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Research Article

In silico approaches illustrate the evolutionary pattern and protein-small molecule interactions of quinolone synthase from Aegle marmelos Correa

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Pages 195-209 | Received 07 Oct 2017, Accepted 15 Dec 2017, Published online: 24 Jan 2018

References

  • Ahmed, A., & Daneshtalab, M. (2012). Nonclassical biological activities of quinolone derivatives. Journal of Pharmacy & Pharmaceutical Sciences, 15, 52–72.
  • Ashkenazy, H., Erez, E., Martz, E., Pupko, T., & Ben-Tal, N. (2010). ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Research, 38, W529–W533. doi:10.1093/nar/gkq399
  • Austin, M. B., & Noel, J. P. (2003). The chalcone synthase superfamily of type III polyketide synthases. Natural Product Reports, 20, 79–110.10.1039/b100917f
  • Bendl, J., Stourac, J., Salanda, O., Pavelka, A., Wieben, E. D., Zendulka, J., … Damborsky, J. (2014). PredictSNP: Robust and accurate consensus classifier for prediction of disease-related mutations. PLoS Computational Biology, 10, e1003440. doi:10.1371/journal.pcbi.1003440
  • Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., … Schwede, T. (2014). SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42(W1), W252–W258. doi:10.1093/nar/gku340
  • Choi, Y., & Chan, A. P. (2015). PROVEAN web server: A tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics, 31(16), 2745–2747. doi:10.1093/bioinformatics/btv195
  • Delport, W., Poon, A. F., Frost, S. D., & Kosakovsky Pond, S. L. (2010). Datamonkey 2010: A suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics, 26(19), 2455–2457. doi:10.1093/bioinformatics/btq429
  • Dereeper, A., Guignon, V., Blanc, G., Audic, S., Buffet, S., Chevenet, F., … Gascuel, O. (2008). Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Research, 36(Web Server issue), W465–W469. doi:10.1093/nar/gkn180
  • Dundas, J., Ouyang, Z., Tseng, J., Binkowski, A., Turpaz, Y., & Liang, J. (2006). CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids research, 34, W116–W118. doi: 10.1093/nar/gkl282
  • Felsenstein, J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783–791. doi:10.1111/j.1558-5646.1985.tb00420.x
  • Ferrer, J. L., Jez, J. M., Bowman, M. E., Dixon, R. A., & Noel, J. P. (1999). Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis. Nature Structural & Molecular Biology, 6, 775–784. doi:10.1038/11553
  • Fu, Y. X., & Li, W. H. (1993). Statistical tests of neutrality of mutations. Genetics, 133, 693–709.
  • Heeb, S., Fletcher, M. P., Chhabra, S. R., Diggle, S. P., Williams, P., & Cámara, M. (2011). Quinolones: From antibiotics to autoinducers. FEMS Microbiology Reviews, 35, 247–274. doi:10.1111/j.1574-6976.2010.00247.x
  • Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences., 8, 275–282.
  • Kiefer, F., Arnold, K., Kunzli, M., Bordoli, L., & Schwede, T. (2009). The SWISS-MODEL Repository and associated resources. Nucleic Acids Research, 37, D387–D392. doi:10.1093/nar/gkn750
  • Kimura, M. (1983). The neutral theory of molecular evolution. Cambridge: Cambridge University Press.10.1017/CBO9780511623486
  • Kimura, M., & Ohta, T. (1974). On some principles governing molecular evolution. Proceedings of the National Academy of Sciences, 71(7), 2848–2852.10.1073/pnas.71.7.2848
  • Koonin, E. V., & Wolf, Y. I. (2010). Constraints and plasticity in genome and molecular-phenome evolution. Nature Reviews Genetics, 11(7), 487–498. doi:10.1038/nrg2810
  • Koskela, S., Elomaa, P., Helariutta, Y., Soderholm, P., & Vuorela, P. (2001). Two bioactive compounds and a novel chalcone synthase like enzyme identified in Gerbera hybrida. Acta Horticulturae, 560, 271–274.10.17660/ActaHortic.2001.560.52
  • Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1874. doi:10.1093/molbev/msw054
  • Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., & … Higgins D. G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947–2948. doi:10.1093/bioinformatics/btm404
  • Letunic, I, & Bork, P. (2016). Interactive tree of life (iTOL) v3: An online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research, 8(44)(W1):W242–W245. doi: 10.1093/nar/gkw290
  • Li, H., Liang, J., Chen, H., Ding, G., Ma, B., & He, N. (2016). Evolutionary and functional analysis of mulberry type III polyketide synthases. BMC Genomics, 17, 540. doi:10.1186/s12864-016-2843-7
  • Li, L., Aslam, M., Rabbi, F., Vanderwe, M. C., Ashton, N. W., & Suh, D. Y. (2017). PpORS, an ancient type III polyketide synthase, is required for integrity of leaf cuticle and resistance to dehydration in the moss, Physcomitrella patens. Planta, 1–15. Retrieved from https://link.springer.com/article/10.1007/s00425-017-2806-5#citeas
  • Lim, Y. P., Go, M. K., & Yew, W. S. (2016). Exploiting the biosynthetic potential of type III polyketide synthases. Molecules, 21, 806. doi:10.3390/molecules21060806
  • Liu, K., Warnow, T. J., Holder, M. T., Nelesen, S. M., Yu, J., Stamatakis, A., & Linder, C. R. (2012). SATé-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Systematic Biology., 61(1), 90–106. doi:10.1093/sysbio/syr095
  • Lovell, S. C., Davis, I. W., Arendall, W. B., de Bakker, P. I. W., Word, J. M., Prisant, M. G., … Richardson, D. C. (2002). Structure validation by Calpha geometry: Phi., psi and Cbeta deviation. Proteins: Structure, Function, and Genetics, 50, 437–450. doi:10.1002/prot.10286
  • Lukacin, R., Schreiner, S., & Matern, U. (2001). Transformation of acridone synthase to chalcone synthase. FEBS Letters, 508, doi:10.1016/S0014-5793(01)03061-7
  • Mallika, V., Aiswarya, G., Gincy, P. T., Remakanthan, A., & Soniya, E. V. (2016). Type III polyketide synthase repertoire in Zingiberaceae: Computational insights into the sequence, structure and evolution. Development Genes and Evolution, 226(4), 269–285. doi:10.1007/s00427-016-0548-1
  • Meslet-Cladière, L., Delage, L., Leroux, C. J.-J., Goulitquer, S., Leblanc, C., Creis, E., ... Potin, P. (2013). Structure/function analysis of a type III polyketide synthase in the brown alga ectocarpus siliculosus reveals a biochemical pathway in phlorotannin monomer biosynthesis. The Plant Cell, 25(8), 3089–3103. doi:10.1105/tpc.113.111336
  • Mittal, A. (2012). Self-generated and reproducible dynamics in ‘gene years’ represent life. Journal of Biomolecular Structure and Dynamics, 29(4), 609–611. doi: 10.1080/073911012010525002
  • Mittal, A., & Jayaram, B. (2011a). Backbones of folded proteins reveal novel invariant amino acid neighborhoods. Journal of Biomolecular Structure and Dynamics, 28(4), 443–454. doi:10.1080/073911011010524954
  • Mittal, A., & Jayaram, B. (2011b). The newest view on protein folding: Stoichiometric and spatial unity in structural and functional diversity. Journal of Biomolecular Structure and Dynamics, 28(4), 669–674.10.1080/073911011010524984
  • Mittal, A., Jayaram, B., Shenoy, S., & Bawa, T. J. (2010). A stoichiometry driven universal spatial organization of backbones of folded proteins: Are these Chargaff’s rules for protein folding? Journal of Biomolecular Structure and Dynamics, 28, 133–142. doi:10.1080/07391102.2010.10507349
  • Mori, T., Shimokawa, Y., Matsui, T., Kinjo, K., Kato, R., Noguchi, H., … Abe, I. (2013). Cloning and structure-function analyses of quinolone- and acridone-producing novel type III polyketide synthases from citrus microcarpa. Journal of Biological Chemistry, 288, 28845–28858. doi:10.1074/jbc.M113.493155
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). Autodock4 and AutoDockTools4: Automated docking with selective receptor flexiblity. Journal of Computational Chemistry, 30, 2785–2791. doi:10.1002/jcc.21256
  • Quan, L., Lv, Q., & Zhang, Y. (2016). STRUM: Structure-based stability change prediction upon single-point mutation. Bioinformatics, 32, 2911–2919. doi:10.1093/bioinformatics/btw361
  • Resmi, M. S., Verma, P., Gokhale, R. S., & Soniya, E. V. (2013). Identification and characterization of a type III polyketide synthase involved in quinolone alkaloid biosynthesis from Aegle marmelos correa. Journal of Biological Chemistry, 288, 7271–7281. doi:10.1074/jbc.M112.429886
  • Resmi, M. S., Vivek, P. J., & Soniya, E. V. (2015). Over-expression of bael quinolone synthase in tobacco improves plant vigor under favorable conditions, drought, or salt stress. FEBS Letters, 589(3), 332–341. doi: 10.1016/j.febslet.2014.12.016
  • Robert, X., & Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research, 42, W320–W324. doi:10.1093/nar/gku316
  • Rozas, J. (2009). DNA sequence polymorphism analysis using DnaSP. Bioinformatics for DNA sequence analysis, 537, 337–350. doi:10.1007/978-1-59745-251-9_17
  • Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4), 406–425.
  • Sanders, I. F. (2008). Sequencing of Medicago truncatula genome and studies of metabolic gene organization and expression profile. (PhD dissertation). The University of Oklahoma. [ProQuest http://gradworks.umi.com/33/07/3307965.html]
  • Schroder, J. (1997). A family of plant-specific polyketide synthases: Facts and predictions. Trends in Plant Science, 2, 373–378.10.1016/S1360-1385(97)87121-X
  • Schroeder, J., & Schroeder, G. (1990). Stilbene and chalcone synthases: Related enzymes with key functions in plant-specific pathways. Zeitschrift für Naturforschung C , 45, 1–8.
  • Sharma, G.N., Dubey, S. K., Sharma, P., & Sati, N. (2011). Medicinal values of bael (Aegle marmelos) (L.) corr.: A review. International Journal of Current Pharmaceutical Review and Research. 1(3), 12–22.
  • Shimizu, Y., Ogata, H., & Goto, S. (2017). Type III polyketide synthases: Functional classification and phylogenomics. ChemBioChem, 18(1), 50–65. doi: 10.1002/cbic.201600522.
  • Steinway, S. N., Dannenfelser, R., Laucius, C. D., Hayes, J. E., & Nayak, S. (2010). JCoDA: A tool for detecting evolutionary selection. BMC Bioinformatics, 11, 284. doi:10.1186/1471-2105-11-284
  • Stewart, C., Jr, Vickery, C. R., Burkart, M. D., & Noel, J. P. (2013). Confluence of structural and chemical biology: Plant polyketide synthases as biocatalysts for bio-based future. Current Opinion in Plant Biology, 16, 365–372. doi:10.1016/j.pbi.2013.02.004
  • Su, X., Sun, X., Cheng, X., Wang, Y., Abdullah, M., Li, M., … Lin, Y. (2017). Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton. PeerJ, 5, e3974. doi:10.7717/peerj.3974
  • Tajima, F. (1993). Simple methods for testing molecular clock hypothesis. Genetics, 135, 599–607.
  • 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. Retrieved from http://doi.org/10.1002/jcc.21334
  • Tuller, T., Kupiec, M., & Ruppin, E. (2008). Evolutionary rate and gene expression across different brain regions. Genome Biology, 9(9), R142. doi:10.1186/gb-2008-9-9-r142
  • Watanabe, K., Praseuth, A. P., & Wang, C. C. (2007). A comprehensive and engaging overview of the type III family of polyketide synthases. Current Opinion in Chemical Biology, 11, 279–286. doi:10.1016/j.cbpa.2006.11.041
  • Zhang, J., Yu, L., & Yang, Z. (2011). Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure, 19, 1784–1795. doi:10.1016/j.str.2011.09.022
  • Zhou, L., Wang, Y., & Peng, Z. (2011). Molecular characterization and expression analysis of chalcone synthase gene during flower development in tree peony (Paeoniasuffruticosa). African Journal of Biotechnology, 10, 1275–1284.

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