We study light-regulated de-etiolation responses downstream of plant photoreceptors. We also explore Arabidopsis seed development. We take protein interaction, genetic, epigenetic, and genomic approaches.

Red/far-red light-absorbing phytochromes and blue/UV-A light-absorbing cryptochromes regulate seedling de-etiolation. PIF4 is a critical signaling hub downstream of the photoreceptors as well as temperature and hormonal regulatory pathways. Its expression peaks in the morning and afternoon. Excess light toward noon damages the photosynthetic apparatus and plants need a balanced photomorphogenesis to avoid photodamage. Upregulation of PIF4 expression by the interaction of SHB1 with the circadian clock proteins CCA1/LHY under red light represents a desensitization step. We study how SHB1 and CCA1/LHY regulate PIF expression after dawn. As noon approaches and ambient temperature tends to increase, the SHB1-CCA1 interaction sustains PIF4 expression to trigger plant thermomorphogenic responses. Moreover, we also study proteins that work together with PIF4 regulating thermomorphogenesis and mechanisms that repress PIF4 expression toward evening.

Double fertilization in angiosperms leads to the formation of a diploid embryo and a triploid endosperm. Seed development in Arabidopsis and some dicots undergoes an initial phase of active endosperm proliferation followed by a second phase in which embryo grows at the expense of the endosperm. In many dicots, the embryo grows to full size and the mature seed contains only a single layer of endosperm cells. However, excess endosperm proliferation always enlarges the final mature seeds. We study how endosperm proliferation is triggered by a few key genes such as IKU2, a LRR receptor protein kinase. IKU2 is specifically expressed in Arabidopsis endosperm at 2 to 3 Days after Pollination (DAP) and is then repressed at 4 to 5 DAP. Its activation is likely through an epigenetic mechanism. By contrast, IKU2 is continuously expressed in Brachypodium and rice. Second, we explore how IKU2 expression is repressed after 4 to 5 DAP for a phase transition to embryo development. Last, seed development in major seed crops such as soybean and canola follows a very similar path as Arabidopsis. Enhancing the potential for large seed sizes represents one of the most promising and less explored avenues for significant increases in agricultural yields.

Zhang, S., Mohanty, D., Muzaffar, A. and Ni, M. (2024). Two MADS-box proteins, AGL9 and AGL15, recruit the FIS-PRC2 complex to trigger the phase transition from endosperm proliferation to embryo development in Arabidopsis. Molecular Plant 17, 1110–1128, https://doi.org/10.1016/j.molp.2024.05.011.

Wu, D., Wei, Y., Zhao, X., Li, B., Zhang, H., Xu, G., Lv, J., Zhang, D., Zhang, X., and Ni, M. (2022). Ancestralfunction but divergent epigenetic regulation of HAIKU2 reveals routes of seed developmental evolution. Molecular Plant https://doi.org/10.1016/j.molp.2022.09.002.

Wang, S., Sun, Q., Zhang, M., Yin, C., and Ni, M. (2021). WRKY2 and WRKY10 regulate the circadian expression of PIF4 during the day through interactions with CCA1/LHY and phyB. Plant Communicationshttps://doi.org/10.1016/j.xplc.2021.100265.

Sun, Q., Wang, S., Xu, G., Kang, X., Zhang, M, and Ni, M. (2019). SHB1 and CCA1 interaction desensitizes light responses and enhances thermomorphogenesis. Nature communications https://doi.org/10.1038/s41467-019-11071-6.

Kang, X., Xu, G., Lee, B., Chen, C., Zhang, H., Kuang, R., and Ni, M. (2018). HRB2 and BBX21 interaction modulates Arabidopsis ABI5 locus and stomatal aperture. Plant Cell Environ. doi: 10.1111/pce.13336.

Zhang, H., Cheng, F., Xiao, Y., Kang, X., Wang, X., Kuang, R., and Ni, M. (2017). Global analysis of canola genes targeted by SHORT HYPOCOTYL UNDER BLUE 1 during endosperm and embryo development. Plant Journal doi:10.1111/tpj.13542.

Xiao, Y., Sun, Q., Kang, X., Chen, C., and Ni, M. (2016). SHORT HYPOCOTYL UNDER BLUE1 or HAIKU2 mixexpression alters canola and Arabidopsis seed development. New Phytol. 209: 636-49. doi: 10.1111/nph.13632

Raschke, A., Ibañez, C., Ullrich, K.K., Anwer, M.U., Becker, S., Glöckner, A., Trenner, J., Denk, K., Saal, B., Sun, X., Ni, M., Davis, S.J., Delker, C., Quint, M. (2015). Natural variants of ELF3 affect thermomorphogenesis by transcriptionally modulating PIF4-dependent auxin response genes. BMC Plant Biol doi: 10.1186/s12870-015-0566-6.

Kang, X., Li, W., Zhou, Y., and Ni, M. (2013). A WRKY transcription factor recruits SYG1-like protein SHB1 to activate gene expression and seed cavity enlargement. PLoS Genetics. 9(3): e1003347.

Sun, X., Kang, X., and Ni, M. (2012). Hypersensitive to Red and Blue 1 and its modification by Protein Phosphatase 7 are implicated in the control of Arabidopsis stomatal aperture. PLoS Genetics 8(5): e1002674.

Sun X., and Ni M. (2011). HYPOSENSITIVE TO LIGHT, an alpha/beta fold protein, acts downstream of HY5 to regulate Arabidopsis seedling de-etiolation. Molecular Plant 4, 116-126.

Zhou Y., and Ni, M. (2010). SHB1 truncations and mutations alter its association with a signaling protein complex. Plant Cell 22, 703-715.

Zhou Y., and Ni, M. (2009). SHB1 plays dual roles in photoperiodic and autonomous flowering. Developmental Biology 331, 50-57.

Zhou Y., Zhang, X., Kang, X., Zhao, X., Zhang, X., and Ni, M. (2009). SHORT HYPOCOTYL UNDER BLUE1 associates with MINISEED3 and HAIKU2 promoters in vivo to control Arabidopsis seed development. Plant Cell 21, 106-117.

Kang, X., Zhou, Y., Sun, X., and Ni, M. (2007). HYPERSENSITIVE TO RED AND BLUE 1 and its C-terminal regulatory function control FLOWERING LOCUS T expression. Plant Journal 52, 937-948.

Chen, M., and Ni, M. (2006). RED AND FAR-RED INSENSITIVE 2, a RING-domain zinc-finger protein, negatively regulates CONSTANS expression and photoperiodic flowering. Plant Journal 46, 823-833.

Kang, X., and Ni, M. (2006). Arabidopsis SHORT HYPOCOTYL UNDER BLUE 1 contains SPX and EXS domains and acts in cryptochrome signaling. Plant Cell 18, 921-934.

Chen, M., and Ni, M. (2006). RED AND FAR-RED INSENSITIVE 2, a RING-domain zinc-finger protein, mediates phytochrome-controlled seedling de-etiolation responses. Plant Physiology 140, 457-465.

Kang, X., Chong, J., and Ni, M. (2005). HYPERSENSITIVE TO RED AND BLUE 1, a ZZ-type zinc finger protein, regulates phytochrome B-mediated red and cryptochrome-mediated blue light responses. Plant Cell 17, 822-835.

Ni, M., Tepperman, J., and Quail, P.H. (1999). Binding of phytochrome B to its nuclear signaling partner PIF3 is reversibly induced by light. Nature 400, 781-784.

Ni, M., Tepperman, J., and Quail, P.H. (1998). PIF3, a phytochrome interacting factor necessary for photoinduced signal transduction, is a basic helix-loop-helix protein. Cell 95, 657-667.

Ni, M., Dehesh, K., Tepperman, J., and Quail, P.H. (1996). GT-2: In vivo transcriptional activation activity and definition of twin novel DNA-binding domains with reciprocal target-site selectivity. Plant Cell 8, 1041-1059.