1、Methylation of phytohormones and functional dissection

Plant hormones are essential for many aspects during development. We intend to study, at both the molecular and cellular level, the role of methylation of the phytohormones in plant development (including leaf flatness, branching, etc.), so that new layers of understanding would be added to the complexity of regulation of the phytohormone activities. In 2014, we report that ADP1, a putative MATE (multidrug and toxic compound extrusion) transporter, plays an essential role in regulating lateral organ outgrowth by reducing the level of auxin biosynthesis in the local meristematic regions (Li RX et al., PLoS Genetics, 2014) and by post-transcriptionally regulating auxin transporters (Li JR et al., Plant Sig. Behav., 2014) to maintain normal architecture of Arabidopsis.

2、Molecular mechanisms involved in Arabidopsis male-female interactions and embryogenesis

We are interested in dissecting the molecular mechanisms involved in sexual reproduction in Arabidopsis, especially pollen tube journey to female gametophyte and fertilization. By using reverse genetic approach, we focus on peptide signals, receptor-like kinases (RLKs) and RING-type E3 ligases. Over the past two decades, many peptides including small cysteine-rich peptides (CRPs) and non-CRPs were found to play key roles for plant reproduction, mainly acting as the signaling cues in this male-female communication (Qu L-J et al., J. Exp. Bot., 2015). We conducted systematic high-throughput RNA-seq analysis of ovules before and after fertilization and found that CRP genes represent the major class of genes specifically expressed in the female gametophyte during ovule maturation, fertilization and early seed development in Arabidopsis (Huang QP et al., J. Integr. Plant Biol., 2015).Moreover, our findings further indicate that the understanding of the role(s) of these mobile ligands and their corresponding receptors represents a key to understand and manipulate cell-cell communication events during plant reproduction. In 2013, we identified two receptor-like cytoplasmic kinases (RLCKs), Lost In Pollen Tube Guidance 1 (LIP1) and 2 (LIP2), that are involved in AtLURE1-mediated micropylar pollen tube guidance in Arabidopsis, which will facilitate to identify and characterize the other components of the receptor complex in pollen tube guidance in Arabidopsis (Liu JJ et al., Curr. Biol., 2013). In collaboration with Prof. Chai’s group from Tsinghua University, we solved the crystal structure of CLE peptide TDIF in complex with its receptor PXY, a leucine-rich repeat receptor-like kinase (LRR-RLK), which provides a structural template to understand the recognition mechanisms of CLE peptides by their receptors, and will facilitate to identify the receptors for other uncharacterized CLE peptides (Zhang HQ et al., Cell Res., 2016). Furthermore, we show that SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERKs) serve as co-receptors in the CLE41/TDIF-PXY signaling to regulate plant vascular development. Crystal structure of the PXY-TDIF-SERK2 complex reveals that the last amino acid of TDIF conserved among CLEs and other evolutionary-related peptides is important for the interaction between SERK2 and PXY (Zhang HQ et al., Mol. Plant, 2016). As for RING-type E3 ligases, we found that Arabidopsis APC4 played critical roles in female gametogenesis and embryogenesis, possibly as a connector in APC/C, and that regulation of auxin distribution may be involved in these processes (Wang YB et al., Plant J., 2012). We identified a group of female-specific small GPI-anchored proteins, early nodulin-like proteins (ENODLs or ENs), are required for pollen tube reception, and play an essential role in male-female communication and fertilization (Hou YN et al., Curr. Biol., 2016). We identified the Arabidopsis VPS41 (AtVPS41), encoded by a single-copy gene with sequence similarity to yeast Vps41p, as a new factor controlling pollen tube-stigma interaction. The AtVPS41-mediated late stage of the endocytic pathway is essential for pollen tube-stigma interaction in Arabidopsis (Hao LH et al., PNAS, 2016).

3、Functional analysis of transcription factors in Arabidopsis

We have been systematically analyzing the functions of transcription factors in Arabidopsis (Qu and Zhu, Curr. Opin. Plant Biol., 2006; Zhang XB et al., Plant J., 2007; Guo Y et al., Plant Cell, 2009). In 2011, weestablished a functional characterization platform to analyze those transcription factors through yeast-two-hybrid and yeast one-hybrid assays (Ou B et al., Mol. Plant, 2011). We identified a transcriptional repressor TIE1 forms tertiary complexes with TCPs and TPL/TPRs and modulates the activities of TCP transcription factors during leaf development (Tao Q et al., Plant Cell, 2013).We identified an AP2/EREBP family transcription factor TRANSLUCENT GREEN (TG), whose overexpression in transgenic plants confers enhanced drought tolerance and vitrified leaves by activating the expression of aquaporin genes (Zhu DL et al., Mol. Plant, 2014).In early 2015, we clarified a fifteen-year-old mystery by demonstrating that SPOROCYTELESS / NOZZLE (SPL/NZZ), an essential factor for sporogenesis and the megasporocyte specification during Arabidopsis ovule development, is actually a transcription repressor that recruits TPL/TPR co-repressors to inhibit the CINCINNATA (CIN)-like TCP transcription factors during ovule development (Wei BY et al., Cell Res., 2015). I also found that a subunit of Arabidopsis Mediator complex MED16 interacted with another subunit MED25 and regulated iron homeostasis, which increases our understanding on complex transcriptional regulation of plant iron homeostasis(Yang Y et al., Plant J., 2014). Recently, in collaboration with Prof. Takashi Aoyama from Kyoto University, we identified five bHLH transcription factor genes as the direct targets of GL2, the central transcription factor in Arabidopsis root hair development, thus for the first time to have integrated the two processes (i.e., cell fate determination and morphological differentiation of root hair cells) into a regulatory cascade (Lin Q et al., Plant Cell, 2015). We identified the critical functions of two plant-specific proteins containing RNA recognition motifs, RZ-1B and RZ-1C, in regulating RNA splicing, gene expression, and many key aspects of plant development including flowering via interaction with proteins including SR proteins (Wu Z et al., Plant Cell, 2016)。

4、Innovation of new technology for gene editing in plants

We successfully applied the CRISPR/Cas9 system to knock out two functional genes in rice, making my lab one of the four first labs that successfully establishes this powerful technique platform in plants in the world, paving the way for large scale genome editing in rice, which is important for quality improvement and yield increase of rice (Miao J et al., Cell Res., 2013). We have also established several efficient CRISPR/Cas9 knock-out systems in Arabidopsis in 2014.

Sheng Zhong, Li Zhang, Zijun Lan, Zihan Song, Dandan Liu, Sufan Yuan, Yuan Wang, Luhan Li, Wenhao Li, Qiyun Li, Han Lu, Nina Ning, Shuaihua Zhi, Xuefei Li, Hongboyu Yang, Yaxiao Liu, Xin Quan, Xiaowen Xu