Transcriptomic dynamics of ABA response in Brassica napus guard cells

Abstract

Drought has a significant, negative impact on crop production; and these effects are poised to increase with climate change. Plants acclimate to drought and water stress through diverse physiological responses, primarily mediated by the hormone abscisic acid (ABA). Because plants lose the majority of their water through stomatal pores on aerial surfaces of plants, stomatal closure is one of the rapid responses mediated by ABA to reduce transpirational water loss. The dynamic changes in the transcriptome of stomatal guard cells in response to ABA have been investigated in the model plant Arabidopsis thaliana. However, guard cell transcriptomes have not been analyzed in agronomically valuable crops such as a major oilseed crop, rapeseed. In this study, we investigated the dynamics of ABA-regulated transcriptomes in stomatal guard cells of Brassica napus and conducted comparison analysis with the transcriptomes of A. thaliana. We discovered changes in gene expression indicating alterations in a host of physiological processes, including stomatal movement, metabolic reprogramming, and light responses. Our results suggest the existence of both immediate and delayed responses to ABA in Brassica guard cells. Furthermore, the transcription factors and regulatory networks mediating these responses are compared to those identified in Arabidopsis. Our results imply the continuing evolution of ABA responses in Brassica since its divergence from a common ancestor, involving both protein-coding and non-coding nucleotide sequences. Together, our results will provide a basis for developing strategies for molecular manipulation of drought tolerance in crop plants.

References

[1] AgarwalPK, JhaB. Transcription factors in plants and ABA dependent and independent abiotic stress signalling. Biol Plant, 2010, 54: 201-212

[2] Allender CJ, King GJ (2010) Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers. BMC Plant Biol 10:54. https://doi.org/10.1186/1471-2229-10-54

[3] Altman D, Bland J (1983) Measurement in medicine: the analysis of method comparison studies. J R Stat Soc Ser D-Stat 2:307–317. https://doi.org/10.2307/2987937

[4] AndersS, PylPT, HuberW. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics, 2015, 31(2): 166-169

[5] BaderJS, ChaudhuriA, RothbergJM, ChantJ. Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol, 2004, 22: 78-85

[6] Bak G, Lee EJ, Lee Y et al (2013) Rapid structural changes and acidification of guard cell vacuoles during stomatal closure require phosphatidylinositol 3,5-bisphosphate. Plant Cell 25:2202–2216. https://doi.org/10.1105/tpc.113.110411

[7] Benjamini Y, Hochberg Y (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J R Stat Soc Ser B-Stat Methodol 57(1):289–300. https://doi.org/10.2307/2346101

[8] Bininda-EmondsOR. transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. BMC Bioinformatics, 2005, 6: 156

[9] BlancG, HokampK, WolfeKH. A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome. Genome Res, 2003, 13: 137-144

[10] Bland J, Altman D (1999) Measuring agreement in method comparison studies. Stat Methods Med Res 8(2):135–160. https://doi.org/10.1177/096228029900800204

[11] BoyerJS. Plant productivity and environment. Science, 1982, 218(4571): 443-448

[12] Caspi R, Billington R, Ferrer L et al (2016) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 44:D471–480. https://doi.org/10.1093/nar/gkv1164

[13] Celli F, Malapela T, Wegner K et al (2015) AGRIS: providing access to agricultural research data exploiting open data on the web. F1000Res 4:110. https://doi.org/10.12688/f1000research.6354.1

[14] ChalhoubB, DenoeudF, LiuS, ParkinI, a. P., Tang, H., Wang, X., … Wincker, P.. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014, 345: 950-953

[15] Charif D, Lobry JR (2007) SeqinR 1.0–2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis. In: Bastolla U, Porto M, Roman HE (eds) Structural Approaches to Sequence Evolution. Biological and Medical Physics, Biomedical Engineering. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-35306-5_10

[16] ChenK, LiGJ, BressanRA, SongCP, ZhuJK, ZhaoY. Abscisic acid dynamics, signaling, and functions in plants. J Integr Plant Biol, 2020, 62(1): 25-54

[17] DaiA. Increasing drought under global warming in observations and models. Nat Clim Chang, 2012, 3: 52-58

[18] Davuluri R, Sun H, Palaniswamy S (2003) AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics 4:25. https://doi.org/10.1186/1471-2105-4-25

[19] Ermolaeva M, Wu M, Eisen J et al (2003) The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol 51(6):859–866. https://doi.org/10.1023/a:1023001130337

[20] FabregasN, YoshidaT, FernieAR. Role of Raf-like kinases in SnRK2 activation and osmotic stress response in plants. Nat Commun, 2020, 11(1): 6184

[21] Federal Emergency Management Agency (1995) National Mitigation Strategy: Partnerships for Building Safer Communities. FEMA, Washington, DC, USA

[22] Franco-ZorrillaJM, Lopez-VidrieroI, CarrascoJL, GodoyM, VeraP, SolanoR. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A, 2014, 111(6): 2367-2372

[23] Fujita M, Fujita Y, Maruyama K et al (2004) A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stress-signaling pathway. Plant J 39(6):863–876. https://doi.org/10.1111/j.1365-313x.2004.02171.x

[24] García-LeónD, StandardiG, StaccioneA. An integrated approach for the estimation of agricultural drought costs. Land Use Pol, 2021, 100

[25] GaureS. OLS with multiple high dimensional category variables. Comput Stat Data Anal, 2013, 66: 8-18

[26] GhoshUK, IslamMN, SiddiquiMN, CaoX, KhanMAR. Proline, a multifaceted signalling molecule in plant responses to abiotic stress: understanding the physiological mechanisms. Plant Biol (stuttg), 2022, 24(2): 227-239

[27] GodaH, SasakiE, AkiyamaK, Mauyama-NakashitaA, NakabayashiK, LiW, OgawaM, YamauchY, PrestonJ, AokiK, KibaT, TakatsutoS, FujiokaS, AsamiT, NakanoT, KatoH, MizunoT, SakakibaraH, YamaguchiS, NambaraE, KamiyY, TakahashiH, HiraiMY, SakuraiT, ShinozakiK, SaitoK, YoshidaS, ShimadaY. The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. Plant J, 2008, 55(3): 526-542

[28] GuptaA, Rico-MedinaA, Cano-DelgadoAI. The physiology of plant responses to drought. Science, 2020, 368(6488): 266-269

[29] HauserF, WaadtR, SchroederJI. (2011) Evolution of abscisic acid synthesis and signaling mechanisms. Curr Biol, 2011, 21(9): R346-355

[30] Hmida-SayariA, Gargouri-BouzidR, BidaniA, JaouaL, SavouréA, JaouaS. Overexpression of Δ1-pyrroline-5-carboxylate synthetase increases proline production and confers salt tolerance in transgenic potato plants. Plant Sci, 2005, 169(4): 746-752

[31] HsuPK, DubeauxG, TakahashiY, SchroederJI. Signaling mechanisms in abscisic acid-mediated stomatal closure. Plant J, 2021, 105(2): 307-321

[32] JonnsonR. Breeding for improved oil and meal quality in rape (Brassica napus L.) and turnip rape (Brassica campestris L.). Hereditas, 2009, 87: 205-218

[33] Kesari R, Lasky JR, Villamor JG et al (2012) Intron-mediated alternative splicing of Arabidopsis P5CS1 and its association with natural variation in proline and climate adaptation. Proc Natl Acad Sci U S A 109(23):9197–9202. https://doi.org/10.1073/pnas.1203433109

[34] Kilian J, Whitehead D, Horak J et al (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J 50(2):347–363. https://doi.org/10.1111/j.1365-313X.2007.03052.x

[35] KimD, PerteaG, TrapnellC, PimentelH, KelleyR, SalzbergSL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol, 2013, 14(4): R36

[36] Kishor P, Hong Z, Miao G et al (1995) Overexpression of delta-1-pyrroline-5-carboxylate synthetase increases proline production and confers osmotolerance in transgenic plants. Plant Physiol 108(4):1387–1394. https://doi.org/10.1104/pp.108.4.1387

[37] Kiyosue T, Yamaguchi-Shinozaki K, Shinozaki K (1994) Cloning of cDNAs for genes that are early-responsive to dehydration stress (ERDs) in Arabidopsis thaliana L.: identification of three ERDs as HSP cognate genes. Plant Mol Biol 25(5):791–798. https://doi.org/10.1007/bf00028874

[38] KomatsuK, TakezawaD, SakataY. Decoding ABA and osmostress signalling in plants from an evolutionary point of view. Plant Cell Environ, 2020, 43(12): 2894-2911

[39] KondraZP, StefanssonBR. Inheritance of erucic and eicosenic acid content of rapeseed oil (Brassica napus). Can J Genet Cytol, 1965, 7: 505-510

[40] KuromoriT, FujitaM, TakahashiF, Yamaguchi-ShinozakiK, ShinozakiK. Inter-tissue and inter-organ signaling in drought stress response and phenotyping of drought tolerance. Plant J, 2022, 109(2): 342-358

[41] Kushiro T, Okamoto M, Nakabayashi K et al (2004) The Arabidopsis cytochrome P450 CYP707A encodes ABA 8'-hydroxylases: key enzymes in ABA catabolism. EMBO J 23(7):1647–1656. https://doi.org/10.1038/sj.emboj.7600121

[42] Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948. https://doi.org/10.1093/bioinformatics/btm404

[43] LiW-H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol, 1993, 36(1): 96-99

[44] LiangX, ZhangL, NatarajanSK, BeckerDF. Proline mechanisms of stress survival. Antioxid Redox Signal, 2013, 19(9): 998-1011

[45] Lopez-AnidoCB, VaténA, SmootNK, SharmaN, GuoV, GongY, GilMXA, WeimerAK, BergmannDC. Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf. Dev Cell, 2021, 56(7): 1043-1055

[46] LoveMI, HuberW, AndersS. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 2014, 15(12): 550

[47] Lozano-JusteJ, AlrefaeiAF, RodriguezPL. Plant Osmotic Stress Signaling: MAPKKKs Meet SnRK2s. Trends Plant Sci, 2020, 25(12): 1179-1182

[48] MekonnenMM, HoekstraAY. Water footprint benchmarks for crop production: A first global assessment. Ecol Ind, 2014, 46: 214-223

[49] MrowkaR, PatzakA, HerzelH. Is There a Bias in Proteome Research?. Genome Res, 2001, 11: 1971-1973

[50] NakashimaK, Yamaguchi-ShinozakiK, ShinozakiK. The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat. Front Plant Sci, 2014, 5: 170

[51] Narusaka Y, Nakashima K, Shinwari ZK et al (2003). Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J 34:137–148. https://doi.org/10.1046/j.1365-313X.2003.01708.x

[52] Okamoto M, Kuwahara A, Seo M, Kushiro T et al (2006) CYP707A1 and CYP707A2, which encode abscisic acid 8'-hydroxylases, are indispensable for proper control of seed dormancy and germination in Arabidopsis. Plant Physiol 141:97–107. https://doi.org/10.1104/pp.106.079475

[53] ParkinIAP, SharpeAG, KeithDJ, LydiateDJ. Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape). Genome, 1995, 38: 1122-1131

[54] Qiu D, Morgan C, Shi J et al (2006) A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content. Theor Appl Genet 114:67–80. https://doi.org/10.1007/s00122-006-0411-2

[55] RodriguesJ, InzeD, NelissenH, SaiboNJM. Source-Sink Regulation in Crops under Water Deficit. Trends Plant Sci, 2019, 24(7): 652-663

[56] SamarasY, BressanRA, CsonkaLN, Garcia-RiosMG, PainoD, RhodesD. Proline accumulation during drought and salinity, 1995Oxford, UKBios Scientific Publishers, Oxford161-187

[57] SeoM, KoshibaT. Complex regulation of ABA biosynthesis in plants. Trends Plant Sci, 2002, 7(1): 41-48

[58] SharmaS, VersluesPE. Mechanisms independent of abscisic acid (ABA) or proline feedback have a predominant role in transcriptional regulation of proline metabolism during low water potential and stress recovery. Plant Cell Environ, 2010, 33(11): 1838-1851

[59] ShinozakiK, Yamaguchi-ShinozakiK. Molecular responses to drought and cold stress. Curr Opin Biotechnol, 1996, 7: 161-167

[60] SofoA, DichioB, XiloyannisC, MasiaA. Lipoxygenase activity and proline accumulation in leaves and roots of olive trees in response to drought stress. Physiol Plant, 2004, 121: 58-65

[61] SongK, OsbornTC. Polyphyletic origins of Brassica napus : new evidence based on organelle and nuclear RFLP analyses. Genome, 1992, 35: 992-1001

[62] TrenberthKE, DaiA, van der SchrierG, JonesPD, BarichivichJ, BriffaKR, SheffieldJ. Global warming and changes in drought. Nat Clim Chang, 2013, 4: 17-22

[63] VersluesPE, BrayEA. Role of abscisic acid (ABA) and Arabidopsis thaliana ABA-insensitive loci in low water potential-induced ABA and proline accumulation. J Exp Bot, 2006, 57(1): 201-212

[64] WaldA. Tests of Statistical Hypotheses Concerning Several Parameters When the Number of Observations is Large. Trans Am Math Soc, 1943, 54(3): 426-482

[65] WangR-S, PandeyS, LiS, GookinTE, ZhaoZ, AlbertR, AssmannSM. Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells. BMC Genomics, 2011, 12: 216

[66] WaniAS, AhmadA, HayatS, TahirI. Is foliar spray of proline sufficient for mitigation of salt stress in Brassica juncea cultivars?. Environ Sci Pollut Res Int, 2016, 23: 13413-13423

[67] YamadaM, MorishitaH, UranoK, ShiozakiN, Yamaguchi-ShinozakiK, ShinozakiK, YoshibaY. Effects of free proline accumulation in petunias under drought stress. J Exp Bot, 2005, 56(417): 1975-1981

[68] Yang Y, Lai K, Tai P et al (1999) Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J Mol Evol 48(5):597–604. https://doi.org/10.1007/pl00006502

[69] YoshidaT, MogamiJ, Yamaguchi-ShinozakiK. ABA-dependent and ABA-independent signaling in response to osmotic stress in plants. Curr Opin Plant Biol, 2014, 21: 133-139

[70] ZhuJK. Salt and drought stress signal transduction in plants. Annu Rev Plant Biol, 2002, 53: 247-273

Funding

National Science Foundation(IOS-1025837)

National Institute of Health (US)(GM060396)

National Research Foundation of Korea(2020R1A4A1019408)