The In Silico Characterization of Lycopene Forming Phytoene Desaturase (CrtI) Protein from Wheat Leaf Rust Fungi (Puccinia triticina)


  • Yehezkiel Vieri Polandos School of Life Sciences and Technology, Institut Teknologi Bandung
  • Fenny Martha Dwivany School of Life Sciences and Technology, Institut Teknologi Bandung
  • Karlia Meitha School of Life Sciences and Technology, Institut Teknologi Bandung



carotenoid, bioparts, biofortification, molecular docking, pro-vitamin A


Carotenoid is a highly economical compound with a variety of bioactivities. However, 98% of total carotenoid used is still being manufactured by chemical-based synthesis, reducing bioactivities and is not environmentally friendly, hence the use of biofortification approach is sought.Lycopene forming phytoene desaturase (CrtI) is one of the key enzymes with the potential to develop as bioparts in recombinant carotenoid biosynthesis. CrtI from Puccinia triticina and Blakeslea trispora are considered as promising candidates due to the high amount of carotenoid inthe fungi. This research aims to characterize CrtI enzyme from P. triticina and B. trispora and the interaction with substrate, i.e.,15 cis-phytoene. The results showed that CrtI from P. triticina protein has 2 unique motifs, determining the three-dimensional CrtI protein structure. According to docking analysis, CrtI enzyme from P. triticina is predicted to bind to the substrate more spontaneously as indicated by the lower energy of affinity (-8.3 kcal mol-1) and more residues interaction compared to CrtI from Blakeslea trispora. In conclusion, the CrtI protein from P. triticina is suggested as the candidate for further exploration to design expression in a recombinant system.


] Cuttriss, A. J., Cazzonelli, C. I., Wurtzel, E. T., & Pogson, B. J. 2011. Carotenoids. B978-0-12-386479-6.00005-6

] Ellison, S. L. 2016. Carotenoids: Physiology. In Encyclopedia of Food and Health. Elsevier. https://doi. org/10.1016/B978-0-12-384947-2.00120-3

] Gong, M., & Bassi, A. 2016. Carotenoids from microalgae: A review of recent developments. Biotechnology Advances, 34(8).

] Singh, U., Praharaj, C. S., Chaturvedi, S. K., & Bohra, A. 2016. Biofortification: Introduction, Approaches, Limitations, and Challenges. In Biofortification of Food Crops. Springer India.

] Sandmann, G. 2002.Combinatorial Biosynthesis of Carotenoids in a Heterologous Host: A Powerful Approach for the Biosynthesis of Novel Structures. ChemBioChem, 3(7), 629.

] Paul, J.-Y., Khanna, H., Kleidon, J., Hoang, P., Geijskes, J., Daniells, J., Zaplin, E., Rosenberg, Y., James, A., Mlalazi, B., Deo, P., Arinaitwe, G., Namanya, P., Becker, D., Tindamanyire, J., Tushemereirwe, W., Harding, R., & Dale, J. (2017). Golden bananas in the field: elevated fruit pro-vitamin A from the expression of a single banana transgene. Plant Biotechnology Journal, 15(4).

] Paine, J. A., Shipton, C. A., Chaggar, S., Howells, R. M., Kennedy, M. J., Vernon, G., Wright, S. Y., Hinchliffe, E., Adams, J. L., Silverstone, A. L., & Drake, R. (2005). Improving the nutritional value of Golden Rice through increased pro-vitamin A content. Nature Biotechnology, 23(4).

] Mishiba, K.-I., Nishida, K., Inoue, N., Fujiwara, T., Teranishi, S., Iwata, Y., Takeda, S., & Koizumi, N. 2020. Genetic engineering of eggplant accumulating ?-carotene in fruit. Plant Cell Reports, 39(8). s00299-020-02546-8

] Nisar, N., Li, L., Lu, S., Khin, N. C., & Pogson, B. J. 2015. Carotenoid Metabolism in Plants. Molecular Plant, 8(1), 68?82.

] Wang, L., Liu, Z., Jiang, H., & Mao, X. 2021. Biotechnology advances in ?-carotene production by microorganisms. Trends in Food Science & Technology, 111.

] Gao, S., Tong, Y., Zhu, L., Ge, M., Zhang, Y., Chen, D., Jiang, Y., & Yang, S. 2017. Iterative integration of multiple-copy pathway genes in Yarrowia lipolytica for heterologous ?-carotene production. Metabolic Engineering, 41, 192?201.

] Li, X.-R., Tian, G.-Q., Shen, H.-J., & Liu, J.-Z. 2015. Metabolic engineering of Escherichia coli to produce zeaxanthin. Journal of Industrial Microbiology and Biotechnology, 42(4).

] Mlalazi, B., Welsch, R., Namanya, P., Khanna, H., Geijskes, R. J., Harrison, M. D., Harding, R., Dale, J. L., & Bateson, M. 2012. Isolation and functional characterisation of banana phytoene synthase genes as potential cisgenes. Planta, 236(5), 1585?1598. https://doi. org/10.1007/s00425-012-1717-8

] Schaub, P., Yu, Q., Gemmecker, S., Poussin-Courmontagne, P., Mailliot, J., McEwen, A. G., Ghisla, S., Al-Babili, S., Cavarelli, J., & Beyer, P. 2012. On the Structure and Function of the Phytoene Desaturase CRTI from Pantoea ananatis, a Membrane-Peripheral and FAD-Dependent Oxidase/Isomerase. PLoS ONE, 7(6), e39550.

] Wang, E., Dong, C., Park, R. F., & Roberts, T. H. 2018. Carotenoid pigments in rust fungi: Extraction, separation, quantification and characterisation. Fungal Biology Reviews, 32(3), 166?180. fbr.2018.02.002

] Papadaki, E., & Mantzouridou, F. T. 2021. Natural ?-Carotene Production by Blakeslea trispora Cultivated in Spanish-Style Green Olive Processing Waste waters. Foods, 10(2), 327. foods10020327

] Sen, T., Barrow, C. J., & Deshmukh, S. K. 2019. Microbial Pigments in the Food Industry?Challenges and the Way Forward. Frontiers in Nutrition, 6. https://doi. org/10.3389/fnut.2019.00007

] Garner K. L. 2021. Principles of synthetic biology. Essays Biochem. 2;65(5):791-811. EBC20200059

] Larroude, M., Celinska, E., Back, A., Thomas, S., Nicaud, J.-M., & Ledesma-Amaro, R. 2018. A synthetic biology approach to transform Yarrowia lipolytica into a competitive biotechnological producer of ?-carotene. Biotechnology and Bioengineering, 115(2), 464?472.

] Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35(6), 1547?1549. https://doi. org/10.1093/molbev/msy096

] Lu, S., Wang, J., Chitsaz, F., Derbyshire, M. K., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Marchler, G. H., Song, J. S., Thanki, N., Yamashita, R. A., Yang, M., Zhang, D., Zheng, C., Lanczycki, C. J., & Marchler-Bauer, A. (2020). CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Research, 48(D1), D265?D268. nar/gkz991

] Liu, W., Xie, Y., Ma, J., Luo, X., Nie, P., Zuo, Z., Lahrmann, U., Zhao, Q., Zheng, Y., Zhao, Y., Xue, Y., & Ren, J. (2015). IBS: an illustrator for the presentation and visualization of biological sequences: Fig. 1. Bioinformatics, 31(20), 3359?3361.

] Bailey, T. L., & Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings. International Conference on Intelligent Systems for Molecular Biology, 2, 28?36.

] Blum, M., Chang, H.-Y., Chuguransky, S., Grego, T., Kandasaamy, S., Mitchell, A., Nuka, G., Paysan-Lafosse, T., Qureshi, M., Raj, S., Richardson, L., Salazar, G. A., Williams, L., Bork, P., Bridge, A., Gough, J., Haft, D. H., Letunic, I., Marchler-Bauer, A., ? Finn, R. D. 2021. The InterPro protein families and domains database: 20 years on. Nucleic Acids Research, 49(D1), D344?D354.

] Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. 2015. The I-TASSER Suite: protein structure and function prediction. Nature Methods, 12(1), 7?8. https://

] Berman, H.M., Henrick, K., Nakamura, H. (2003) Announcing the worldwide Protein Data Bank Nature Structural Biology 10 (12): 980.

] Schringer, L., & DeLano, W. (2020). PyMOL. Retrieved from

] Colovos, C., & Yeates, T. O. 1993. Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511?1519. https://doi. org/10.1002/pro.5560020916

] Trott, O., & Olson, A. J. 2010. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455?461.

] Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A. Efficient and robust RNAseq process for cultured bacteria and complex community transcriptomes. (2012). Genome Biol. 2012;13(3):R23. doi: 10.1186/gb-2012-13-3-r23

] Miller, M. E., Zhang, Y., Omidvar, V., Sperschneider, J., Schwessinger, B., Raley, C., Palmer, J. M., Garnica, D., Upadhyaya, N., Rathjen, J., Taylor, J. M., Park, R. F., Dodds, P. N., Hirsch, C. D., Kianian, S. F., & Figueroa, M. 2018. De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae , the Causal Agent of Oat Crown Rust. MBio, 9(1).

] Yan, Z., Wang, C., Lin, J., & Cai, J. 2013.Medium optimization using mathematical statistics for production of ?-Carotene by Blakeslea trispora and fermenting process regulation. Food Science and Biotechnology, 22(6), 1667?1673.

] Rodruez-Sz, M., de la Fuente, J. L., & Barredo, J. L. 2010. Xanthophyllomyces dendrorhous for the industrial production of astaxanthin. Applied Microbiology and Biotechnology, 88(3), 645?658. s00253-010-2814-x

] Guo, Z., Li, B., Cheng, L.-T., Zhou, S., McCammon, J. A., & Che, J. 2015. Identification of Protein?Ligand Binding Sites by the Level-Set Variational Implicit-Solvent Approach. Journal of Chemical Theory and Computation, 11(2), 753?765.

] Fujiwara, K., Toda, H. & Ikeguchi, M. 2012. Dependence of ?-helical and ?-sheet amino acid propensities on the overall protein fold type. BMC Struct Biol. 12 (18).

] Gtl, F., Greis, A., Bu?ko, T., & Hafner, J. 2012. Van der Waals interactions between hydrocarbon molecules and zeolites: Periodic calculations at different levels of theory, from density functional theory to the random phase approximation and Mler-Plesset perturbation theory. The Journal of Chemical Physics, 137(11), 114111.

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