园艺-分子生物合辑Horticulture — Genetics · Breeding
|A novel long non-coding RNA, DIR, increases drought tolerance in cassava by modifying stress-related gene expression
DONG Shi-man1, 4, XIAO Liang3, LI Zhi-bo1, 4, SHEN Jie1, 4, YAN Hua-bing3, LI Shu-xia1, 2, LIAO Wen-bin1, 2, PENG Ming1, 2
1 Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, P.R.China
2 Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, P.R.China
3 Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, P.R.China
4 College of Tropical Crops, Hainan University, Haikou 570228, P.R.China
本研究鉴定了一个新的lncRNA，命名为干旱诱导型lncRNA（DIR，DROUGHT-INDUCED INTERGENIC lncRNA)。基因表达分析表明，干旱胁迫显著诱导了DIR的表达，而植物激素脱落酸和茉莉酸处理不影响DIR的表达。此外，过表达DIR基因可增强转基因木薯脯氨酸的积累从而提升抗旱性。RNA测序分析发现，DIR优先影响与干旱相关的转录基因和代谢相关基因。利用RNA下拉技术（RNA pull-down）联合质谱分析发现DIR与325个蛋白存在相互作用。蛋白-蛋白互作分析（Protein-protein interaction analysis，PPI）发现，mRNA胞质运输和蛋白质翻译质控通路相关的蛋白质被显著富集。这些结果表明，DIR与其互作蛋白可通过调控mRNAs或蛋白质的代谢来响应干旱胁迫。因此，干旱胁迫下通过调节DIR的表达有提高木薯产量的潜力。
Cassava is an important tropical cash crop. Severe drought stresses affect cassava productivity and quality, and cause great economic losses in agricultural production. Enhancing the drought tolerance of cassava can effectively improve its yield. Long non-coding RNAs (lncRNAs) are present in a wide variety of eukaryotes. Recently, increasing evidence has shown that lncRNAs play a critical role in the responses to abiotic stresses. However, the function of cassava lncRNAs in the drought response remains largely unknown. In this study, we identified a novel lncRNA, DROUGHT-INDUCED INTERGENIC lncRNA (DIR). Gene expression analysis showed that DIR was significantly induced by drought stress treatment, but did not respond to abscisic acid (ABA) or jasmonic acid (JA) treatments. In addition, overexpression of the DIR gene enhanced proline accumulation and drought tolerance in transgenic cassava. RNA-seq analysis revealed that DIR preferentially affected drought-related genes that were linked to transcription and metabolism. Moreover, RNA pull-down mass spectrometry analysis showed that DIR interacted with 325 proteins. A protein–protein interaction (PPI) analysis found a marked enrichment in proteins associated with the mRNA export and protein quality control pathways. Collectively, these results suggest that DIR and its interacting proteins that regulate mRNA or protein metabolism are involved in mediating the drought stress response. Thus, regulating DIR expression has potential for improving cassava yield under drought conditions.
Received: 16 November 2021
Accepted: 06 May 2022
|Fund: This work was supported by the National Key Research and Development Program of China (2018YFD1000500, 2019YFD1000500, and 2019YFD1001105), the Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences (1630052021026 and 1630052022008), the National Natural Science Foundation of China (31960440), the Hainan Provincial Natural Science Foundation of China (320MS097), and the Natural Science Foundation of China (31701484).
|About author: Correspondence PENG Ming, E-mail: email@example.com; LIAO Wen-bin, E-mail: firstname.lastname@example.org; LI Shu-xia, E-mail: email@example.com; YAN Hua-bing, E-mail: firstname.lastname@example.org
Cite this article:
DONG Shi-man, XIAO Liang, LI Zhi-bo, SHEN Jie, YAN Hua-bing, LI Shu-xia, LIAO Wen-bin, PENG Ming.
A novel long non-coding RNA, DIR, increases drought tolerance in cassava by modifying stress-related gene expression. Journal of Integrative Agriculture, 21(9): 2588-2602.
| Ahmad P, Rasool S, Gul A, Sheikh S A, Akram N A, Ashraf M, Kazi A M, Gucel S. 2016. Jasmonates: Multifunctional roles in stress tolerance. Frontiers in Plant Science, 7, 813.
An D, Ma Q, Wang H, Yang J, Zhou W, Zhang P. 2017. Cassava C-repeat binding factor 1 gene responds to low
temperature and enhances cold tolerance when over-
expressed in Arabidopsis and cassava. Plant Molecular Biology, 94, 109–124.
An D, Ma Q, Yan W, Zhou W, Liu G, Zhang P. 2016. Divergent regulation of cbf regulon on cold tolerance and plant phenotype in cassava overexpressing Arabidopsis CBF3 gene. Frontiers in Plant Science, 7, 1866.
Baruah P M, Kashyap P, Krishnatreya D B, Bordoloi K S, Gill S S, Agarwala N. 2021. Identification and functional analysis of drought responsive lncRNAs in tea plant. Plant Gene, 27, 100311.
Bates L S, Waldren R P, Teare I D. 1973. Rapid determination of free proline for water-stress studies. Plant and Soil, 39, 205–207.
Bhatia G, Singh A, Verma D, Sharma S, Singh K. 2020.
Genome-wide investigation of regulatory roles of lncRNAs in response to heat and drought stress in Brassica juncea
(Indian mustard). Environmental and Experimental Botany, 171, 103922.
Cagirici H B, Alptekin B, Budak H. 2017. RNA sequencing and co-expressed long non-coding RNA in modern and wild wheats. Scientific Reports, 7, 10670.
Cilano K, Mazanek Z, Khan M, Metcalfe S, Zhang X N. 2016. A new mutation, hap1-2, reveals a C terminal domain function in atmago protein and its biological effects in male gametophyte development in Arabidopsis thaliana. PLoS ONE, 11, e0148200.
Cox J, Mann M. 2008. MaxQuant enables high peptide identi-
fication rates, individualized p.p.b.-range mass accuracies and
proteome-wide protein quantification. Nature Biotechnology, 26, 1367–1372.
Cui M, Zhang W, Zhang Q, Xu Z, Zhu Z, Duan F, Wu R. 2011.
Induced over-expression of the transcription factor OsDREB2A
improves drought tolerance in rice. Plant Physiology and Biochemistry, 49, 1384–1391.
Ding Z, Wu C, Tie W, Yan Y, He G, Hu W. 2019. Strand-specific RNA-seq based identification and functional prediction of lncRNAs in response to melatonin and simulated drought stresses in cassava. Plant Physiology and Biochemistry, 140, 96–104.
Dong Y, Wang C, Han X, Tang S, Liu S, Xia X, Yin W. 2014. A novel bHLH transcription factor PebHLH35 from Populus euphratica confers drought tolerance through regulating stomatal development, photosynthesis and growth in Arabidopsis. Biochemical and Biophysical Research Communications, 450, 453–458.
Dubovskaya L V, Bakakina Y S, Kolesneva E V, Sodel D L, McAinsh M R, Hetherington A M, Volotovski I D. 2011. cGMP-dependent ABA-induced stomatal closure in the
ABA-insensitive Arabidopsis mutant abi1-1. New Phytologist, 191, 57–69.
EL-Sharkawy M A. 2004. Cassava biology and physiology. Plant Molecular Biology, 53, 621–641.
Fahad S, Bajwa A A, Nazir U, Anjum S A, Farooq A, Zohaib A, Sadia S, Nasim W, Adkins S, Saud S, Ihsan M Z, Alharby H, Wu C, Wang D, Huang J. 2017. Crop production under drought and heat stress: Plant responses and management options. Frontiers in Plant Science, 8, 1147.
Golicz A A, Bhalla P L, Singh M B. 2018. lncRNAs in plant and animal sexual reproduction. Trends in Plant Science, 23, 195–205.
Gowda N K, Kandasamy G, Froehlich M S, Dohmen R J, Andreasson C. 2013. Hsp70 nucleotide exchange factor Fes1 is essential for ubiquitin-dependent degradation of misfolded cytosolic proteins. Proceedings of the National Academy of Sciences of the United States of America, 110, 5975–5980.
Guo J, Sun B, He H, Zhang Y, Tian H, Wang B. 2021. Current understanding of bHLH transcription factors in plant abiotic stress tolerance. International Journal of Molecular Sciences, 22, 4921.
Guttman M, Rinn J L. 2012. Modular regulatory principles of large non-coding RNAs. Nature, 482, 339–346.
Hirayama T, Shinozaki K. 2010. Research on plant abiotic stress responses in the post-genome era: Past, present and future. Plant Journal, 61, 1041–1052.
Jeong J S, Kim Y S, Baek K H, Jung H, Ha S H, Do Choi Y, Kim M, Reuzeau C, Kim J K. 2010. Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiology, 153, 185–197.
Jin R, Kim B H, Ji C Y, Kim H S, Li H M, Ma D F, Kwak S S. 2017. Overexpressing IbCBF3 increases low temperature and drought stress tolerance in transgenic sweetpotato. Plant Physiology and Biochemistry, 118, 45–54.
Khan S A, Li M Z, Wang S M, Yin H J. 2018. Revisiting the role of plant transcription factors in the battle against abiotic stress. International Journal of Molecular Sciences, 19, 1634.
Kim D, Langmead B, Salzberg S L. 2015. HISAT: A fast spliced aligner with low memory requirements. Nature Methods, 12, 357–360.
Kodaira K S, Qin F, Tran L S, Maruyama K, Kidokoro S, Fujita
Y, Shinozaki K, Yamaguchi-Shinozaki K. 2011. Arabidopsis Cys2/His2 zinc-finger proteins AZF1 and AZF2 negatively
regulate abscisic acid-repressive and auxin-inducible genes under abiotic stress conditions. Plant Physiology, 157, 742–756.
Li B, Dewey C N. 2011. RSEM accurate transcript quantification from RNA-Seq data with or without a reference genome. Biochemical and Biophysical Research Communications, 12, 323.
Li S, Yu X, Cheng Z, Yu X, Ruan M, Li W, Peng M. 2017a. Global gene expression analysis reveals crosstalk between response mechanisms to cold and drought stresses in cassava seedlings. Frontiers in Plant Science, 8, 1259.
Li S, Yu X, Lei N, Cheng Z, Zhao P, He Y, Wang W, Peng M. 2017b. Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava. Scientific Reports, 7, 45981.
Li Z, Jing W, Peng Y, Zhang X Q, Ma X, Huang L K, Yan Y H.
2015. Spermine alleviates drought stress in white clover with different resistance by influencing carbohydrate meta-
bolism and dehydrins synthesis. PLoS ONE, 10, e0120708.
Love M I, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 550.
Mao K, Dong Q, Li C, Liu C, Ma F. 2017. Genome wide identi- fication and characterization of apple bHLH transcription factors and expression analysis in response to drought and salt stress. Frontiers in Plant Science, 8, 480.
Mao X, Zhang H, Qian X, Li A, Zhao G, Jing R. 2012. TaNAC2, a NAC-type wheat transcription factor conferring enhanced multiple abiotic stress tolerances in Arabidopsis. Journal of Experimental Botany, 63, 2933–2946.
Merkle T. 2011. Nucleo-cytoplasmic transport of proteins and RNA in plants. Plant Cell Reports, 30, 153–176.
Muthusamy M, Uma S, Backiyarani S, Saraswathi M S. 2015. Genome-wide screening for novel, drought stress- responsive long non-coding RNAs in drought-stressed leaf transcriptome of drought-tolerant and -susceptible banana (Musa spp) cultivars using Illumina high-throughput sequencing. Plant Biotechnology Reports, 9, 279–286.
Ohta M, Matsui K, Hiratsu K, Shinshi H. 2001. Repression domains of class II ERF transcriptional repressors share an essential motif for active repression. American Society of Plant Biologists, 13, 1959–1968.
Pendle A F, Clark G P, Boon R, Lewandowska D, Lam Y W, Andersen J, Mann M, Lamond A I, Brown J W, Shaw P J. 2005. Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Molecular Biology of the Cell, 16, 260–269.
Pertea M, Pertea G M, Antonescu C M, Chang T C, Mendell J T , Salzberg S L. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology, 33, 290–295.
Qin T, Zhao H, Cui P, Albesher N, Xiong L. 2017. A nucleus- localized long non-coding RNA enhances drought and salt stress tolerance. Plant Physiology, 175, 1321–1336.
Quan M, Chen J, Zhang D. 2015. Exploring the secrets of long noncoding RNAs. International Journal of Molecular Sciences, 16, 5467–5496.
Ren Z, He S, Zhou Y, Zhao N, Jiang T, Zhai H, Liu Q. 2020. A sucrose non-fermenting-1-related protein kinase-1 gene, IbSnRK1, confers salt, drought and cold tolerance in sweet potato. The Crop Journal, 8, 905–917.
Rogers S O, Bendich A J. 1985. Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Molecular Biology, 5, 69–76.
Sun H, Hu M, Li J, Chen L, Li M, Zhang S, Zhang X, Yang X. 2018. Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton. BMC Plant Biology, 18, 150.
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou K P, Kuhn M, Bork P, Jensen L J, von Mering C. 2015. STRING v10: Protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Research, 43, D447–D452.
Tang Y, Bao X, Zhi Y, Wu Q, Guo Y, Yin X, Zeng L, Li J, Zhang J, He W, Liu W, Wang Q, Jia C, Li Z , Liu K. 2019.
Overexpression of a MYB family gene, OsMYB6, increases drought and salinity stress tolerance in transgenic rice. Frontiers in Plant Science, 10, 168.
Tian T, Liu Y, Yan H, You Q, Yi X, Du Z, Xu W, Su Z. 2017. agriGO v2.0: A GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Research, 45, W122–W129.
Wang A, Hu J, Gao C, Chen G, Wang B, Lin C, Song L, Ding Y, Zhou G. 2019. Genome-wide analysis of long non-coding RNAs unveils the regulatory roles in the heat tolerance of Chinese cabbage (Brassica rapa ssp. chinensis). Scientific Reports, 9, 5002.
Wang B, Guo X, Zhao P, Ruan M, Yu X, Zou L, Yang Y, Li X, Deng D, Xiao J, Xiao Y, Hu C, Wang X, Wang X, Wang W, Peng M. 2017. Molecular diversity analysis, drought related marker-traits association mapping and discovery of excellent alleles for 100-day old plants by EST-SSRs in cassava germplasms (Manihot esculenta Cranz). PLoS ONE, 12, e0177456.
Wang F, Chen H W, Li Q T, Wei W, Li W, Zhang W K, Ma B, Bi Y D, Lai Y C, Liu X L, Man W Q, Zhang J S, Chen S Y. 2015. GmWRKY27 interacts with GmMYB174 to reduce expression of GmNAC29 for stress tolerance in soybean plants. Plant Journal, 83, 224–236.
Wang F, Tong W, Zhu H, Kong W, Peng R, Liu Q, Yao Q. 2016. A novel Cys2/His2 zinc finger protein gene from sweetpotato, IbZFP1, is involved in salt and drought tolerance in transgenic Arabidopsis. Planta, 243, 783–797.
Wang H, Niu Q W, Wu H W, Liu J, Ye J, Yu N, Chua N H. 2015. Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits. Plant Journal, 84, 404–416.
Wang Y, Luo X, Sun F, Hu J, Zha X, Su W, Yang J. 2018. Overexpressing lncRNA LAIR increases grain yield and regulates neighbouring gene cluster expression in rice. Nature Communication, 9, 3516.
Wei Y, Liu W, Hu W, Yan Y, Shi H. 2020. The chaperone MeHSP90 recruits MeWRKY20 and MeCatalase1 to regulate drought stress resistance in cassava. New Phytologist, 226, 476–491.
Wu J, Chen J, Wang L, Wang S. 2017. Genome-wide
investigation of WRKY transcription factors involved in terminal drought stress response in common bean. Frontiers in Plant Science, 8, 380.
Xiao J J, Zhang R X, Khan A, Ul Haq S, Gai W X, Gong Z H. 2021. CaFtsH06, a novel filamentous thermosensitive protease gene, is involved in heat, salt, and drought stress tolerance of pepper (Capsicum annuum L.). International Journal of Molecular Sciences, 22, 6953.
Yu T F, Xu Z S, Guo J K, Wang Y X, Abernathy B, Fu J D, Chen X, Zhou Y B, Chen M, Ye X G, Ma Y Z. 2017. Improved drought tolerance in wheat plants overexpressing a synthetic bacterial cold shock protein gene SeCspA. Scientific Reports, 7, 44050.
Zhang B, Chang L, Sun W, Ullah A, Yang X. 2021. Over- expression of an expansin-like gene, GhEXLB2 enhanced drought tolerance in cotton. Plant Physiology and Biochemistry, 162, 468–475.
Zhang P, Potrykus I, Puonti-Kaerlas J. 2000. Efficient production of transgenic cassava using negative and positive selection. Transgenic Research, 9, 405–415.
Zhu M, Meng X, Cai J, Li G, Dong T, Li Z. 2018. Basic leucine
zipper transcription factor SlbZIP1 mediates salt and drought stress tolerance in tomato. BMC Plant Biology, 18, 83.
Zou J J, Wei F J, Wang C, Wu J J, Ratnasekera D, Liu W X, Wu W H. 2010. Arabidopsis calcium-dependent protein kinase CPK10 functions in abscisic acid- and Ca2+-mediated stomatal regulation in response to drought stress. Plant Physiology, 154, 1232–1243.
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