Abstract
Lipoxygenases (LOXs) namely 9-LOXs and 13-LOXs catalyse the oxygenation of polyunsaturated fatty acids to produce fatty acid hydroperoxides which are crucial in growth, development and stress responses in plants. Here, we isolated and characterized a 2723-bp cDNA encoding a distinct 861-aa 9-LOX form, designated StKCLX-1, using tuber total RNA from an Indian potato cultivar, Kufri Chipsona-1 through RT-PCR. A total of 17 LOX genes distributed in different chromosomes were identified and characterized in the potato genome. Multiple sequence alignment revealed highly conserved amino acids in the crucial domains, motifs and variable N-terminal regions between the LOX classes. A total of 36 LOXs from potato, tomato and Arabidopsis were used in phylogenetic analysis. A 3-D structure of StKCLX-1 was predicted by AlphaFold tool, validated through the predicted local-distance difference test (pLDDT) and Ramachandran Plot. Molecular docking predicted the nature of receptor-ligand interactions. STRING database was used to predict the protein-protein interactions. Expression patterns of the LOXs in the potato organs were examined by Expression Atlas and semi-quantitative RT-PCR. 9-LOX activity was noticed at early stages of tuberization, and significantly increased in the freshly-harvested mature tubers. This report would be useful in gaining insights into the structure-function relationships of the LOXs and corresponding multigene family-prerequisites for understanding tuber development in potato.
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References
Aksenova NP, Konstantinova TN, Golyanovskaya SA, Sergeeva LI, Romanov GA (2012) Hormonal regulation of tuber formation in potato plants. Russ J Plant Physiol 59:451–466. https://doi.org/10.1134/S1021443712040024
Allmann S, Halitschke R, Schuurink RC, Baldwin IT (2010) Oxylipin channelling in Nicotiana attenuata: lipoxygenase 2 supplies substrates for green leaf volatile production. Plant Cell Environ 33:2028–2040. https://doi.org/10.1111/j.1365-3040.2010.02203.x
Axelrod B (1974) Lipoxygenases. In: Whitaker JR (ed) Food Related Enzymes. ACS, Washington DC, pp 324–348
Bannenberg G, Martínez M, Hamberg M, Castresana C (2009) Diversity of the enzymatic activity in the lipoxygenase gene family of Arabidopsis thaliana. Lipids 44:85–95. https://doi.org/10.1007/s11745-008-3245-7
Brash AR (1999) Lipoxygenases: occurrence, functions, catalysis, and acquisition of substrate. J Biol Chem 274:23679–23682. https://doi.org/10.1074/jbc.274.34.23679
Caldelari D, Wang G, Farmer EE, Dong X (2011) Arabidopsis lox3 lox4 double mutants are male sterile and defective in global proliferative arrest. Plant Mol Biol 5:25–33. https://doi.org/10.1007/s11103-010-9701-9
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinfo 10:1–9. https://doi.org/10.1186/1471-2105-10-421
Chauvin A, Caldelari D, Wolfender JL, Farmer EE (2013) Four 13-lipoxygenases contribute to rapid jasmonate synthesis in wounded Arabidopsis thaliana leaves: a role for lipoxygenase 6 in responses to long-distance wound signals. New Phytol 197:566–575. https://doi.org/10.1111/nph.12029
Chen G, Hackett R, Walker D, Taylor A, Lin Z, Grierson D (2004) Identification of a specific isoform of tomato lipoxygenase (TomloxC) involved in the generation of fatty acid-derived flavor compounds. Plant Physiol 136:2641–2651. https://doi.org/10.1104/pp.104.041608
Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2:1511–1519. https://doi.org/10.1002/pro.5560020916
Corpet F (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16:10881–10890. https://doi.org/10.1093/nar/16.22.10881
Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Austine-Orimoloye O, Azov AG, Barnes I, Bennett R, Berry A (2022) Ensembl 2022. Nucleic Acids Res 50:D988–D995. https://doi.org/10.1093/nar/gkab1049
DeLano WL (2002) Pymol: An open-source molecular graphics tool. CCP4 Newsl Protein Crystallogr 40:82–92
Dhiman G, Lohia N, Jain S, Baranwal M (2016) Metadherin peptides containing CD4+ and CD8+ T cell epitopes as a therapeutic vaccine candidate against cancer. Microbiol Immunol 60:646–652. https://doi.org/10.1111/1348-0421.12436
Doolittle RF (1989) Redundancies in protein sequences. In: Fasman GD (ed) Prediction of protein structure and the principles of protein conformation. Springer, New York, pp 599–623
Dutt S, Manjul AS, Raigond P, Singh B, Siddappa S, Bhardwaj V, Kawar PG, Patil VU, Kardile HB (2017) Key players associated with tuberization in potato: potential candidates for genetic engineering. Crit Rev Biotechnol 37:942–957. https://doi.org/10.1080/07388551.2016.1274876
Fernie AR, Willmitzer L (2001) Molecular and biochemical triggers of potato tuber development. Plant Physiol 127:1459–1465. https://doi.org/10.1104/pp.010764
Ferrie BJ, Beaudoin N, Burkhart W, Bowsher CG, Rothstein SJ (1994) The cloning of two tomato lipoxygenase genes and their differential expression during fruit ripening. Plant Physiol 106:109–118. https://doi.org/10.1104/pp.106.1.109
Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31:3784–3788. https://doi.org/10.1093/nar/gkg563
Genova AD, Goverse A, Massa AN et al (2011) The Potato Genome Consortium Genome sequence and analysis of the tuber crop potato. Nature 475:189–195. https://doi.org/10.1038/nature10158
Gökmen V, Bahçeci S, Acar J (2002) Characterization of crude lipoxygenase extract from green pea using a modified spectrophotometric method. Eur Food Res Technol 215:42–45. https://doi.org/10.1007/s00217-002-0518-x
Gorina S, Ogorodnikova A, Mukhtarova L, Toporkova Y (2022) Gene expression analysis of potato (Solanum tuberosum L.) lipoxygenase cascade and oxylipin signature under abiotic stress. Plants 11:683. https://doi.org/10.3390/plants11050683
Griffiths A, Barry C, Alpuche-Solis AG, Grierson D (1999) Ethylene and developmental signals regulate expression of lipoxygenase genes during tomato fruit ripening. J Exp Bot 50:793–798. https://doi.org/10.1093/jxb/50.335.793
Guruprasad K, Reddy BB, Pandit MW (1990) Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng Des Sel 4:155–161. https://doi.org/10.1093/protein/4.2.155
Halitschke R, Baldwin IT (2003) Antisense LOX expression increases herbivore performance by decreasing defense responses and inhibiting growth-related transcriptional reorganization in Nicotiana attenuata. The Plant J 36:794–807. https://doi.org/10.1046/j.1365-313X.2003.01921.x
Hannapel DJ, Chen H, Rosin FM, Banerjee AK, Davies PJ (2004) Molecular controls of tuberization. Am J Potato Res 81:263–274. https://doi.org/10.1007/BF02871768
Hayward S, Cilliers T, Swart P (2017) Lipoxygenases: from isolation to application. Compr Rev Food Sci Food Saf 16:199–211. https://doi.org/10.1111/1541-4337.12239
He Y, Fukushige H, Hildebrand DF, Gan S (2002) Evidence supporting a role of jasmonic acid in Arabidopsis leaf senescence. Plant Physiol 128:876–884. https://doi.org/10.1104/pp.010843
Heitz T, Bergey DR, Ryan CA (1997) A gene encoding a chloroplast-targeted lipoxygenase in tomato leaves is transiently induced by wounding, systemin, and methyl jasmonate. Plant Physiol 114:1085–1093. https://doi.org/10.1104/pp.114.3.1085
Heo L, Park H, Seok C (2013) GalaxyRefine: Protein structure refinement driven by side-chain repacking. Nucleic Acids Res 41:W384–W388. https://doi.org/10.1093/nar/gkt458
Hoseney RC, Faubion JM (1981) A mechanism for the oxidative gelation of wheat flour water-soluble pentosans. Cereal Chem 58:421–424
Jackson SD, Willmitzer L (1994) Jasmonic acid spraying does not induce tuberisation in short-day-requiring potato species kept in non-inducing conditions. Planta 194:155–159. https://doi.org/10.1007/BF01101673
Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195–202. https://doi.org/10.1006/jmbi.1999.3091
Joo YC, Oh DK (2012) Lipoxygenases: potential starting biocatalysts for the synthesis of signaling compounds. Biotechnol Advan 30:1524–1532. https://doi.org/10.1016/j.biotechadv.2012.04.004
Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A, Bridgland A (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596:583–589. https://doi.org/10.1038/s41586-021-03819-2
Kaur Y, Das N (2023) Gibberellin 2-Oxidases in Potato (Solanum tuberosum L.): Cloning Characterization in Silico Analysis and Molecular Docking. Mol Biotechnol. https://doi.org/10.1007/s12033-023-00745-8
Kaur G, Sharma S, Das N (2020) Comparison of catalase activity in different organs of the potato (Solanum tuberosum L.) cultivars grown under field condition and purification by three-phase partitioning. Acta Physiol Plant 42:1–11. https://doi.org/10.1007/s11738-019-3002-y
Kessel A, Ben-Tal N (2002) Free energy determinants of peptide association with lipid bilayers. Curr Top Membr 5:205–253. https://doi.org/10.1016/S1063-5823(02)52010-X
Kessler A, Halitschke R, Baldwin IT (2004) Silencing the jasmonate cascade: induced plant defenses and insect populations. Sci 305:665–668. https://doi.org/10.1126/science.1096931
Kolomiets MV, Hannapel DJ, Chen H, Tymeson M, Gladon RJ (2001) Lipoxygenase is involved in the control of potato tuber development. Plant Cell 13:613–626. https://doi.org/10.1105/tpc.13.3.613
Kuhn H, Banthiya S, Van Leyen K (2015) Mammalian lipoxygenases and their biological relevance. Biochimica et Biophysica Acta (BBA)-Mol Cell Biol Lipids 1851:308–330. https://doi.org/10.1016/j.bbalip.2014.10.002
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547. https://doi.org/10.1093/molbev/msy096
Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291. https://doi.org/10.1107/S0021889892009944
León J, Royo J, Vancanneyt G, Sanz C, Silkowski H, Griffiths G, Sánchez-Serrano JJ (2002) Lipoxygenase H1 gene silencing reveals a specific role in supplying fatty acid hydroperoxides for aliphatic aldehyde production. J Biol Chem 277:416–423. https://doi.org/10.1074/jbc.M107763200
Liburdi K, Benucci I, Lombardelli C, Esti M (2017) Identification and characterization of lipoxygenase in fresh culinary herbs. Int J Food Prop 20:1470–1478. https://doi.org/10.1080/10942912.2016.1211678
Liu SQ, Liu XH, Jiang LW (2011) Genome-wide identification, phylogeny and expression analysis of the lipoxygenase gene family in cucumber. Genet Mol Res 10:2613–2636. https://doi.org/10.4238/2011.October.25.9
Liu F, Li H, Wu J, Wang B, Tian N, Liu J, Sun X, Wu H, Huang Y, Lü P, Cheng C (2021) Genome-wide identification and expression pattern analysis of lipoxygenase gene family in banana. Sci Rep 11:9948. https://doi.org/10.1038/s41598-021-89211-6
Liu Y, Yang X, Gan J, Chen S, Xiao ZX, Cao Y (2022) CB-Dock 2: Improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting. Nucleic Acids Res 50:W159–W164. https://doi.org/10.1093/nar/gkac394
Lüthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356:83–85. https://doi.org/10.1038/356083a0
Melan MA, Dong X, Endara ME, Davis KR, Ausubel FM, Peterman TK (1993) An Arabidopsis thaliana lipoxygenase gene can be induced by pathogens, abscisic acid, and methyl jasmonate. Plant Physiol 101:441–450. https://doi.org/10.1104/pp.101.2.441
Melan MA, Enriquez AL, Peterman TK (1994) The LOX1 gene of Arabidopsis is temporally and spatially regulated in germinating seedlings. Plant Physiol 105:385–393. https://doi.org/10.1104/pp.105.1.385
Mwenda CM, Matsui K (2014) The importance of lipoxygenase control in the production of green leaf volatiles by lipase-dependent and independent pathways. Plant Biotech 31:445–452. https://doi.org/10.5511/plantbiotechnology.14.0924a
Nam KH, Kong F, Matsuura H, Takahashi K, Nabeta K, Yoshihara T (2008) Temperature regulates tuber-inducing lipoxygenase-derived metabolites in potato (Solanum tuberosum). J Plant Physiol 165:233–238. https://doi.org/10.1016/j.jplph.2007.04.003
Nookaraju A, Kappachery S, Yu JW, Park SW (2011) Rhizobacteria influence potato tuberization through enhancing lipoxygenase activity. Am J Potato Res 88:441–449. https://doi.org/10.1007/s12230-011-9210-7
O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open Babel: An open chemical toolbox. J Cheminfo 3:1–14. https://doi.org/10.1186/1758-2946-3-33
Pakhomova S, Boeglin WE, Neau DB, Bartlett SG, Brash AR, Newcomer ME (2019) An ensemble of lipoxygenase structures reveals novel conformations of the Fe coordination sphere. Protein Sci 28:920–927. https://doi.org/10.1002/pro.3602
Podolyan A, White J, Jordan B, Winefield C (2010) Identification of the lipoxygenase gene family from Vitis vinifera and biochemical characterisation of two 13-lipoxygenases expressed in grape berries of Sauvignon Blanc. Funct Plant Biol 37:767–784. https://doi.org/10.1071/FP09271
Porta H, Rocha-Sosa M (2002) Plant lipoxygenases Physiological and molecular features. Plant Physiol 130:15–21. https://doi.org/10.1104/pp.010787
Reddy PS, Kumar TC, Reddy MN, Sarada C, Reddanna P (2000) Differential formation of octadecadienoic acid and octadecatrienoic acid products in control and injured/infected potato tubers. Biochim Biophys Acta 1483:294–300. https://doi.org/10.1016/S1388-1981(99)00191-2
Rosahl S (1996) Lipoxygenases in plants-their role in development and stress response. Zeitschrift für Naturforschung C 51:123–138. https://doi.org/10.1515/znc-1996-3-401
Royo J, Vancanneyt G, Pérez AG, Sanz C, Störmann K, Rosahl S, Sánchez-Serrano JJ (1996) Characterization of three potato lipoxygenases with distinct enzymatic activities and different organ-specific and wound-regulated expression patterns. J Biol Chem 271:21012–21019. https://doi.org/10.1074/jbc.271.35.21012
Saidi A, Hajibarat Z (2021) Phytohormones: plant switchers in developmental and growth stages in potato. J Genet Eng Biotechnol 19:1–17. https://doi.org/10.1186/s43141-021-00192-5
Sambrook J, Fritsch ER, Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
Sarde SJ, Kumar A, Remme RN, Dicke M (2018) Genome-wide identification, classification and expression of lipoxygenase gene family in pepper. Plant Mol Biol 98:375–387. https://doi.org/10.1007/s11103-018-0785-y
Sarkar D (2008) The signal transduction pathways controlling in planta tuberization in potato: an emerging synthesis. Plant Cell Rep 27:1–8. https://doi.org/10.1007/s00299-007-0457-x
Schneider C, Pratt DA, Porter NA, Brash AR (2007) Control of oxygenation in lipoxygenase and cyclooxygenase catalysis. Chem Biol 14:473–488. https://doi.org/10.1016/j.chembiol.2007.04.007
Sievers F, Higgins DG (2018) Clustal Omega for making accurate alignments of many protein sequences. Protein Sci 27:135–145. https://doi.org/10.1002/pro.3290
Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ (2016) The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible. Nucleic Acids Res 45:D362–D368. https://doi.org/10.1093/nar/gkw937
Truebestein L, Leonard TA (2016) Coiled-coils: The long and short of it. Bioessays 38:903–916. https://doi.org/10.1002/bies.201600062
Van de Wal MHBJ, Jacobsen E, Visser R (2001) Multiple allelism as a control mechanism in metabolic pathways: GBSSI allelic composition affects the activity of granule-bound starch synthase I and starch composition in potato. Mol Genet Genom 265:1011–1021. https://doi.org/10.1007/s004380100496
VanDoorn A, Kallenbach M, Borquez AA, Baldwin IT, Bonaventure G (2010) Rapid modification of the insect elicitor N-linolenoyl-glutamate via a lipoxygenase-mediated mechanism on Nicotiana attenuata leaves. BMC Plant Biol 10:1–1. https://doi.org/10.1186/1471-2229-10-164
Vellosillo T, Martínez M, Lopez MA, Vicente J, Cascon T, Dolan L, Hamberg M, Castresana C (2007) Oxylipins produced by the 9-lipoxygenase pathway in Arabidopsis regulate lateral root development and defense responses through a specific signaling cascade. Plant Cell 19:831–846. https://doi.org/10.1105/tpc.106.046052
Viswanath KK, Varakumar P, Pamuru RR, Basha SJ, Mehta S, Rao AD (2020) Plant lipoxygenases and their role in plant physiology. J Plant Biol 63:83–95. https://doi.org/10.1007/s12374-020-09241-x
Yan L, Zhai Q, Wei J, Li S, Wang B, Huang T, Du M, Sun J, Kang L, Li CB, Li C (2013) Role of tomato lipoxygenase D in wound-induced jasmonate biosynthesis and plant immunity to insect herbivores. PLoS Genetics 9:e1003964. https://doi.org/10.1371/journal.pgen.1003964
Zhang C, Cao S, Jin Y, Ju L, Chen Q, Xing Q, Qi H (2017a) Melon 13-lipoxygenase CmLOX18 may be involved in C6 volatiles biosynthesis in fruit. Sci Rep 7:2816. https://doi.org/10.1038/s41598-017-02559-6
Zhang H, Fen XU, Yu WU, Hu HH, Dai XF (2017b) Progress of potato staple food research and industry development in China. J Integr Agric 16:2924–2932. https://doi.org/10.1016/S2095-3119(17)61736-2
Zhou G, Ren N, Qi J, Lu J, Xiang C, Ju H, Cheng J, Lou Y (2014) The 9-lipoxygenase Osr9-LOX1 interacts with the 13-lipoxygenase-mediated pathway to regulate resistance to chewing and piercing-sucking herbivores in rice. Physiol Plant 152:59–69. https://doi.org/10.1111/ppl.12148
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Kaur, Y., Das, N. Molecular, in silico and expression studies on lipoxygenases (LOXs) in potato (Solanum tuberosum L.). 3 Biotech 13, 419 (2023). https://doi.org/10.1007/s13205-023-03839-x
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DOI: https://doi.org/10.1007/s13205-023-03839-x