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آنالیز این‌سیلیکو اعضای خانواده ژنی CBL در گیاه هالوفیت آلوروپوس لیتورالیس و گیاه مدل آرابیدوپسیس تالیانا | ||
| فصلنامه علمی زیست فناوری گیاهان زراعی | ||
| مقاله 2، دوره 10، شماره 2 - شماره پیاپی 32، اسفند 1399، صفحه 17-35 اصل مقاله (1.5 M) | ||
| نوع مقاله: علمی پژوهشی | ||
| شناسه دیجیتال (DOI): 10.30473/cb.2021.57064.1827 | ||
| نویسندگان | ||
| مژده عرب1؛ حمید نجفی زرینی2؛ قربانعلی نعمت زاده3؛ سید حمیدرضا هاشمی پطرودی* 4 | ||
| 1دانشجوی کارشناسی‌ارشد بیوتکنولوژی کشاورزی، دانشگاه علوم کشاورزی و منابع طبیعی ساری، ایران | ||
| 2دانشیار گروه بیوتکنولوژی، دانشگاه علوم کشاورزی و منابع طبیعی ساری، ساری، ایران | ||
| 3استاد گروه مهندسی ژنتیک و بیولوژی، پژوهشکده ژنتیک و زیست‌فناوری کشاورزی طبرستان، دانشگاه علوم کشاورزی و منابع طبیعی ساری ، ایران | ||
| 4گروه مهندسی ژنتیک و بیولوژی، پژوهشکده ژنتیک و زیست فناوری کشاورزی طبرستان، دانشگاه علوم کشاورزی و منابع طبیعی ساری | ||
| چکیده | ||
| پروتئین‌های شبه‌کالسینئورین B (CBLs) به‌عنوان یک مولکول پیام‌رسان ثانویه زیرخانواده گروه حس‌گرهای کلسیم بوده، و در تنظیم فرآیندهای فیزیولوژیکی و رشد و نمو گیاهان نقش مهمی دارند. در این مطالعه به منظور بررسی این‌سیلیکو و مقایسه خصوصیات پروتئین‌های دخیل در پیام رسانی کلسیم در گیاهان شورپسند و شیرین‌پسند، اعضای زیرخانواده ژنی CBL در دو گیاه آلوروپوس لیتورالیس و آرابیدوپسیس تالیانا مورد مطالعه قرار گرفت. بر اساس همولوژی توالی و روابط اورتولوژی با ژن‌های آرابیدوپسیس، شش ژن شناسایی شده در ژنوم آلوروپوس در قالب سه گروه پروتئینی AlCBL4، AlCBL2 وAlCBL10 دسته‌بندی شدند. بررسی خانواده ژنی AlCBL بر مبنای همردیفی چندگانه در گیاه آلوروپوس لیتورالیس موید حضور چهار دمین EF-hand در تمام این ژن‌ها بوده که ساختاری را برای اتصال یون کلسیم فراهم می‌نماید. شباهت بالای خصوصیات فیزیکوشیمیایی اکثر پروتئین‌های آلوروپوس به آرابیدوپسیس و داشتن رابطه قوی اورتولوژی با یکدیگر ممکن است دلالت بر محفوظ ماندن کارکرد و عملکرد این ژن‌ها در فرایند تکاملی بوده باشد. تجزیه و تحلیل الگوهای بیانی AtCBLs در اندام‌های مختلف و تحت تنش‌های غیر زنده مختلف نشان داد به دلیل انشقاق عملکردی و ساختاری، این ژن‌ها از الگوی بیان منحصربفردی برخوردارند. الگوی بیانی متفاوت در داده‌های ترانسکریپتوم AlCBLs نیز دلیلی بر الگوی عملکردی متفاوت این ژن‌هاست. نتایج بدست آمده در این تحقیق می‌تواند اطلاعات ارزشمندی در مورد نقش این خانواده ژنی و سازوکار‌های عملکردی آنها در تحمل به تنش‌های غیر زیستی برای مطالعات آتی مهیا سازد. | ||
| کلیدواژه‌ها | ||
| خانواده ژنی؛ حسگر کلسیم؛ هالوفیت؛ CBL؛ آنالیز این‌سیلیکو | ||
| موضوعات | ||
| بیوانفورماتیک | ||
| عنوان مقاله [English] | ||
| In silico analysis of CBL gene family in the halophyte plant Aeluropus littoralis and the model plant Arabidopsis thaliana | ||
| نویسندگان [English] | ||
| Mozhdeh Arab1؛ Hamid Najafi Zarrini2؛ Ghorbanali Nematzadeh3؛ Seyyed Hamidreza Hashemi-petroudi4 | ||
| 1M.Sc. Student in Plant Breeding, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran. | ||
| 2Associated Professor, Department of Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran | ||
| 3Professors, Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU) | ||
| 4Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU) | ||
| چکیده [English] | ||
| Calcineurin B-like proteins (CBLs), which act as a secondary messenger molecule in the subfamily of the calcium sensor gene family, play a key role in regulating physiological processes, plant growth and development. In order to identification and comparison of proteins involving in calcium signaling in two model of halophyte and glycophyte plants, in silico analysis of the CBL gene family were done in Aeluropus littoralis and Arabidopsis thaliana. Based on sequence homology and orthological relationships with Arabidopsis genes, 6 genes identified in Aeluropus were classified into three protein groups: AlCBL4, AlCBL2 and AlCBL10. Multiple sequence allignment of the CBL gene family in Aeluropus littoralis confirmed the presence of four EF-hand domains in all genes, which provide a structure for calcium ion binding. The high similarity of the physicochemical properties of most Aeluropus proteins to Arabidopsis as well as the strong orthological relationship with each other may indicate the preservation of the function of these genes in the evolutionary process. Analysis of AtCBLs expression patterns in different organs/ abiotic stresses showed that these genes have unique expression profiles due to functional and structural convergent. Different expression profiles of AlCBLs in Aeluropus transcriptome would be an evidence for the functional divergent of these genes. The results obtained from this study can provide valuable information about the properties of this gene family and their functional roles in tolerating to abiotic stresses for future studies. | ||
| کلیدواژه‌ها [English] | ||
| Gene family, Calcium sensor, Halophyte, CBL, In silico analysis | ||
| مراجع | ||
|
Aminfar Z, Rabiei B, Tohidfar M, Mirjalili MH (2019) Meta-analysis of Transcriptomics related to the genes of the mevalonate (MVA) and the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways for isoprenoids biosynthesis in plants. Crop Biotechnology. 9(25): 1-17.
Armenteros JJA, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, Von Heijne G, Nielsen H (2019) SignalP 5.0 improves signal peptide predictions using deep neural networks. Nature biotechnology. 37(4): 420-423.
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37: 202-208.
Barhoumi Z, Djebali W, Abdelly C, Chaïbi W, Smaoui A (2008) Ultrastructure of Aeluropus littoralis leaf salt glands under NaCl stress. Protoplasma. 233(3-4): 195-202.
Barhoumi Z, Djebali W, Chaïbi W, Abdelly C, Smaoui A (2007) Salt impact on photosynthesis and leaf ultrastructure of Aeluropus littoralis. Journal of plant research. 120(4): 529-537.
Batistič O, Waadt R, Steinhorst L, Held K, Kudla J (2010) CBL‐mediated targeting of CIPKs facilitates the decoding of calcium signals emanating from distinct cellular stores. The Plant Journal. 61(2): 211-222.
Cheong YH, Kim K-N, Pandey GK, Gupta R, Grant JJ, Luan S (2003) CBL1, a calcium sensor that differentially regulates salt, drought, and cold responses in Arabidopsis. The Plant Cell. 15(8): 1833-1845.
Cheong YH, Pandey GK, Grant JJ, Batistic O, Li L, Kim BG, Lee SC, Kudla J, Luan S (2007) Two calcineurin B‐like calcium sensors, interacting with protein kinase CIPK23, regulate leaf transpiration and root potassium uptake in Arabidopsis. The Plant Journal. 52(2): 223-239.
Dodd AN, Kudla J, Sanders D (2010) The language of calcium signaling. Annual review of plant biology. 61: 593-620.
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A (2019) The Pfam protein families database in 2019. Nucleic acids research. 47(D1): D427-D432.
Evrard A (2013). Cell type-specific transcriptional responses of plants to salinity.
Fatemi F, Hashemi-Petroudi SH, Nematzadeh G, Askari H, Abdollahi MR (2019) Exploiting differential gene expression to discover ionic and osmotic-associated transcripts in the halophyte grass Aeluropus littoralis. Biological procedures online. 21(1): 1-16.
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39(4): 783-791.
Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM. (ed) The proteomics protocols handbook, Humana Press, New York City, New York, United States, pp571-607.
Ghorbani HR, Samizadeh Lahiji H, Nematzadeh G-A (2017) Expression pattern analysis of transcription factors from Aeluropus littoralis in response to salt stress and recovery condition. Journal of Plant Molecular Breeding. 5(1): 19-30.
Hall T, Biosciences I, Carlsbad C (2011) BioEdit: an important software for molecular biology. GERF Bull Biosci. 2(1): 60-61.
Hashemi-Petroudi S, Nematzadeh G, Mohammadi S, Kuhlmann M (2020a) Expression pattern analysis of heat shock transcription factors (HSFs) gene family in Aeluropus littoralis under salinity stress. Environmental Stresses in Crop Sciences. 13(2).
Hashemi-Petroudi SH, Mohammadi S (2020b) Identification of the ERF gene family in Aeluropus littoralis halophyte plant and analysis of their expression pattern in response to salt stress. Crop Biotechnology. 9(29): 53-66.
Hashemi-Petroudi SH, Nematzadeh G, Kuhlmann M (2019) Identification and analysis of a DEVIL paralog gene cluster in Aeluropus littoralis by a comparative genomic approach. Crop Biotechnology. 9(25): 75-87.
Hashemi SH, Arab M, Dolatabadi B, Kuo Y-T, Baez MA, Himmelbach A, Nematzadeh G, Maibody SaMM, Schmutzer T, Mälzer M (2020) Initial Description of the Genome of Aeluropus littoralis, a Halophile Grass.
Hashemi SH, Nematzadeh G, Ahmadian G, Yamchi A, Kuhlmann M (2016) Identification and validation of Aeluropus littoralis reference genes for Quantitative Real-Time PCR Normalization. Journal of Biological Research-Thessaloniki. 23(1): 1-13.
Hashemipetroudi S, Nematzadeh G, Ahmadian G, Yamchi A, Kuhlmann M (2016) Expression analysis of salt stress related expressed sequence tags (ESTs) from Aeluropus littoralis by quantitative real-time PCR. Biosci. Biotech. Res. Comm. 9(3): 445-456.
Horton P, Park K-J, Obayashi T, Fujita N, Harada H, Adams-Collier C, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res. 35: 585-587.
Hu B, Jin J, Guo A-Y, Zhang H, Luo J, Gao G (2014) GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 31(8): 1296-1297.
Hulo N, Bairoch A, Bulliard V, Cerutti L, De Castro E, Langendijk-Genevaux PS, Pagni M, Sigrist CJ (2006) The PROSITE database. Nucleic acids research. 34(suppl_1): D227-D230.
Jalili MM, Haddad MA, Housaindokht MR (2019) Biocomputational Investigations of Structural and Functional Properties of Cry Proteins for Malaria Biocontrol.
Jiang M, Zhao C, Zhao M, Li Y, Wen G (2020) Phylogeny and Evolution of Calcineurin B-Like (CBL) Gene Family in Grass and Functional Analyses of Rice CBLs. Journal of Plant Biology. 1-14.
Jones P, Binns D, Chang H-Y, Fraser M, Li W, Mcanulla C, Mcwilliam H, Maslen J, Mitchell A, Nuka G (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics. 30(9): 1236-1240.
Jung H-J, Kayum MA, Thamilarasan SK, Nath UK, Park J-I, Chung M-Y, Hur Y, Nou I-S (2017) Molecular characterisation and expression profiling of calcineurin B-like (CBL) genes in Chinese cabbage under abiotic stresses. Functional Plant Biology. 44(7): 739-750.
Karami Lake B, Sohani M, Abedi A (2020) Bioinformatical study of Calcium/cation (CaCA) antiporters gene family in maize (Zea mays L.). Crop Biotechnology. 9(29): 21-37.
Kim K-N, Cheong YH, Gupta R, Luan S (2000) Interaction specificity of Arabidopsis calcineurin B-like calcium sensors and their target kinases. Plant physiology. 124(4): 1844-1853.
Kolukisaoglu Ü, Weinl S, Blazevic D, Batistic O, Kudla J (2004) Calcium sensors and their interacting protein kinases: genomics of the Arabidopsis and rice CBL-CIPK signaling networks. Plant physiology. 134(1): 43-58.
Kudla J, Becker D, Grill E, Hedrich R, Hippler M, Kummer U, Parniske M, Romeis T, Schumacher K (2018) Advances and current challenges in calcium signaling. New Phytologist. 218(2): 414-431.
Kudla J, Xu Q, Harter K, Gruissem W, Luan S (1999) Genes for calcineurin B-like proteins in Arabidopsis are differentially regulated by stress signals. Proceedings of the National Academy of Sciences. 96(8): 4718-4723.
Letunic I, Bork P (2018) 20 years of the SMART protein domain annotation resource. Nucleic acids research. 46(D1): D493-D496.
Lewit-Bentley A, Réty S (2000) EF-hand calcium-binding proteins. Current opinion in structural biology. 10(6): 637-643.
Li J, Jiang M-M, Ren L, Liu Y, Chen H-Y (2016) Identification and characterization of CBL and CIPK gene families in eggplant (Solanum melongena L.). Molecular Genetics and Genomics. 291(4): 1769-1781.
Li L, Kim B-G, Cheong YH, Pandey GK, Luan S (2006) A Ca2+ signaling pathway regulates a K+ channel for low-K response in Arabidopsis. Proceedings of the National Academy of Sciences. 103(33): 12625-12630.
Li R, Zhang J, Wei J, Wang H, Wang Y, Ma R (2009) Functions and mechanisms of the CBL–CIPK signaling system in plant response to abiotic stress. Progress in Natural Science. 19(6): 667-676.
Lu T, Zhang G, Sun L, Wang J, Hao F (2017) Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton. PeerJ. 5: e3653.
Luan S (2009) The CBL–CIPK network in plant calcium signaling. Trends in plant science. 14(1): 37-42.
Ma X, Gai W-X, Qiao Y-M, Ali M, Wei A-M, Luo D-X, Li Q-H, Gong Z-H (2019) Identification of CBL and CIPK gene families and functional characterization of CaCIPK1 under Phytophthora capsici in pepper (Capsicum annuum L.). BMC genomics. 20(1): 775.
Ma X, Li Q-H, Yu Y-N, Qiao Y-M, Gong Z-H (2020) The CBL–CIPK Pathway in Plant Response to Stress Signals. International Journal of Molecular Sciences. 21(16): 5668.
Martínez-Atienza J, Jiang X, Garciadeblas B, Mendoza I, Zhu J-K, Pardo JM, Quintero FJ (2007) Conservation of the salt overly sensitive pathway in rice. Plant physiology. 143(2): 1001-1012.
Mohanta TK, Kumar P, Bae H (2017) Genomics and evolutionary aspect of calcium signaling event in calmodulin and calmodulin-like proteins in plants. BMC plant biology. 17(1): 38.
Nagae M, Nozawa A, Koizumi N, Sano H, Hashimoto H, Sato M, Shimizu T (2003) The crystal structure of the novel calcium-binding protein AtCBL2 from Arabidopsis thaliana. Journal of Biological Chemistry. 278(43): 42240-42246.
Pandey GK, Cheong YH, Kim K-N, Grant JJ, Li L, Hung W, D'angelo C, Weinl S, Kudla J, Luan S (2004) The calcium sensor calcineurin B-like 9 modulates abscisic acid sensitivity and biosynthesis in Arabidopsis. The Plant Cell. 16(7): 1912-1924.
Pandey GK, Kanwar P, Pandey A, 2014. Global comparative analysis of CBL-CIPK gene families in plants. Springer.
Podell S, Gribskov M (2004) Predicting N-terminal myristoylation sites in plant proteins. BMC genomics. 5(1): 37.
Sánchez-Barrena MJ, Martínez-Ripoll M, Zhu J-K, Albert A (2005) The structure of the Arabidopsis thaliana SOS3: molecular mechanism of sensing calcium for salt stress response. Journal of molecular biology. 345(5): 1253-1264.
Sanyal S, Rao S, Mishra L, Sharma M, Pandey G (2016) Plant Stress Responses Mediated by CBL–CIPK Phosphorylation Network. (ed) The Enzymes, Elsevier, pp31-64.
Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT (2000) A gene expression database for the molecular pharmacology of cancer. Nat. Genet. 24(3): 236.
Shi J, Kim K-N, Ritz O, Albrecht V, Gupta R, Harter K, Luan S, Kudla J (1999) Novel protein kinases associated with calcineurin B–like calcium sensors in Arabidopsis. The Plant Cell. 11(12): 2393-2405.
Sigrist CJ, De Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret L, Xenarios I (2012) New and continuing developments at PROSITE. Nucleic Acids Res. 41(D1): D344-D347.
Sun Z, Qi X, Li P, Wu C, Zhao Y, Zhang H, Wang Z (2008) Overexpression of aThellungiella halophila CBl9 homolog, ThCBL9, confers salt and osmotic tolerances in transgenic Arabidopsis thaliana. Journal of Plant Biology. 51(1): 25-34.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular biology and evolution. 30(12): 2725-2729.
Wang M, Gu D, Liu T, Wang Z, Guo X, Hou W, Bai Y, Chen X, Wang G (2007) Overexpression of a putative maize calcineurin B-like protein in Arabidopsis confers salt tolerance. Plant Molecular Biology. 65(6): 733-746.
Wu Y, Ding N, Zhao X, Zhao M, Chang Z, Liu J, Zhang L (2007) Molecular characterization of PeSOS1: the putative Na+/H+ antiporter of Populus euphratica. Plant molecular biology. 65(1-2): 1.
Xu J, Li H-D, Chen L-Q, Wang Y, Liu L-L, He L, Wu W-H (2006) A protein kinase, interacting with two calcineurin B-like proteins, regulates K+ transporter AKT1 in Arabidopsis. Cell. 125(7): 1347-1360.
Yang Y, Zhang C, Tang R-J, Xu H-X, Lan W-Z, Zhao F, Luan S (2019) Calcineurin B-Like proteins CBL4 and CBL10 mediate two independent salt tolerance pathways in Arabidopsis. International journal of molecular sciences. 20(10): 2421.
Yin X, Wang Q, Chen Q, Xiang N, Yang Y, Yang Y (2017) Genome-wide identification and functional analysis of the calcineurin B-like protein and calcineurin B-like protein-interacting protein kinase gene families in turnip (Brassica rapa var. rapa). Frontiers in plant science. 8: 1191.
Zhang H, Yang B, Liu W-Z, Li H, Wang L, Wang B, Deng M, Liang W, Deyholos MK, Jiang Y-Q (2014) Identification and characterization of CBL and CIPK gene families in canola (Brassica napus L.). BMC plant biology. 14(1): 8.
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