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بررسی مقایسه‌ای خانواده ژنی CCCH Zinc finger در آرابیدوپسیس تالیانا و برنج

نوع مقاله : علمی پژوهشی

نویسندگان

1 دانشجوی کارشناسی ارشد بیوتکنولوژی کشاورزی، دانشگاه علوم کشاورزی و منابع طبیعی ساری، ایران

2 دانشیار، گروه بیوتکنولوژی و به‌نژادی، دانشگاه علوم کشاورزی و منابع طبیعی ساری، ساری، ایران

3 استادیار، گروه مهندسی ژنتیک و بیولوژی، پژوهشکده ژنتیک و زیست‌فناوری کشاورزی طبرستان، دانشگاه علوم کشاورزی و منابع طبیعی ساری ، ایران

4 دانشیار گروه بیوتکنولوژی و به‌نژادی، دانشگاه علوم کشاورزی و منابع طبیعی ساری، ساری، ایران

چکیده

ژن‌های خانواده زینک‌فینگر CCCH (C3HZNF)، کد کننده پروتئین‌هایی با سه سیستئین و یک هیستیدین می‌باشند. پروتئین‌های این خانواده دسته مهمی از فاکتورهای رونویسی زینک فینگر بوده که در فعالیت‌های مختلف از جمله رشد و نمو گیاه و پاسخ به تنش‌های زیستی و غیر زیستی و در واقع در مقاومت به تنش‌ها موثر می‌باشند. در این مقاله از داده‌های پروتئینی C3HZNF دو گیاه آرابیدوپسیس و برنج برای تجزیه و تحلیل روابط فیلوژنتیک، ساختار اگزون/ اینترون، سازماندهی موتیف‌ها/ دامنه ها استفاده شد. این بررسی‌ها نشان از همولوژی بالای این ژن‌ها با ژن‌های CCCH در برنج داشتند. تجزیه و تحلیل ساختار ژنی نشان داد که AtC3Hها دارای تعداد اگزون‌های متغیری می‌باشند، اما به طور کلی ژن‌هایی با 1 و 7 اگزون، بیشترین تعداد را در بر می‌گیرند. بررسی ویژگی‌های فیزیکی و شیمیایی پروتئین‌های این خانواده نشان داد که AtC3H36 پایدارترین پروتئین در بین اعضای این خانواده می‌باشد همچنین بیشترین نقطه ایزوالکتریک متعلق به پروتئین AtC3H7 (96/9) است. مشاهدات نشان داد اعضای این خانواده ژنی دارای 1 تا 6 دمین Znf C3H و مجموعا 17 دمین عملکردی می‌باشند. مقایسه‌ی فیلوژنی بین پروتئین‌های C3H در برنج و Arabidopsis نشان داد که این پروتئین‌‌ها از حفاظت شدگی بالایی برخوردارند. در آنالیز فیلوژنتیکی مقایسه‌ای AtC3H وOsC3H، ژن‌های اورتولوگ در یک گروه‌ قرار گرفتند. به عنوان مثال،OsC3H8 همولوژی نزدیکی با HUA1 در Arabidopsis (AtC3H37) نشان داد، که این ژن در توسعه گل نقش دارد. این مطالعه اطلاعات ارزشمندی در مورد خانواده مهم ژنی CCCH zinc finger در گیاه آرابیدوپسیس و برنج ارائه می‌دهد. این اطلاعات می‌تواند در درک نحوه عمل این ژن‌ها برای کمک به مقاومت گیاه در هنگام مواجه با تنش-های زیستی و غیر زیستی کمک کننده باشد.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Comparative study of CCCH Zinc finger gene family in Arabidopsis thaliana and rice

نویسندگان [English]

  • Parisa Ramezanpoor 1
  • Hamid Najafi Zarini 2
  • Hamidreza Hashemi 3
  • Gholamali Ranjbar 4

1 Department of Biotechnology Sari Agricultural Sciences and Natural Resources University, Sari, Iran

2 Associate Professor, Department of Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU) Sari, Iran.

3 Assistant Professor, Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU) Sari, Iran.

4 Associate Professor, Department of Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran.3. Professor, Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari A

چکیده [English]

Zincfinger CCCH (C3HZNF) genes encode proteins with three cysteines and one histidine. The proteins of this family are an important group of zinc finger transcription factors that are effective in various activities such as plant growth and response to biotic and abiotic stresses and actually They are effective in stresses tolarance. In this article, C3HZNF protein data of Arabidopsis and rice plants were used to analyze phylogenetic relationships, exon/intron structure, motifs/domains organization. These studies showed the high homology of these genes with CCCH genes in rice. Analysis of the gene structure showed that AtC3Hs have a variable number of exons, but in general, genes with 1 and 7 exons contain the largest number. study the physical and chemical properties of this family showed that AtC3H36 is the most stable protein among the members of this family, and the highest isoelectric point belongs to the AtC3H7(9.96) protein. The observations showed that the members of this gene family have 1 to 6 Znf C3H domains and a total of 17 functional domains. Phylogeny comparison between C3H proteins in rice and Arabidopsis showed that these proteins are highly conserved. In the comparative phylogenetic analysis of AtC3H and OsC3H, the orthologous genes were placed in one group. For example, OsC3H8 showed close homology to HUA1 in Arabidopsis (AtC3H37), suggesting that this gene is involved in flower development. This study provides valuable information about the important CCCH zinc finger gene family in Arabidopsis and rice. This information can be helpful in understanding how these genes work to help plant tolarance when faced with biotic and abiotic stresses.

کلیدواژه‌ها [English]

  • "؛ abiotic stress"؛ motif"؛
  • "؛ transcription factors"؛
مراجع
Ai Q, Pan W, Zeng Y, Li Y, Cui L (2022) CCCH Zinc finger genes in Barley: genome-wide identification, evolution, expression and haplotype analysis. BMC Plant Biology. 22(1): 117. Arab M, Kazemitabar SK, Hashemi-Petroudi SH (2022) Bioinformatics analysis of CBL gene family members in Sesamum indicum under drought stress. Crop Biotechnology. 11(2): 17-31. Arab M, Najafi Zarrini H, Nematzadeh G, Hashemi-Petroudi SH (2021) Comparative study of cis-regulatory elements in the promoter regions of calcineurin B-like genes (CBLs) of Aeluropus, Arabidopsis and rice plants. Crop Biotechnology. Aravind L, Koonin EV (1999) G-patch: a new conserved domain in eukaryotic RNA-processing proteins and type D retroviral polyproteins. Trends in Biochemical Sciences. 24(9): 342-344. 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(Web Server issue): W202-208. Birkenbihl R, Somssich I (2011) Transcriptional Plant Responses Critical for Resistance Towards Necrotrophic Pathogens. Frontiers in Plant Science. 2. Blomme J, Van Aken O, Van Leene J, Jégu T, De Rycke R, De Bruyne M, Vercruysse J, Nolf J, Van Daele T, De Milde L, Vermeersch M, Des Francs-Small CC, De Jaeger G, Benhamed M, Millar AH, Inzé D, Gonzalez N (2017) The Mitochondrial DNA-Associated Protein SWIB5 Influences mtDNA Architecture and Homologous Recombination. Plant Cell. 29(5): 1137-1156. Callebaut I, Mornon J-P (2010) LOTUS, a new domain associated with small RNA pathways in the germline. Bioinformatics. 26(9): 1140-1144. Chai G, Kong Y, Zhu M, Yu L, Qi G, Tang X, Wang Z, Cao Y, Yu C, Zhou G (2015) Arabidopsis C3H14 and C3H15 have overlapping roles in the regulation of secondary wall thickening and anther development. Journal of experimental botany. 66. Chai G, Qi G, Cao Y, Wang Z, Yu L, Tang X, Yu Y, Wang D, Kong Y, Zhou G (2014) Poplar PdC3H17 and PdC3H18 are direct targets of PdMYB3 and PdMYB21, and positively regulate secondary wall formation in Arabidopsis and poplar. New Phytologist. 203(2): 520-534. Chen F, Liu H-L, Wang K, Gao Y-M, Wu M, Xiang Y (2020) Identification of CCCH Zinc Finger Proteins Family in Moso Bamboo (Phyllostachys edulis), and PeC3H74 Confers Drought Tolerance to Transgenic Plants. Frontiers in Plant Science. 11. Chen X, Meyerowitz EM (1999) HUA1 and HUA2 Are Two Members of the Floral Homeotic AGAMOUS Pathway. Molecular Cell. 3(3): 349-360. Cléry A, Blatter M, Allain FHT (2008) RNA recognition motifs: boring? Not quite. Current Opinion in Structural Biology. 18(3): 290-298. Costa P, Arndt K (2000) Synthetic Lethal Interactions Suggest a Role for the Saccharomyces cerevisiae Rtf1 Protein in Transcription Elongation. Genetics. 156: 535-547. De Mello G, Stocker M, Dappert A, Dasler R, Demeranville T, Garza K, Graef F, Mcentyre J, Schindler U, Kotarski RR (2017) Services that Enable Integration and Cross-Linking Across Different Types of Identifiers and Data Types. Deng H, Liu H, Li X, Xiao J, Wang S (2012) A CCCH-type zinc finger nucleic acid-binding protein quantitatively confers resistance against rice bacterial blight disease. Plant Physiol. 158(2): 876-889. Freund C, Dötsch V, Nishizawa K, Reinherz EL, Wagner G (1999) The GYF domain is a novel structural fold that is involved in lymphoid signaling through proline-rich sequences. Nature Structural Biology. 6(7): 656-660. Fuller-Pace FV (2006) DExD/H box RNA helicases: multifunctional proteins with important roles in transcriptional regulation. Nucleic acids research. 34 (15): 4206-4215. Gamsjaeger R, Liew CK, Loughlin FE, Crossley M, Mackay JP (2007) Sticky fingers: zinc-fingers as protein-recognition motifs. Trends in Biochemical Sciences. 32(2): 63-70. García-Mayoral M, Hollingworth D, Masino L, Díaz-Moreno I, Kelly G, Gherzi R, Chou C-F, Chen C-Y, Ramos A (2007) The Structure of the C-Terminal KH Domains of KSRP Reveals a Noncanonical Motif Important for mRNA Degradation. Structure (London, England : 1993). 15: 485-498. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel R, Bairoch A (2003) ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic acids research. 31: 3784-3788. Han G, Lu C, Guo J, Qiao Z, Sui N, Qiu N, Wang B (2020) C2H2 Zinc Finger Proteins: Master Regulators of Abiotic Stress Responses in Plants. Frontiers in Plant Science. 11. Han G, Qiao Z, Li Y, Wang C, Wang B (2021) The roles of CCCH zinc-finger proteins in plant abiotic stress tolerance. International journal of molecular sciences. 22(15): 8327. 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. Isalan M (2013) Zinc Fingers. In: Lennarz WJ ,Lane MD. (ed) Encyclopedia of Biological Chemistry (Second Edition), Academic Press, Waltham, pp 575-579. Jiang A-L, Xu Z-S, Zhao G-Y, Cui X-Y, Chen M, Li L-C, Ma Y-Z (2014) Genome-Wide Analysis of the C3H Zinc Finger Transcription Factor Family and Drought Responses of Members in Aegilops tauschii. Plant Molecular Biology Reporter. 32(6): 1241-1256. Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D’angelo C, Bornberg‐Bauer E, Kudla J, Harter K (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV‐B light, drought and cold stress responses. The Plant Journal. 50(2): 347-363. Klug A (1999) Zinc finger peptides for the regulation of gene expression. Journal of Molecular Biology. 293(2): 215-218. Letunic I, Copley R, Schmidt S, Ciccarelli F, Doerks T, Schultz J, Ponting C, Bork P (2004) SMART 4.0: Towards genomic data integration. Nucleic acids research. 32: D142-144. Lin PC, Pomeranz MC, Jikumaru Y, Kang SG, Hah C, Fujioka S, Kamiya Y, Jang JC (2011) The Arabidopsis tandem zinc finger protein AtTZF1 affects ABA- and GA-mediated growth, stress and gene expression responses. Plant J. 65(2): 253-268. Liu C, Xu X, Kan J, Cheng Z, Chang Y, Lin J, Li H (2020) Genome-wide analysis of the C3H zinc finger family reveals its functions in salt stress responses of Pyrus betulaefolia. PeerJ. 8: e9328. Maris C, Dominguez C, Allain FHT (2005) The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. The FEBS Journal. 272(9): 2118-2131. Moglia A, Gianoglio S, Acquadro A, Valentino D, Milani AM, Lanteri S, Comino C (2019) Identification of DNA methyltransferases and demethylases in Solanum melongena L., and their transcription dynamics during fruit development and after salt and drought stresses. PLoS One. 14(10): e0223581. Mottola A, Ramírez‐Zavala B, Hünniger K, Kurzai O, Morschhäuser J (2021) The zinc cluster transcription factor Czf1 regulates cell wall architecture and integrity in Candida albicans. Molecular Microbiology. 116(2): 483-497. Ohi Melanie D, Link Andrew J, Ren L, Jennings Jennifer L, Mcdonald WH, Gould Kathleen L (2002) Proteomics Analysis Reveals Stable Multiprotein Complexes in Both Fission and Budding Yeasts Containing Myb-Related Cdc5p/Cef1p, Novel Pre-mRNA Splicing Factors, and snRNAs. Molecular and Cellular Biology. 22(7): 2011-2024. Peng X, Zhao Y, Cao J, Zhang W, Jiang H, Li X, Ma Q, Zhu S, Cheng B (2012) CCCH-Type Zinc Finger Family in Maize: Genome-Wide Identification, Classification and Expression Profiling under Abscisic Acid and Drought Treatments. PLOS ONE. 7(7): e40120. Pi B, He X, Ruan Y, Jang J-C, Huang Y (2018) Genome-wide analysis and stress-responsive expression of CCCH zinc finger family genes in Brassica rapa. BMC Plant Biology. 18(1): 1-15. Pi B, Pan J, Xiao M, Hu X, Zhang L, Chen M, Liu B, Ruan Y, Huang Y (2021) Systematic analysis of CCCH zinc finger family in Brassica napus showed that BnRR-TZFs are involved in stress resistance. BMC Plant Biology. 21(1): 555. Pradhan S, Kant C, Verma S, Bhatia S (2017) Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.). PLOS ONE. 12(7): e0180469. Punta M, Coggill P, Eberhardt R, Mistry J, Tate J, Boursnell C, Pang N, Forslund S, Ceric G, Clements J, Heger A, Holm L, Sonnhammer E, Eddy S, Bateman A, Finn R (2011) The Pfam protein families database. Nucleic acids research. 40: D290-301. Ren J, Wen L, Gao X, Jin C, Xue Y, Yao X (2009) DOG 1.0: illustrator of protein domain structures. Cell Research. 19(2): 271-273. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Schölkopf B, Weigel D, Lohmann JU (2005) A gene expression map of Arabidopsis thaliana development. Nature genetics. 37(5): 501-506. Schmitz R, Hong L, Michaels S, Amasino R (2006) FRIGIDA-ESSENTIAL 1 interacts genetically with FRIGIDA and FRIGIDA-LIKE 1 to promote the winter-annual habit of Arabidopsis thaliana. Development (Cambridge, England). 132: 5471-5478. Seong SY, Shim JS, Bang SW, Kim J-K (2020) Overexpression of OsC3H10, a CCCH-Zinc Finger, Improves Drought Tolerance in Rice by Regulating Stress-Related Genes. Plants. 9(10): 1298. Singh N, Swain S, Singh A, Nandi AK (2018) AtOZF1 Positively Regulates Defense Against Bacterial Pathogens and NPR1-Independent Salicylic Acid Signaling. Mol Plant Microbe Interact. 31(3): 323-333. Sun J, Jiang H, Xu Y, Li H, Wu X, Xie Q, Li C (2007) The CCCH-type zinc finger proteins AtSZF1 and AtSZF2 regulate salt stress responses in Arabidopsis. Plant Cell Physiol. 48(8): 1148-1158.mura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular biology and evolution. 30. Vieira WA, Coetzer TL (2016) Localization and interactions of Plasmodium falciparum SWIB/ MDM2 homologues. Malar J 15, 32 DOI: 10.1186/ s12936-015-1065-9. Wan F-X, Gao J, Wang G-L, Niu Y, Wang L-Z, Zhang X-G, Wang Y-Q, Pan Y (2021) Genome-wide identification of NAC transcription factor family and expression analysis of ATAF subfamily members under abiotic stress in eggplant. Scientia Horticulturae. 289: 110424. Wang D, Guo Y, Wu C, Yang G, Li Y, Zheng C (2008) Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice. BMC Genomics. 9(1): 44. Wang X-L, Zhong Y, Cheng Z-M (2014) Evolution and Expression Analysis of the CCCH Zinc Finger Gene Family in Vitis vinifera. The Plant Genome. 7(3): plantgenome2014.2005.0019. Yan Z, Jia J, Yan X, Shi H, Han Y (2017) Arabidopsis KHZ1 and KHZ2, two novel non-tandem CCCH zinc-finger and K-homolog domain proteins, have redundant roles in the regulation of flowering and senescence. Plant Molecular Biology. 95(6): 549-565. Yuan S, Xu B, Zhang J, Xie Z, Cheng Q, Yang Z, Cai Q, Huang B (2015) Comprehensive analysis of CCCH-type zinc finger family genes facilitates functional gene discovery and reflects recent allopolyploidization event in tetraploid switchgrass. BMC Genomics. 16(1): 129.
فصلنامه علمی زیست فناوری گیاهان زراعی
دوره 12، شماره 39 - شماره پیاپی 39
آذر 1401
صفحه 85-107
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