فیلوژنی مولکولی و واگرایی عملکردی یوریدین دی فسفات گلیکوزیل ترانسفرازهای (UGT) موجود در جنس زعفران و همولوگ‌های آن در سایر گیاهان

Abhiman, S., Daub, C. O., & Sonnhammer, E. L. L. (2006). Prediction of function divergence in protein families using the substitution rate variation parameter alpha. Molecular Biology and Evolution, 23(7), 1406–1413. https://doi.org/10.1093/molbev/msl002.

Ahmed, A., Peters, N. R., Fitzgerald, M. K., Watson, J. A., Hoffmann, F. M., & Thorson, J. S. (2006). Colchicine glycorandomization influences cytotoxicity and mechanism of action. Journal of the American Chemical Society, 128(44), 14224–14225. https://doi.org/10.1021/ja064686s.

Ahrazem, O., Diretto, G., Argandoña, J., Rubio-Moraga, Á., Julve, J. M., Orzáez, D., Granell, A., & Gómez-Gómez, L. (2017). Evolutionarily distinct carotenoid cleavage dioxygenases are responsible for crocetin production in Buddleja davidii. Journal of Experimental Botany, 68(16), 4663–4677. https://doi.org/10.1093/jxb/erx277.

Ahrazem, O., Rubio-Moraga, A., Mozos, A. T., & Gómez-Gómez, M. L. (2014). Genomic organization of a UDP-glucosyltransferase gene determines differential accumulation of specific flavonoid glucosides in tepals. Plant Cell, Tissue and Organ Culture (PCTOC), 119, 227–245. https://doi.org/10.1007/s11240-014-0528-y.

Ahrazem, O., Rubio-Moraga, A., Trapero-Mozos, A., Climent, M. F. L., Gómez-Cadenas, A., & Gómez-Gómez, L. (2015). Ectopic expression of a stress-inducible glycosyltransferase from saffron enhances salt and oxidative stress tolerance in Arabidopsis while alters anchor root formation. Plant Science, 234, 60–73. https://doi.org/10.1016/j.plantsci.2015.02.004.

Arnau, V., Gallach, M., Lucas, J. I., & Marín, I. (2006). UVPAR: fast detection of functional shifts in duplicate genes. BMC Bioinformatics, 7(1), 1–12. https://doi.org/10.1186/1471-2105-7-174.

Bharatham, K., Zhang, Z. H., & Mihalek, I. (2011). Determinants, discriminants, conserved residues-a heuristic approach to detection of functional divergence in protein families. PLoS One, 6(9), e24382. https://doi.org/10.1371/journal.pone.0024382.

Breton, C., Fournel-Gigleux, S., & Palcic, M. M. (2012). Recent structures, evolution and mechanisms of glycosyltransferases. Current Opinion in Structural Biology, 22(5), 540–549. https://doi.org/10.1016/j.sbi.2012.06.007.

Breton, C., & Imberty, A. (1999). Structure/function studies of glycosyltransferases. Current Opinion in Structural Biology, 9(5), 563–571. https://doi.org/10.1016/S0959-440X(99)00006-8.

Caballero-Ortega, H., Pereda-Miranda, R., & Abdullaev, F. I. (2007). HPLC quantification of major active components from 11 different saffron (Crocus sativus L.) sources. Food Chemistry, 100(3), 1126–1131. https://doi.org/10.1016/j.foodchem.2005.11.020.

Chagoyen, M., García-Martín, J. A., & Pazos, F. (2016). Practical analysis of specificity-determining residues in protein families. Briefings in Bioinformatics, 17(2), 255–261. https://doi.org/10.1093/bib/bbv045.

Christodoulou, E., Kadoglou, N. P. E., Kostomitsopoulos, N., & Valsami, G. (2015). Saffron: a natural product with potential pharmaceutical applications. Journal of Pharmacy and Pharmacology, 67(12), 1634–1649. https://doi.org/10.1111/jphp.12456.

del Sol Mesa, A., Pazos, F., & Valencia, A. (2003). Automatic methods for predicting functionally important residues. Journal of Molecular Biology, 326(4), 1289–1302. https://doi.org/10.1016/S0022-2836(02)01451-1.

Demurtas, O. C., Frusciante, S., Ferrante, P., Diretto, G., Azad, N. H., Pietrella, M., Aprea, G., Taddei, A. R., Romano, E., & Mi, J. (2018). Candidate enzymes for saffron crocin biosynthesis are localized in multiple cellular compartments. Plant Physiology, 177(3), 990–1006. https://doi.org/10.1104/pp.17.01815.

Diretto, G., Ahrazem, O., Rubio‐Moraga, Á., Fiore, A., Sevi, F., Argandoña, J., & Gómez‐Gómez, L. (2019). UGT709G1: a novel uridine diphosphate glycosyltransferase involved in the biosynthesis of picrocrocin, the precursor of safranal in saffron (Crocus sativus). New Phytologist, 224(2), 725–740. https://doi.org/10.1111/nph.16079.

Gu, X. (2003). Functional divergence in protein (family) sequence evolution. Origin and Evolution of New Gene Functions, 133–141. https://doi.org/10.1007/978-94-010-0229-5_4

Gu, X. (2006). A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. Molecular Biology and Evolution, 23(10), 1937–1945. https://doi.org/10.1093/molbev/msl056.

Gu, X., Zou, Y., Su, Z., Huang, W., Zhou, Z., Arendsee, Z., & Zeng, Y. (2013). An update of DIVERGE software for functional divergence analysis of protein family. Molecular Biology and Evolution, 30(7), 1713–1719. https://doi.org/10.1093/molbev/mst069.

Holm, L., Laiho, A., Törönen, P., & Salgado, M. (2023). DALI shines a light on remote homologs: One hundred discoveries. Protein Science, 32(1), e4519. https://doi.org/10.1002/pro.4519.

Illergård, K., Ardell, D. H., & Elofsson, A. (2009). Structure is three to ten times more conserved than sequence—a study of structural response in protein cores. Proteins: Structure, Function, and Bioinformatics, 77(3), 499–508. https://doi.org/10.1002/prot.22458.

Lai, C., Yang, N., Yusuyin, M., Zhang, D., Yang, Y., Li, C., & Xu, H. (2022). Characterization of a novel crocetin glycosyltransferase UGTCs4 involved in two steps of glycosylation in crocin biosynthesis from crocus cultured cell.

Le Roy, J., Huss, B., Creach, A., Hawkins, S., & Neutelings, G. (2016). Glycosylation is a major regulator of phenylpropanoid availability and biological activity in plants. Frontiers in Plant Science, 7, 735. https://doi.org/10.3389/fpls.2016.00735.

Li, L., Shakhnovich, E. I., & Mirny, L. A. (2003). Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proceedings of the National Academy of Sciences, 100(8), 4463–4468. https://doi.org/10.1073/pnas.0737647100.

Liang, Z., Yang, M., Xu, X., Xie, Z., Huang, J., Li, X., & Yang, D. (2014). Isolation and purification of geniposide, crocin-1, and geniposidic acid from the fruit of Gardenia jasminoides Ellis by high-speed counter-current chromatography. Separation Science and Technology, 49(9), 1427–1433. https://doi.org/10.1080/01496395.2013.879179.

Lim, E., & Bowles, D. J. (2004). A class of plant glycosyltransferases involved in cellular homeostasis. The EMBO Journal, 23(15), 2915–2922. https://doi.org/10.1038/sj.emboj.7600295.

López-Jimenez, A. J., Frusciante, S., Niza, E., Ahrazem, O., Rubio-Moraga, Á., Diretto, G., & Gómez-Gómez, L. (2021). A new glycosyltransferase enzyme from family 91, UGT91P3, is responsible for the final glucosylation step of crocins in saffron (Crocus sativus l.). International Journal of Molecular Sciences, 22(16), 8815. https://doi.org/10.3390/ijms22168815.

Mandai, T., Yoneyama, M., Sakai, S., Muto, N., & Yamamoto, I. (1992). The crystal structure and physicochemical properties of L-ascorbic acid 2-glucoside. Carbohydrate Research, 232(2), 197–205. https://doi.org/10.1016/0008-6215(92)80054-5.

Meng, L., Liu, X., He, C., Xu, B., Li, Y., & Hu, Y. (2020). Functional divergence and adaptive selection of KNOX gene family in plants. Open Life Sciences, 15(1), 346–363. https://doi.org/10.1515/biol-2020-0036.

Mirny, L. A., & Gelfand, M. S. (2002). Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. Journal of Molecular Biology, 321(1), 7–20. https://doi.org/10.1016/S0022-2836(02)00587-9.

Modolo, L. V, Blount, J. W., Achnine, L., Naoumkina, M. A., Wang, X., & Dixon, R. A. (2007). A functional genomics approach to (iso) flavonoid glycosylation in the model legume Medicago truncatula. Plant Molecular Biology, 64, 499–518. https://doi.org/10.1007/s11103-007-9167-6.

Moraga, Á. R., Mozos, A. T., Ahrazem, O., & Gómez-Gómez, L. (2009). Cloning and characterization of a glucosyltransferase from Crocus sativusstigmas involved in flavonoid glucosylation. BMC Plant Biology, 9(1), 1–16. https://doi.org/10.1186/1471-2229-9-109.

Nagatoshi, M., Terasaka, K., Owaki, M., Sota, M., Inukai, T., Nagatsu, A., & Mizukami, H. (2012). UGT75L6 and UGT94E5 mediate sequential glucosylation of crocetin to crocin in Gardenia jasminoides. FEBS Letters, 586(7), 1055–1061. https://doi.org/10.1016/j.febslet.2012.03.003.

Naylor, G. J. P., & Gerstein, M. (2000). Measuring shifts in function and evolutionary opportunity using variability profiles: a case study of the globins. Journal of Molecular Evolution, 51, 223–233. https://doi.org/10.1007/s002390010084.

Nguyen Ba, A. N., Strome, B., Hua, J. J., Desmond, J., Gagnon-Arsenault, I., Weiss, E. L., Landry, C. R., & Moses, A. M. (2014). Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences. PLoS Computational Biology, 10(12), e1003977. https://doi.org/10.1371/journal.pcbi.1003977.

Offen, W., Martinez‐Fleites, C., Yang, M., Kiat‐Lim, E., Davis, B. G., Tarling, C. A., Ford, C. M., Bowles, D. J., & Davies, G. J. (2006). Structure of a flavonoid glucosyltransferase reveals the basis for plant natural product modification. The EMBO Journal, 25(6), 1396–1405. https://doi.org/10.1016/j.febslet.2012.03.003.

Ohno, S. (2013). Evolution by gene duplication. Springer Science & Business Media.

Pennisi, E. (2021). Protein structure prediction now easier, faster. American Association for the Advancement of Science. doi: 10.1126/science.373.6552.262.

Pfister, S., Meyer, P., Steck, A., & Pfander, H. (1996). Isolation and structure elucidation of carotenoid− glycosyl esters in gardenia fruits (gardenia jasminoides ellis) and saffron (crocus sativus linne). Journal of Agricultural and Food Chemistry, 44(9), 2612–2615. https://doi.org/10.1021/jf950713e.

Pu, X., He, C., Yang, Y., Wang, W., Hu, K., Xu, Z., & Song, J. (2020). In vivo production of five crocins in the engineered Escherichia coli. ACS Synthetic Biology, 9(5), 1160–1168. https://doi.org/10.1021/acssynbio.0c00039.

Rahimi, S., Kim, J., Mijakovic, I., Jung, K.-H., Choi, G., Kim, S.-C., & Kim, Y.-J. (2019). Triterpenoid-biosynthetic UDP-glycosyltransferases from plants. Biotechnology Advances, 37(7), 107394. https://doi.org/10.1016/j.biotechadv.2019.04.016.

Swint-Kruse, L. (2016). Using evolution to guide protein engineering: the devil is in the details. Biophysical Journal, 111(1), 10–18. http://dx.doi.org/10.1016/j.bpj.2016.05.030.

Trapero, A., Ahrazem, O., Rubio-Moraga, A., Jimeno, M. L., Gómez, M. D., & Gómez-Gómez, L. (2012). Characterization of a glucosyltransferase enzyme involved in the formation of kaempferol and quercetin sophorosides in Crocus sativus. Plant Physiology, 159(4), 1335–1354. https://doi.org/10.1104/pp.112.198069.

Tunyasuvunakool, K., Adler, J., Wu, Z., Green, T., Zielinski, M., Žídek, A., Bridgland, A., Cowie, A., Meyer, C., & Laydon, A. (2021). Highly accurate protein structure prediction for the human proteome. Nature, 596(7873), 590–596. https://doi.org/10.1038/s41586-021-03828-1.

Umesono, K., & Evans, R. M. (1989). Determinants of target gene specificity for steroid/thyroid hormone receptors. Cell, 57(7), 1139–1146.

Verma, V. V., Gupta, R., & Goel, M. (2015). Phylogenetic and evolutionary analysis of functional divergence among Gamma glutamyl transpeptidase (GGT) subfamilies. Biology Direct, 10(1), 1–21. https://doi.org/10.1186/s13062-015-0080-7.

Vogt, T., & Jones, P. (2000). Glycosyltransferases in plant natural product synthesis: characterization of a supergene family. Trends in Plant Science, 5(9), 380–386.

Wang, M., Ji, Q., Lai, B., Liu, Y., & Mei, K. (2023). Structure-function and engineering of plant UDP-glycosyltransferase. Computational and Structural Biotechnology Journal. https://doi.org/10.1016/j.csbj.2023.10.046.

Wang, X. (2009). Structure, mechanism and engineering of plant natural product glycosyltransferases. FEBS Letters, 583(20), 3303–3309. https://doi.org/10.1016/j.febslet.2009.09.042.

Weymouth-Wilson, A. C. (1997). The role of carbohydrates in biologically active natural products. Natural Product Reports, 14(2), 99–110.

Winterhalter, P., & Rouseff, R. L. (2001). Carotenoid-derived aroma compounds. ACS Publications.

Xi, L., & Qian, Z. (2006). Pharmacological properties of crocetin and crocin (digentiobiosyl ester of crocetin) from saffron. Natural Product Communications, 1(1), 1934578X0600100112. https://doi.org/10.1177/1934578X0600100

Zhang, C., Griffith, B. R., Fu, Q., Albermann, C., Fu, X., Lee, I.-K., Li, L., & Thorson, J. S. (2006). Exploiting the reversibility of natural product glycosyltransferase-catalyzed reactions. Science, 313(5791), 1291–1294. doi: 10.1126/science.113002.