The characterisation of phytoene synthase-1 and 2, and 1-D-deoxy-xylulose 5-phosphate synthase genes from red chilli pepper (Capsicum annuum)

References

• Berry, H. M., Lai, F., Kende, A., Rickett, D. V., Baxter, C. J., Enfissi, E. M. A., & Fraser, P. D. (2021). Understanding colour retention in red chilli pepper fruit using a metabolite profiling approach. Food Chemistry: Molecular Sciences, 2, 2637–2650. https://doi.org/10.1016/j.fochms.2021.100013
   Google Scholar
• Berry, H. M., Rickett, D. V., Baxter, C. J., Enfissi, E. M. A., & Fraser, P. D. (2019). Carotenoid biosynthesis and sequestration in red chilli pepper fruit and its impact on colour intensity traits. Journal of Experimental Botany, 70(10), 100013. https://doi.org/10.1093/jxb/erz086
   Web of Science ®Google Scholar
• Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T. G., Bertoni, M., Bordoli, L., & Schwede, T. (2014). SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42(W1), 252–258. https://doi.org/10.1093/nar/gku340
   PubMed Web of Science ®Google Scholar
• Bouvier, F., d’Harlingue, A., Suire, C., Backhaus, R. A., & Camara, B. (1998). Dedicated roles of plastid transketolases during the early onset of isoprenoid biogenesis in pepper fruits1. Plant Physiology, 117(4), 1423–1431. https://doi.org/10.1104/pp.117.4.1423
   PubMed Web of Science ®Google Scholar
• Britton, G. (1995). Structure and properties of carotenoids in relation to function. FASEB Journal, 9(15), 1551–1558. https://doi.org/10.1096/fasebj.9.15.8529834
   PubMed Web of Science ®Google Scholar
• Cao, H., Luo, H., Yuan, H., Eissa, M. A., Thannhauser, T. W., Welsch, R., Hao, Y. J., Cheng, L., & Li, L. (2019). A neighboring aromatic-aromatic amino acid combination governs activity divergence between tomato phytoene synthases. Plant Physiology, 180(4), 1988–2003. https://doi.org/10.1104/pp.19.00384
   PubMed Web of Science ®Google Scholar
• Cazzonelli, C. I. (2011). Goldacre review: Carotenoids in nature: Insights from plants and beyond. Functional Plant Biology, 38(11), 833–847. https://doi.org/10.1071/FP11192
   PubMed Web of Science ®Google Scholar
• Congdon, N., & West, K. P. J. (1999). Nutrition and the eye. Current Opinion in Opthalmology, 10(6), 464–473. https://doi.org/10.1097/00055735-199912000-00016
   Google Scholar
• Corpet, F. (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Research, 16(22), 10881–10890.
   PubMed Web of Science ®Google Scholar
• Deruère, J., Römer, S., d'Harlingue, A., Backhaus, R. A., Kuntz, M. & Camara, B. (1994). Fibril assembly and carotenoid overaccumulation in chromoplasts: a model for supramolecular lipoprotein structures. Plant Cell, 6(1), 119–133. https://doi.org/10.1105/tpc.6.1.119
   PubMed Web of Science ®Google Scholar
• Enfissi, E. M. A., Barneche, F., Ahmed, I., Lichtlé, C., Gerrish, C., McQuinn, R. P., Giovannoni, J. J., Lopez-Juez, E., Bowler, C., Bramley, P. M., & Fraser, P. D. (2010). Integrative transcript and metabolite analysis of nutritionally enhanced DE-ETIOLATED1 downregulated tomato fruit. The Plant Cell, 22(4), 1190–1215. https://doi.org/10.1105/tpc.110.073866
   PubMed Web of Science ®Google Scholar
• Fraser, P. D., Kiano, J. W., Truesdale, M. R., Schuch, W., & Bramley, P. M. (1999). Phytoene synthase-2 enzyme activity in tomato does not contribute to carotenoid synthesis in ripening fruit. Plant Molecular Biology, 40(4), 687–698. https://doi.org/10.1023/A:1006256302570
   PubMed Web of Science ®Google Scholar
• Fraser, P. D., Romer, S., Shipton, C. A., Mills, P. B., Kiano, J. W., Misawa, N., Drake, R. G., Schuch, W. & Bramley, P. M. (2002). Evaluation of transgenic tomato plants expressing an additional phytoene synthase in a fruit-specific manner. Proc. Natl. Acad. Sci. U.S.A., 99(2), 1092–1097. https://doi.org/10.1073/pnas.241374598
   PubMed Web of Science ®Google Scholar
• Gallagher, C. E., Matthews, P. D., Li, F., & Wurtzel, E. T. (2004). Gene duplication in the carotenoid biosynthetic pathway preceded evolution of the grasses. Plant Physiology, 135(3), 1776–1783. https://doi.org/10.1104/pp.104.039818
   PubMed Web of Science ®Google Scholar
• Giorio, G., Stigliani, A. L., & D’Ambrosio, C. (2008). Phytoene synthase genes in tomato (Solanumlycopersicum L.) - new data on the structures, the deduced amino acid sequences and the expression patterns. The FEBS Journal, 275(3), 527–535. https://doi.org/10.1111/j.1742-4658.2007.06219.x
   PubMed Web of Science ®Google Scholar
• Gu, P., Ishii, Y., Spencer, T. A., & Shechter, I. (1998). Function-structure studies and identification of three enzyme domains involved in the catalytic activity in rat hepatic squalene synthase. Journal of Biological Chemistry, 273(20), 12515–12525. https://doi.org/10.1074/jbc.273.20.12515
   PubMed Web of Science ®Google Scholar
• Guzman, I., Hamby, S., Romero, J., Bosland, P. W., & O’Connell, M. A. (2010). Variability of carotenoid biosynthesis in orange colored Capsicum spp. Plant Science, 179(1–2), 49–59. https://doi.org/10.1016/j.plantsci.2010.04.014
   PubMed Web of Science ®Google Scholar
• Hepworth, S. R. (2002). Antagonistic regulation of flowering-time gene SOC1 by CONSTANS and FLC via separate promoter motifs. The EMBO Journal, 21(16), 4327–4337. https://doi.org/10.1093/emboj/cdf432
   PubMed Web of Science ®Google Scholar
• Huh, J. H., Kang, B. C., Nahm, S. H., Kim, S., Ha, K. S., Lee, M. H., & Kim, B. D. (2001). A candidate gene approach identified phytoene synthase as the locus for mature fruit color in red pepper (Capsicum spp.). Theoretical and Applied Genetics, 102(4), 524–530. https://doi.org/10.1007/s001220051677
   Web of Science ®Google Scholar
• Hurtado-Hernandez, H., & Smith, P. G. (1985). Inheritance of mature fruit color in Capsicum annuum L. The Journal of Heredity, 76(3), 211–213. https://doi.org/10.1093/oxfordjournals.jhered.a110070
   Web of Science ®Google Scholar
• Jeong, H., Kang, M., Jung, A., Han, K., Lee, J., Jo, J., Lee, H., An, J., Kim, S., & Kang, B. (2019). Single-molecule real-time sequencing reveals diverse allelic variations in carotenoid biosynthetic genes in pepper (Capsicum spp.). Plant Biotechnol J, 17(6), 1081–1093. https://doi.org/10.1111/pbi.13039
   PubMed Web of Science ®Google Scholar
• Jeong, M. J., & Shih, M. C. (2003). Interaction of a GATA factor with cis-acting elements involved in light regulation of nuclear genes encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase in Arabidopsis. Biochemical & Biophysical Research Communications, 300(2), 555–562. https://doi.org/10.1016/S0006-291X(02)02892-9
   PubMed Web of Science ®Google Scholar
• Karniel, U., Adler Berke, N., Mann, V. & Hirschberg, J. (2022). Perturbations in the Carotenoid Biosynthesis Pathway in Tomato Fruit Reactivate the Leaf-Specific Phytoene Synthase 2. Front. Plant Sci., 13. https://doi.org/10.3389/fpls.2022.84474810.3389/fpls.2022.844748.s001
   PubMed Web of Science ®Google Scholar
• Kim, K. N., & Guiltinan, M. J. (1999). Identification of cis-acting elements important for expression of the starch-branching enzyme I gene in maize endosperm. Plant Physiology, 121(1), 225–236. https://doi.org/10.1104/pp.121.1.225
   PubMed Web of Science ®Google Scholar
• Krinsky, N. I., & Johnson, E. J. (2005). Carotenoid actions and their relation to health and disease. Molecular Aspects of Medicine, 26(6), 459–516. https://doi.org/10.1016/j.mam.2005.10.001
   PubMedGoogle Scholar
• Kumar, S., Stecher, G., Li, M., Knyaz, C., Tamura, K., & Battistuzzi, F. U. (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
   PubMed Web of Science ®Google Scholar
• Lee, S. B., Kim, J. E., Kim, H. T., Lee, G. M., Kim, B. S., & Lee, J. M. (2020). Genetic mapping of the c1 locus by GBS-based BSA-seq revealed pseudo-response regulator 2 as a candidate gene controlling pepper fruit color. Theoretical and Applied Genetics, 133(6), 1–14. https://doi.org/10.1007/s00122-020-03565-5
   PubMed Web of Science ®Google Scholar
• Lefebvre, V., Kuntz, M., Camara, B., & Palloix, A. (1998). The capsanthin-capsorubin synthase gene: A candidate gene for the y locus controlling the red fruit colour in pepper. Plant Molecular Biology, 36(5), 785–789. https://doi.org/10.1023/A:1005966313415
   PubMed Web of Science ®Google Scholar
• Lois, L. M., Rodríguez-Concepción, M., Gallego, F., Campos, N., & Boronat, A. (2000). Carotenoid biosynthesis during tomato fruit development: Regulatory role of 1-deoxy-D-xylulose 5-phosphate synthase. Plant Journal, 22(6), 503–513. https://doi.org/10.1046/j.1365-313x.2000.00764.x
   PubMed Web of Science ®Google Scholar
• Pandit, J., Danley, D. E., Schulte, G. K., Mazzalupo, S., Pauly, T. A., Hayward, C. M., Hamanaka, E. S., Thompson, J. F., & Harwood, H. J. (2000). Crystal structure of human squalene synthase. A key enzyme in cholesterol biosynthesis. Journal of Biological Chemistry, 275(39), 30610–30617. https://doi.org/10.1074/jbc.M004132200
   PubMed Web of Science ®Google Scholar
• Popovsky, S., & Paran, I. (2000). Molecular genetics of the y locus in pepper: Its relation to capsanthin-capsorubin synthase and to fruit color. TAG. Theoretical and Applied Genetics, 101(1–2), 86–89. https://doi.org/10.1007/s001220051453
   Web of Science ®Google Scholar
• Qin, C., Yu, C., Shen, Y., Fang, X., Chen, L., Min, J., Cheng, J., Zhao, S., Xu, M., Luo, Y., Yang, Y., Wu, Z., Mao, L., Wu, H., Ling-Hu, C., Zhou, H., Lin, H., González-Morales, S., Trejo-Saavedra, D. L. … Zhang, Z. (2014). Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proceedings of the National Academy of Sciences, 111(14), 5135–5140. https://doi.org/10.1073/pnas.1400975111
   PubMed Web of Science ®Google Scholar
• Rodríguez-Concepción, M. (2004). The MEP pathway: A new target for the development of herbicides, antibiotics and antimalarial drugs. Current Pharmaceutical Design, 10(19), 2391–2400. https://doi.org/10.2174/1381612043384006
   PubMed Web of Science ®Google Scholar
• Romer, S., Hugueney, P., Bouvier, F., Camara, B., & Kuntz, M. (1993). Expression of genes encoding early carotenoid biosynthetic enzymes in Capsicum annuum. Biochemical & Biophysical Research Communications, 196(3), 1414–1421. https://doi.org/10.1006/bbrc.1993.2410
   PubMed Web of Science ®Google Scholar
• Shahmuradov, I. A., & Solovyev, V. V. (2015). Nsite, NsiteH and NsiteM computer tools for studying transcription regulatory elements. Bioinformatics, 31(21), 3544–3545. https://doi.org/10.1093/bioinformatics/btv404
   PubMed Web of Science ®Google Scholar
• Shumskaya, M., Bradbury, L. M. T., Monaco, R. R., & Wurtzel, E. T. (2012). Plastid localization of the key carotenoid enzyme phytoene synthase is altered by isozyme, allelic variation, and activity. The Plant Cell, 24(9), 3725–3741. https://doi.org/10.1105/tpc.112.104174
   PubMed Web of Science ®Google Scholar
• Small, I., Peeters, N., Legeai, F., & Lurin, C. (2004). Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics, 4(6), 1581–1590. https://doi.org/10.1002/pmic.200300776
   PubMed Web of Science ®Google Scholar
• Thorup, T. A., Tanyolac, B., Livingstone, K. D., Popovsky, S., Paran, I., & Jahn, M. (2000). Candidate gene analysis of organ pigmentation loci in the Solanaceae. Proceedings of the National Academy of Sciences, 97(21), 11192–11197. https://doi.org/10.1073/pnas.97.21.11192
   PubMed Web of Science ®Google Scholar
• Yanagisawa, S. (2000). Dof1 and Dof2 transcription factors are associated with expression of multiple genes involved in carbon metabolism in maize. Plant Journal, 21(3), 281–288. https://doi.org/10.1046/j.1365-313x.2000.00685.x
   PubMed Web of Science ®Google Scholar
• Zhou, X., Welsch, R., Yang, Y., Álvarez, D., Riediger, M., Yuan, H., Fish, T., Liu, J., Thannhauser, T. W., & Li, L. (2015). Arabidopsis or proteins are the major posttranscriptional regulators of phytoene synthase in controlling carotenoid biosynthesis. Proceedings of the National Academy of Sciences, 112(11), 3558–3563. https://doi.org/10.1073/pnas.1420831112
   PubMed Web of Science ®Google Scholar