Gravity is a critical environmental factor regulating directional growth and morphogenesis in pla... more Gravity is a critical environmental factor regulating directional growth and morphogenesis in plants, and gravitropism is the process by which plants perceive and respond to the gravity vector. The cytoskeleton is proposed to play important roles in gravitropism, but the underlying mechanisms are obscure. Here we use genetic screening in Physcomitrella patens, to identify a locus GTRC, that when mutated, reverses the direction of protonemal gravitropism. GTRC encodes a processive minus-end-directed KCHb kinesin, and its N-terminal, C-terminal and motor domains are all essential for transducing the gravity signal. Chimeric analysis between GTRC/KCHb and KCHa reveal a unique role for the N-terminus of GTRC in gravitropism. Further study shows that gravity-triggered normal asymmetric distribution of actin filaments in the tip of protonema is dependent on GTRC. Thus, our work identifies a microtubule-based cellular motor that determines the direction of plant gravitropism via mediating ...
Seed dispersal: theory and its application in a changing world, 2007
This chapter briefly reviews some of the key challenges in understanding the impact of seed consu... more This chapter briefly reviews some of the key challenges in understanding the impact of seed consumers on plant dispersal and demography, and provides an overview of a case study in oaks (Quercus) from Pennsylvania, Maryland, Virginia and southern Indiana, USA, that serves to illustrate many of these issues.
Arabidopsis thaliana seedlings undergo photomorphogenic development even in darkness when the fun... more Arabidopsis thaliana seedlings undergo photomorphogenic development even in darkness when the function of DE-ETIOLATED1 (DET1), a repressor of photomorphogenesis, is disrupted. However, the mechanism by which DET1 represses photomorphogenesis remains unclear. Our results indicate that DET1 directly interacts with a group of transcription factors known as the phytochrome-interacting factors (PIFs). Furthermore, our results suggest that DET1 positively regulates PIF protein levels primarily by stabilizing PIF proteins in the dark. Genetic analysis showed that each pif single mutant could enhance the det1-1 phenotype, and ectopic expression of each PIF in det1-1 partially suppressed the det1-1 phenotype, based on hypocotyl elongation and cotyledon opening angles observed in darkness. Genomic analysis also revealed that DET1 may modulate the expression of light-regulated genes to mediate photomorphogenesis partially through PIFs. The observed interaction and regulation between DET1 and ...
The G-box is a cis-acting element found within the promoters of many plant genes where it mediate... more The G-box is a cis-acting element found within the promoters of many plant genes where it mediates expression in response to a variety of different stimuli. This palindromic DNA motif (CCACGTGG) is composed of two identical half sites, the base pairs of which we have numbered -4 to +4 (numbering from 5' to 3'). Both half sites are involved in the binding of the bZIP protein GBF1, a member of the GBF family of Arabidopsis thaliana. Here we demonstrate using the random binding site selection method that GBF1 interacts with, in addition to the palindromic G-box, other DNA motifs that fall into seven distinct groups. All groups share the ACGT core sequence, common to most DNA motifs bound by plant bZIP proteins so far characterized. Our studies demonstrate that a high affinity GBF1 binding site is further defined by the following two parameters: first, all sites contain a G residue at position +3 (as in ACGTG) and secondly, only certain base pair combinations are allowed at posi...
Proceedings of the National Academy of Sciences of the United States of America, Jan 15, 2014
Seedling photomorphogenesis is a sophisticated developmental process that is controlled by both t... more Seedling photomorphogenesis is a sophisticated developmental process that is controlled by both the transcriptional and posttranscriptional regulation of gene expression. Here, we identify an Arabidopsis noncoding RNA, designated hidden treasure 1 (HID1), as a factor promoting photomorphogenesis in continuous red light (cR). We show that HID1 acts through phytochrome-interacting factor 3 (PIF3), which encodes a basic helix-loop-helix transcription factor known to be a key repressor of photomorphogenesis. Knockdown of HID1 in hid1 mutants leads to a significant increase in the expression of PIF3, which in turn drives the development of elongated hypocotyls in cR. We identified two major stem-loops in HID1 that are essential for its modulation of hypocotyl growth in cR-grown seedlings. Furthermore, our data reveal that HID1 is assembled into large nuclear protein-RNA complex(es) and that it associates with the chromatin of the first intron of PIF3 to repress its transcription. Strikin...
The G-box is an important regulatory element found in the promoters of many different genes. Four... more The G-box is an important regulatory element found in the promoters of many different genes. Four members of an Arabidopsis gene family encoding basic leucine zipper proteins (GBFs) which bind the G-box have previously been cloned. To study GBFs, a polyclonal antibody was raised against GBF1 expressed in bacteria. This antibody also recognized GBF2 and GBF3. Immunoblot analysis of nuclear and cytoplasmic fractions from Arabidopsis and soybean (SB-M) cell cultures indicated that over 90% of proteins detected with anti-GBF1 were cytoplasmic. Electrophoretic mobility shift assays indicated that over 90% of G-box binding activity was cytoplasmic. DNA affinity chromatography demonstrated that each protein detected with anti-GBF1 specifically bound the G-box. To study individual GBFs, DNA constructs fusing GBF1, GBF2 and GBF4 to GUS were made and assayed by transient expression in SB-M protoplasts. Of GUS:GBF1 proteins, 50-62% were localized in the cytoplasm under all conditions tested, while 97% of GUS:GBF4 was localized in the nucleus. By contrast, whereas about 50% of GUS:GBF2 was found in the cytoplasm of dark-grown cells, over 80% of this protein was found in the nucleus in cells cultured under blue light. Deletion analysis of GBF1 identified a region between amino acids 112 and 164 apparently required for cytoplasmic retention. These results suggest the intriguing possibility that limitation of nuclear access may be an important control on GBF activity. In particular, GBF2 is apparently specifically imported into the nucleus in response to light.
We present high-resolution maps of DNA methylation and H3K4 di- and trimethylation of two entire ... more We present high-resolution maps of DNA methylation and H3K4 di- and trimethylation of two entire chromosomes and two fully sequenced centromeres in rice (Oryza sativa) shoots and cultured cells. This analysis reveals combinatorial interactions between these epigenetic modifications and chromatin structure and gene expression. Cytologically densely stained heterochromatin had less H3K4me2 and H3K4me3 and more methylated DNA than the less densely stained euchromatin, whereas centromeres had a unique epigenetic composition. Most transposable elements had highly methylated DNA but no H3K4 methylation, whereas more than half of protein-coding genes had both methylated DNA and di- and/or trimethylated H3K4. Methylation of DNA but not H3K4 was correlated with suppressed transcription. By contrast, when both DNA and H3K4 were methylated, transcription was only slightly reduced. Transcriptional activity was positively correlated with the ratio of H3K4me3/H3K4me2: genes with predominantly H3K...
As more and more genetically modified organisms (GMO) are commercialized, efficient and inexpensi... more As more and more genetically modified organisms (GMO) are commercialized, efficient and inexpensive assays are required for their quick detection. An event-specific detection strategy based on the unique and specific sequences of integration junctions is useful because of its high specificity. This study developed a system for detecting six GM maize lines (Bt11, Bt176, GA21, MON810, NK603, and T25) using optical silicon thin-film biosensor chips. Aldehyde-labeled probes were arrayed and covalently attached to a hydrazine-derivatized chip surface. Biotinylated PCR amplicons were then hybridized with the probes. After washing and brief incubation with an anti-biotin IgG horseradish peroxidase conjugate and a precipitable horseradish peroxidase substrate, biotinylated PCR amplicons perfectly matched with the probes can be visualized by the color change on the chip surface (gold to blue/purple). This assay is extremely robust, exhibits high sensitivity and specificity, and is flexible from low through moderate to high throughput.
Plants use light as a source of both energy and information about their environment. One of the w... more Plants use light as a source of both energy and information about their environment. One of the ways they use the information is to adjust their development to suit prevailing light conditions. Perhaps the most striking example of this plasticity comes from ...
Annual Review of Plant Physiology and Plant Molecular Biology, 1995
... Substantial progress has been made in identifying steps in signal transduction from light per... more ... Substantial progress has been made in identifying steps in signal transduction from light perception to ... Gene fusions have also demonstrated that light negatively regulates PHYA (19) and NPR genes (118 ... Similarly, mutation of the G-box in the parsley CHS promoter resulted in ...
Gravity is a critical environmental factor regulating directional growth and morphogenesis in pla... more Gravity is a critical environmental factor regulating directional growth and morphogenesis in plants, and gravitropism is the process by which plants perceive and respond to the gravity vector. The cytoskeleton is proposed to play important roles in gravitropism, but the underlying mechanisms are obscure. Here we use genetic screening in Physcomitrella patens, to identify a locus GTRC, that when mutated, reverses the direction of protonemal gravitropism. GTRC encodes a processive minus-end-directed KCHb kinesin, and its N-terminal, C-terminal and motor domains are all essential for transducing the gravity signal. Chimeric analysis between GTRC/KCHb and KCHa reveal a unique role for the N-terminus of GTRC in gravitropism. Further study shows that gravity-triggered normal asymmetric distribution of actin filaments in the tip of protonema is dependent on GTRC. Thus, our work identifies a microtubule-based cellular motor that determines the direction of plant gravitropism via mediating ...
Seed dispersal: theory and its application in a changing world, 2007
This chapter briefly reviews some of the key challenges in understanding the impact of seed consu... more This chapter briefly reviews some of the key challenges in understanding the impact of seed consumers on plant dispersal and demography, and provides an overview of a case study in oaks (Quercus) from Pennsylvania, Maryland, Virginia and southern Indiana, USA, that serves to illustrate many of these issues.
Arabidopsis thaliana seedlings undergo photomorphogenic development even in darkness when the fun... more Arabidopsis thaliana seedlings undergo photomorphogenic development even in darkness when the function of DE-ETIOLATED1 (DET1), a repressor of photomorphogenesis, is disrupted. However, the mechanism by which DET1 represses photomorphogenesis remains unclear. Our results indicate that DET1 directly interacts with a group of transcription factors known as the phytochrome-interacting factors (PIFs). Furthermore, our results suggest that DET1 positively regulates PIF protein levels primarily by stabilizing PIF proteins in the dark. Genetic analysis showed that each pif single mutant could enhance the det1-1 phenotype, and ectopic expression of each PIF in det1-1 partially suppressed the det1-1 phenotype, based on hypocotyl elongation and cotyledon opening angles observed in darkness. Genomic analysis also revealed that DET1 may modulate the expression of light-regulated genes to mediate photomorphogenesis partially through PIFs. The observed interaction and regulation between DET1 and ...
The G-box is a cis-acting element found within the promoters of many plant genes where it mediate... more The G-box is a cis-acting element found within the promoters of many plant genes where it mediates expression in response to a variety of different stimuli. This palindromic DNA motif (CCACGTGG) is composed of two identical half sites, the base pairs of which we have numbered -4 to +4 (numbering from 5' to 3'). Both half sites are involved in the binding of the bZIP protein GBF1, a member of the GBF family of Arabidopsis thaliana. Here we demonstrate using the random binding site selection method that GBF1 interacts with, in addition to the palindromic G-box, other DNA motifs that fall into seven distinct groups. All groups share the ACGT core sequence, common to most DNA motifs bound by plant bZIP proteins so far characterized. Our studies demonstrate that a high affinity GBF1 binding site is further defined by the following two parameters: first, all sites contain a G residue at position +3 (as in ACGTG) and secondly, only certain base pair combinations are allowed at posi...
Proceedings of the National Academy of Sciences of the United States of America, Jan 15, 2014
Seedling photomorphogenesis is a sophisticated developmental process that is controlled by both t... more Seedling photomorphogenesis is a sophisticated developmental process that is controlled by both the transcriptional and posttranscriptional regulation of gene expression. Here, we identify an Arabidopsis noncoding RNA, designated hidden treasure 1 (HID1), as a factor promoting photomorphogenesis in continuous red light (cR). We show that HID1 acts through phytochrome-interacting factor 3 (PIF3), which encodes a basic helix-loop-helix transcription factor known to be a key repressor of photomorphogenesis. Knockdown of HID1 in hid1 mutants leads to a significant increase in the expression of PIF3, which in turn drives the development of elongated hypocotyls in cR. We identified two major stem-loops in HID1 that are essential for its modulation of hypocotyl growth in cR-grown seedlings. Furthermore, our data reveal that HID1 is assembled into large nuclear protein-RNA complex(es) and that it associates with the chromatin of the first intron of PIF3 to repress its transcription. Strikin...
The G-box is an important regulatory element found in the promoters of many different genes. Four... more The G-box is an important regulatory element found in the promoters of many different genes. Four members of an Arabidopsis gene family encoding basic leucine zipper proteins (GBFs) which bind the G-box have previously been cloned. To study GBFs, a polyclonal antibody was raised against GBF1 expressed in bacteria. This antibody also recognized GBF2 and GBF3. Immunoblot analysis of nuclear and cytoplasmic fractions from Arabidopsis and soybean (SB-M) cell cultures indicated that over 90% of proteins detected with anti-GBF1 were cytoplasmic. Electrophoretic mobility shift assays indicated that over 90% of G-box binding activity was cytoplasmic. DNA affinity chromatography demonstrated that each protein detected with anti-GBF1 specifically bound the G-box. To study individual GBFs, DNA constructs fusing GBF1, GBF2 and GBF4 to GUS were made and assayed by transient expression in SB-M protoplasts. Of GUS:GBF1 proteins, 50-62% were localized in the cytoplasm under all conditions tested, while 97% of GUS:GBF4 was localized in the nucleus. By contrast, whereas about 50% of GUS:GBF2 was found in the cytoplasm of dark-grown cells, over 80% of this protein was found in the nucleus in cells cultured under blue light. Deletion analysis of GBF1 identified a region between amino acids 112 and 164 apparently required for cytoplasmic retention. These results suggest the intriguing possibility that limitation of nuclear access may be an important control on GBF activity. In particular, GBF2 is apparently specifically imported into the nucleus in response to light.
We present high-resolution maps of DNA methylation and H3K4 di- and trimethylation of two entire ... more We present high-resolution maps of DNA methylation and H3K4 di- and trimethylation of two entire chromosomes and two fully sequenced centromeres in rice (Oryza sativa) shoots and cultured cells. This analysis reveals combinatorial interactions between these epigenetic modifications and chromatin structure and gene expression. Cytologically densely stained heterochromatin had less H3K4me2 and H3K4me3 and more methylated DNA than the less densely stained euchromatin, whereas centromeres had a unique epigenetic composition. Most transposable elements had highly methylated DNA but no H3K4 methylation, whereas more than half of protein-coding genes had both methylated DNA and di- and/or trimethylated H3K4. Methylation of DNA but not H3K4 was correlated with suppressed transcription. By contrast, when both DNA and H3K4 were methylated, transcription was only slightly reduced. Transcriptional activity was positively correlated with the ratio of H3K4me3/H3K4me2: genes with predominantly H3K...
As more and more genetically modified organisms (GMO) are commercialized, efficient and inexpensi... more As more and more genetically modified organisms (GMO) are commercialized, efficient and inexpensive assays are required for their quick detection. An event-specific detection strategy based on the unique and specific sequences of integration junctions is useful because of its high specificity. This study developed a system for detecting six GM maize lines (Bt11, Bt176, GA21, MON810, NK603, and T25) using optical silicon thin-film biosensor chips. Aldehyde-labeled probes were arrayed and covalently attached to a hydrazine-derivatized chip surface. Biotinylated PCR amplicons were then hybridized with the probes. After washing and brief incubation with an anti-biotin IgG horseradish peroxidase conjugate and a precipitable horseradish peroxidase substrate, biotinylated PCR amplicons perfectly matched with the probes can be visualized by the color change on the chip surface (gold to blue/purple). This assay is extremely robust, exhibits high sensitivity and specificity, and is flexible from low through moderate to high throughput.
Plants use light as a source of both energy and information about their environment. One of the w... more Plants use light as a source of both energy and information about their environment. One of the ways they use the information is to adjust their development to suit prevailing light conditions. Perhaps the most striking example of this plasticity comes from ...
Annual Review of Plant Physiology and Plant Molecular Biology, 1995
... Substantial progress has been made in identifying steps in signal transduction from light per... more ... Substantial progress has been made in identifying steps in signal transduction from light perception to ... Gene fusions have also demonstrated that light negatively regulates PHYA (19) and NPR genes (118 ... Similarly, mutation of the G-box in the parsley CHS promoter resulted in ...
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