Jian-Kang Zhu

Shanghai Institutes for Biological Sciences, Shanghai, Shanghai Shi, China

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Publications (77)635.52 Total impact

  • Chunzhao Zhao, Zhaobo Lang, Jian-Kang Zhu
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    ABSTRACT: CBF transcription factors, which play important roles in cold acclimation, regulate the expression of approximately 170 cold-responsive genes, termed the CBF regulon. Recent work by Park et al. showed that CBF regulon genes and other cold-responsive genes are regulated by a complex network that involves many early cold-induced transcription factors. Copyright © 2015 Elsevier Ltd. All rights reserved.
    Trends in Plant Science 06/2015; DOI:10.1016/j.tplants.2015.06.001 · 13.48 Impact Factor
  • Pengcheng Wang, Jian-Kang Zhu, Zhaobo Lang
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    ABSTRACT: Nitric oxide (NO) plays important roles in plant development, and biotic and abiotic stress responses. In a recent study, we showed that endogenous NO negatively regulates abscisic (ABA) signaling in guard cells by inhibiting sucrose nonfermenting 1 (SNF1)-related protein kinase 2.6 (SnRK2.6)/open stomata 1(OST1) through S-nitrosylation. Application of NO breaks seed dormancy and alleviates the inhibitory effect of ABA on seed germination and early seedling growth, but it is unclear how NO functions at the stages of seed germination and early seedling development. Here, we show that like SnRK2.6, SnRK2.2 can be inactivated by S-nitrosoglutathione (GSNO) treatment through S-nitrosylation. SnRK2.2 and the closely related SnRK2.3 are known to play redundant roles in ABA inhibition of seed germination in Arabidopsis. We found that treatment with the NO donor SNP phenocopies the snrk2.2snrk2.3 double mutant in conferring ABA insensitivity at the stages of seed germination and early seedling growth. Our results suggest that NO negatively regulates ABA signaling in germination and early seedling growth through S-nitrosylation of SnRK2.2 and SnRK2.3.
    Plant signaling & behavior 05/2015; DOI:10.1080/15592324.2015.1031939
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    ABSTRACT: Paramutation is an epigenetic phenomenon that has been observed in a number of multicellular organisms. The epigenetically silenced state of paramutated alleles is not only meiotically stable but also "infectious" to active homologous alleles. The molecular mechanism of paramutation remains unclear, but components involved in RNA-directed DNA methylation (RdDM) are required. Here, we report a multi-copy pRD29A-LUC transgene in Arabidopsis thaliana that behaves like a paramutation locus. The silent state of LUC is induced by mutations in the DNA glycosylase gene ROS1. The silent alleles of LUC are not only meiotically stable but also able to transform active LUC alleles into silent ones, in the absence of ros1 mutations. Maintaining silencing at the LUC gene requires action of multiple pathways besides RdDM. Our study identified specific factors that are involved in the paramutation-like phenomenon and established a model system for the study of paramutation in Arabidopsis. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
    Cell Reports 05/2015; 107(8). DOI:10.1016/j.celrep.2015.04.034 · 7.21 Impact Factor
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    Proceedings of the National Academy of Sciences 05/2015; 112(18):201505811. DOI:10.1073/pnas.1505811112 · 9.81 Impact Factor
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    ABSTRACT: CRISPR/Cas9 and TALEN are currently the two systems of choice for genome editing. We have studied the efficiency of the TALEN system in rice as well as the nature and inheritability of TALEN-induced mutations and found important features of this technology. The N287C230 TALEN backbone resulted in low mutation rates (0-6.6%), but truncations in its C-terminal domain dramatically increased efficiency to 25%. In most transgenic T0 plants, TALEN produced a single prevalent mutation accompanied by a variety of low-frequency mutations. For each independent T0 plant, the prevalent mutation was present in most tissues within a single tiller as well as in all tillers examined, suggesting that TALEN-induced mutations occurred very early in the development of the shoot apical meristem. Multigenerational analysis showed that TALEN-induced mutations were stably transmitted to the T1 and T2 populations in a normal Mendelian fashion. In our study, the vast majority of TALEN-induced mutations (~81%) affected multiple bases and ~70% of them were deletions. Our results contrast with published reports for the CRISPR/Cas9 system in rice, in which the predominant mutations affected single bases and deletions accounted for only 3.3% of the overall mutations. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
    Plant Biotechnology Journal 04/2015; DOI:10.1111/pbi.12372 · 5.68 Impact Factor
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    ABSTRACT: Cell polarization is linked to fate determination during asymmetric division of plant stem cells, but the underlying molecular mechanisms remain unknown. In Arabidopsis, BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE (BASL) is polarized to control stomatal asymmetric division. A mitogen-activated protein kinase (MAPK) cascade determines terminal stomatal fate by promoting the degradation of the lineage determinant SPEECHLESS (SPCH). Here, we demonstrate that a positive-feedback loop between BASL and the MAPK pathway constitutes a polarity module at the cortex. Cortical localization of BASL requires phosphorylation mediated by MPK3/6. Phosphorylated BASL functions as a scaffold and recruits the MAPKKK YODA and MPK3/6 to spatially concentrate signaling at the cortex. Activated MPK3/6 reinforces the feedback loop by phosphorylating BASL and inhibits stomatal fate by phosphorylating SPCH. Polarization of the BASL-MAPK signaling feedback module represents a mechanism connecting cell polarity to fate differentiation during asymmetric stem cell division in plants. Copyright © 2015 Elsevier Inc. All rights reserved.
    Developmental Cell 04/2015; DOI:10.1016/j.devcel.2015.02.022 · 10.37 Impact Factor
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    ABSTRACT: During the transition from water to land, plants had to cope with the loss of water through transpiration, the inevitable result of photosynthetic CO2 fixation on land [1, 2]. Control of transpiration became possible through the development of a new cell type: guard cells, which form stomata. In vascular plants, stomatal regulation is mediated by the stress hormone ABA, which triggers the opening of the SnR kinase OST1-activated anion channel SLAC1 [3, 4]. To understand the evolution of this regulatory circuit, we cloned both ABA-signaling elements, SLAC1 and OST1, from a charophyte alga, a liverwort, and a moss, and functionally analyzed the channel-kinase interactions. We were able to show that the emergence of stomata in the last common ancestor of mosses and vascular plants coincided with the origin of SLAC1-type channels capable of using the ancient ABA drought signaling kinase OST1 for regulation of stomatal closure.
    Current Biology 03/2015; · 9.92 Impact Factor
  • Xiangqiang Zhan, Jian-Kang Zhu, Zhaobo Lang
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    ABSTRACT: Cold temperatures trigger the ICE1-CBF-COR transcriptional cascade in plants, which reprograms gene expression to increase freezing tolerance. In this issue of Developmental Cell, Ding et al. (2015) report that cold stress activates the protein kinase OST1 to phosphorylate and thereby stabilize and stimulate ICE1. This enhances plant tolerance to freezing temperatures. Copyright © 2015 Elsevier Inc. All rights reserved.
    Developmental Cell 02/2015; 32(3):257-8. DOI:10.1016/j.devcel.2015.01.004 · 10.37 Impact Factor
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    ABSTRACT: Although researchers have established that DNA methylation and active demethylation are dynamically regulated in plant cells, the molecular mechanism for regulation of active DNA demethylation is not well understood. By using an Arabidopsis line expressing the ProRD29A:LUC and Pro35S:NPTII transgenes, we isolated an mbd7 (Methyl-CpG-binding domain protein 7) mutant. The mbd7 mutation causes an inactivation of the Pro35S:NPTII transgene but does not affect the expression of the ProRD29A:LUC transgene. The silencing of the Pro35S:NPTII reporter gene is associated with DNA hypermethylation of the reporter gene. MBD7 physically interacts with ROS5/IDM2, a protein in the small heat shock protein family. MBD7 prefers to target the genomic loci with high densities of DNA methylation around chromocenters. The gypsy type LTR retrotransposons mainly distributed around chromocenters are most affected by mbd7 in all transposons. Our results suggest that MBD7 is required for active DNA demethylation and antisilencing of the genomic loci with high densities of DNA methylation in Arabidopsis. Copyright © 2015, American Society of Plant Biologists.
    Plant physiology 01/2015; 167(3). DOI:10.1104/pp.114.252106 · 7.39 Impact Factor
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    Jian-Kang Zhu, Yang Zhao, Zhulong Chan
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    ABSTRACT: Embodiments of the present invention relate generally to drought tolerant transgenic plants and methods of creating the drought tolerant transgenic plants. In one embodiment, plants are transformed such that a PYL polypeptide is overexpressed in the plant. In an embodiment, the plant is transformed with a cassette or vector that comprises a polynucleotide encoding for one or more of the PYL polypeptides, which may be under the control of an inducible or constitutive promoter. In embodiments, overexpression of PYL13 results in plants having increased drought tolerance, such as a decreased transpiration rate, a decreased stomatal conductance, an increased photosynthetic rate, accelerated stress responsive gene expression, and increased water use efficiency, and/or an increased survival rate compared to a control plant. In some embodiments, other PYL proteins having the single point mutations identified in PYL13 are expressed in the plant.
    Ref. No: US 2015-0074844, Year: 01/2015
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    ABSTRACT: The phytohormone abscisic acid (ABA) plays important roles in plant development and adaptation to environmental stress. ABA induces the production of nitric oxide (NO) in guard cells, but how NO regulates ABA signaling is not understood. Here, we show that NO negatively regulates ABA signaling in guard cells by inhibiting open stomata 1 (OST1)/sucrose nonfermenting 1 (SNF1)-related protein kinase 2.6 (SnRK2.6) through S-nitrosylation. We found that SnRK2.6 is S-nitrosylated at cysteine 137, a residue adjacent to the kinase catalytic site. Dysfunction in the S-nitrosoglutathione (GSNO) reductase (GSNOR) gene in the gsnor1-3 mutant causes NO overaccumulation in guard cells, constitutive S-nitrosylation of SnRK2.6, and impairment of ABA-induced stomatal closure. Intro-duction of the Cys137 to Ser mutated SnRK2.6 into the gsnor1-3/ ost1-3 double-mutant partially suppressed the effect of gsnor1-3 on ABA-induced stomatal closure. A cysteine residue correspond-ing to Cys137 of SnRK2.6 is present in several yeast and human protein kinases and can be S-nitrosylated, suggesting that the S-nitrosylation may be an evolutionarily conserved mechanism for protein kinase regulation. NO | ABA | drought | GSNOR | stomata
    Proceedings of the National Academy of Sciences 12/2014; 112(2). DOI:10.1073/pnas.1423481112 · 9.81 Impact Factor
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    ABSTRACT: Due to its ability to be rapidly generated and propagated over long distances, H2O2 is an important second messenger for biotic and abiotic stress signaling in plants. In response to low water potential and high salt concentrations sensed in the roots of plants, the stress hormone abscisic acid (ABA) activates NADPH oxidase to generate H2O2, which is propagated in guard cells in leaves to induce stomatal closure and prevent water loss from transpiration. Using a reconstituted system, we demonstrate that H2O2 reversibly prevents the protein phosphatase HAB1, a key component of the core ABA-signaling pathway, from inhibiting its main target in guard cells, SnRK2.6/OST1 kinase. We have identified HAB1 C186 and C274 as H2O2-sensitive thiols and demonstrate that their oxidation inhibits both HAB1 catalytic activity and its ability to physically associate with SnRK2.6 by formation of intermolecular dimers.
    PLoS ONE 12/2014; 9(12):e113643. DOI:10.1371/journal.pone.0113643 · 3.53 Impact Factor
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    ABSTRACT: RNA-binding proteins play crucial roles in RNA processing and function as regulators of gene expression. Recent studies have defined the structural basis for RNA recognition by diverse RNA-binding motifs. While many RNA-binding proteins recognize RNA sequence non-specifically by associating with 5' or 3' RNA ends, sequence-specific recognition by RNA-binding proteins is typically achieved by combining multiple modular domains to form complex binding surfaces. In this review, we present examples of structures from different classes of RNA-binding proteins, identify the mechanisms utilized by them to target specific RNAs, and describe structural principles of how protein-protein interactions affect RNA recognition specificity. We also highlight the structural mechanism of sequence-dependent and -independent interactions in the Cas9-RNA-DNA complex.
    Cellular and Molecular Life Sciences CMLS 11/2014; 72(6). DOI:10.1007/s00018-014-1779-9 · 5.86 Impact Factor
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    ABSTRACT: Comprehending the reasons for the natural variation and distribution of life-forms in different environments has been a major motivational force for biology since antiquity. With Mendel's discoveries, Darwin's natural selection theories became armed with the concept of genotype.How a genotype is inherited, selected, and how this results in a phenotype have become a spirited debate that has ultimately led to our ideas of genetics and epigenetics. The concept of genetic memory that arose from developmental biology has underpinned the desire to understand the molecular basis of epigenetics. This has finally led to uncovering of many of the molecular building blocks and regulatory pathways of epigenetics. The possibility that the environment through epigenetic regulation may direct trait inheritance has even begun to question some of our fundamental paradigms of the function of the environment in shaping evolution. Some direct role of the environment in heritable phenotype variation cannot be ruled out now. This has blurred our concepts of transgenerational and developmental genetics so much that understanding the connections between these processes has taken an enormously important status in biology. The pace of growth of our knowledge of the biochemical participants in the epigenetic informational system has been truly impressive. Major epigenetic marks involve covalent chemical modifications to DNA and to histones. How these modifications and noncoding RNAs are organized into an epigenetic informational system is being intensively investigated.Understanding the way in which the environment controls the connections and use of epigenetic marks with the DNA sequence code promises to expose a rich new world of biology and new toolboxes that will afford stunning new capabilities in agriculture, medicine, and all practical applications of biology. This chapter discusses the sea change in our understanding of genome–environment interactions.
    Plant Breeding Reviews: Volume 38, 11/2014: pages 69-142; , ISBN: 9781118916834
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    ABSTRACT: The SU(VAR)3-9-like histone methyltransferases usually catalyze repressive histone H3K9 methylation and are involved in transcriptional gene silencing in eukaryotic organisms. We identified a putative SU(VAR)3-9-like histone methyltransferase SUVR2 by a forward genetic screen and demonstrated that it is involved in transcriptional gene silencing at genomic loci targeted by RNA-directed DNA methylation (RdDM). We found that SUVR2 has no histone methyltransferase activity and the conserved catalytic sites of SUVR2 are dispensable for the function of SUVR2 in transcriptional silencing. SUVR2 forms a complex with its close homolog SUVR1 and associate with three previously uncharacterized SNF2-related chromatin-remodeling proteins CHR19, CHR27, and CHR28. SUVR2 was previously thought to be a component in the RdDM pathway. We demonstrated that SUVR2 contributes to transcriptional gene silencing not only at a subset of RdDM target loci but also at many RdDM-independent target loci. Our study suggests that the involvement of SUVR2 in transcriptional gene silencing is related to nucleosome positioning mediated by its associated chromatin-remodeling proteins.Cell Research advance online publication 25 November 2014; doi:10.1038/cr.2014.156.
    Cell Research 11/2014; DOI:10.1038/cr.2014.156 · 11.98 Impact Factor
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    ABSTRACT: CYCLIN-DEPENDENT KINASE8 (CDK8) is a widely studied component of eukaryotic Mediator complexes. However, the biological and molecular functions of plant CDK8 are not well understood. Here, we provide evidence for regulatory functions of Arabidopsis thaliana CDK8 in defense and demonstrate its functional and molecular interactions with other Mediator and non-Mediator subunits. The cdk8 mutant exhibits enhanced resistance to Botrytis cinerea but susceptibility to Alternaria brassicicola. The contributions of CDK8 to the transcriptional activation of defensin gene PDF1.2 and its interaction with MEDIATOR COMPLEX SUBUNIT25 (MED25) implicate CDK8 in jasmonate-mediated defense. Moreover, CDK8 associates with the promoter of AGMATINE COUMAROYLTRANSFERASE to promote its transcription and regulate the biosynthesis of the defense-active secondary metabolites hydroxycinnamic acid amides. CDK8 also interacts with the transcription factor WAX INDUCER1, implying its additional role in cuticle development. In addition, overlapping functions of CDK8 with MED12 and MED13 and interactions between CDK8 and C-type cyclins suggest the conserved configuration of the plant Mediator kinase module. In summary, while CDK8's positive transcriptional regulation of target genes and its phosphorylation activities underpin its defense functions, the impaired defense responses in the mutant are masked by its altered cuticle, resulting in specific resistance to B. cinerea.
    The Plant Cell 10/2014; DOI:10.1105/tpc.114.128611 · 9.58 Impact Factor
  • Huiming Zhang, Jian-Kang Zhu
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    ABSTRACT: Long non-coding RNAs (lncRNAs) can be important regulators of various biological processes such as RNA-directed DNA methylation (RdDM). In the RdDM pathway, recruitment of the DNA methylation complex is mediated through complementary pairing between scaffold RNAs and Argonaute-associated siRNAs. Scaffold RNAs are chromatin-associated lncRNAs transcribed by RNA polymerase Pol V or Pol II, while siRNAs originate from Pol IV- or Pol II-dependent production of lncRNAs. In contrast to the vast literature on co-transcriptional and post-transcriptional processing of mRNAs, information is limited for lncRNA regulation that enables their production and function. Recently Arabidopsis RRP6L1, a plant paralog of the conserved nuclear RNA surveillance protein Rrp6, was shown to mediate RdDM through retention of lncRNAs in the chromatin, thereby revealing that accumulation of functional lncRNAs requires more than simply RNA polymerases. By focusing on the canonical RdDM pathway, here we summarize recent evidence that indicate co-transcriptional and/or post-transcriptional regulation of lncRNAs, and highlight the emerging theme of lncRNA regulation by RNA processing factors.
    RNA Biology 07/2014; 11(7). DOI:10.4161/rna.29731 · 5.38 Impact Factor
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    ABSTRACT: Kinase mediated phosphorylation signaling is extensively involved in cellular functions and human diseases, and unraveling phosphorylation networks requires the identification of substrates targeted by kinases, which has remained challenging. We report here a novel proteomic strategy to identify the specificity and direct substrates of kinases by coupling phosphoproteomics with a sensitive stable isotope labeled kinase reaction. A whole cell extract was moderately dephosphorylated and subjected to in vitro kinase reaction under the condition in which 18O-ATP is the phosphate donor. The phosphorylated proteins are then isolated and identified by mass spectrometry, in which the heavy phosphate (+85.979 Da) labeled phosphopeptides reveal the kinase specificity. The in vitro phosphorylated proteins with heavy phosphates are further overlapped with in vivo kinase-dependent phosphoproteins for the identification of direct substrates with high confidence. The strategy allowed us to identify 46 phosphorylation sites on 38 direct substrates of extracellular signal-regulated kinase 1, including multiple known substrates and novel substrates, highlighting the ability of this high throughput method for direct kinase substrate screening.
    Molecular &amp Cellular Proteomics 07/2014; DOI:10.1074/mcp.O114.038588 · 7.25 Impact Factor
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    ABSTRACT: DNA methylation is a conserved epigenetic mark that controls genome stability, development and environmental responses in many eukaryotes. DNA methylation can be guided by non-coding RNAs that include small interfering RNAs and scaffold RNAs. Although measurement of DNA methylation and regulatory non-coding RNAs is desirable for many biologists who are interested in exploring epigenetic regulation in their areas, conventional methods have limitations and are technically challenging. For instance, traditional siRNA detection through RNA hybridization requires relatively large amount of small RNAs and involves radioactive isotopes. An alternative approach is RT-qPCR that employs stem loop primers during reverse transcription; however, it requires a prerequisite that the exact sequences of siRNAs should be known.
    Plant Methods 06/2014; 10:18. DOI:10.1186/1746-4811-10-18 · 2.59 Impact Factor
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    ABSTRACT: DNA methylation is a reversible epigenetic mark regulating genome stability and function in many eukaryotes. In Arabidopsis, active DNA demethylation depends on the function of the ROS1 subfamily of genes that encode 5-methylcytosine DNA glycosylases/lyases. ROS1-mediated DNA demethylation plays a critical role in the regulation of transgenes, transposable elements and some endogenous genes; however, there have been no reports of clear developmental phenotypes in ros1 mutant plants. Here we report that, in the ros1 mutant, the promoter region of the peptide ligand gene EPF2 is hypermethylated, which greatly reduces EPF2 expression and thereby leads to a phenotype of overproduction of stomatal lineage cells. EPF2 gene expression in ros1 is restored and the defective epidermal cell patterning is suppressed by mutations in genes in the RNA-directed DNA methylation pathway. Our results show that active DNA demethylation combats the activity of RNA-directed DNA methylation to influence the initiation of stomatal lineage cells.
    Nature Communications 06/2014; 5:4062. DOI:10.1038/ncomms5062 · 10.74 Impact Factor

Publication Stats

2k Citations
635.52 Total Impact Points

Institutions

  • 2012–2015
    • Shanghai Institutes for Biological Sciences
      Shanghai, Shanghai Shi, China
  • 2011–2015
    • Purdue University
      • Department of Horticulture and Landscape Architecture
      ウェストラファイエット, Indiana, United States
  • 2013
    • Tsinghua University
      • School of Life Sciences
      Peping, Beijing, China
    • Van Andel Research Institute
      Grand Rapids, Michigan, United States
  • 2009–2013
    • University of California, Riverside
      • • Institute for Integrative Genome Biology
      • • Department of Botany and Plant Sciences
      Riverside, California, United States
  • 2007
    • Maria Curie-Sklodowska University in Lublin
      Lyublin, Lublin Voivodeship, Poland