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Divergence in the ABA gene regulatory network underlies differential growth control

Nature Plants volume 8, pages 549–560 (2022)Cite this article

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Abstract

The phytohormone abscisic acid (ABA) is a central regulator of acclimation to environmental stress; however, its contribution to differences in stress tolerance between species is unclear. To establish a comparative framework for understanding how stress hormone signalling pathways diverge across species, we studied the growth response of four Brassicaceae species to ABA treatment and generated transcriptomic and DNA affinity purification and sequencing datasets to construct a cross-species gene regulatory network (GRN) for ABA. Comparison of genes bound directly by ABA-responsive element binding factors suggests that cis-factors are most important for determining the target loci represented in the ABA GRN of a particular species. Using this GRN, we reveal how rewiring of growth hormone subnetworks contributes to stark differences in the response to ABA in the extremophyte Schrenkiella parvula. Our study provides a model for understanding how divergence in gene regulation can lead to species-specific physiological outcomes in response to hormonal cues.

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Fig. 1: Comparative analysis of stress response in the Brassicaceae family.
Fig. 2: RNA-Seq identifies conserved and species-specific ABA-responsive pathways.
Fig. 3: Global AREB/ABF binding landscape demonstrates dependency between promoter sequence and TF interaction.
Fig. 4: A high-confidence AREB/ABF regulatory network in Brassicaceae.
Fig. 5: Rewiring of the AREB/ABF–auxin network is associated with altered growth response to ABA in S. parvula.

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Data availability

All data are available in the manuscript, in the Supplementary material or in the following databases: high-throughput sequencing data sets are available through the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) under BioProject ID PRJNA682697. The Sisymbrium irio gene models are deposited in the CoGe database (https://genomevolution.org/) with the Genome ID 57216. Supplementary data are available on FigShare (https://doi.org/10.6084/m9.figshare.14033822). Genome browser view of data can be found on Jbrowse: http://jbrowsedap.s3-website-us-west-1.amazonaws.com

Code availability

The custom scripts developed in this study are publicly available in the GitHub repository at https://github.com/dinnenylab/BrassicaceaeGRN.

References

  1. Kazachkova, Y. et al. Halophytism: what have we learnt from Arabidopsis thaliana relative model systems? Plant Physiol. 178, 972–988 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Zhu, J.-K. The next top models. Cell 163, 18–20 (2015).

    Article  CAS  Google Scholar 

  3. Oh, D.-H., Dassanayake, M., Bohnert, H. J. & Cheeseman, J. M. Life at the extreme: lessons from the genome. Genome Biol. 13, 241 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  4. Wu, H.-J. et al. Insights into salt tolerance from the genome of Thellungiella salsuginea. Proc. Natl Acad. Sci. USA 109, 12219–12224 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Dassanayake, M. et al. The genome of the extremophile crucifer Thellungiella parvula. Nat. Genet. 43, 913–918 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Yang, R. et al. The reference genome of the halophytic plant Eutrema salsugineum. Front. Plant Sci. 4, 46 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Wang, X.-J. et al. Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum. Mol. Ecol. 27, 2943–2955 (2018).

    Article  PubMed  Google Scholar 

  8. Inan, G. et al. Salt cress. A halophyte and cryophyte Arabidopsis relative model system and its applicability to molecular genetic analyses of growth and development of extremophiles. Plant Physiol. 135, 1718–1737 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Marín-de la Rosa, N. et al. Drought resistance is mediated by divergent strategies in closely related Brassicaceae. New Phytol. 223, 783–797 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  10. Gong, Q., Li, P., Ma, S., Indu Rupassara, S. & Bohnert, H. J. Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana. Plant J. 44, 826–839 (2005).

    Article  CAS  PubMed  Google Scholar 

  11. Oh, D.-H. et al. Loss of halophytism by interference with SOS1 expression. Plant Physiol. 151, 210–222 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Oh, D.-H. et al. Genome structures and transcriptomes signify niche adaptation for the multiple-ion-tolerant extremophyte Schrenkiella parvula. Plant Physiol. 164, 2123–2138 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Wang, G. et al. Cross species multi-omics reveals cell wall sequestration and elevated global transcript abundance as mechanisms of boron tolerance in plants. New Phytol. 230, 1985–2000 (2021).

    Article  CAS  PubMed  Google Scholar 

  14. Cutler, S. R., Rodriguez, P. L., Finkelstein, R. R. & Abrams, S. R. Abscisic acid: emergence of a core signaling network. Annu. Rev. Plant Biol. 61, 651–679 (2010).

    Article  CAS  PubMed  Google Scholar 

  15. Hauser, F., Waadt, R. & Schroeder, J. I. Evolution of abscisic acid synthesis and signaling mechanisms. Curr. Biol. 21, R346–R355 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Li, X., Chen, L., Forde, B. G. & Davies, W. J. The biphasic root growth response to abscisic acid in Arabidopsis involves interaction with ethylene and auxin signalling pathways. Front. Plant Sci. 8, 1493 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Miao, R. et al. Low ABA concentration promotes root growth and hydrotropism through relief of ABA INSENSITIVE 1-mediated inhibition of plasma membrane H+-ATPase 2. Sci. Adv. 7, eabd4113 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Geng, Y. et al. A spatio-temporal understanding of growth regulation during the salt stress response in Arabidopsis. Plant Cell 25, 2132–2154 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Duan, L. et al. Endodermal ABA signaling promotes lateral root quiescence during salt stress in Arabidopsis seedlings. Plant Cell 25, 324–341 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Yoshida, T. et al. Four Arabidopsis AREB/ABF transcription factors function predominantly in gene expression downstream of SnRK2 kinases in abscisic acid signalling in response to osmotic stress. Plant Cell Environ. 38, 35–49 (2015).

    Article  CAS  PubMed  Google Scholar 

  21. Yamaguchi-Shinozaki, K. & Shinozaki, K. A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6, 251–264 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Marcotte, W. R. Jr, Russell, S. H. & Quatrano, R. S. Abscisic acid-responsive sequences from the Em gene of wheat. Plant Cell 1, 969–976 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Haudry, A. et al. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat. Genet. 45, 891–898 (2013).

    Article  CAS  PubMed  Google Scholar 

  24. Oh, D.-H. & Dassanayake, M. Landscape of gene transposition-duplication within the Brassicaceae family. DNA Res. 26, 21–36 (2019).

    Article  CAS  PubMed  Google Scholar 

  25. Tran, K.-N. et al. Multiple paths lead to salt tolerance – pre-adaptation vs dynamic responses from two closely related extremophytes. Preprint at bioRxiv https://doi.org/10.1101/2021.10.23.465591 (2021).

  26. Li, C., Qi, Y., Zhao, C., Wang, X. & Zhang, Q. Transcriptome profiling of the salt stress response in the leaves and roots of halophytic Eutrema salsugineum. Front. Genet. 12, 770742 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Deprost, D. et al. The Arabidopsis TOR kinase links plant growth, yield, stress resistance and mRNA translation. EMBO Rep. 8, 864–870 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. McLeay, R. C. & Bailey, T. L. Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. BMC Bioinformatics 11, 165 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Yoshida, T. et al. AREB1, AREB2, and ABF3 are master transcription factors that cooperatively regulate ABRE-dependent ABA signaling involved in drought stress tolerance and require ABA for full activation. Plant J. 61, 672–685 (2010).

    Article  CAS  PubMed  Google Scholar 

  30. O’Malley, R. C. et al. Cistrome and epicistrome features shape the regulatory DNA landscape. Cell 165, 1280–1292 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  31. Bartlett, A. et al. Mapping genome-wide transcription-factor binding sites using DAP-seq. Nat. Protoc. 12, 1659–1672 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Maizel, A. et al. The floral regulator LEAFY evolves by substitutions in the DNA binding domain. Science 308, 260–263 (2005).

    Article  CAS  PubMed  Google Scholar 

  33. Guo, Y., Mahony, S. & Gifford, D. K. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Comput. Biol. 8, e1002638 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Sun, Y. & Dinneny, J. R. Q&A: How do gene regulatory networks control environmental responses in plants? BMC Biol. 16, 38 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  35. Dinneny, J. R. et al. Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science 320, 942–945 (2008).

    Article  CAS  PubMed  Google Scholar 

  36. Thole, J. M., Beisner, E. R., Liu, J., Venkova, S. V. & Strader, L. C. Abscisic acid regulates root elongation through the activities of auxin and ethylene in Arabidopsis thaliana. G3 (Bethesda) 4, 1259–1274 (2014).

    Article  CAS  Google Scholar 

  37. Spollen, W. G., LeNoble, M. E., Samuels, T. D., Bernstein, N. & Sharp, R. E. Abscisic acid accumulation maintains maize primary root elongation at low water potentials by restricting ethylene production. Plant Physiol. 122, 967–976 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Qin, H., He, L. & Huang, R. The coordination of ethylene and other hormones in primary root development. Front. Plant Sci. 10, 874 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  39. Song, L. et al. A transcription factor hierarchy defines an environmental stress response network. Science 354, aag1550 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  40. Majda, M. & Robert, S. The role of auxin in cell wall expansion. Int. J. Mol. Sci. 19, 951 (2018).

    Article  PubMed Central  CAS  Google Scholar 

  41. Miao, Z.-Q. et al. HOMEOBOX PROTEIN 52 mediates the crosstalk between ethylene and auxin signaling during primary root elongation by modulating auxin transport-related gene expression. Plant Cell 30, 2761–2778 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Velasquez, S. M., Barbez, E., Kleine-Vehn, J. & Estevez, J. M. Auxin and cellular elongation. Plant Physiol. 170, 1206–1215 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Liu, G. et al. Local transcriptional control of YUCCA regulates auxin promoted root-growth inhibition in response to aluminium stress in Arabidopsis. PLoS Genet. 12, e1006360 (2016).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  44. Wang, Q. et al. A phosphorylation-based switch controls TAA1-mediated auxin biosynthesis in plants. Nat. Commun. 11, 679 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. He, W. et al. A small-molecule screen identifies l-kynurenine as a competitive inhibitor of TAA1/TAR activity in ethylene-directed auxin biosynthesis and root growth in Arabidopsis. Plant Cell 23, 3944–3960 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Stepanova, A. N. et al. TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development. Cell 133, 177–191 (2008).

    Article  CAS  PubMed  Google Scholar 

  47. Jarvis, D. E., Ryu, C.-H., Beilstein, M. A. & Schumaker, K. S. Distinct roles for SOS1 in the convergent evolution of salt tolerance in Eutrema salsugineum and Schrenkiella parvula. Mol. Biol. Evol. 31, 2094–2107 (2014).

    Article  CAS  PubMed  Google Scholar 

  48. Ali, Z. et al. TsHKT1;2, a HKT1 homolog from the extremophile Arabidopsis relative Thellungiella salsuginea, shows K(+) specificity in the presence of NaCl. Plant Physiol. 158, 1463–1474 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Ali, A. et al. A single amino-acid substitution in the sodium transporter HKT1 associated with plant salt tolerance. Plant Physiol. 171, 2112–2126 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  50. Rodríguez-Leal, D., Lemmon, Z. H., Man, J., Bartlett, M. E. & Lippman, Z. B. Engineering quantitative trait variation for crop improvement by genome editing. Cell 171, 470–480.e8 (2017).

    Article  PubMed  CAS  Google Scholar 

  51. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    Article  CAS  PubMed  Google Scholar 

  52. Waterhouse, R. M. et al. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol. Biol. Evol. 35, 543–548 (2018).

    Article  CAS  PubMed  Google Scholar 

  53. Pertea, M., Kim, D., Pertea, G. M., Leek, J. T. & Salzberg, S. L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat. Protoc. 11, 1650–1667 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  55. Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).

    Article  CAS  PubMed  Google Scholar 

  56. Maere, S., Heymans, K. & Kuiper, M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21, 3448–3449 (2005).

    Article  CAS  PubMed  Google Scholar 

  57. Wang, G., Oh, D.-H. & Dassanayake, M. GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. BMC Bioinformatics 21, 139 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  58. Fornes, O. et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 48, D87–D92 (2019).

    PubMed Central  Google Scholar 

  59. Virtanen, P. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261–272 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Emms, D. M. & Kelly, S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16, 157 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  61. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Wu, R. et al. The 6xABRE synthetic promoter enables the spatiotemporal analysis of ABA-mediated transcriptional regulation. Plant Physiol. 177, 1650–1665 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Longabaugh, W. J. R. BioTapestry: a tool to visualize the dynamic properties of gene regulatory networks. Methods Mol. Biol. 786, 359–394 (2012).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We acknowledge M. Galli and M.C. Yee for advice on experimental design; Carnegie Institution for Science, Department of Plant Biology and G. Huntress for providing access to computing resources and data management; undergraduates R. Gates and J. Pulido for their summer engagements with this study; and C. Pires for Sisymbrium irio seeds. D.-H.O. and M.D. also acknowledge the Louisiana State University High Performance Computing services (HPC@LSU) for providing computational resources needed for data analyses. US Department of Energy’s Biological and Environmental Research program (Grant DE-SC0020358, to J.R.D., D.-H.O and M.D.), Carnegie Institution for Science endowment (to J.R.D.), National Science Foundation (MCB-1616827 and NSF-IOS-EDGE-1923589, to D.-H.O. and M.D.) Rural Development Administration (RDA), South Korea (Next-Generation BioGreen21 program PJ01317301 to D.-H.O. and M.D.), National Science Foundation Graduate Research Fellowship (to Y.S.), and HHMI-Simons Faculty Scholar (to J.R.D.).

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Author notes

  1. These authors contributed equally: Ying Sun, Dong-Ha Oh.

Authors and Affiliations

  1. Department of Biology, Stanford University, Stanford, CA, USA

    Ying Sun, Lina Duan, Prashanth Ramachandran, Andrea Ramirez & José R. Dinneny

  2. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA

    Dong-Ha Oh, Kieu-Nga Tran, Guannan Wang & Maheshi Dassanayake

  3. Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA

    Anna Bartlett

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Contributions

Y.S., L.D. and P.R. performed the experiments. Y.S., D.-H.O., P.R., A.R., A.B., K.-N.T., G.W. and J.R.D. analysed the data. Y.S., D.-H.O. and J.R.D. wrote the manuscript. L.D., P.R. and M.D. contributed to the manuscript preparation.

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Correspondence to José R. Dinneny.

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Supplementary information

Supplementary Information

Supplementary Text 1 and 2, Figs. 1–10 and Tables 1–4.

Reporting Summary

Supplementary Data 1

RNA- and DAP-Seq results for all 1-to-1 orthologous groups (OGs).

Supplementary Data 2

RNA- and DAP-Seq results for all genes organized as OrthNets.

Supplementary Data 3

GO enrichment among ABA-responsive DEGs and overlaps between salt and ABA responses.

Supplementary Data 4

Results of PiP analyses.

Supplementary Data 5

JASPAR motifs enriched among promoters of ABA-induced and repressed DEGs.

Supplementary Data 6

All DAP-Seq peak coordinates with annotations.

Supplementary Data 7

Conserved GRN.

Supplementary Data 8

ABA, auxin, and ethylene GRNs.

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Sun, Y., Oh, DH., Duan, L. et al. Divergence in the ABA gene regulatory network underlies differential growth control. Nat. Plants 8, 549–560 (2022). https://doi.org/10.1038/s41477-022-01139-5

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