بررسی ساختار و قرابت پروتئین‌های دهیدرین توسط ابزارهای بیوانفورماتیک در گیاهان تک‌لپه و دولپه

نوع مقاله : علمی پژوهشی

نویسندگان

1 بخش تحقیقات زراعی و باغی، مرکز تحقیقات و آموزش کشاورزی و منابع طبیعی استان کرمانشاه، سازمان تحقیقات، آموزش و ترویج کشاورزی، کرمانشاه

2 بخش تحقیقات زراعی و باغی، مرکز تحقیقات و آموزش کشاورزی و منابع طبیعی استان کرمانشاه، سازمان تحقیقات، آموزش و ترویج کشاورزی، کرمانشاه،

چکیده

پروتئین‌های گروه دهیدرین (Dehydrin: DHN)، گروهی از پروتئین‌های مهم دخیل در پاسخ به تنش‌های غیر زیستی مانند سرما و خشکی در گیاهان هستند. این پروتئین‌ها به گروهی از پروتئین‌های محافظت‌کننده از سایر پروتئین‌ها به نام type II Late embryogenesis abundant تعلق دارند. با توجه به اهمیت پروتئین‌های گروه دهیدرین در گیاهان، در این تحقیق روابط تکاملی این گروه در گیاهان مختلف موردبررسی قرار گرفت. بدین منظور توالی‌های پروتئین‌های دهیدرین گیاهان مختلف از سایت NCBI استخراج و هم‌ردیف گردید. نتایج وجود نواحی حفاظت‌شده ازجمله موتیف K و S که به ترتیب در واکنش با دیگر پروتئین‌های تحت تنش و محافظت از آن‌ها و همچنین انتقال پروتئین‌های گروه دهیدرین از سیتوپلاسم به هسته نقش دارند را در بین ژن‌های مورد بررسی نشان داد. درخت فیلوژنی بر پایه نواحی حفاظت‌شده و با روش Neighbor Joining رسم گردید و توالی خطی و درصد اسیدآمینه‌های موجود در ساختار این پروتئین‌ها به‌همراه توالی مکمل ژنومی آن‌ها نیز مورد بررسی قرار گرفت. نتایج نشان داد که پروتئین‌های گروه دهیدرین دولپه‌ای و تک‌لپه‌ای‌ها به دو گروه مجزا تفکیک‌شده و در هر گروه نیز بر اساس نزدیکی و دوری جنس‌های مختلف گیاهی در کلاسترهای مجزا قرار گرفتند. همچنین گیاهان تک و دولپه ازلحاظ توالی خطی اسیدآمینه و درصد آن‌ها هم اختلاف بالایی را نشان دادند. از طرفی، بررسی توالی ژنومی این گیاهان نشان‌دهنده وجود ساختارهای حفاظت‌شده و مشابه بود.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Structure and similarity of dehydrin proteins using bioinformatics tools in monocotyledons ‎and dicotyledons plants

نویسندگان [English]

  • Armin Saed-Moucheshi 1
  • Ali Shirkhani 2
1 Crop and Horticulture Reseach Department, Kermanshah Agricultural and Natural Resources Research and Education Center (AREEO), Kermanshah, Iran.
2 Crop and Horticulture Reseach Department, Kermanshah Agricultural and Natural Resources Research and Education Center (AREEO), Kermanshah, Iran.
چکیده [English]

Dehydrin (DHN) proteins are a group of proteins that effectively respond to abiotic stresses such as cold and drought stress in plants. These proteins are a subset of protective greater group of proteins called type II Late embryogenesis abundant which are protecting other proteins from stresses shock. Due to the significant effect of dehydrin proteins in plants, specialy under abiotic stresses, the aims of this study were to survey the linear structure along with phylogeny relationship of this proteins’ group in different plants species. The protein linear sequences of different plant species were downloaded from NCBI site and then were aligned using MegaX software. The results of aligning showed highly conserved segments within the considered sequences such as K- and S-segments that are respectively responsible for covering other proteins and protecting them from damaging effects of stresses and transporting dehydrin proteins from cytoplasm to nucleus. Using the sequences’ alignment, phylogenic tree was extracted using Neighbor joining method. Furthermore, linear sequence order of amino acids and their ratio in the structure of these protein were evaluated. Folowing that, the composition of these proteins genomic sequences were considered to compare with the results of amino acids evaluation. The results indicated that dicotyledon and monocotyledon plants can be clearly separated into two distinguished classes based on the amino acid structure of DHN proteins. Similarly, The ratio and order of DNHs linear sequences were distinctly altered between mono- and di-cotyledon plants. Evaluation of genomic base pairs of these proteins showed that there are numerous unchanged motifs with eighter no or a little difference shared among the genomic sequences of DHN proteins.

کلیدواژه‌ها [English]

  • Abiotic stress
  • K and S motifs
  • Late embryogenesis abundant proteins
  • Neighbor Joining

مراجع

Borovskii, G. B., Stupnikova, I. V., Antipina, A. I., Vladimirova, S. V., & Voinikov, V. K. (2002). Accumulation of dehydrin-like proteins in the mitochondria of cereals in response to cold, freezing, drought and ABA treatment. BMC Plant Biology, 2, 1-7. Decena, M. A., Gálvez-Rojas, S., Agostini, F., Sancho, R., Contreras-Moreira, B., Des Marais, D. L., Hernandez, P., & Catalán, P. (2021). Comparative genomics, evolution, and drought-induced expression of dehydrin genes in model Brachypodium grasses. Plants, 10(12), 2664-2681. Koag, M.-C., Wilkens, S., Fenton, R. D., Resnik, J., Vo, E., & Close, T. J. (2009). The K-segment of maize DHN1 mediates binding to anionic phospholipid vesicles and concomitant structural changes. Plant physiology, 150(3), 1503-1514. Malik, A. A., Veltri, M., Boddington, K. F., Singh, K. K., & Graether, S. P. (2017). Genome analysis of conserved dehydrin motifs in vascular plants. Frontiers in plant science, 8, 252-268. Saavedra, L., Svensson, J., Carballo, V., Izmendi, D., Welin, B., & Vidal, S. (2006). A dehydrin gene in Physcomitrella patens is required for salt and osmotic stress tolerance. The Plant Journal, 45(2), 237-249. Sun, Y., Liu, L., Sun, S., Han, W., Irfan, M., Zhang, X., Zhang, L., & Chen, L. (2021). AnDHN, a dehydrin protein from Ammopiptanthus nanus, mitigates the negative effects of drought stress in plants. Frontiers in plant science, 12, 788-838. Velasco-Conde, T., Yakovlev, I., Majada, J. P., Aranda, I., & Johnsen, Ø. (2012). Dehydrins in maritime pine (Pinus pinaster) and their expression related to drought stress response. Tree genetics & genomes, 8, 957-973. Battaglia, M., Olvera-Carrillo, Y., Garciarrubio, A., Campos, F., & Covarrubias, A. A. (2008). The enigmatic LEA proteins and other hydrophilins. Plant physiology, 148(1), 6-24. Borovskii, G. B., Stupnikova, I. V., Antipina, A. I., Vladimirova, S. V., & Voinikov, V. K. (2002). Accumulation of dehydrin-like proteins in the mitochondria of cereals in response to cold, freezing, drought and ABA treatment. BMC Plant Biology, 2, 1-7. Close, T. J., Kortt, A. A., & Chandler, P. M. (1989). A cDNA-based comparison of dehydration-induced proteins (dehydrins) in barley and corn. Plant molecular biology, 13, 95-108. Danyluk, J., Houde, M., Rassart, É., & Sarhan, F. (1994). Differential expression of a gene encoding an acidic dehydrin in chilling sensitive and freezing tolerant gramineae species. FEBS letters, 344(1), 20-24. Decena, M. A., Gálvez-Rojas, S., Agostini, F., Sancho, R., Contreras-Moreira, B., Des Marais, D. L., Hernandez, P., & Catalán, P. (2021). Comparative genomics, evolution, and drought-induced expression of dehydrin genes in model Brachypodium grasses. Plants, 10(12), 2664-2681. Farah Yachash, S., Nazeri, S., & Mino Chehar, Z. (2019). In silico investigation of the process of molecular evolution and expansion of the geranyl geranyl diphosphate synthase protein family in plants. Journal of Cellular and Molecular Research (Iranian Biology Journal), 33(3), 326-342. Hanin, M., Brini, F., Ebel, C., Toda, Y., Takeda, S., & Masmoudi, K. (2011). Plant dehydrins and stress tolerance: versatile proteins for complex mechanisms. Plant signaling & behavior, 6(10), 1503-1509. Jiménez-Bremont, J. F., Maruri-López, I., Ochoa-Alfaro, A. E., Delgado-Sánchez, P., Bravo, J., & Rodríguez-Kessler, M. (2013). LEA gene introns: is the intron of dehydrin genes a characteristic of the serine-segment? Plant Molecular Biology Reporter, 31, 128-140. Lan, T., Gao, J., & Zeng, Q.-Y. (2013). Genome-wide analysis of the LEA (late embryogenesis abundant) protein gene family in Populus trichocarpa. Tree genetics & genomes, 9, 253-264. Liu, C.-C., Li, C.-M., Liu, B.-G., Ge, S.-J., Dong, X.-M., Li, W., Zhu, H.-Y., Wang, B.-C., & Yang, C.-P. (2012). Genome-wide identification and characterization of a dehydrin gene family in poplar (Populus trichocarpa). Plant Molecular Biology Reporter, 30, 848-859. Saavedra, L., Svensson, J., Carballo, V., Izmendi, D., Welin, B., & Vidal, S. (2006). A dehydrin gene in Physcomitrella patens is required for salt and osmotic stress tolerance. The Plant Journal, 45(2), 237-249. Sheikh Asadi, M., Naderi, R., Kafi, M., Fatahi Moghadam, M., & Eslami, A. (2019). Study of molecular phylogeny and structure of matk protein in Lilium ledebourii [Baker] Boiss. Journal of plant production research, 27(4), 181-191. Smith, M. A., & Graether, S. P. (2022). The disordered dehydrin and its role in plant protection: A biochemical perspective. Biomolecules, 12(2), 294-307. Stival Sena, J., Giguère, I., Rigault, P., Bousquet, J., & Mackay, J. (2018). Expansion of the dehydrin gene family in the Pinaceae is associated with considerable structural diversity and drought-responsive expression. Tree Physiology, 38(3), 442-456. Sun, X., Xi, D. H., Feng, H., Du, J. B., Lei, T., Liang, H. G., & Lin, H. H. (2009). The dual effects of salicylic acid on dehydrin accumulation in water-stressed barley seedlings. Russian journal of plant physiology, 56, 348-354. Sun, Y., Liu, L., Sun, S., Han, W., Irfan, M., Zhang, X., Zhang, L., & Chen, L. (2021). AnDHN, a dehydrin protein from Ammopiptanthus nanus, mitigates the negative effects of drought stress in plants. Frontiers in plant science, 12, 788-838. Tripepi, M., Pöhlschroder, M., & Beatrice Bitonti, M. (2011). Diversity of dehydrins in Oleae europaea plants exposed to stress. The Open Plant Science Journal, 5(1), 308-320. Velasco-Conde, T., Yakovlev, I., Majada, J. P., Aranda, I., & Johnsen, Q. (2012). Dehydrins in maritime pine (Pinus pinaster) and their expression related to drought stress response. Tree genetics & genomes, 8, 957-973. Verma, G., Dhar, Y. V., Srivastava, D., Kidwai, M., Chauhan, P. S., Bag, S. K., Asif, M. H., & Chakrabarty, D. (2017). Genome-wide analysis of rice dehydrin gene family: Its evolutionary conservedness and expression pattern in response to PEG induced dehydration stress. PLoS One, 12(5), 176-193.. Yang, Y., He, M., Zhu, Z., Li, S., Xu, Y., Zhang, C., Singer, S. D., & Wang, Y. (2012). Identification of the dehydrin gene family from grapevine species and analysis of their responsiveness to various forms of abiotic and biotic stress. BMC Plant Biology, 12, 1-17. Yousef Zaei, S., Mahdinjad, N., Fakheri, B., & Ganjali, P. (2019). Identification of DHN5 gene and investigation of its evolutionary relationships in cultivated wheat and its ancestors. Modern genetics, 15(4), 361-370. Zan, T., Li, L., Li, J., Zhang, L., & Li, X. (2020). Genome-wide identification and characterization of late embryogenesis abundant protein-encoding gene family in wheat: evolution and expression profiles during development and stress. Gene, 736, 1444-1452. Zhang, J., Xia, H., Liang, D., Lin, L., Deng, H., Lv, X., Wang, Z., Wang, J., & Xiong, B. (2021). Genome-wide identification and expression profiling of the dehydrin gene family in Actinidia chinensis. Scientia Horticulturae, 280, 1099-1130.

فایل ها

هم رسانی

ارجاع به این مقاله

آمار