شناسایی و ارزیابی ژن‌های حفاظت‌شده NAC مورد هدف miR164 در گیاهAeluropus littoralis در پاسخ به تنش‌های غیرزیستی

نوع مقاله : علمی پژوهشی

نویسندگان

1 گروه به نژادی گیاهی، دانشکده علوم زراعی، دانشگاه علوم کشاورزی و منابع طبیعی ساری

2 هیئت علمی دانشگاه علوم کشاورزی و منابع طبیعی ساری و رئیس پژوهشکده ژنتیک و زیست فناوری طبرستان

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

4 گروه مهندسی ژنتیک و بیولوژی، پژوهشکده ژنتیک و زیست فناوری کشاورزی طبرستان، دانشگاه علوم کشاورزی و منابع طبیعی ساری

چکیده

MicroRNAها گروه بزرگی از RNAهای کوچک و غیرکدکننده هستند که با برش mRNA مورد هدف و یا مهار ترجمه، بیان این ژن‌ها را تنظیم می‌کنند. خانواده miR164 گیاهی بسیار حفاظت‌شده بوده و از طریق تنظیم ژن‌های NAC مورد هدف خود، در پاسخ گیاهان به تنش‌های غیرزیستی نقش دارند. در مطالعه حاضر، 68 ژن بالقوه کدکننده دمین NAC در Aeluropus littoralis به‌عنوان یک گیاه هالوفیت از خانواده Poaceae شناسایی شد. در میان ژن‌های AlNAC شناسایی شده، 4 ژن به‌عنوان هدف miR164 پیش‌بینی شدند. حفظ‌شدگی بالای جایگاه‌های تششخیص miR164 در ژن‌های AlNAC حاکی از نقش ضروری جایگاه‌های هدف در کارکرد طبیعی این ژن‌ها به‌عنوان عوامل رونویسی می‌باشد. الگوی بیان ژن انتخابی AlNAC1L.1 در پاسخ به تنش‌های شوری و خشکی و فیتوهورمون ABA در بافت‌های برگ، ساقه و ریشه با استفاده از RT-qPCR مورد بررسی قرار گرفت. نتایج نشان داد که ژن AlNAC1L.1 در زمان 6 ساعت بعد از اعمال تنش در تمامی بافت‌ها کاهش بیان نشان می‌دهد. در بین تیمارها، تیمار سدیم‌کلرید 600 میلی‌مولار بیان AlNAC1L.1 را در بافت‌های برگ، ساقه و ریشه به ترتیب حدود 217- ، 26- و 9- برابر کاهش داد. بنابراین، AlNAC1L.1 به‌عنوان ارتولوگ ژن OMTN6 (ژن NAC هدف miR164 در برنج) می‌تواند نقش تنظیم‌کننده منفی در پاسخ به تیمار‌های شوری، خشکی و ABA ایفا نماید. این نتایج نشان داد که کارکرد برخی از پروتئین‌های NAC می‌تواند در بین گونه‌ها حفاظت‌شده باشد. در مجموع، این یافته‌ها منبع مفیدی برای تجزیه و تحلیل بیشتر میان‌کنش‌های بین ژن‌های NAC و خانواده miR164 در پاسخ به تنش‌های غیرزیستی فراهم آورده است.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Identification and evaluation of conserved miR164-targeted Aeluropus littoralis NAC genes in response to abiotic stress

نویسندگان [English]

  • Samira Mohammadi 1
  • Ghorbanali Nematzadeh 2
  • Hamid Najafi Zarini 3
  • Seyyed Hamidreza Hashemi-petroudi 4
1 Department of Plant Biotechnology and breeding, Sari Agricultural Sciences and Natural Resources University
2 . Department of Biotechnology and breeding. Sari Agricultural Sciences and Natural Resources University (SANRU). Sari. Iran
3 Associate professor. Department of Biotechnology and breeding. Sari Agricultural Sciences and Natural Resources University (SANRU). Sari. Iran
4 Department of Genetic Engineering and Biology, Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University (SANRU)
چکیده [English]

MicroRNAs are a large class of small and non-coding RNAs that regulate gene expression by binding target mRNA, which leads to cleavage or translational inhibition. Plant miR164 family is highly conserved and is involved in the responses of plants to biotic stresses through the regulation of their target NAC genes. In the present study, 68 putative NAC domain-encoding genes (NACs) were identified in Aeluropus littoralis, a halophyte plant of family Poaceae. Among the AlNAC genes identified, 4 were predicted putative targets for regulation by miR164. The high conservation of miR164 recognition sites in AlNAC genes indicates the essential role of target sites in the normal function of these genes as transcription factors. Expression profile of AlNAC1L.1 candidate gene in response to salt and drought stresses and ABA phytohormone in leaf, stem and root tissues was analyzed by RT-qPCR. The results showed that AlNAC1L.1 gene down-regulated in all tissues at 6 hours after applying stresses. Among the treatments, 600 mM NaCl treatment reduced AlNAC1L.1 expression in leaf, stem and root tissues to about -217, -26 and -9 folds, respectively. Therefore, the AlNAC1L.1 which is ortholog of known Oryza miR164-targeted NAC gene OMTN6, may play negative regulatory role in response to salt, drought and ABA treatments. These results indicated that function of some NAC proteins might be conserved among species. Collectively, these findings provided a useful resource for further analysis of the interactions between NAC genes and their intricate regulation by miR164 in response to abiotic stresses.

کلیدواژه‌ها [English]

  • Abiotic stress
  • miR164
  • NAC Transcription Factors
  • post-transcriptional regulation
  • stress-responses
Akdogan G, Tufekci ED, Uranbey S, Unver T (2016) miRNA-based drought regulation in wheat. Funct. Integr. Genomics. 16(3): 221-233. Baker CC, Sieber P, Wellmer F, Meyerowitz EM (2005) The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis. Curr. Biol. 15(4): 303-315. Cohen D, Bogeat-Triboulot M-B, Tisserant E, Balzergue S, Martin-Magniette M-L, Lelandais G, Ningre N, Renou J-P, Tamby J-P, Le Thiec D (2010) Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes. BMC Genomics. 11(1): 630. Dai X, Zhuang Z, Zhao PX (2018) psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res. 46(W1): W49-W54. Fang Y, Xie K, Xiong L (2014) Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice. J. Exp. Bot. 65(8): 2119-2135. Feng H, Duan X, Zhang Q, Li X, Wang B, Huang L, Wang X, Kang Z (2014) The target gene of tae‐miR164, a novel NAC transcription factor from the NAM subfamily, negatively regulates resistance of wheat to stripe rust. Mol. Plant Pathol. 15(3): 284-296. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A (2015) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44: 279-285. Ge W, Zhang Y, Cheng Z, Hou D, Li X, Gao J (2017) Main regulatory pathways, key genes and micro RNAs involved in flower formation and development of moso bamboo (Phyllostachys edulis). Plant Biotechnol. J. 15(1): 82-96. Gonçalves B, Hasson A, Belcram K, Cortizo M, Morin H, Nikovics K, Vialette‐Guiraud A, Takeda S, Aida M, Laufs P (2015) A conserved role for CUP‐SHAPED COTYLEDON genes during ovule development. Plant J. 83(4): 732-742. Guo HS, Xie Q, Fei JF, Chua NH (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell. 17(5): 1376-1386. Guo Y, Cai Z, Gan S (2004) Transcriptome of Arabidopsis leaf senescence. Plant, Cell Environ. 27(5): 521-549. Guo Y, Zhao S, Zhu C, Chang X, Yue C, Wang Z, Lin Y, Lai Z (2017) Identification of drought-responsive miRNAs and physiological characterization of tea plant (Camellia sinensis L.) under drought stress. BMC Plant Biol. 17(1): 1-20. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41: 95-98. Hashemi-Petroudi S, Mohammadi S (2021) Identification, classification and expression analysis of DREB transcription factor gene family in Aeluropus littoralis under salinity stress. J. Plant Res. 34(1): 224-235. Hashemi-Petroudi SH, Mohammadi S (2020) Identification of the ERF gene family in Aeluropus littoralis halophyte plant and analysis of their expression pattern in response to salt stress. Crop Biotechnol. 9(29): 53-66. Hashemi-Petroudi SH, Nematzadeh G, Mohammadi S, Kuhlmann M (2019) Analysis of Expression Pattern of Genome and Analysis of HSP90 Gene Family in Aeluropus littoralis under Salinity Stress. J. Crop Breed. 11(31): 134-143. Hashemi-Petroudi SH, Nematzadeh G, Mohammadi S, Kuhlmann M (2020) Expression pattern analysis of heat shock transcription factors (HSFs) gene family in Aeluropus littoralis under salinity stress. Env. Stresses Crop Sci. 13(2): 571-581. Hernández Y, Sanan-Mishra N (2017) miRNA mediated regulation of NAC transcription factors in plant development and environment stress response. Plant Gene. 11: 190-198. Hu G, Lei Y, Wang L, Liu J, Tang Y, Zhang Z, Chen A, Peng Q, Yang Z, Wu J (2018) The ghr-miR164 and GhNAC100 module participates in cotton plant defence against Verticillium dahliae. bioRxiv. 440826. Huang Q, Wang Y, Li B, Chang J, Chen M, Li K, Yang G, He G (2015) TaNAC29, a NAC transcription factor from wheat, enhances salt and drought tolerance in transgenic Arabidopsis. BMC Plant Biol. 15(1): 1-15. Jeong D-H, Park S, Zhai J, Gurazada SGR, De Paoli E, Meyers BC, Green PJ (2011) Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell. 23(12): 4185-4207. Jin W, Wu F (2015) Characterization of miRNAs associated with Botrytis cinerea infection of tomato leaves. BMC Plant Biol. 15(1): 1. 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. Kim JH, Woo HR, Kim J, Lim PO, Lee IC, Choi SH, Hwang D, Nam HG (2009) Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis. Science. 323(5917): 1053-1057. Kozomara A, Birgaoanu M, Griffiths-Jones S (2019) miRBase: from microRNA sequences to function. Nucleic Acids Res. 47(D1): D155-D162. Lakhwani D, Pandey A, Sharma D, Asif MH, Trivedi PK (2020) Novel microRNAs regulating ripening-associated processes in banana fruit. Plant Growth Regul. 90(2): 223-235. Lan Y, Su N, Shen Y, Zhang R, Wu F, Cheng Z, Wang J, Zhang X, Guo X, Lei C (2012) Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice. BMC Genomics. 13(1):1-10. Lee MH, Jeon HS, Kim HG, Park OK (2017) An Arabidopsis NAC transcription factor NAC4 promotes pathogen‐induced cell death under negative regulation by microRNA164. New Phytol. 214(1): 343-360. Letunic I, Doerks T, Bork P (2014) SMART: recent updates, new developments and status in 2015. Nucleic Acids Res. 43(D1):D257-D260. Li B, Qin Y, Duan H, Yin W, Xia X (2011) Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. J. Exp. Bot. 62(11): 3765-3779. Li J, Guo G, Guo W, Guo G, Tong D, Ni Z, Sun Q, Yao Y (2012) miRNA164-directed cleavage of ZmNAC1 confers lateral root development in maize (Zea mays L.). BMC Plant Biol. 12(1): 220. Lu S, Sun Y-H, Shi R, Clark C, Li L, Chiang VL (2005) Novel and mechanical stress–responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell. 17(8): 2186-2203. Lu X, Dun H, Lian C, Zhang X, Yin W, Xia X (2017) The role of peu-miR164 and its target PeNAC genes in response to abiotic stress in Populus euphratica. Plant Physiol. Biochem. 115: 418-438. Lu Y-B, Qi Y-P, Yang L-T, Guo P, Li Y, Chen L-S (2015) Boron-deficiency-responsive microRNAs and their targets in Citrus sinensis leaves. BMC Plant Biol. 15(1): 271. Luan Y, Cui J, Zhai J, Li J, Han L, Meng J (2015) High-throughput sequencing reveals differential expression of miRNAs in tomato inoculated with Phytophthora infestans. Planta. 241(6): 1405-1416. Mallory AC, Reinhart BJ, Jones‐Rhoades MW, Tang G, Zamore PD, Barton MK, Bartel DP (2004) MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region. EMBO J. 23(16): 3356-3364. Nair MM, Krishna T, Alagu M (2020) Bioinformatics insights into microRNA mediated gene regulation in Triticum aestivum during multiple fungal diseases. Plant Gene. 21: 100219. Naqvi AR, Haq QM, Mukherjee SK (2010) MicroRNA profiling of tomato leaf curl new delhi virus (tolcndv) infected tomato leaves indicates that deregulation of mir159/319 and mir172 might be linked with leaf curl disease. Virol. J. 7(1): 281. Olsen AN, Ernst HA, Leggio LL, Skriver K (2005) NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci. 10(2): 79-87. Pandey R, Joshi G, Bhardwaj AR, Agarwal M, Katiyar-Agarwal S (2014) A comprehensive genome-wide study on tissue-specific and abiotic stress-specific miRNAs in Triticum aestivum. PLoS One. 9(4): e95800. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell. 110(4): 513-520. Sánchez-Montesino R, Bouza-Morcillo L, Marquez J, Ghita M, Duran-Nebreda S, Gómez L, Holdsworth MJ, Bassel G, Oñate-Sánchez L (2019) A regulatory module controlling GA-mediated endosperm cell expansion is critical for seed germination in Arabidopsis. Mol. plant. 12(1): 71-85. Sievers F, Higgins DG (2021) The clustal omega multiple alignment package. (ed) Multiple Sequence Alignment, Springer, pp 3-16. Sosa-Valencia G, Palomar M, Covarrubias AA, Reyes JL (2017a) The legume miR1514a modulates a NAC transcription factor transcript to trigger phasiRNA formation in response to drought. J. Exp. Bot. 68(8): 2013-2026. Sosa-Valencia G, Romero-Pérez PS, Palomar VM, Covarrubias AA, Reyes JL (2017b) Insights into the function of the phasiRNA-triggering miR1514 in response to stress in legumes. Plant Signal. Behav. 12(3): e1284724. Stender EG, O'shea C, Skriver K (2015) Subgroup-specific intrinsic disorder profiles of arabidopsis NAC transcription factors: Identification of functional hotspots. Plant Signal. Behav. 10(6): e1010967. Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P (2019) STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47(D1): D607-D613. Wang L, Zhao H, Chen D, Li L, Sun H, Lou Y, Gao Z (2016) Characterization and primary functional analysis of a bamboo NAC gene targeted by miR164b. Plant Cell Rep. 35(6): 1371-1383. Wang M, Wang Q, Zhang B (2013) Response of miRNAs and their targets to salt and drought stresses in cotton (Gossypium hirsutum L.). Gene. 530(1): 26-32. Wilkins O, Waldron L, Nahal H, Provart NJ, Campbell MM (2009) Genotype and time of day shape the Populus drought response. Plant J. 60(4): 703-715. Xie Q, Frugis G, Colgan D, Chua N-H (2000) Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. Genes Dev. 14(23): 3024-3036. Yamaguchi M, Ohtani M, Mitsuda N, Kubo M, Ohme-Takagi M, Fukuda H, Demura T (2010) VND-INTERACTING2, a NAC domain transcription factor, negatively regulates xylem vessel formation in Arabidopsis. Plant Cell. 22(4): 1249-1263. You J, Zhang L, Song B, Qi X, Chan Z (2015) Systematic analysis and identification of stress-responsive genes of the NAC gene family in Brachypodium distachyon. PloS one. 10(3): e0122027. Yuan F, Xu Y, Leng B, Wang B (2019) Beneficial effects of salt on halophyte growth: Morphology, cells, and genes. Open life sci. 14(1): 191-200. Zeng S, Liu Y, Pan L, Hayward A, Wang Y (2015) Identification and characterization of miRNAs in ripening fruit of Lycium barbarum L. using high-throughput sequencing. Front. Plant Sci. 6: 778. Zhao J-P, Jiang X-L, Zhang B-Y, Su X-H (2012) Involvement of microRNA-mediated gene expression regulation in the pathological development of stem canker disease in Populus trichocarpa. PLoS One. 7(9): e44968. Zhou M, Li D, Li Z, Hu Q, Yang C, Zhu L, Luo H (2013) Constitutive expression of a miR319 gene alters plant development and enhances salt and drought tolerance in transgenic creeping bentgrass. Plant Physiol. 161(3): 1375-1391.