
Werck-Reichhart, D. & Feyereisen, R. Cytochromes P450: a success story. Genome Biol. 1, REVIEWS3003 (2000).
Nelson, D. R. A world of cytochrome P450s. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 368, 20120430 (2013).
Payne, A. H. Hormonal regulation of cytochrome P450 enzymes, cholesterol side-chain cleavage and 17 alpha-hydroxylase/C17-20 lyase in Leydig cells. Biol. Reprod. 42, 399–404 (1990).
Mizutani, M. Impacts of diversification of cytochrome P450 on plant metabolism. Biol. Pharm. Bulletin 35, 824–832 (2012).
Käppeli, O. Cytochromes P-450 of yeasts. Microbiol. Rev. 50, 244–258 (1986).
Anzenbacher, P. & Anzenbacherová, E. Cytochromes P450 and metabolism of xenobiotics. Cell. Mol. Life. Sci. 58, 737–747 (2001).
Chen, W. et al. Fungal cytochrome P450 monooxygenases: their distribution, structure, functions, family expansion, and evolutionary origin. Genome Biol. Evol. 6, 1620–1634 (2014).
Fukuda, R. Metabolism of hydrophobic carbon sources and regulation of it in n-alkane-assimilating yeast Yarrowia lipolytica. Biosci. Biotechnol. Biochem. 77, 1149–1154 (2013).
Rojo, F. Enzymes for aerobic degradation of alkanes. In Handbook of Hydrocarbon and Lipid Microbiology, (ed. Timis, K. N.) 480–499 (Springer-Velarg, 2010).
Van Bogaert, I. N. A. et al. The role of cytochrome P450 monooxygenases in microbial fatty acid metabolism. FEBS J. 278, 206–221 (2011).
Kretschmer, M., Wang, J. & Kronstad, J. W. Peroxisomal and mitochondrial β-oxidation pathways influence the virulence of the pathogenic fungus Cryptococcus neoformans. Eukaryot. Cell 11, 1042–1054 (2012).
Singh, S. N., Kumari, B. & Mishra, S. Microbial degradation of alkanes. In Microbial Degradation of Xenobiotics, (ed. Singh, S. N.) 439–469 (Springer-Velarg, 2012).
Ohkuma, M. et al. CYP52 (cytochrome P450alk) multigene family in Candida maltosa: identification and characterization of eight members. DNA Cell Biol. 4, 163–173 (1995).
Craft, D. L., Madduri, K. M., Eshoo, M. & Ron-Wilson, C. Identification and characterization of the CYP52 family of Candida tropicalis ATCC 20336, important for the conversion of fatty acids and alkanes to β, ω-Dicarboxylic acids. Appl. Environ. Microbiol. 69, 5983–5991 (2003).
Kim, D., Cryle, M. J., De Voss, J. J. & Ortiz de Montellano, P. R. Functional expression and characterization of cytochrome P450 52A21 from Candida albicans. Arch. Biochem. Biophys. 464, 213–220 (2007).
Hirakawa, K. et al. Yas3p, an Opi1 family transcription factor, regulates cytochrome P450 expression in response to n-alkanes in Yarrowia lipolytica. J. Biol. Chem. 284, 7126–7137 (2009).
Moktali, V. et al. Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes. BMC Genomics 13, 525 (2012).
Iwama, R., Kobayashi, S., Ishimaru, C. & Ohta, A. Functional roles and substrate specificities of twelve cytochromes P450 belonging to CYP52 family in n-alkane assimilating yeast Yarrowia lipolytica. Fungal Genet. Biol. 91, 43–54 (2016).
Iida, T., Sumita, T., Ohta, A. & Takagi, M. The cytochrome P450ALK multigene family of an n-alkane-assimilating yeast, Yarrowia lipolytica: cloning and characterization of genes coding for new CYP52 family members. Yeast 16, 1077–1087 (2000).
Ortiz-Alvarez, J. et al. Candida pseudoglaebosa and Kodamaea ohmeri are capable of degrading alkanes in presence of heavy metals. J. Basic Microbiol. 59, 792–806 (2019).
Dujon, B. Yeast evolutionary genomics. Nat. Rev.Genet. 11, 512–524 (2010).
Mohanta, T. K. & Bae, H. The diversity of fungal genome. Biol. Proced. Online 17, 1–9 (2015).
Dujon, B. A. & Louis, E. J. Genome diversity and evolution in the budding yeasts (Saccharomycotina). Genetics 206, 717–750 (2017).
Butler, G. et al. Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature 459, 657–662 (2009).
Génolevures Consortium. et al. Comparative genomics of protoploid Saccharomycetaceae. Genome Res. 19, 1696–1709 (2009).
Loira, N., Dulermo, T., Nicaud, J. M. & Sherman, D. J. A. genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. BMC Syst. Biol. 6, 35 (2012).
Kafri, R., Levy, M. & Pilpel, Y. The regulatory utilization of genetic redundancy through responsive backup circuits. Proc. Natl. Acad. Sci. 103, 11653–11658 (2006).
DeLuna, A. et al. Exposing the fitness contribution of duplicated genes. Nat. Genet. 40, 676–681 (2008).
Diss, G., Ascencio, D., Deluna, A. & Landry, C. R. Molecular mechanisms of paralogous compensation and the robustness of cellular networks. J. Exp. Zool. B. Mol. Dev. Evol. 322, 488–499 (2014).
Gagnon-Arsenault, I. et al. Gene duplication can impart fragility, not robustness, in the yeast protein interaction network. Science 355, 630–634 (2017).
Pires, J. C. & Conant, G. C. Robust yet fragile: expression noise, protein misfolding, and gene dosage in the evolution of genomes. Ann. Rev. Genet. 50, 113–131 (2016).
Dujon, B. et al. Genome evolution in yeasts. Nature 430, 35–44 (2004).
Parra-Ortega, B., Cruz-Torres, H., Villa-Tanaca, L. & Hernández-Rodríguez, C. Phylogeny and evolution of the aspartyl protease family from clinically relevant Candida species. Mem. Inst. Oswaldo Cruz 104, 505–512 (2009).
Ames, R. M., Money, D. & Lovell, S. C. Inferring gene family histories in yeast identifies lineage specific expansions. PLoS ONE 9, e99480 (2014).
Cortés-Acosta, E. et al. Polymorphism in the regulatory regions of genes CgYPS1 and CgYPS7 encoding yapsins in Candida glabrata is associated with changes in expression levels. FEMS Yeast Res. 17, fox077 (2017).
Cliften, P. F., Fulton, R. S., Wilson, R. K. & Johnston, M. After the duplication: gene loss and adaptation in Saccharomyces genomes. Genetics 172, 863–872 (2006).
Naseeb, S., Ames, R. M., Delneri, D. & Lovell, S. C. Rapid functional and evolutionary changes follow gene duplication in yeast. Proc. Biol. Sci. 284, 20171393 (2017).
Wolfe, K. H. Origin of the Yeast Whole-Genome Duplication. PLoS Biol. 13, e1002221 (2015).
Pérez-Brito, D. et al. Genetic diversity of Clavispora lusitaniae isolated from Agave fourcroydes Lem, as revealed by DNA fingerprinting. J. Microbiol. 53, 14–20 (2015).
Durrens, P. et al. Genome sequence of the yeast Clavispora lusitaniae type strain CBS 6936. Genome Announc. 5, pii: e00724-17 (2012).
Zieniuk, B. & Fabiszewska, A. Yarrowia lipolytica: a beneficious yeast in biotechnology as a rare opportunistic fungal pathogen: a minireview. World J. Microbiol. Biotechnol. 35, 10 (2019).
Hassanshahian, M., Tebyanian, H. & Cappello, S. Isolation and characterization of two crude oil-degrading yeast strains, Yarrowia lipolytica PG-20 and PG-32, from the Persian Gulf. Mar. Pollut. Bull. 64, 1386–1391 (2012).
Flores, M., Corral, S., Cano-García, L., Salvador, A. & Belloch, C. Yeast strains as potential aroma enhancers in dry fermented sausages. Int. J. Food Microbiol. 212, 16–24 (2015).
Fan, M. Y., Xie, R. J. & Qin, G. Bioremediation of petroleum-contaminated soil by a combined system of biostimulation-bioaugmentation with yeast. Environ. Technol. 35, 391–399 (2014).
Gargouri, B., Mhiri, N., Karray, F., Aloui, F. & Sayadi, S. Isolation and characterization of hydrocarbon-degrading yeast strains from petroleum contaminated industrial wastewater. Biomed. Res. Int. 2015, 929424 (2015).
Rehman, A. & Anjum, M. S. Multiple metal tolerance and biosorption of cadmium by Candida tropicalis isolated from industrial effluents: glutathione as detoxifying agent. Environ. Monit. Assess. 174, 585–595 (2011).
Ilyas, S. & Rehman, A. Oxidative stress, glutathione level and antioxidant response to heavy metals in multi-resistant pathogen, Candida tropicalis. Environ. Monit. Assess. 187, 4115 (2015).
Zuza-Alves, D. L., Silva-Rocha, W. P. & Chaves, G. M. An update on Candida tropicalis based on basic and clinical approaches. Front. Microbiol. 8, 1927 (2017).
Martini, C., Tauk-Tornisielo, S. M., Codato, C. B., Bastos, R. G. & Ceccato-Antonini, S. R. A strain of Meyerozyma guilliermondii isolated from sugarcane juice is able to grow and ferment pentoses in synthetic and bagasse hydrolysate media. World J. Microbiol. Biotechnol. 32, 80 (2016).
Karimi, M. & Hassanshahian, M. Isolation and characterization of phenol degrading yeasts from wastewater in the coking plant of Zarand, Kerman. Braz. J. Microbiol. 47, 18–24 (2016).
Savini, V. et al. What do we know about Candida guilliermondii? A voyage throughout past and current literature about this emerging yeast. Mycoses 54, 434–441 (2016).
Sánchez-Martínez, G. & Wagner, M. R. Host preference and attack pattern of Dendroctonus rhizophagus (Coleoptera: Curculionidae:Scolytinae): a bark beetle specialist on pine regeneration. Environ. Entomol. 38, 1197–1204 (2009).
Strom, B. L., Smith, S. L. & Brownie, C. Attractant and disruptant semiochemicals for Dendroctonus jeffreyi (Coleoptera: Curculionidae: Scolytinae). Environ. Entomol. 42, 323–332 (2013).
Kurtzman, C. P. & Fell, J. W. The yeast, A taxonomy Study (Elsevier-Science, 1997).
Lin, Z. & Li, W. H. Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts. Mol. Biol. Evol. 28, 131–142 (2011).
Berthelot, C. et al. Adaptation of proteins to the cold in Antarctic fish: a role for methionine? Genome Biol. Evol. 11, 220–231 (2019).
Libuda, D. E. & Winston, F. Amplification of histone genes by circular chromosome formation in Saccharomyces cerevisiae. Nature 443, 1003–1007 (2006).
Meunchan, M. et al. Comprehensive analysis of a yeast lipase family in the Yarrowia clade. PLoS One 10, e0143096 (2015).
Godinho, C. P., Dias, P. J., Ponçot, E. & Sá-Correia, I. The paralogous genes PDR18and SNQ2, encoding multidrug resistance ABC transporters, derive from a recent duplication event, PDR18 being specific to the Saccharomyces genus. Front. Genet. 9, 476 (2018).
Kondrashov, F. A. Gene duplication as a mechanism of genomic adaptation to a changing environment. Proc. Biol. Sci. 279, 5048–5057 (2012).
Mattenberger, F., Sabater-Muñoz, B., Toft, C. & Fares, M. A. The phenotypic plasticity of duplicated genes in Saccharomyces cerevisiae and the origin of adaptations. G3 (Bethesda) 7, 63–75 (2017).
Chase, J. M. Ecological niche theory. In The theory of ecology. (eds. Scheinerand, M. & Willig, M. R.) 93–108 (University of Chicago Press, 2011).
Bak, S. et al. Cytochromes P450. Arabidopsis Book 9, e0144 (2011).
Sezutsu, H., Le Goff, G. & Feyereisen, R. Origins of P450 diversity. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 368, 20120428 (2013).
Voordeckers, K. et al. Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication. PLoS Biology 10 (2012).
Siddiq, M. A., Hochberg, G. K. & Thornton, J. W. Evolution of protein specificity: insights from ancestral protein reconstruction. Curr. Opin. Struct. Biol. 47, 113–122 (2017).
Newton, M. S., Arcus, V. L., Gerth, M. L. & Patrick, W. M. Enzyme evolution: innovation is easy, optimization is complicated. Curr. Opin. Struct. Biol. 48, 110–116 (2018).
Syed, K. & Mashele, S. S. Comparative analysis of P450 signature motifs EXXR and CXG in the large and diverse kingdom of fungi: identification of evolutionarily conserved amino acid patterns characteristic of P450 family. PLoS One 17, e95616 (2014).
Sirim, D., Widmann, M., Wagner, F. & Pleiss, J. Prediction and analysis of the modular structure of cytochrome P450 monooxygenases. BMC Struct. Biol. 10, 34 (2010).
Risso, V. A. et al. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Mol. Biol. Evol. 32, 440–455 (2015).
Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113 (2004).
Gouy., S., Guindon, S. & Gascuel, O. SeaView version 4: a multiplatform graphical user interphase for sequence alignment and phylogenetic three building. Mol. Biol. Evol. 27, 221–224 (2014).
Darriba, D., Taboada, G. L. & Posada, D. ProtTest 3: fast selection of best-fit models of protein evolution. Mol. Biol. Evol. 27, 1164–1165 (2011).
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
Letunic, I. & Bork, P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44, W242–W245 (2016).
Nei, M. & Li, W. H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76, 5269–5273 (1979).
Lockhart, S. R. et al. Development and verification of fingerprinting probes for Candida glabrata. Microbiology 143, 3733–3746 (1997).
Bautista-Muñoz, C., Boldo, X. M., Villa-Tanaca, L. & Hernández-Rodríguez, C. Identification of Candida spp. by randomly amplified polymorphic DNA analysis and differentiation between Candida albicans and Candida dubliniensis by direct PCR methods. J. Clin. Microbiol. 41, 414–420 (2003).
Rohlf, F.J. NTSYS-pc 2.0e. Exeter Software, New York (1998).
Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
Aszodi, A., Munro, R. E. & Taylor, W. R. Distance geometry based comparative modelling. Fold. Des. 2, S3–S6 (1997).
Webb, B. & Sali, A. Protein Structure Modelling with MODELLER. Methods Mol. Biol. 1654, 39–54 (2017).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thorton, J. M. PROCHECK: a program to check the stereochemical quality of protein structure. J. Appl. Cryst. 26, 283–291 (1993).
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).
Phillips, J. C., Braun, R. & Wang., W. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802 (2005).
Huang, J. et al. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat. Methods 14, 71–73 (2017).
Morris, G. & Huey, R. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. 30, 2785–2791 (2009).
Campanella, J. J., Bitincka, L. & Smalley, J. MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinformatics 4, 29 (2003).
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