Skip to main content

miRNAs control HAM1 functions at the single-cell-layer level and are essential for normal embryogenesis in Arabidopsis

Abstract

Key message

miR171a controls HAM1 functions within the protodermal cells of the embryo, and these controls are essential for normal embryogenesis in Arabidopsis.

Abstract

Arabidopsis thaliana miR171a is known to bind to and cleave mRNAs of three HAIRY MERISTEM (HAM) genes that encode members of the GRAS family transcriptional regulators. The molecular functions of the HAM genes are still being elucidated in Arabidopsis. However, detailed expression patterns of miR171a and the effects of the failure of miR171a to suppress HAM genes were unknown till now. Here, we show the detailed expression patterns of miR171a and HAM1 using green fluorescent protein and confocal scanning microscopy. Our observations revealed that miR171a was expressed in the surface cell layer of the embryo and shoot apical meristem, and it controlled HAM1 functions. To determine the impact of the failure of miR171a to suppress of HAM1, we introduced seven synonymous mutations into the miR171a target site of the HAM1 gene (modified HAM1, mHAM1) and generated transgenic plants that had mHAM1 driven by HAM1 native promoter. The mHAM1 transgenic plants showed organogenic defects. These results indicate that the control of HAM1 functions at the single-cell-layer level by miR171a is essential for proper organ formation in Arabidopsis.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

References

  1. Achkar NP, Cambiagno DA, Manavella PA (2016) miRNA biogenesis: a dynamic pathway. Trends Plant Sci 21:1034–1044. https://doi.org/10.1016/j.tplants.2016.09.003

    CAS  Article  PubMed  Google Scholar 

  2. Aida M, Ishida T, Tasaka M (1999) Shoot apical meristem and cotyledon formation during Arabidopsis embryogenesis: interaction among the CUP-SHAPED COTYLEDON and SHOOT MERISTEMLESS genes. Development 126:1563–1570

    CAS  PubMed  Google Scholar 

  3. 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 15:303–315. https://doi.org/10.1016/j.cub.2005.02.017

    CAS  Article  PubMed  Google Scholar 

  4. Bologna NG, Voinnet O (2014) The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Annu Rev Plant Biol 65:473–503. https://doi.org/10.1146/annurev-arplant-050213-035728

    CAS  Article  PubMed  Google Scholar 

  5. Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16:735–743. https://doi.org/10.1046/j.1365-313x.1998.00343.x

    CAS  Article  PubMed  Google Scholar 

  6. Emery JF, Floyd SK, Alvarez J, Eshed Y, Hawker NP, Izhaki A, Baum SF, Bowman JL (2003) Radial patterning of Arabidopsis shoots by class IIIHD-ZIP and KANADI genes. Curr Biol 13:1768–1774. https://doi.org/10.1016/j.cub.2003.09.035

    CAS  Article  PubMed  Google Scholar 

  7. Engstrom EM, Andersen CM, Gumulak-Smith J, Hu J, Orlova E, Sozzani R, Bowman JL (2011) Arabidopsis homologs of the petunia hairy meristem gene are required for maintenance of shoot and root indeterminacy. Plant Physiol 155:735–750. https://doi.org/10.1104/pp.110.168757

    CAS  Article  PubMed  Google Scholar 

  8. Hardtke CS, Berleth T (1998) The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development. EMBO J 17:1405–1411. https://doi.org/10.1093/emboj/17.5.1405

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  9. Hibara K, Karim MR, Takada S, Taoka KI, Furutani M, Aida M, Tasaka M (2006) Arabidopsis CUP-SHAPED COTYLEDON3 regulates postembryonic shoot meristem and organ boundary formation. Plant Cell 18:2946–2957. https://doi.org/10.1105/tpc.106.045716

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. Huang J, Fujimoto M, Fujiwara M, Fukao Y, Arimura S, Tsutsumi N (2015) Arabidopsis dynamin-related proteins, DRP2A and DRP2B, function coordinately in post-Golgi trafficking. Biochem Biophys Res Commun 456:238–244. https://doi.org/10.1016/j.bbrc.2014.11.065

    CAS  Article  PubMed  Google Scholar 

  11. Karimi M, Inze D, Depicker A (2002) GATEWAY((TM)) vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci 7:193–195. https://doi.org/10.1016/s1360-1385(02)02251-3

    CAS  Article  PubMed  Google Scholar 

  12. Klepikova AV, Kasianov AS, Gerasimov ES, Logacheva MD, Penin AA (2016) A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling. Plant J 88:1058–1070. https://doi.org/10.1111/tpj.13312

    CAS  Article  PubMed  Google Scholar 

  13. Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42:D68–D73. https://doi.org/10.1093/nar/gkt1181

    Article  Google Scholar 

  14. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small rnas with antisense complementarity to lin-14. Cell 75:843–854. https://doi.org/10.1016/0092-8674(93)90529-y

    CAS  Article  PubMed  Google Scholar 

  15. Li C, Zhang BH (2016) MicroRNAs in control of plant development. J Cell Physiol 231:303–313. https://doi.org/10.1002/jcp.25125

    CAS  Article  PubMed  Google Scholar 

  16. Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297:2053–2056. https://doi.org/10.1126/science.1076311

    CAS  Article  PubMed  Google Scholar 

  17. Mallory AC, Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38:S31–S36. https://doi.org/10.1038/ng1791

    Article  Google Scholar 

  18. Manavella PA, Koenig D, Rubio-Somoza I, Burbano HA, Becker C, Weigel D (2013) Tissue-specific silencing of Arabidopsis SU(VAR)3–9 HOMOLOG8 by miR171a. Plant Physiol 161:805–812. https://doi.org/10.1104/pp.112.207068

    CAS  Article  PubMed  Google Scholar 

  19. McConnell JR, Barton MK (1998) Leaf polarity and meristem formation in Arabidopsis. Development 125:2935–2942

    CAS  PubMed  Google Scholar 

  20. Meunier J, Lemoine F, Soumillon M, Liechti A, Weier M, Guschanski K, Hu HY, Khaitovich P, Kaessmann H (2013) Birth and expression evolution of mammalian microRNA genes. Genome Res 23:34–45. https://doi.org/10.1101/gr.140269.112

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  21. Miyashima S, Honda M, Hashimoto K, Tatematsu K, Hashimoto T, Sato-Nara K, Okada K, Nakajima K (2013) A comprehensive expression analysis of the Arabidopsis MICRORNA165/6 gene family during embryogenesis reveals a conserved role in meristem specification and a non-cell-autonomous function. Plant Cell Physiol 54:375–384. https://doi.org/10.1093/pcp/pcs188

    CAS  Article  PubMed  Google Scholar 

  22. Montes RAC, Rosas-Cardenas FD, De Paoli E, Accerbi M, Rymarquis LA, Mahalingam G et al. (2014) Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs. Nat Commun. https://doi.org/10.1038/ncomms4722

    Google Scholar 

  23. Odat O, Gardiner J, Sawchuk MG, Verna C, Donner TJ, Scarpella E (2014) Characterization of an allelic series in the MONOPTEROS gene of Arabidopsis. Genesis 52:127–133. https://doi.org/10.1002/dvg.22729

    CAS  Article  PubMed  Google Scholar 

  24. Ohnishi T, Takanashi H, Mogi M, Takahashi H, Kikuchi S, Yano K et al (2011) Distinct gene expression profiles in egg and synergid cells of rice as revealed by cell type-specific microarrays. Plant Physiol 155:881–891. https://doi.org/10.1104/pp.110.167502

    CAS  Article  PubMed  Google Scholar 

  25. Raman S, Greb T, Peaucelle A, Blein T, Laufs P, Theres K (2008) Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana. Plant J 55:65–76. https://doi.org/10.1111/j.1365-313X.2008.03483.x

    CAS  Article  PubMed  Google Scholar 

  26. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616–1626. https://doi.org/10.1101/gad.1004402

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  27. Rodriguez RE, Schommer C, Palatnik JF (2016) Control of cell proliferation by microRNAs in plants. Curr Opin Plant Biol 34:68–76. https://doi.org/10.1016/j.pbi.2016.10.003

    CAS  Article  PubMed  Google Scholar 

  28. Scheres B, Wolkenfelt H, Willemsen V, Terlouw M, Lawson E, Dean C, Weisbeek P (1994) Embryonic origin of the Arabidopsis primary root and root-meristem initials. Development 120:2475–2487

    CAS  Google Scholar 

  29. Schulze S, Schafer BN, Parizotto EA, Voinnet O, Theres K (2010) LOST MERISTEMS genes regulate cell differentiation of central zone descendants in Arabidopsis shoot meristems. Plant J 64:668–678. https://doi.org/10.1111/j.1365-313X.2010.04359.x

    CAS  Article  PubMed  Google Scholar 

  30. Stuurman J, Jaggi F, Kuhlemeier C (2002) Shoot meristem maintenance is controlled by a GRAS-gene mediated signal from differentiating cells. Genes Dev 16:2213–2218. https://doi.org/10.1101/gad.230702

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  31. Szemenyei H, Hannon M, Long JA (2008) TOPLESS mediates auxin-dependent transcriptional repression during Arabidopsis embryogenesis. Science 319:1384–1386. https://doi.org/10.1126/science.1151461

    CAS  Article  PubMed  Google Scholar 

  32. Wang L, Mai YX, Zhang YC, Luo Q, Yang HQ (2010) MicroRNA171c-targeted SCL6-II, SCL6-III, and SCL6-IV genes regulate shoot branching in Arabidopsis. Mol Plant 3:794–806. https://doi.org/10.1093/mp/ssq042

    Article  PubMed  Google Scholar 

  33. Willmann MR, Poethig RS (2007) Conservation and evolution of miRNA regulatory programs in plant development. Curr Opin Plant Biol 10:503–511. https://doi.org/10.1016/j.pbi.2007.07.004

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. Zhou GK, Kubo M, Zhong RQ, Demura T, Ye ZH (2007) Overexpression of miR165 affects apical meristem formation, organ polarity establishment and vascular development in Arabidopsis. Plant Cell Physiol 48:391–404. https://doi.org/10.1093/pcp/pcm008

    CAS  Article  PubMed  Google Scholar 

  35. Zhou Y, Liu X, Engstrom EM, Nimchuk ZL, Pruneda-Paz JL, Tarr PT, Yan A, Kay SA, Meyerowitz EM (2015) Control of plant stem cell function by conserved interacting transcriptional regulators. Nature 517:377–380. https://doi.org/10.1038/nature13853

    CAS  Article  PubMed  Google Scholar 

Download references

Funding

This research was supported by Grants-in-Aid for Scientific Research on Priority Areas (Grant 18075005 to N.T.) and Exploratory Research (Grant 26660004 to H.T.) from the Ministry of Education, Culture, Sports, Science, and Technology of Japan.

Author information

Affiliations

Authors

Contributions

HT designed the study, and wrote the initial draft of the manuscript. MM contributed to constructing expression vectors. HS and YH contributed to analysis and observation of transgenic plants. TO and NT helped supervise the project. All authors discussed the results and contributed to the final manuscript.

Corresponding author

Correspondence to Nobuhiro Tsutsumi.

Ethics declarations

Conflict of interest

The authors declare no competing or financial interests.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 2343 KB)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Takanashi, H., Sumiyoshi, H., Mogi, M. et al. miRNAs control HAM1 functions at the single-cell-layer level and are essential for normal embryogenesis in Arabidopsis. Plant Mol Biol 96, 627–640 (2018). https://doi.org/10.1007/s11103-018-0719-8

Download citation

Keywords

  • Embryogenesis
  • HAM1/SCL27
  • miR171a
  • Post-transcriptional regulation