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Molecular Cloning of an Amino Acid Permease Gene and Structural Characterization of the Protein in Common Bean (Phaseolus vulgaris L.)

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Plants synthesize amino acids by collateral metabolic pathways using primary elements carbon and oxygen from air, hydrogen from water in soil and nitrogen from soil. Following synthesis, amino acids are immediately used for metabolism, transient storage or transported to the phloem. Different families of transporters have been identified for import of amino acids into plant cells. The first identified amino acid transporter, amino acid permease 1 (AAP1) in Arabidopsis belongs to a family of eight members and transports acidic, neutral, and basic amino acids. Legumes fix atmospheric nitrogen through a symbiotic relationship with root nodules bacteria. Following fixation, nitrogen is reduced to amino acids and is exported via different amino acid transporters. However, information is lacking about the structure of these important classes of amino acid transporter proteins in plant. We have amplified AAP from Phaseolus vulgaris, an economically important leguminous plant grown all over the world, and sequenced. The sequence has been characterized in silico and a three-dimensional structure of AAP has been predicted and validated. The information obtained not only enhances the knowledge about the structure of an amino acid permease gene in P. vulgaris, but will also help in designing protein–ligand studies using this protein as well.

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  1. 1.

    Okumoto, S., & Pilot, G. (2011). Amino acid export in plants: A missing link in nitrogen cycling. Molecular Plant,4, 453–463.

  2. 2.

    Lalonde, S., Wipf, D., & Frommer, W. B. (2004). Transport mechanisms for organic forms of carbon and nitrogen between source and sink. Annual Review of Plant Biology,55, 341–372.

  3. 3.

    Martinoia, E., Maeshima, M., & Neuhaus, H. E. (2007). Vacuolar transporters and their essential role in plant metabolism. Journal of Experimental Botany,58, 83–102.

  4. 4.

    Lunn, J. E. (2007). Compartmentation in plant metabolism. Journal of Experimental Botany,58, 35–47.

  5. 5.

    Elashry, A., Okumoto, S., Siddique, S., et al. (2013). The AAP gene family for amino acid permeases contributes to development of the cyst nematode Heterodera schachtii in roots of Arabidopsis. Plant Physiology and Biochemistry,70, 379–386.

  6. 6.

    Rentsch, D., Schmidt, S., & Tegeder, M. (2007). Transporters for uptake and allocation of organic nitrogen compounds in plants. Federation of European Biochemical Societies Letters,581, 2281–2289.

  7. 7.

    Tegeder, M., & Rentsch, D. (2010). Uptake and partitioning of amino acids and peptides. Molecular Plant,3, 997–1011.

  8. 8.

    Tegeder, M. (2014). Transporters involved in source to sink partitioning of amino acids and ureides: Opportunities for crop improvement. Journal of Experimental Botany,65, 1865–1878.

  9. 9.

    Ortiz-Lopez, A., Chang, H. C., & Bush, D. R. (2000). Amino acid transporters in plants. Biochimica et Biophysica Acta,1465, 275–280.

  10. 10.

    Frommer, W. B., Hummel, S., & Riesmeier, J. W. (1993). Expression cloning in yeast of a cDNA encoding a broad specificity amino acid permease from Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America,90, 5944–5948.

  11. 11.

    Hsu, L. C., Chiou, T. J., Chen, L., et al. (1993). Cloning a plant amino acid transporter by functional complementation of a yeast amino acid transport mutant. Proceedings of the National Academy of Sciences of the United States of America,90, 7441–7445.

  12. 12.

    Fischer, W. N., Kwart, M., Hummel, S., et al. (1995). Substrate specificity and expression profile of amino acid transporters (AAPs) in Arabidopsis. Journal of Biological Chemistry,270, 16315–16320.

  13. 13.

    Tegeder, M. (2012). Transporters for amino acids in plant cells: Some functions and many unknowns. Current Opinion in Plant Biology,15, 315–321.

  14. 14.

    Lalanne, E., Mathieu, C., Roche, O., Vedel, F., et al. (1997). Structure and specific expression of a Nicotiana sylvestris putative amino-acid transporter gene in mature and in vitro germinating pollen. Plant Molecular Biology,35, 855–864.

  15. 15.

    Zhao, Y., Xu, Y., Wang, Z., Zhang, J., et al. (2017). Genome-wide identification and characterization of an amino acid permease gene family in Nicotiana tabacum. RSC Advances,7, 38081–38090.

  16. 16.

    Koch, W., Kwart, M., Laubner, M., Heineke, D., et al. (2003). Reduced amino acid content in transgenic potato tubers due to antisense inhibition of the leaf H+/amino acid symporter StAAP1. The Plant Journal,33, 211–220.

  17. 17.

    Neelam, A., Marvier, A. C., Hall, J. L., & Williams, L. E. (1999). Functional characterization and expression analysis of the amino acid permease RcAAP3 from castor bean. Plant Physiology,120, 1049–1056.

  18. 18.

    Schulze, W., Frommer, W. B., & Ward, J. M. (1999). Transporters for ammonium, amino acids and peptides are expressed in pitchers of the carnivorous plant Nepenthes. The Plant Journal,17, 637–646.

  19. 19.

    Miranda, M., Borisjuk, L., Tewes, A., Heim, U., et al. (2001). Amino acid permeases in developing seeds of Viciafaba L.: Expression precedes storage protein synthesis and is regulated by amino acid supply. The Plant Journal,28, 61–71.

  20. 20.

    Cheng, L., Yuan, H. Y., Ren, R., Zhao, S. Q., et al. (2016). Genome-wide identification, classification, and expression analysis of amino acid transporter gene family in Glycine max. Frontiers in Plant Science,7, 515.

  21. 21.

    Akbar, M., Moghaddam, M., Valizadeh, M., & Kooshk, M. H. (2013). Genetic diversity of common bean genotypes as revealed by seed storage proteins and some agronomic traits. Plant Breeding and Seed Science. https://doi.org/10.2478/v10129-011-0075-1.

  22. 22.

    Tan, Q., Grennan, A. K., Pe´lissier, H. C., Rentsch, D., et al. (2008). Characterization and expression of French bean amino acid transporter PvAAP1. Plant Science,174, 348–356.

  23. 23.

    Basak, J., Kundagrami, S., Ghose, T. K., & Pal, A. (2004). Development of Yellow Mosaic Virus (YMV) resistance linked DNA marker in Vignamungo from populations segregating for YMV-reaction. Molecular Breeding,14, 375–383.

  24. 24.

    Altschul, S. F., Madden, T. L., Schäffer, A. A., & Zhang, J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research,25, 3389–3402.

  25. 25.

    Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., et al. (2003). ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research,31, 3784–3788.

  26. 26.

    Geourjon, C., & Deléage, G. (1995). SOPMA: Significant improvement in protein secondary structure prediction by consensus prediction from multiple alignments. Computer Applications in the Biosciences,11, 681–684.

  27. 27.

    Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics,9, 40.

  28. 28.

    Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography,26, 283–291.

  29. 29.

    Bailey, T. L., Boden, M., Buske, F. A., Frith, M., et al. (2009). MEME SUITE: Tools for motif discovery and searching. Nucleic Acids Research,37, W202–W208.

  30. 30.

    Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., et al. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols,10, 845–858.

  31. 31.

    Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005). PatchDock and SymmDock: Servers for rigid and symmetric docking. Nucleic Acids Research,33, W363–367.

  32. 32.

    Pradeep, N. V., Anupama, A., Vidyashree, K. G., & Lakshmi, P. (2012). In silico characterization of industrial important cellulases using computational tools. Advances in Life Science and Technology,4, 2224–7181.

  33. 33.

    Ertugrul, F., & Ibrahim, K. (2014). In silico sequence analysis and homology modeling of predicted beta-amylase 7-like protein in Brachypodium distachyon L. Journal of BioScience and Biotechnology,3, 61–67.

  34. 34.

    Singh, N., Upadhyay, S., Jaiswar, A., & Mishra, N. (2016). In silico analysis of protein. JSM Bioinformatics, Genomics and Proteomics,1, 1007.

  35. 35.

    Yadav, N. K., Sarika, Iquebal, M. A., & Akram, M. (2011). In-silico analysis and homology modelling of coat-protein of Mungbean Yellow Mosaic India Virus. Journal of Food Legumes,24, 138–141.

  36. 36.

    Nakashima, H., & Nishikawa, K. (1992). The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins. FEBS Letters,303, 141–146.

  37. 37.

    Weber, E., Chevallier, M. R., & Jund, R. (1988). Evolutionary relationship and secondary structure predictions in four transport proteins of Saccharomyces cerevisiae. Journal of Molecular Evolution,27, 341–350.

  38. 38.

    Vandenbol, M., Jauniaux, J. C., & Grenson, M. (1989). Nucleotide sequence of the Saccharomyces cerevisiae PUT4 proline-permease-encoding gene: Similarities between CAN1, HIP1 and PUT4 permeases. Gene,83, 153–159.

  39. 39.

    Reizer, J., Reizer, A., Saier, M. H., Jr., Finley, K., Kakuda, D., & Macleod, C. L. (1993). Mammalian integral membrane receptors are homologous to facilitators and antiporters of yeast, fungi, and eubacteria. Protein Science,2, 20–30.

  40. 40.

    Geourjon, C., & Deléage, G. (1995). SOPMA: Significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Computer Applications in the Biosciences,11, 681–684.

  41. 41.

    Fitzkee, N. C., & Rose, G. D. (2004). Reassessing random-coil statistics in unfolded proteins. Proceedings of the National Academy of Sciences,101, 12497–12502.

  42. 42.

    Kumar, S., Tsai, C., & Nussinov, R. (2000). Factors enhancing protein thermostability. Protein Engineering,13, 179–191.

  43. 43.

    Meng, X. Y., Zhang, H. X., Mezei, M., & Cui, M. (2011). Molecular docking: A powerful approach for structure-based drug discovery. Current Computer-Aided Drug Design,1(7), 146–157.

  44. 44.

    McConkey, B. J., Sobolev, V., & Edelman, M. (2002). The performance of current methods in ligand-protein docking. Current Science,83, 845–855.

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Correspondence to Jolly Basak.

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Chakraborty, N., Besra, A. & Basak, J. Molecular Cloning of an Amino Acid Permease Gene and Structural Characterization of the Protein in Common Bean (Phaseolus vulgaris L.). Mol Biotechnol 62, 210–217 (2020). https://doi.org/10.1007/s12033-020-00240-4

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  • Amino acid permease
  • Phaseolus vulgaris
  • Homology modeling
  • Molecular docking