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Research Articles

An in-silico approach to unravel the structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS): a critical enzyme for sennoside biosynthesis in Cassia angustifolia Vahl

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Pages 3848-3861 | Received 30 Dec 2022, Accepted 13 May 2023, Published online: 27 May 2023

Reference

  • Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindah, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
  • Alam, M. S., Sharma, M., Kumar, R., Das, J., Rode, S., Kumar, P., Prasad, R., & Sharma, A. K. (2022). In silico identification of potential phytochemical inhibitors targeting farnesyl diphosphate synthase of cotton bollworm (Helicoverpa armigera). Journal of Biomolecular Structure and Dynamics, 41(5) 1978-1987. https://doi.org/10.1080/07391102.2022.2025904
  • Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389–3402. https://doi.org/10.1093/NAR/25.17.3389
  • Aruw, K., Bapi, D., & Reddy, G. S. (2012). Effect of organic manures, biofertilizers and inorganic fertilizers on growth and yield of seena (Cassia angustifolia Vahl.). Asian Journal of Horticulture, 7(1), 144–147.
  • Bailey, A. G., & Lowe, C. P. (2009). Milch shake: An efficient method for constraint dynamics applied to alkanes. Journal of Computational Chemistry, 30(15), 2485–2493. https://doi.org/10.1002/JCC.21237
  • Berendsen, H. J. C., Postma, J. P. M., Van Gunsteren, W. F., Dinola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
  • Berezin, C., Glaser, F., Rosenberg, J., Paz, I., Pupko, T., Fariselli, P., Casadio, R., & Ben-Tal, N. (2004). ConSeq: The identification of functionally and structurally important residues in protein sequences. Bioinformatics (Oxford, England), 20(8), 1322–1324. https://doi.org/10.1093/bioinformatics/bth070
  • Berman, H., Henrick, K., & Nakamura, H. (2003). Announcing the worldwide Protein Data Bank. Nature Structural & Molecular Biology, 10(12), 980–980. https://doi.org/10.1038/nsb1203-980
  • Bhattacharya, S., & Kumar, P. (2012). An insilico approach to structural elucidation of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Arabidopsis thaliana: Hints for herbicide design. Phytochemistry, 73(1), 7–14. https://doi.org/10.1016/J.PHYTOCHEM.2011.09.005
  • Chen, M. R., Zhao, J., Fu, S. F., Yu, J. Q., Zhang, X., Zhang, Q. Y., & Zhou, Z. H. (2019). Clinical practice of Chinese medicine navel therapy for chronic diarrhea: A literature review. Journal of Gastroenterology and Hepatology, 34(4), 643–649. https://doi.org/10.1111/JGH.14549
  • Chey, W. D., Camilleri, M., Chang, L., Rikner, L., & Graffner, H. (2011). A randomized placebo-controlled phase IIb trial of A3309, a bile acid transporter inhibitor, for chronic idiopathic constipation. The American Journal of Gastroenterology, 106(10), 1803–1812. https://doi.org/10.1038/AJG.2011.162
  • Chey, W. D., Camilleri, M., Chang, L., Rikner, L., & Graffner, H. (2014). Erratum: A randomized placebo-controlled phase IIb trial of A3309, a bile acid transporter inhibitor, for chronic idiopathic constipation. American Journal of Gastroenterology, 109(5), 782. https://doi.org/10.1038/ajg.2011.224
  • Colovos, C., & Yeates, T. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science: A Publication of the Protein Society, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
  • Cross, P. J., Dobson, R. C. J., Patchett, M. L., & Parker, E. J. (2011). Tyrosine latching of a regulatory gate affords allosteric control of aromatic amino acid biosynthesis. The Journal of Biological Chemistry, 286(12), 10216–10224. https://doi.org/10.1074/JBC.M110.209924
  • Cross, P. J., Pietersma, A. L., Allison, T. M., Wilson-Coutts, S. M., Cochrane, F. C., & Parker, E. J. (2013). Neisseria meningitidis expresses a single 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase that is inhibited primarily by phenylalanine. Protein Science: A Publication of the Protein Society, 22(8), 1087–1099. https://doi.org/10.1002/PRO.2293
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
  • Deb, B., Prichard, D. O., & Bharucha, A. E. (2020). Constipation and fecal incontinence in the elderly. Current Gastroenterology Reports, 22(11), 1–16. https://doi.org/10.1007/S11894-020-00791-1/FIGURES/2
  • Dhanani, T., Singh, R., Reddy, N., Trivedi, A., & Kumar, S. (2017). Comparison on extraction yield of sennoside A and sennoside B from senna (Cassia angustifolia) using conventional and non-conventional extraction techniques and their quantification using a validated HPLC-PDA detection method. Natural Product Research, 31(9), 1097–1101. https://doi.org/10.1080/14786419.2016.1258562
  • Doong, R. L., Gander, J. E., Ganson, R. J., & Jensen, R. A. (1992). The cytosolic isoenzyme of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase in Spinacia oleracea and other higher plants: Extreme substrate ambiguity and other properties. Physiologia Plantarum, 84(3), 351–360. https://doi.org/10.1111/j.1399-3054.1992.tb04675.x
  • Ford, A. C., & Suares, N. C. (2011). Effect of laxatives and pharmacological therapies in chronic idiopathic constipation: Systematic review and meta-analysis. Gut, 60(2), 209–218. https://doi.org/10.1136/GUT.2010.227132
  • Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D., Bairoch, A. (2003). ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31(13), 3784–3788. https://doi.org/10.1093/nar/gkg563
  • Grant, B. J., Skjaerven, L., & Yao, X.-Q. (2021). The Bio3D packages for structural bioinformatics. Protein Science: A Publication of the Protein Society, 30(1), 20–30. https://doi.org/10.1002/PRO.3923
  • Graziana, A., & Boudet, A. M. (1980). 3-Deoxy-D-arabino heptulosonate 7-phosphate synthase from Zea mays: General properties and regulation by tryptophan. Plant and Cell Physiology, 21(5), 793–802. https://doi.org/10.1093/oxfordjournals.pcp.a076054
  • Gruenberg, M., Irla, M., Myllek, S., & Draths, K. (2021). Characterization of two 3-deoxy-D-arabino-heptulosonate 7-phosphate synthases from Bacillus methanolicus. Protein Expression and Purification, 188, 105972. https://doi.org/10.1016/j.pep.2021.105972
  • Gupta, D. N., Dalal, V., Savita, B. K., Alam, M. S., Singh, A., Gubyad, M., Ghosh, D. K., Kumar, P., & Sharma, A. K. (2022). Biochemical characterization and structure-based in silico screening of potent inhibitor molecules against the 1 cys peroxiredoxin of bacterioferritin comigratory protein family from Candidatus Liberibacter asiaticus. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2022.2096118
  • Hartmann, M., Schneider, T. R., Pfeil, A., Heinrich, G., Lipscomb, W. N., & Braus, G. H. (2003). Evolution of feedback-inhibited β/α barrel isoenzymes by gene duplication and a single mutation. Proceedings of the National Academy of Sciences of the United States of America, 100(3), 862–867. https://doi.org/10.1073/PNAS.0337566100
  • Hietala, P., Marvola, M., Parviainen, T., & Lainonen, H. (1987). Laxative potency and acute toxicity of some anthraquinone derivatives, senna extracts and fractions of senna extracts. Pharmacology & toxicology, 61(2), 153-156. https://doi.org/10.1111/j.1600-0773.1987.tb01794.x
  • Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., Cuche, B. A., De Castro, E., Lachaize, C., Langendijk-Genevaux, P. S., & Sigrist, C. J. A. (2008). The 20 years of PROSITE. Nucleic Acids Research, 36(Database), D245–D249. https://doi.org/10.1093/nar/gkm977
  • Inoue, K., Shiobara, Y., Nayeshiro, H., Inouye, H., Wilson, G., & Zenk, M. H. (1984). Biosynthesis of anthraquinones and related compounds in Galium mollugo cell suspension cultures. Phytochemistry, 23(2), 307–311. https://doi.org/10.1016/S0031-9422(00)80323-4
  • Jensen, R. A., Xie, G., Calhoun, D. H., & Bonner, C. A. (2002). The correct phylogenetic relationship of KdsA (3-deoxy-D-manno-octulosonate 8-phosphate synthase) with one of two independently evolved classes of AroA (3-deoxy-D-arabino-heptulosonate 7-phosphate synthase). Journal of Molecular Evolution, 54(3), 416–423. https://doi.org/10.1007/s00239-001-0031-z
  • Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., & Madden, T. L. (2008). NCBI BLAST: A better web interface. Nucleic Acids Research, 36(Web Server), W5–W9. https://doi.org/10.1093/nar/gkn201
  • Junia, R., Jain, N., Sohal, J., Sharma, D., Khare, N., & Aseri, G. K. (2021). Comparative impact of bioinoculants on nutrient uptake, enzyme activities and growth of Cassia angustifolia Vhal (Senna) and Cyamopsis tetragonoloba (L.) (Guar) in Feldspar mine spoil. South African Journal of Botany, 140, 434–443. https://doi.org/10.1016/j.sajb.2020.12.006
  • Kibbe, W. A. (2007). OligoCalc: An online oligonucleotide properties calculator. Nucleic Acids Research, 35(Web Server issue), W43–W46. https://doi.org/10.1093/NAR/GKM234
  • Konc, J., Miller, B. T., Štular, T., Lešnik, S., Woodcock, H. L., Brooks, B. R., & Janežič, D. (2015). ProBiS-CHARMMing: Web interface for prediction and optimization of ligands in protein binding sites. Journal of Chemical Information and Modeling, 55(11), 2308–2314. https://doi.org/10.1021/acs.jcim.5b00534
  • König, V., Pfeil, A., Braus, G. H., & Schneider, T. R. (2004). Substrate and metal complexes of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from saccharomyces cerevisiae provide new insights into the catalytic mechanism. Journal of Molecular Biology, 337(3), 675–690. https://doi.org/10.1016/J.JMB.2004.01.055
  • Kumar, A., Kumar Verma, D., Ac, J., & Tk, V. (2018). Opportunities and challenges in the cultivation of senna (Cassia angustifolia (Vahl.)). International Journal of Herbal Medicine, 6(4), 41–43.
  • Kumari, R., Kumar, R., & Lynn, A, Open Source Drug Discovery Consortium. (2014). G-mmpbsa –A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/CI500020M
  • Laskowski, R. A., Rullmann, J. A. C., MacArthur, M. W., Kaptein, R., & Thornton, J. M. (1996). AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular NMR, 8(4), 477–486. https://doi.org/10.1007/BF00228148
  • Leistner, E. (1975). [Isolation, identification and biosynthesis of anthraquinones in cell suspension cultures of Morinda citrifolia (author’s transl)]. Planta Medica, Suppl, 214–224. https://doi.org/10.1055/S-0028-1105797
  • LeLeiko, N. S., Mayer-Brown, S., Cerezo, C., & Plante, W. (2020). Constipation. Pediatrics in Review, 41(8), 379–392. https://doi.org/10.1542/PIR.2018-0334
  • 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. https://doi.org/10.1093/nar/gkz991
  • Maeda, H., & Dudareva, N. (2012). The shikimate pathway and aromatic amino acid biosynthesis in plants, Annual Review of Plant Biology, 63, 73–105. https://doi.org/10.1146/ANNUREV-ARPLANT-042811-105439
  • Mangmeesri, P., Wongsuphasawat, K., Gritsanapan, W., & Viseshsindh, W. (2013). Laxative effectiveness of cassia angustifolia in thai constipated patients. Thai Journal of Pharmaceutical Sciences, 38 (Suppl.), 268–270.
  • Manhas, A., Patel, D., Lone, M. Y., & Jha, P. C. (2019). Identification of natural compound inhibitors against PfDXR: A hybrid structure-based molecular modeling approach and molecular dynamics simulation studies. Journal of Cellular Biochemistry, 120(9), 14531–14543. https://doi.org/10.1002/JCB.28714
  • Mayrose, I., Graur, D., Ben-Tal, N., & Pupko, T. (2004). Comparison of site-specific rate-inference methods for protein sequences: Empirical Bayesian methods are superior. Molecular Biology and Evolution, 21(9), 1781–1791. https://doi.org/10.1093/molbev/msh194
  • Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E. L. L., Tosatto, S. C. E., Paladin, L., Raj, S., Richardson, L. J., Finn, R. D., & Bateman, A. (2021). Pfam: The protein families database in 2021. Nucleic Acids Research, 49(D1), D412–D419. https://doi.org/10.1093/nar/gkaa913
  • Nanumala, S. K., Nischal, Y., Sarika, M., & Shravya, G. S. S. (2014). Hypolipidemic activity of ethanolic extracts of cassia angustifolia in triton-X 100 induced hyperlipidemia in Rats. Asian Journal of Pharmaceutical and Clinical Research, 7(SUPPL. 1), 189–191.
  • Nazmi, A. R., Schofield, L. R., Dobson, R. C. J., Jameson, G. B., & Parker, E. J. (2014). Destabilization of the homotetrameric assembly of 3-deoxy-d-arabino- heptulosonate-7-phosphate synthase from the hyperthermophile pyrococcus furiosus enhances enzymatic activity. Journal of Molecular Biology, 426(3), 656–673. https://doi.org/10.1016/J.JMB.2013.11.008
  • Parrinello, M., & Rahman, A. (1980). Crystal structure and pair potentials: A molecular-dynamics study. Physical Review Letters, 45(14), 1196–1199. https://doi.org/10.1103/PhysRevLett.45.1196
  • Patel, B., Patel, D., Parmar, K., Chauhan, R., Singh, D. D., & Pappachan, A. (2018). L. donovani XPRT: Molecular characterization and evaluation of inhibitors. Biochimica et Biophysica Acta. Proteins and Proteomics, 1866(3), 426–441. https://doi.org/10.1016/J.BBAPAP.2017.12.002
  • Patel, D., Athar, M., & Jha, P. C. (2021). Exploring ruthenium-based organometallic inhibitors against plasmodium falciparum calcium dependent kinase 2 (PfCDPK2): A combined ensemble docking, QM/MM and molecular dynamics study. ChemistrySelect, 6(32), 8189–8199. https://doi.org/10.1002/slct.202101801
  • Patel, R., Chudasama, R., Solanki, R., Patel, P., Parmar, K., & Munshi, N. S. (2020). Structure prediction and molecular docking studies of aromatic hydrocarbon sensing proteins TbuT, HbpR and PhnR to detect priority pollutants. Journal of Environmental Science and Health. Part A, Toxic/Hazardous Substances & Environmental Engineering, 55(2), 126–141. https://doi.org/10.1080/10934529.2019.1672457
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/JCC.20084
  • Combet, C., Blanchet, C., Geourjon, C., & Deleage, G. (2000). NPS@: network protein sequence analysis. Trends in biochemical sciences, 25(3), 147–150.
  • Reddy, N. R. R., Mehta, R. H., Soni, P. H., Makasana, J., Gajbhiye, N. A., Ponnuchamy, M., & Kumar, J. (2015). Next generation sequencing and transcriptome analysis predicts biosynthetic pathway of sennosides from senna (Cassia angustifolia Vahl.), a non-model plant with potent laxative properties. Plos One, 10(6), e0129422. https://doi.org/10.1371/journal.pone.0129422
  • Reinink, M., & Borstlap, A. C. (1982). 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from pea leaves: Inhibition by L-tyrosine. Plant Science Letters, 26(2–3), 167–171. https://doi.org/10.1016/0304-4211(82)90088-8
  • Rice, P., Longden, L., & Bleasby, A. (2000). EMBOSS: The European molecular biology open software suite. Trends in Genetics: TIG, 16(6), 276–277. https://doi.org/10.1016/S0168-9525(00)02024-2
  • Rio, D. C., Ares, M., Hannon, G. J., & Nilsen, T. W. (2010). Purification of RNA using TRIzol (TRI Reagent). Cold Spring Harbor Protocols, 2010(6), pdb.prot5439. https://doi.org/10.1101/PDB.PROT5439
  • Schofield, L. R., Patchett, M. L., & Parker, E. J. (2004). Expression, purification, and characterization of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Pyrococcus furiosus. Protein Expression and Purification, 34(1), 17–27. https://doi.org/10.1016/j.pep.2003.11.008
  • Schüttelkopf, A. W., & Van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
  • Scott, W. R. P., Hünenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Krüger, P., & Van Gunsteren, W. F. (1999). The GROMOS biomolecular simulation program package. The Journal of Physical Chemistry A, 103(19), 3596–3607. https://doi.org/10.1021/jp984217f
  • Sehgal, S. A., Hammad, M. A., Tahir, R. A., Akram, H. N., & Ahmad, F. (2018). Current therapeutic molecules and targets in neurodegenerative diseases based on in silico drug design. Current Neuropharmacology, 16(6), 649–663. https://doi.org/10.2174/1570159X16666180315142137
  • Sharma, A., & Rao, S. (2017). Constipation: Pathophysiology and current therapeutic approaches. Handbook of Experimental Pharmacology, 239, 59-74.https://doi.org/10.1007/164_2016_111
  • Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J. D., & Higgins, D. G. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal omega. Molecular Systems Biology, 7(1), 539. https://doi.org/10.1038/MSB.2011.75
  • Sterritt, O. W., Kessans, S. A., Jameson, G. B., & Parker, E. J. (2018). A pseudoisostructural type II DAH7PS enzyme from Pseudomonas aeruginosa: Alternative evolutionary strategies to control shikimate pathway flux. Biochemistry, 57(18), 2667–2678. https://doi.org/10.1021/ACS.BIOCHEM.8B00082/SUPPL_FILE/BI8B00082_SI_001.PDF
  • Suzich, J. A., Dean, J. F. D., & Herrmann, K. M. (1985). 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from carrot root (Daucus carota) is a hysteretic enzyme. Plant Physiology, 79(3), 765–770. https://doi.org/10.1104/PP.79.3.765
  • Suzuki, N., Sakuta, M., & Shimizu, S. (1996). Purification and characterization of a cytosolic isozyme of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from cultured carrot cells. Journal of Plant Physiology, 149(1–2), 19–22. https://doi.org/10.1016/S0176-1617(96)80167-2
  • Tian, W., Chen, C., Lei, X., Zhao, J., & Liang, J. (2018). CASTp 3.0: Computed atlas of surface topography of proteins. Nucleic Acids Research, 46(W1), W363–W367. https://doi.org/10.1093/nar/gky473
  • 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. https://doi.org/10.1002/JCC.21334
  • Ur. Rehman, N., Khan, A., Al-Harrasi, A., Hussain, H., Wadood, A., Riaz, M., & Al-Abri, Z. (2018). New α-Glucosidase inhibitors from the resins of Boswellia species with structure–glucosidase activity and molecular docking studies. Bioorganic Chemistry, 79(April), 27–33. https://doi.org/10.1016/j.bioorg.2018.04.020
  • Warren, G. L., Do, T. D., Kelley, B. P., Nicholls, A., & Warren, S. D. (2012). Essential considerations for using protein–ligand structures in drug discovery. Drug Discovery Today, 17(23–24), 1270–1281. https://doi.org/10.1016/J.DRUDIS.2012.06.011
  • Wass, M. N., Kelley, L. A., & Sternberg, M. J. E. (2010). 3DLigandSite: Predicting ligand-binding sites using similar structures. Nucleic Acids Research, 38(suppl_2), W469–W473. https://doi.org/10.1093/nar/gkq406
  • Webby, C. J., Jiao, W., Hutton, R. D., Blackmore, N. J., Baker, H. M., Baker, E. N., Jameson, G. B., & Parker, E. J. (2010). Synergistic allostery, a sophisticated regulatory network for the control of aromatic amino acid biosynthesis in Mycobacterium tuberculosis. The Journal of Biological Chemistry, 285(40), 30567–30576. https://doi.org/10.1074/JBC.M110.111856
  • Wu, J., & Woodard, R. W. (2006). New insights into the evolutionary links relating to the 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase subfamilies. The Journal of Biological Chemistry, 281(7), 4042–4048. https://doi.org/10.1074/JBC.M512223200
  • Xu, D., & Zhang, Y. (2011). Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical Journal, 101(10), 2525–2534. https://doi.org/10.1016/j.bpj.2011.10.024
  • Yang, J., Zhang, Y., & I-Tasser, T. (2015). I-TASSER server: New development for protein structure and function predictions, Nucleic Acids Research, 43(W1), W174–W181. https://doi.org/10.1093/nar/gkv342
  • Ying, S., Su, M., Wu, Y., Zhou, L., Fu, R., Li, Y., Guo, H., Luo, J., Wang, S., & Zhang, Y. (2020). Trichome regulator SlMIXTA-like directly manipulates primary metabolism in tomato fruit. Plant Biotechnology Journal, 18(2), 354–363. https://doi.org/10.1111/PBI.13202
  • Yokoyama, R., de Oliveira, M. V. V., Kleven, B., & Maeda, H. A. (2021). The entry reaction of the plant shikimate pathway is subjected to highly complex metabolite-mediated regulation. The Plant Cell, 33(3), 671–696. https://doi.org/10.1093/plcell/koaa042
  • Yokoyama, R., Kleven, B., Gupta, A., Wang, Y., & Maeda, H. A. (2022). 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase as the gatekeeper of plant aromatic natural product biosynthesis. Current Opinion in Plant Biology, 67, 102219. https://doi.org/10.1016/j.pbi.2022.102219
  • Yoo, H., Shrivastava, S., Lynch, J. H., Huang, X. Q., Widhalm, J. R., Guo, L., Carter, B. C., Qian, Y., Maeda, H. A., Ogas, J. P., Morgan, J. A., Marshall-Colón, A., & Dudareva, N. (2021). Overexpression of arogenate dehydratase reveals an upstream point of metabolic control in phenylalanine biosynthesis. The Plant Journal: For Cell and Molecular Biology, 108(3), 737–751. https://doi.org/10.1111/TPJ.15467
  • Zhang, C., Freddolino, P. L., & Zhang, Y. (2017). COFACTOR: Improved protein function prediction by combining structure, sequence and protein–protein interaction information, Nucleic Acids Research, 45(W1), W291–W299. https://doi.org/10.1093/nar/gkx366
  • Zhao, H., Gao, H., Ji, K., Yan, B., Li, Q., Mo, S., Zheng, M., Ou, Q., Wu, B., Li, N., & Jiang, C. (2019). Isolation and biochemical characterization of a metagenome-derived 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase gene from subtropical marine mangrove wetland sediments. AMB Express, 9(1), 19. https://doi.org/10.1186/S13568-019-0742-4
  • Zhou, L., Wu, J., Vijayalakshmi, J., Shumilin, I. A., Bauerle, R., Kretsinger, R. H., & Woodard, R. W. (2012). Structure and characterization of the 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Aeropyrum pernix. Bioorganic Chemistry, 40(1), 79–86. https://doi.org/10.1016/j.bioorg.2011.09.002

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