Bioinformatics Based Structural Analysis of Cytochrome P450 genes in Candida tropicalis
https://dx.doi.org/10.4314/njpar.v43i2.17
Keywords:
Genome, Gene duplication, Evolutionary history, Cytochrome P450, Candida tropicalisAbstract
Cytochrome P450 is a superfamily of enzymes that contain heme as a cofactor that functions as monooxygenases. These proteins are responsible for the oxidation of fatty acids, steroids, and xenobiotics, and the synthesis and breakdown of various hormones. Candida tropicalis has been identified as the leading cause of Candidemia, a bloodstream infection that contributes to the high mortality rate worldwide. So far, no research has reported a detailed study of the cytochrome P450 genes in the genome of Candida tropicalis. Hence, a detailed analysis involving the identification and characterisation of cytochrome P450 genes from the Candida tropicalis genome would provide valuable information about the evolutionary history and functions of the Cytochrome P450 gene family. In this study, 32 Cytochrome P450 genes were identified in Candida tropicalis, which were further grouped into four clades. The results show that most cytochrome P450 families in Candida tropicalis have a close phylogenetic relationship.And diversity might have mainly been a result of gene duplication. Clans and family groupings, alongside their putative functions and subcellular localisation, also showed the possible relationship between the genes’ cellular location and their functions. The results obtained from this study pave the way for a broader and more detailed analysis of the specific functions of each of the Cytochrome P450 genes in Candida tropicalis, as well as possible ways of altering their functions to find a way of curbing/eradicating the negative effect of Candida tropicalis and its contribution to the high rate of mortality worldwide.
References
Doddapaneni, H., Chakraborty, R., and Yadav, J. S. (2005). Genome-wide structural and evolutionary analysis of the P450 monooxygenase genes (P450ome) in the white rot fungus Phanerochaete chrysosporium: evidence for gene duplications and extensive gene clustering.
BMC Genomics,6: 92.
Kelly, D. E., Krasevec, N., Mullins, J., and Nelson, D.R. (2009). The CYPome (cytochrome P450 complement) of Aspergillus nidulans. Fungal Genetics and Biology, 46, S53–S61.
Zarafi, A.B. and Dauda, W.P. (2019). Exploring the importance of fungi in agricultural biotechnology. International Journal of Agricultural Science and Veterinary Medicine, 7: 1-12.
Lamb, D. C., Skaug, T., Song, H. L., Jackson, C. J., Podust, L. M., Waterman, M. R., and Kelly, S. L. (2002). The cytochrome P450 complement (CYPome) of Streptomyces coelicolor A3 (2). Journal of Biological Chemistry, 277(27): 24000-24005.
Soanes, D. M., Alam, I., Cornell, M., Wong, H. M., Hedeler, C., Paton, N. W., Rattray, M., Hubbard, S. J., Oliver, S. G. and Talbot, N.J. (2008). Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis. PLoS One, 3(6):
p.e2300.
Nelson, D. R. (2006). "Cytochrome P450 Nomenclature, 2004." In Cytochrome P450 protocols, Totowa, NJ, Humana Press, pp.1-10.
Mastromarino, P., Vitali, B. and Mosca, L.(2013). Bacterial vaginosis: a review on clinical trials with probiotics. New Microbiology, 36(3): 229-238.
Brown, G. D., Denning, D. W., Gow, N. A., Levitz, S. M., Netea, M. G., and White, T. C. (2012). Hidden killers: human fungal infections. Science Translational Medicine, 4(165), 165rv13-165rv13.
Marcos-Zambrano, L. J., Escribano, P., Bouza, E. and Guinea, J. (2014). Production of biofilm by Candida and nonCandida spp. isolates causing fungemia: comparison of biomass production and metabolic activity and development of cutoff points. International Journal of Medical Microbiology, 304(8), 1192-1198. doi:10.1016/j.ijmm.2014.08.012
Choi, M. J., Won, E. J., Shin, J. H., Kim, S. H., Lee, W. G., Kim, M. N., Lee, K., Shin, .G., Suh, S.P., Ryang, D. W. and Im, Y. J. (2016). Resistance mechanisms and clinical features of fluconazole-non susceptible Candida tropicalis isolates compared with fluconazole-less-susceptible isolates. Antimicrobial Agents and Chemotherapy, 60: 3653–3661. doi: 10.1128/AAC.02652- 15.
Zuza-Alves, D. L., Silva-Rocha, W. P. and Chaves, G. M. (2017). An update on Candida tropicalis based on basic and clinical approaches. Frontiers in microbiology, 8: 1927.
Rao, R. S., Jyothi, C. P., Prakasham, R. S., Sarma, P. N., and Rao, L. V. (2006). Xylitol production from corn fiber and sugarcane bagasse hydrolysates by Candida tropicalis. Bioresource Technology, 97: 1974–1978. doi: 10.1016/j.biortech.2005.08.015
Ra, C. H., Jung, J. H., Sunwoo, I. Y., Kang, C. H., Jeong, G. T. and Kim, S. K.(2015). Detoxification of Eucheuma spinosum hydrolysates with activated carbon for ethanol production by the salt-tolerant yeast Candida tropicalis. Journal of Microbiology and Biotechnology, 25:856–862. doi: 10.4014/jmb.1409.09038
Syed, K., and Yadav, J. S. (2012). P450 monooxygenases (P450ome) of the model white rot fungus Phanerochaete chrysosporium. Critical Reviews in Microbiology, 38(4): 339–363.
Newsome, A. W., Nelson, D., Corran, A., Kelly, S. L., and Kelly, D. E. (2013). The cytochrome P450 complement (CYP ome) of Mycosphaerella graminicola. Biotechnology and Applied Biochemistry, 60(1): 52-64.
Lah, L., Haridas, S., Bohlmann, J., and Breuil, C. (2013). The cytochromes P450 of Grosmanniaclavigera: genome organisation, phylogeny, and expression inresponse to pine host chemicals. Fungal Genetics and Biology, 50: 72–81.
Chadha, S., Sayaji, T. M., Ravindra, B., Alan, K., Andrea, A., Igor, V. G., Irina, S. D. and Prasun, K. M. (2018). Genomewide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships. Fungal Biology and Biotechnology, 5(1): 1-15. https://doi.org/10.1186/s40694-018-0056-3
Dauda, W. P., Glen, E., Abraham, P., Adetunji, C. O., Morumda, D., Abraham, S. E., Wabba, G. P., Ogwuche, I. O., and Azameti, M. K. (2021). Comparative Phylogenomic Analysis of Cytochrome P450 Monooxygenases from Fusarium Species 3- 8.https://doi.org/10.21203/rs.3.rs-
/v1
Dauda, W. P., Morumda, D., Abraham, P., Adetunji, C. O., Ghazanfar, S., Glen, E., Abraham, S. E., Peter, G. W., Ogra, I. O., Ifeanyi, U. J., Musa, H., Azameti, M. K., Paray, B. A., and Gulnaz, A. (2022). Genome-Wide Analysis of Cytochrome P450s of Alternaria species: Evolutionary Origin, Family Expansion and Putative Functions. Journal of Fungi, 8, 324. https://doi.org/10.3390/jof8040324
Dauda, W. P., Abraham, P., Glen, E., Adetunji, C. O., Ghazanfar, S., Ali, S., AlZahrani, M., Azameti, M. K., Alao, S. E. L., Zarafi, A. B., Abraham, M. P., and Musa, H. (2022). Robust Profiling of Cytochrome P450s (P450ome) in Notable Aspergillusspp. Life, 12: 451. https://doi.org/10.3390/life12030451
Park, J., Lee, S., Choi, J., Ahn, K., Park, B., Kang, S., and Lee, Y. H.(2008). Fungal cytochrome P450 database, BMC Genomics, 9:402.
Nelson, D. R. (1999). Cytochrome P450 and the individuality of species. Archives of Biochemistry and Biophysics, 369(1): 1–10.
Marchler-Bauer,A., Lu S,Anderson, J. B., Chitsaz, F., Derbyshire, M. K., DeWeeseScott, C., Fong, J. H., Geer, L. Y., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Jackson, J. D., Ke, Z., Lanczycki, C. J., Lu, F., Marchler, G. H., Mullokandov, M., Omelchenko, M. V., Robertson, C. L., Dong, J. S., Thanki, N., Yamashita, R. A., Zhang, D., Zhang, N., Zheng, C., Bryant, S. H. (2011). CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Research, 39: 225–9.
Dauda, W. P., Abraham, P., Fasogbon, I. V., Adetunji, C. O., Banwo, O. O., Kashina, B. D., and Alegbejo, M. D. (2021). Cassava mosaic virus in Africa: Functional analysis of virus coat proteins based on evolutionary processes and protein structure. Gene Reports, 24: 101239.
Kumar, S., Stecher, G., Li, M., Knyaz, C., and Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution, 35:1547-1549.
Edgar, R. C. (2004). MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5: 113.
Thomas, M., Gerth, S. B., Rolf. F., Christain. N. S. and Derek. P. (2006). Recrafting the neighbour-joining method. BMC Bioinformatics, 1471-2105.
Bailey, T. L., and Elkan, C.(1994). Fitting a mixture model by expectation maximisation to discover motifs in biopolymers. Proceedings/international conference on intelligent systems for molecular biology. - ISMB International Conference on Intelligent. Systems for Molecular Biology, 2:28–36.
Bo, H., Jinpu, J., An-Yuan, G., He, Z, Jingchu, L. and Ge, G. (2015). GSDS 2.0: an upgraded gene features visualisation server. Bioinformatics, 31(8):1296-1297.
Nelson, D. R. (2006). Plant cytochrome P450s from moss to poplar. PhytochemistryReviews, 5(2): 193-204.
Sezutsu, H., Le, G. G., and Feyereisen, R. (2013). Origins of P450 diversity. Philosophical Transactions of the Royal Society B: Biological Sciences, 368:20120428.
Feyereisen, R. (2011). Arthropod CYPomes illustrate the tempo and mode in P450 evolution. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1814(1): 19-28.
Yu, J. H., Wanping, C., Mi-Kyung, L., Colin, J., Sun-Chang, K., and Fusheng, C. (2014). Fungal Cytochrome P450 Monooxygenases: their Distribution, Structure, Functions, Family Expansion, and Evolutionary Origin. Genome of Biology Evolution, 6(7):1620-1634.
Moktali, V., Park, J., Federova-Abrams, N. D., Park, B., Choi, J., Lee, Y-H, Kang, S. (2012). Fungal cytochrome P450 database 1.2. BMC Genomics, 13: 525s.
Eschenfeldt, W. H., Zhang, Y., Samaha, H., Stols, L.,Eirich, L. D., Wilson, C. R., and Donnelly, M. I. (2003). Transformation of fatty acids catalysed by cytochrome P450 monooxygenase enzymes of Candida tropicalis. Applied and Environmental Microbiology, 69(10): 5992-5999.
Skaggs, B. A., Alexander, J. F., Pierson, C. A., Schweitzer, K. S., Chun, K. T., Koegel, C., Barbuch, R., and Bard, M. (1996). Cloning and characterisation of the Saccharomyces cerevisiae C-22 sterol desaturase gene, encoding a second cytochrome P-450 involved in ergosterol
biosynthesis. Gene,169: 105–9.
Becher, R., and Wirsel, S. G. (2012). Fungal cytochrome P450 sterol 14α- demethylase (CYP51) and azole resistance in plant and human pathogens. Applied microbiology and biotechnology, 95(4): 825-840.
Kelly, S. L., and Kelly, D. E. (2013). Microbial cytochromes P450: biodiversity and biotechnology. Where do cytochromes P450 come from, what do they do and what can they do for us?. Philosophical Transactions of the Royal Society B: Biological Sciences, 368(1612): 20120476.
Ichinose, H.(2014). Metabolic diversity and cytochromes P450 of fungi. In: Yamazaki H, (eds). Fifty years of cytochrome P450 research. Tokyo: Springer; 187–205pg.
Werck-Reichhart, D., and Feyereisen, R. (2000). Cytochromes P450: a success story. Genome Biology, 1(6):1-9.
Sogin, M. L., Silberman, J. D. (1998). Evolution of the protists and protistan parasites from the perspective of molecular systematics. Int J Parasitol. ;28:11–20. doi: 10.1016/S0020-7519(97)00181
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2023 Nigerian Journal of Parasitology
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
