CEPCEB Members
Jian-Kang Zhu
Professor of Botany
Presidential Chair
Botany & Plant Sciences
University of California
Riverside, CA 92521
Phone: (909) 827-7117
Fax: (909) 827-7115
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Background Detecting
and responding to environmental perturbations are important for all living organisms.
One of the most important distinguishing features of plants is that they are sessile
and thus have to endure environmental challenges. Our lab is interested in the
molecular mechanisms underlying plant responses to harsh environments such as
soil salinity, drought and cold temperatures. In addition, we are interested in
the mechanisms of transcriptional gene silencing and in the role of epigenetic
gene regulation in stress adaptation. We use a combination of genetic, biochemical,
genomic and proteomic approaches to analyze various levels of gene regulation
(chromatin level/epigenetic, transcriptional, posttranscriptional, and protein
activity) and to understand stress signaling and stress tolerance. Our long-term
goals are to elucidate the signaling pathways used by plants in responding to
environmental stresses and to identify key genes for modifying the responses of
crops to environmental stresses. This knowledge ultimately will lead to major
contributions to agriculture and the environment. Back
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Salt
Stress, the SOS Pathway and Beyond
Soil salinity, by inhibiting
growth and crop yield, is a severe and increasing constraint on agricultural productivity.
Salinization of arable land arising from poor water management has led to the
decline of past civilizations, and it threatens the long-term sustainability of
many present large-scale irrigation systems. A critical aspect of salt tolerance
is for plant cells to maintain a low concentration of the toxic sodium ion (Na+)
in the cytosol. . We are interested in the signaling cascades controlling Na+
homeostasis in the model plant Arabidopsis thaliana. Recently, through
the identification of Arabidopsis mutants that are salt overly sensitive
(sos) and the cloning and characterization of the SOS genes, we have discovered
a novel signaling pathway that mediates ion homeostasis and is in part responsible
for salt tolerance in Arabidopsis (Figure 1). In this pathway, a
myristoylated calcium-binding protein, SOS3, senses cytosolic calcium changes
elicited by salt stress. SOS3 physically interacts with and activates the protein
kinase, SOS2. The SOS3/SOS2 kinase complex phosphorylates and activates the transport
activity of the plasma membrane Na+/H+ exchanger encoded by the SOS1 gene.
In addition to its transport function, preliminary results suggest that SOS1 may
also have a regulatory role, and may even be a novel sensor for Na+. Our current
research is focused on the putative sensory role of SOS1, and the characterization
of additional regulatory components as well as new targets of the SOS signaling
pathway. |  | | Figure
1. Regulation of Na+ homeostasis by the SOS pathway. High Na+ stress initiates
a calcium signal that stimulates the SOS3-SOS2 protein kinase complex, which then
activates the Na+/H+ exchange activity of SOS1 and regulates the expression of
some salt-responsive genes. In addition, SOS3-SOS2 may activate or suppress the
activities of other transporters involved in Na+ homeostasis. | | Using
the SOS pathway as a paradigm, we have extended our work to the entire family
of 9 SOS3-like calcium-binding proteins (designated as SCaBPs) and 24 SOS2-like
protein kinases (PKS) in Arabidopsis. Members of the two protein families interact
specifically to form distinct protein kinase complexes, and our work has implicated
several of them in decoding calcium signals elicited by various environmental
and hormonal stimuli. The function of the remaining SCaBP and PKS proteins are
being investigated using biochemical and reverse genetics approaches. Our very
recent work has provided new evidence for small RNA species that can modulate
gene expression under stress; their role in stress tolerance will be an important
facet of future research in this laboratory. |
Back
to Top Drought
and Abscisic Acid Signaling  | Drought
is the most significant limiting factor for plant agriculture worldwide. Upon
drought stress, plants accumulate the phytohormone abscisic acid (ABA), which
in turn controls many adaptive responses. Our current research is focused on how
plant cells perceive drought stress and the signal transduction cascade leading
to the induction of ABA biosynthesis genes (Figure 2). In addition,
we are interested in the mechanisms of ABA perception and ABA signal transduction. To
facilitate genetic analysis, we have constructed transgenic Arabidopsis plants
with drought stress- and/or ABA-inducible bioluminescence by introducing into
plants chimeric genes consisting of drought/ABA-responsive promoters fused with
the firefly luciferase reporter gene. A large collection of mutants that respond
abnormally to water stress or ABA were recovered, and recent characterization
of some of these mutants has provided many new insights into osmosensing and osmotolerance.
For example, we have demonstrated a paramount role of ABA in osmotic stress-responsive
gene expression, and provided evidence that this hormone is required not only
for the ABA-dependent pathway, but also for the supposedly "ABA-independent"
pathway of osmotic stress signaling. We cloned LOS5/ABA3, a major genetic
locus controlling ABA biosynthesis, and showed that LOS5/ABA3 and several
other ABA biosynthetic genes are positively regulated by the end product, ABA
(Figure 2). Our work on sad1 (sensitive to ABA and drought
1) and several related mutants contributed to the discovery of a surprising role
of RNA metabolism in regulating ABA sensitivity and biosynthesis. In addition,
our work on the fiery1 mutant provided the first mutational evidence supporting
that inositol-1, 4, 5-triphosphate is a second messenger for ABA as well as for
osmotic and cold stress signaling. | Figure
2. Self-regulation and osmotic stress regulation of ABA biosynthesis. | |
Back
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Cold
Stress Signaling and Tolerance
Many plants can increase their
freezing tolerance by a pre-exposure to low, non-freezing temperatures, a process
known as cold acclimation. During cold acclimation, the expression of hundreds
of genes is either up- or down-regulated. Many of the cold up-regulated genes
are also up-regulated by drought, high salt or ABA. These genes encode proteins
that presumably protect cellular structures from dehydration caused by extracellular
ice formation or by salt/drought stress. The induction of these genes by cold
is achieved through a transcriptional cascade (Figure 3). Facilitated
by the firefly luciferase reporter gene driven by cold-responsive promoters (e.g.
RD29A, ZAT10 or CBFs), we have isolated many Arabidopsis mutants
that are defective in cold signal transduction and cold tolerance. The characterization
and cloning of some of the mutations have led to the discovery of several novel
regulators of cold-responsive gene transcription, and of chilling and freezing
tolerance. For example, we have cloned an important negative regulator of cold
responsive gene expression, HOS1, and found that it is a RING finger protein with
an ubiquitin E3 ligase activity, thus implicating a critical role of protein degradation
in cold signaling. HOS1 also provides the first example of a cellular protein
that exhibits cold-regulated nucleocytoplasmic partitioning. More recently, we
have identified the ICE1 protein, a key upstream transcription factor that binds
to the CBF3 promoter and controls the expression of CBF genes in
the cold (Figure 3). Other work in our laboratory has shown a complex
regulation of cold signaling and tolerance by an RNA helicase, a bifunctional
enolase, and by the functional state of mitochondria.  | Figure
3. Cold-activated transcriptional cascade in Arabidopsis. SNOW is a partner
protein of ICE1 (unpublished). |
Back
to Top Gene
Silencing and Stress AdaptationEpigenetic control of gene expression
plays vital roles in development as well as in cellular responses to viruses,
transposons and transgenes in eukaryotes. The silencing of transgenes and endogenous
genes can occur at either the transcriptional (transcriptional gene silencing,
TGS) or posttranscriptional (posttranscriptional gene silencing, PTGS) levels.
While there has been tremendous progress in the understanding of PTGS in recent
years, the mechanism of TGS is not well understood. Little is known about the
initial trigger for DNA methylation that is important for stable TGS. In particular,
the cellular mechanisms for the active suppression of TGS are not known. We have
developed a unique TGS system in the model organism Arabidopsis thaliana.
In this system, an active transgene and a homologous endogenous gene become silenced
when cellular ROS (repressor of silencing)
factors are mutated (Figure 4). We have shown that ROS1 encodes
a DNA glycosylase/lyase that reverses the hypermethylation and TGS of the homologous
genes by active DNA demethylation via a base excision repair mechanism. We hypothesize
that double stranded RNA (or its small RNA products) from the transgene repeat
triggers the silencing of the homologous genes and the ROS factors counter
the production or action of the silencing RNA to prevent RNA-dependent DNA methylation
or participate in the active demethylation of the DNA (Figure 4).
To test this hypothesis, we plan to characterize the putative DNA demethylation
activity of ROS1, to clone other ROS loci, to identify ROS1-interacting
proteins, and to isolate and clone ros1 suppressor mutations. In
related projects, we are investigating the potential role of miRNAs and other
small RNAs in the regulation of stress-responsive genes and in stress adaptation.
 | Figure
4. Suppression of transcriptional gene silencing by ROS (repressor of silencing)
proteins. The RD29A-LUC transgene repeat generates small RNAs that are
proposed to be the diffusible signal for triggering the hypermethylation of the
RD29A promoter at both the transgene and endogenous loci on two different
chromosomes. ROS1 is proposed to counter the silencing activity of the small RNAs
by active demethylation of the promoter DNA. ROS2 and ROS3 have not been cloned,
and may encode proteins that act together with ROS1 in a base excision DNA repair
pathway for demethylation, or function in suppressing the production or action
of the silencing dsRNA or small RNAs. |
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Selected Publications
(Bibliography page)
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