Scallion proteome analysis in Iranian A. stipitatum and A. scabriscapum species to identify proteins with different expression

Document Type : Research Paper

Authors

1 PhD student Agricultural Biotechnology , Dept. Production Engineering and Plant Genetics, Faculty of Agriculture, Lorestan University, Khorramabad, IRAN

2 Corresponding Author, Prof. Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Lorestan University, Khorramabad, I.R. Iran

3 Prof, Dept of Agronomy and Plant Breeding, College of Agriculture and Natural Resources University of Tehran, Karaj, I.R. Iran

4 Prof , Dept. Production Engineering and Plant Genetics, Faculty of Agriculture, Lorestan University, Khorramabad, IRAN

Abstract

Allium includes more than 920 species worldwide. Iran is the main habitat of many wild Allium species. In this study, onion tissue of two species A. stipitatum and A. scabriscapum from two subspecies Melanocrommyum and Reticulatobulbosa were used to evaluate and identify the expression pattern of storage proteins obtained by the SDS-PAGE method. Two-dimensional gel electrophoresis and MALDI TOF/TOF MS mass spectrometry were used to identify protein spots and to observe the expression changes of the two species. Analysis of gels by two-dimensional electrophoresis revealed 138 protein spots. The results showed a slight similarity between the gels and a different expression pattern between the samples, based on which a small number of similar spots were obtained in both gels. The results showed that there were significant differences in the expression profile of onion tissue proteins of these samples. Using the T-test, 9 protein spots with the most significant changes were identified at the 5% probability level, and among them, 3 different spots were identified using Mass spectrometry was selected for identification. The results of mass spectrometry experiments and matching of the obtained data with NCBI and Uniprot databases and bioinformatics tools showed that the tested spots were consistent with Maturasek proteins, Agmatine coumaroyltransferase-1, and a protein with the unknown function called Hypothetical Protein. The findings of this study showed that since the samples belonging to A.stipitatum and A.scabriscapum are of the same genus, but the expression pattern of their stored proteins in onion tissue is very different from each other.

Keywords

Main Subjects

References

Aebersold, R. and Mann, M., 2003. Mass spectrometry-based proteomics. Nature, 422:198-207.
Ahiabor, C., Gordon, A., Ayittey, K. and Agyare, R., 2016. In vitro assessment of antibacterial activity of crude extracts of onion (Allium cepa L.) and shallot (Allium aescalonicum L.) on isolates of Escherichia coli (ATCC 25922), Staphylococcus aureus (ATCC 25923), and Salmonella typhi (ATCC 19430). International Journal of Applied Research, 2:1029-1032.
Barboza, K., Beretta, V., Kozub, P.C., Salinas, C., Morgenfeld, M.M., Galmarini, C.R. and Cavagnaro, P.F., 2018. Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae. Molecular genetics and genomics, 293:1091-1106.
Barthet, M.M., Pierpont, C.L. and Tavernier, E.K., 2020. Unraveling the role of the enigmatic MatK maturase in chloroplast group IIA intron excision. Plant direct, 4:00208.
Bradford, M.M., 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical biochemistry, 72:.248-254.
Burhenne, K., Kristensen, B.K. and Rasmussen, S.K., 2003. A new class of N-hydroxycinnamoyltransferases: purification, cloning, and expression of a barley agmatine coumaroyltransferase (EC 2.3. 1.64). Journal of Biological Chemistry, 278:13919-13927.
Chen, K., Renaut, J., Sergeant, K., Wei, H.U.I. and Arora, R., 2013. Proteomic changes associated with freeze‐thaw injury and post‐thaw recovery in onion (Allium cepa L.) scales. Plant, cell & environment, 36:892-905.
Cvjetko, P., Zovko, M. and Balen, B., 2014. Proteomika u istraživanjima toksičnosti teških metala u biljaka. Arhiv za higijenu rada i toksikologiju, 65:1-17.
Dufoo-Hurtado, M.D., Huerta-Ocampo, J.Á., Barrera-Pacheco, A., Barba de la Rosa, A.P. and Mercado-Silva, E.M., 2015. Low temperature conditioning of garlic (Allium sativum L.)“seed” cloves induces alterations in sprouts proteome. Frontiers in plant science, 6: 332.
El Rabey, H.A., Al-Malki, A.L., Abulnaja, K.O., Ebrahim, M.K., Kumosani, T. and Khan, J.A., 2014. Phylogeny of ten species of the genus Hordeum L. as revealed by AFLP markers and seed storage protein electrophoresis. Molecular biology reports, 41:365-372.
Emre, I., Turgut-Balik, D., Genc, H. and Sahin, A., 2010. Total seed storage protein patterns of some Lathyrus species growing in Turkey using SDS-PAGE. Pakistan Journal of Botany , 42(5):3157-3163.
FARSHADFAR, E. and Farshadfar, M., 2004. Evaluation of genetic diversity in chickpea lines using physiological and RAPD molecular markers. Pajouhesh-Va-Sazandegi jurnal, 13: 63-69 (In Persian).
Fu, J., Zhang, H., Guo, F., Ma, L., Wu, J., Yue, M., Zheng, X., Qiu, Z. and Li, L., 2019. Identification and characterization of abundant repetitive sequences in Allium cepa. Scientific reports, 9(1):1-7.
Ghafoor, A., Ahmad, Z., Qureshi, A.S. and Bashir, M., 2002. Genetic relationship in Vigna mungo (L.) Hepper and V. radiata (L.) R. Wilczek based on morphological traits and SDS-PAGE. Euphytica, 123(3): 367-378.
Görg A, Obermaier C, Boguth G, Harder A, Scheibe B, Wildgruber R, Weiss W. The current state of two‐dimensional electrophoresis with immobilized pH gradients. Electrophoresis:Wiley Analytical Science An International Journal, 21(6):1037-53.
Group, C.P.W., Hollingsworth, P.M., Forrest, L.L., Spouge, J.L., Hajibabaei, M., Ratnasingham, S., van der Bank, M., Chase, M.W., Cowan, R.S., Erickson, D.L. and Fazekas, A.J., 2009. A DNA barcode for land plants. Proceedings of the National Academy of Sciences, 106(31):12794 -12797.
Ipek, M., Ipek, A. and Simon, P.W., 2014. Testing the utility of matK and ITS DNA regions for discrimination of Allium species. Turkish journal of botany, 38(2):203-212.
Karasinski, J., Wrobel, K., Corrales Escobosa, A.R., Konopka, A., Bulska, E. and Wrobel, K., 2017. Allium cepa L. response to Sodium Selenite (Se (IV)) studied in plant roots by a LC-MS-based proteomic approach. Journal of agricultural and food chemistry, 65(19):3995-4004.
Krogh, A., Larsson, B., Von Heijne, G. and Sonnhammer, E.L., 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of molecular biology, 305(3):567-580.
Kumar, O.A. and Tata, S.S., 2010. SDS-PAGE seed storage protein profiles in chili peppers (Capsicum L.). Notulae Scientia Biologicae, 2(3):86-90.
Kyung, K.H., 2012. Antimicrobial properties of allium species. Current opinion in biotechnology, 23(2):142-147.
Ladizinsky, G. and Hymowitz, T., 1979. Seed protein electrophoresis in taxonomic and evolutionary studies. Theoretical and Applied Genetics, 54(4):145-151.
Laemmli, U.K., 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. nature, 227:680-685.
Moradipour Jirandeh, S. Ghamari Zare,  A. Mousavi, A. and Mirjani, L., 2012. Study of morphological and seed storage proteins characteristics of Chelcheragh lily (Lilium ledebourii) populations in Iran. Iranian Journal of Rangelands and Forests Plant Breeding and Genetic Research 20(1): 172-182 (In Persian).
Mujib, A., Ilah, A., Aslam, J., Fatima, S., Siddiqui, Z.H. and Maqsood, M., 2012. Catharanthus roseus alkaloids: application of biotechnology for improving yield. Plant growth regulation, 68(2):111-127.
Murakami, M., Shimada, K., Kawai, M. and Koga, H., 2005. InCeP: Intracellular Pathway Based on mKIAA Protein–Protein Interactions. DNA Research, 12(5):379-387.
Nimrod, G., Schushan, M., Steinberg, D.M. and Ben-Tal, N., 2008. Detection of functionally important regions in “hypothetical proteins” of known structure. Structure, 16(12):1755-1763.
Noormand Moaied, F., Bihamta, M.R., Tabaei Aghdaei, S.R. and Naghavi, M.R., 2021. Study of phylogenetic relationships of different species of Satureja spp. based on nuclear ITS region and chloroplast matK gene. Iranian Journal of Rangelands and Forests Plant Breeding and Genetic Research 28(2): 173-190 (In persian).
O'Farrell, P.H., 1975. High resolution two-dimensional electrophoresis of proteins. Journal of biological chemistry, 250(10): 4007-4021.
Qin, R., Ning, C., Björn, L.O. and Li, S., 2016. Proteomic analysis of Allium cepa var. agrogarum L. roots under copper stress. Plant and soil, 401:197-212.
Rabbani, M.A., Qureshi, A.A., Afzal, M., Anwar, R. and Komatsu, S., 2001. Characterization of mustard (Brassica juncea L.) Czern. & coss.] germplasm by SDS-PAGE of total seed proteins. Pakistan Journal of Botany, 33(2):173-179.
Raj, L.J.M., Britto, S.J., Prabhu, S. and Senthilkumar, S.R., 2011. Phylogenetic relationships of Crotalaria species based on seed protein polymorphism revealed by SDS-PAGE. Plant Science, 2:119-128.
Samah, S., Ventura-Zapata, E. and Valadez-Moctezuma, E., 2015. Fractionation and electrophoretic patterns of seed protein of Opuntia genus. A preliminary survey as a tool for accession differentiation and taxonomy. Biochemical Systematics and Ecology, 58:187-194.
Seregin, A.P., Anačkov, G. and Friesen, N., 2015. Molecular and morphological revision of the Allium saxatile group (Amaryllidaceae): geographical isolation as the driving force of underestimated speciation. Botanical Journal of the Linnean Society, 178(1):67-101.
Sfaxi, I.H., Ezzine, A., Coquet, L., Cosette, P., Jouenne, T. and Marzouki, M.N., 2012. Combined proteomic and molecular approaches for cloning and characterization of copper–zinc superoxide dismutase (Cu, Zn-SOD2) from garlic (Allium sativum). Molecular biotechnology, 52(1):49-58.
Tardieu, A., De Man, W. and This, H., 2010. Using one-dimensional (1D) and two-dimensional (2D) quantitative proton (1 H) nuclear magnetic resonance spectroscopy (q NMR) for the identification and quantification of taste compounds in raw onion (Allium cepa L.) bulbs and in aqueous solutions where onion tissues are soaked. Analytical and bioanalytical chemistry, 398(7):3139-3153.
Uhlen, M., Oksvold, P., Fagerberg, L., Lundberg, E., Jonasson, K., Forsberg, M., Zwahlen, M., Kampf, C., Wester, K., Hober, S. and Wernerus, H., 2010. Towards a knowledge-based human protein atlas. Nature biotechnology, 28(12):1248-1250.
Yousefzadeh, H. Hosseinzadeh Colagar, A. Tabari, M. Sattarian, A and Assadi, M. 2012. Utility of  the ITS region sequence and structure for molecular identification of the Tilia species from Hyrcanian forest, Plant Systematics and Evolution, 298: 947-961.
Zolfaghari, B. Barile, E. Capasso, R. Izzo, AA. Sajjadi, SE. Lanzotti, V. 2006. The Sapogenin Atroviolacegenin and Its Diglycoside Atroviolaceoside from Allium a troviolaceum. Journal of natural products 69 (2):191-195.
Iranian Journal of Rangelands and Forests Plant Breeding and Genetic Research
Volume 29, Issue 2 - Serial Number 58
February 2022
Pages 221-235

Files

Share

How to cite

Statistics