Our lab is currently focused on two separate research areas: light-regulated de-etiolation and stomatal opening responses and Arabidopsis seed development.
Red/far-red light-absorbing phytochromes and blue/UV-A light-absorbing cryptochromes regulate seedling de-etiolation. PIF4 is a critical signaling hub in light, temperature, and hormonal signaling pathways. Its expression peaks in the morning and afternoon. Excess light toward noon damages the photosynthetic apparatus and plants needs to achieve a balanced state of photomorphogenesis to avoid photodamage. Upregulation of PIF4 expression by SHB1 and the circadian clock proteins CCA1/LHY under red light represents a desensitization step. After dawn, the highly expressed CCA1 and LHY bring circadian signals to the regulatory region of the PIF4. Recruitment of SHB1 by CCA1 modulates the red light-specific induction of PIF4 expression thus integrating circadian and light signals. As noon approaches and ambient temperature tend to increase, the SHB1-CCA1 interaction sustained PIF4 expression to trigger plant thermomorphogenic responses. Moreover, two WRKY proteins recognize a WRKY-box near the element bound by CCA1 and LHY in the PIF4 promoter and enhance their binding during the day. The two WRKYs also interact indirectly with SHB1 and requires functional CCA1 or LHY for their interaction. SHB1 in turn associates with the regulatory regions of the two WRKY genes and enhances their expression parallel to the PIF4 expression peaks as a forward regulatory loop.
Double fertilization in angiosperms leads to the formation of a diploid embryo and a triploid endosperm. Seed development in Arabidopsis and in some dicots undergoes an initial phase of active endosperm proliferation in the first few days 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. The mechanisms underlying this control are still not well understood, yet seeds form the bulk of the diet of human population. IKU2 is a LRR receptor protein kinase and a critical player to elicit a subsequent signaling cascade for endosperm proliferation. It is specifically expressed in the endosperm. Its expression peaks at 2 to 3 Days after Pollination (DAP) and is then repressed at 4 to 5 DAP. We first explore how its expression is activated after pollination. Two newly identified transcription factors recruit SHB1 along with a histone modification enzyme to various locus including IKU2 to activate their expression and endosperm proliferation. To explore how IKU2 expression is repressed at 4 to 5 DAP, we identified two transcription factors that recruit FIS-PRC2 to the IKU2 locus at 4 to 5 DAP for a developmental phase transition. On the other hand, seed size is the yield trait that traditional breeding has had the most limited success in improving effectively. 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.
Wu, D., Wei, Y., Zhao, X., Li, B., Zhang, H., Xu, G., Lv, J., Zhang, D., Zhang, X., and Ni, M. (2022). Ancestral HAIKU2 function but divergent epigenetic regulation 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 Communications https://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.