strains of pathogen. Therefore, in the present study, a database (Mtb-HID) has been developed to serve as a unified host–pathogen interaction platform with information on interaction between various strains of MTB and humans. Mtb-HID is different from other databases since it houses information about multiple strains and is an extensive integrated repository of experimental host–pathogen protein–protein interaction (HP-PPIs) data imported from various public databases and derived from interolog-based HP-PPIs. Currently, Mtb-HID hosts records of interaction between five MTB strains and human host. It is freely accessible at http://www.pantlab.co.in/mtb-hid/.

Keywords


Database, Host–Pathogen Interaction, Humans, Mycobacterium tuberculosis.

References





DOI: https://doi.org/10.18520/cs%2Fv118%2Fi2%2F292-297