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. Cryptochromes together with blue/UV-A light-absorbing phototropins also regulate stomatal aperture in a natural environment. The signal transduction cascades that link the perception of light to the de-etiolation and stomatal opening responses are still largely unknown, and hypersensitive to red and blue (hrb) mutants are of particular interest. The hrb mutants were initially isolated for their short hypocotyl phenotype under red and blue light. The hrb mutants are also more resistant to dehydration and show reduced water loss and blue light-regulated stomatal aperture. We have cloned HRB1 gene and mapped hrb2 and hrb3 to chromosomes 2 and 4, respectively. HRB1 encodes a nuclear ZZ-type zinc finger protein. HRB1 physically interacts with a few nuclear proteins through its zinc finger domain, and exists in a protein complex of 312 kDa mostly in its de-phophorylated form. We are exploring the actions and interactions of HRBs with others in the light-mediated signaling pathways, and identifying genes encoding HRB2 and HRB3. The studies on these genetic and biochemical interactions will bring novel insights into HRB1 function and the network structure of the light signaling machinery. Our studies may also open new possibilities to engineer plants to survive desiccation since the stomatal pores are situated in the leaf epidermis to allow CO2 uptake and the loss of water through transpiration. Periodic drought is one of the major environmental factors that limit biomass production and crop yield in a changing global climate, such as increasing CO2 level, temperature elevation, and glacier melting. The stomatal aperture is also regulated by other environmental cues in addition to blue light. Given that hrb plants still respond to ABA, a well-known drought signal, these plants should enjoy the advantages of both constitutive and induced protection under water-limiting conditions.
Double fertilization in angiosperms leads to the formation of a diploid embryo and a triploid endosperm. Seed development in Arabidopsis then 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. As the mature seed size is largely attained during the initial phase, the seed size is coordinately determined by the growth of the maternal ovule, endosperm, and embryo. The mechanisms underlying this control are still not well understood, yet seeds form the bulk of the diet of human population. SHB1 is a positive regulator of Arabidopsis seed development that operates through the regulation of both cell size and cell number. shb1-D, a gain-of-function allele, increases seed size and shb1, a loss-of-function allele, reduces seed size. The increase in shb1-D seed size is associated with the timing of endosperm cellurization, enlargement of chalazal endosperm, and subsequent embryo development. SHB1 regulates the expression of MINI3 and IKU2, a WRKY transcription factor gene and an LRR receptor kinase gene, associates with MINI3 and IKU2 promoters in vivo, and exists in a 305 kDa protein complex. Mutation in either MINI3 or IKU2 retards endosperm development and reduces seed size. We are currently searching for proteins that recruit SHB1 to the MINI3 and IKU2 promoters to control gene expression required for endosperm development. We are also identifying the components within the 305 kDa protein complex and other extragenic suppressors that regulate the activity of SHB1-containing protein complex. Seed size is the yield trait that traditional breeding has had the most limited success in improving effectively and 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.
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.
Chen, C., Xiao, Y., Li, X., and Ni, M. (2012). Light-regulated stomatal aperture in Arabidopsis. Molecular Plant 5, 566-572.
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.
Sun X., Shantharaj D., Kang X., and Ni M. (2010). Transcriptional and hormonal signaling control of Arabidopsis seed development. Current Opinion in Plant Biology 13, 611-620.
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.
Ni, M. (2005). Integration of light signaling with photoperiodic flowering and circadian regulation. Cell Research 15, 559-566.
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.