Loading...

Research on Crops

Intrinsic disordered nature and prediction of secondary structures of pinoresinol lariciresinol reductases 2 in Flax (Linum usitatissimum)

DOI: 10.31830/2348-7542.2024.ROC-1131    | Article Id: ROC-1131 | Page : 570-577
Citation :- Intrinsic disordered nature and prediction of secondary structures of pinoresinol lariciresinol reductases 2 in Flax (Linum usitatissimum). Res. Crop. 25: 570-577
KAPOOR PREEDHI, JOSHI RIDHI, KUNDAN MARIDUL AND RAKHRA GURMEEN gurmeen.25169@lpu.co.in
Address : Department of Biochemistry, Lovely Professional University, Phagwara-144401, Punjab, India
Submitted Date : 27-09-2024
Accepted Date : 30-10-2024
Online Published:

Abstract

Flax (Linum usitatissimum) contains a wide range of essential nutrients, such as proteins, polyunsaturated fatty acids (PUFAs), phenolic compounds, fibers, flavonoids, and lignans. The production of lignans in flax is mainly caused by pinoresinol-lariciresinol reductases (PLRs).  Amongst these, PLR2s play a pivotal function by contributing to the further reduction of lariciresinol to secoisolariciresinol in the biosynthesis of lignans. However, the in-silico analysis of PLR2 gene family interlinking the intrinsic disordered nature and secondary structures that could support this hypothesis is still missing in Flax. Herein, we present the first study of Intrinsic disorder proteins (IDPs) in flax to gain an understanding of their biological functions. This study was conducted from June to August 2024 at the Department of Biochemistry, Lovely Professional University, Phagwara, Punjab, India. The flax genome assembly from Phytozome was used to retrieve 30 PLR2 genes which encode for 30 PLR2 proteins. Further, we used PONDR database to identify the intrinsic disordered nature of the proteins while GOR database was used to predict the secondary structures. For identifying the amino acid composition, Protparam database was used. The results of PONDR database revealed that all the proteins are somewhat disordered whereas amino acid composition marked the presence of disorder-promoting residues in almost all the proteins. Secondary structure predictions by GOR revealed the presence of coils, helices and strands. To relate the structural functional relationship, it is of the utmost importance to have an in-depth knowledge of the balance between intrinsic disorder and secondary structure as this will provide key insights into the dynamic functionality and regulatory mechanisms that are the foundation of complex biological processes.  

Keywords

Disorder environmental flex intrinsic proteins secondary structure

References

Chen, J., Chen, R., Chen, W., Chen, X., Gao, S., Li, Q., Xiao, L., Xiao, Y., Yu, J., Yu, L., Zhang, H. and Zhang, L. (2024). The ERF transcription factor LTF1 activates DIR1 to control stereoselective synthesis of antiviral lignans and stress defense in Isatis indigotica roots. Acta Pharm. Sin. B. 14: 405–20. doi:10.1016/j.apsb.2023.08.011.
Corbin, C., Drouet, S., Mateljak, I., Markulin, L., Decourtil, C., Renouard, S., Lopez, T., Doussot, J., Lamblin, F., Auguin, D., Lainé, E., Fuss, E. and Hano, C. (2017). Functional characterization of the pinoresinol–lariciresinol reductase-2 gene reveals its roles in yatein biosynthesis and flax defense response. Planta 246: 405-20.    doi:10.1007/ s00425-017-2701-0.
Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D. and Bairoch, A. (2003). ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31: 3784–88. doi:10.1093/nar/gkg563.
Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N. and Rokhsar, D. S. (2012). Phytozome: A comparative platform for green plant genomics. Nucleic Acids Res. 40: 1178–86. doi:10.1093/nar/gkr944.
Hano, C. F., Dinkova-Kostova, A. T., Davin, L. B., Cort, J. R. and Lewis, N. G. (2021). Editorial: Lignans: insights into their biosynthesis, metabolic engineering, analytical methods and health benefits. Front. Plant Sci. 11: 2020–22. doi:10.3389/fpls.2020.630327.
Harini, K., Kihara, D. and Michael Gromiha, M. (2023). PDA-Pred: Predicting the binding affinity of protein-DNA complexes using machine learning techniques and structural features. Methods 213:10–17. doi:10.1016/j.ymeth.2023.03.002.
Hemmati, S., Heimendahl, C. B. I. V., Klaes, M., Alfermann, A. W., Schmidt, T. J. and Fuss, E. (2010). Pinoresinol-lariciresinol reductases with opposite enantiospecificity determine the enantiomeric composition of lignans in the different organs of Linum usitatissimum L. Planta Med. 76: 928–34. doi:10.1055/s-0030-1250036.
Hsiao, A. S. (2022). Plant protein disorder: spatial regulation, broad specificity, switch of signaling and physiological status. Front. Plant Sci. 13: 1–6. doi:10.3389/fpls.2022.904446.
Iserte, J. A., Lazar, T., Tosatto, S. C. E., Tompa, P. and Marino-Buslje, C. (2020). Chasing coevolutionary signals in intrinsically disordered proteins complexes. Sci. Rep. 10: 1–9. doi:10.1038/s41598-020-74791-6.
Kloczkowski, A., Ting, K. L., Jernigan, R. L. and Garnier, J. (2002). Protein secondary structure prediction based on the GOR algorithm incorporating multiple sequence alignment information. Polymer (Guildf). 43: 441–49. doi:10.1016/s0032-3861(01)00425-6.
Lundström, O. (2023). Intrinsic disorder and tandem repeats - match made in evolution : Computational studies of molecular evolution. Doctoral Thesis in Biochemistry towards Bioinformatics at Stockholm University, Sweden. ISBN PDF 978-91-8014-560-2.
Maiti, S., Singh, A., Maji, T., Saibo, N. V. and De, S. (2024). Experimental methods to study the structure and dynamics of intrinsically disordered regions in proteins. Curr. Res. Struct. Biol. 7: doi:10.1016/j.crstbi.2024.100138.
Min, T., Kasahara, H., Bedgar, D. L., Youn, B., Lawrence, P. K., Gang, D. R., Halls, S. C., Park, H. J., Hilsenbeck, J. L., Davin, L. B., Lewis, N. G. and Kang, C. H. (2003). Crystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases and their relationship to isoflavone reductases. J. Biol. Chem. 278: 50714–23. doi:10.1074/jbc.M308493200.
Musselman, C.A. and Kutateladze, T.G. (2021). Characterization of functional disordered regions within chromatin-associated proteins. iScience 24: doi:10.1016/j.isci.2021.102070.
Pietrosemoli, N., García-Martín, J. A., Solano, R. and Pazos, F. (2013). Genome-wide analysis of protein disorder in arabidopsis thaliana: implications for plant environmental adaptation. PLoS One 8. doi:10.1371/journal.pone.0055524.
Pritišanac, I., Alderson, T. R., Kolarić, Đ., Zarin, T., Xie, S., Lu, A., Alam, A., Maqsood, A., Youn, J. Y., Forman-Kay, J. D. and Moses, A. M. (2024). A functional map of the human intrinsically disordered proteome. Cold Spring Harbor Laboratory. bioRxiv: The reprint Server for Biology. doi:10.1101/2024.03.15.585291.
Renouard, S., Tribalatc, M. A., Lamblin, F., Mongelard, G., Fliniaux, O., Corbin, C., Marosevic, D., Pilard, S., Demailly, H., Gutierrez, L., Hano, C., Mesnard, F. and Lainé, E. (2014). RNAi-mediated pinoresinol lariciresinol reductase gene silencing in flax (Linum usitatissimum L.) seed coat: Consequences on lignans and neolignans accumulation. J. Plant Physiol. 171: 1372–77. doi:10.1016/j.jplph.2014.06.005.
Ridhi, J., Gurseen, R., Harpreet, S. and Gurmeen, R. (2023). Intrinsic disordered nature and prediction of the secondary structure in wheat dehydrins. Res. J. Biotechnol. 18: 8–13. doi:10.25303/1805rjbt08013.
Salladini, E., Jørgensen, M. L. M., Theisen, F. F. and Skriver, K. (2020). Intrinsic disorder in plant transcription factor systems: Functional implications. Int. J. Mol. Sci. 21: 1–35. doi:10.3390/ijms21249755.
Schuster, B. S., Dignon, G. L., Tang, W. S., Kelley, F. M., Ranganath, A. K., Jahnke, C. N., Simpkins, A. G., Regy, R. M., Hammer, D. A., Good, M. C. and Mittal, J. (2020). Identifying sequence perturbations to an intrinsically disordered protein that determine its phase-separation behavior. Proc. Natl. Acad. Sci. U. S. A. 117. doi:10.1073/pnas.2000223117.
Sulatskaya, A. I., Kosolapova, A. O., Bobylev, A. G., Belousov, M. V., Antonets, K. S., Sulatsky, M. I., Kuznetsova, I. M., Turoverov, K. K., Stepanenko, O. V. and Nizhnikov, A. A. (2021). β-Barrels and amyloids: structural transitions, biological functions, and pathogenesis. Int. J. Mol. Sci. 22: 1–27. doi:10.3390/ijms222111316.
Sun, X., Jones, W. T. and Rikkerink, E. H. A., (2012). GRAS proteins: The versatile roles of intrinsically disordered proteins in plant signalling. Biochem. J. 442: 1–12. doi:10. 1042/BJ20111766.
Sun, X., Rikkerink, E. H. A., Jones, W. T. and Uversky, V. N. (2013). Multifarious roles of intrinsic disorder in proteins illustrate its broad impact on plant biology. Plant Cell. 25: 38-55. doi:10.1105/tpc.112.106062.
Szlachtowska, Z. and Rurek, M. (2023). Plant dehydrins and dehydrin-like proteins: characterization and participation in abiotic stress response. Front. Plant Sci. 14: 1–19. doi:10.3389/fpls.2023.1213188.
Tomanek, L. (2015). Proteomic responses to environmentally induced oxidative stress. J. Exp. Biol. 218: 1867–79.  doi:10.1242/jeb.116475.
Trivedi, R. and Nagarajaram, H. A. (2022). Intrinsically disordered proteins: an overview. Int. J. Mol. Sci. 23: 1–30. doi:10.3390/ijms232214050.
Uversky, V. N. (2013). A decade and a half of protein intrinsic disorder: Biology still waits for physics. Protein Sci. 22: 693-724. doi:10.1002/pro.2261.
Uversky, V. N. (2019). Intrinsically disordered proteins and their “Mysterious” (meta) physics. Front. Phys. 7: 8–23. doi:10.3389/fphy.2019.00010.
Wankhede, D. P., Biswas, D. K., Rajkumar, S. and Sinha, A. K. (2013). Expressed sequence tags and molecular cloning and characterization of gene encoding pinoresinol/lariciresinol reductase from Podophyllum hexandrum. Protoplasma 250: 1239–49.  doi:10.1007/ s00709-013-0505-z. 
Xiao, Y., Ji, Q., Gao, S., Tan, H., Chen, R., Li, Q., Chen, J., Yang, Y., Zhang, L., Wang, Z., Chen, W. and Hu, Z. (2015). Combined transcriptome and metabolite profling reveals that IiPLR1 plays an important role in lariciresinol accumulation in Isatis indigotica. J. Exp. Bot. 66: 6259–71. doi:10.1093/jxb/erv333.
Xiao, Y., Shao, K., Zhou, J., Wang, L., Ma, X., Wu, D., Yang, Y., Chen, J., Feng, J., Qiu, S., Lv, Z., Zhang, L., Zhang, P. and Chen, W. (2021). Structure-based engineering of substrate specificity for pinoresinol-lariciresinol reductases. Nat. Commun. 12: 1–11. doi:10.1038/ s41467-021-23095-y.
Xue, B., Brown, C. J., Dunker, A. K. and Uversky, V. N. (2013). Intrinsically disordered regions of p53 family are highly diversified in evolution. Biochim. Biophys. Acta - Proteins Proteomics. 1834: 725–38. doi:10.1016/j.bbapap.2013.01.012.
Xue, B., Dunbrack, R. L., Williams, R. W., Dunker, A. K. and Uversky, V. N. (2011). PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim Biophys Acta 1804: 996-1010. doi:10.1016/j.bbapap.2010.01.011. 
Yelnazarkyzy, R., Baitelenova, A., Zargar, M., Stybayev, G., Cai, S. Q., Sniazhynski, A. and Kipshakbayeva, G. (2024). Impact of growth conditions on the quality of oil and fiber in various varieties of flax (Linum usitatissimum). Res. on Crops 25: 425-33.
Yousefzadi, M., Sharifi, M., Behmanesh, M., Ghasempour, A., Moyano, E. and Palazon, J. (2012). The effect of light on gene expression and podophyllotoxin biosynthesis in Linum album cell culture. Plant Physiol. Biochem. 56: 41–46. doi:10.1016/j.plaphy.2012.04.010.
Zhang, H., Zhao, Y. and Zhu, J. K. (2020). Thriving under Stress: How plants balance growth and the stress response. Dev. Cell 55: 529–43. doi:10.1016/j.devcel.2020.10.012.


Global Footprints