Post-transcriptional gene regulation by RNA recognition motif (RRM) proteins through binding to c... more Post-transcriptional gene regulation by RNA recognition motif (RRM) proteins through binding to cis-elements in the 3'-untranslated region (3'-UTR) is widely used in eukaryotes to complete various biological processes. Rice MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2) is the RRM protein that functions in the transition to meiosis in proper timing. The MEL2 RRM preferentially associated with the U-rich RNA consensus, UUAGUU[U/A][U/G][A/U/G]U, dependently on sequences and proportionally to MEL2 protein amounts in vitro. The consensus sequences were located in the putative looped structures of the RNA ligand. A genome-wide survey revealed a tendency of MEL2-binding consensus appearing in 3'-UTR of rice genes. Of 249 genes that conserved the consensus in their 3'-UTR, 13 genes spatiotemporally co-expressed with MEL2 in meiotic flowers, and included several genes whose function was supposed in meiosis; such as Replication protein A and OsMADS3. The proteome analysis revealed that the amounts of small ubiquitin-related modifier-like protein and eukaryotic translation initiation factor3-like protein were dramatically altered in mel2 mutant anthers. Taken together with transcriptome and gene ontology results, we propose that the rice MEL2 is involved in the translational regulation of key meiotic genes on 3'-UTRs to achieve the faithful transition of germ cells to meiosis.
Proceedings of The National Academy of Sciences, 2008
Histone modification in chromatin is one of the key control points in gene regulation in eukaryot... more Histone modification in chromatin is one of the key control points in gene regulation in eukaryotic cells. Protein complexes composed of histone acetyltransferase or deacetylase, WD40 repeat protein, and many other components have been implicated in this process. Here, we report the identification and functional characterization of HOS15, a WD40-repeat protein crucial for repression of genes associated with abiotic stress
Investigations of plant responses to abiotic stresses has recently been advanced by new technolog... more Investigations of plant responses to abiotic stresses has recently been advanced by new technologies that promise to move from the analysis of single factors to an integrative understanding of entire systems. We will discuss results from relevant new technologies. First, collections of mutants specifically generated to report altered response to, for example, ionic and osmotic imbalances or pathogen attack. Literally hundreds of such mutants have been characterized to some degree. For many genes that have been recognized in these mutant lines a clear relationship to a specific function in the stress response is difficult to assess. A picture emerges suggesting that any deviation from cellular homeostasis that is perceived by different signaling events leads to responses that are not necessarily specific to the particular stress. Instead, there seems to be an inbuilt element of noise that may serve in eliminating unspecific stress responses and focusing on a specific reaction sequenc...
Using a cDNA microarray containing 7943 ESTs, the behavior of the maize root transcriptome has be... more Using a cDNA microarray containing 7943 ESTs, the behavior of the maize root transcriptome has been monitored in a time course for 72 h after imposition of salinity stress (150 mM NaCI). Under these conditions, root sodium amounts increased faster than in leaves, and root potassium decreased significantly. Although the overall free amino acid concentration was not affected, amino acid composition was changed with proline and asparagine increasing. Microarray analysis identified 916 ESTs representing genes whose steady-state RNA levels were significantly altered at various time points, corresponding to 11% of the ESTs printed. The response of the transcriptome to sub-lethal salt stress was rapid and transient, leading to a burst of changes at the three-hour time point. The salt-regulated ESTs represented 472 tentatively unique genes (TUGs), which, based on functional category analysis, are involved in a broad range of cellular and biochemical activities, prominent amongst which were ...
We report the genome sequence of the nonseed vascular plant, Selaginella moellendorffii, and by c... more We report the genome sequence of the nonseed vascular plant, Selaginella moellendorffii, and by comparative genomics identify genes that likely played important roles in the early evolution of vascular plants and their subsequent evolution
Vascular plants appeared ~410 million years ago, then diverged into several lineages of which onl... more Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
ABSTRACT The common ice plant, Mesembryanthemum crystallinum L., is a eu-halophytic model species... more ABSTRACT The common ice plant, Mesembryanthemum crystallinum L., is a eu-halophytic model species with an environmental stress-initiated switch from C-3 photosynthesis to crassulacean acid metabolism (CAM). Phosphoenolpyruvate carboxylase activity in 6-week-old plants exposed to salt stress for 5 days was similar to 15-fold higher than before stress, indicating the salinity-dependent induction of the C-3 to CAM transition. Five plant protein phosphatase type 2C (PP2C) genes were cloned, representative of. ve of the 10 plant PP2C sub-families. We measured mRNA levels of these PP2Cs and of myo-inositol 1-phosphate synthase (Inps1) in 6-week-old plants before (C-3) and after (CAM) salt stress. Remarkably, four PP2C genes and Inps1 were expressed with a diurnal fluctuation in plants in C-3 mode. After salt-induced CAM induction, the six genes were expressed with more prominent fluctuations than before stress, suggesting that these PP2C genes may be involved in the diurnal regulation of protein phosphorylation in CAM. Under continuous light treatment the expression of two PP2C genes continued to fluctuate, indicating that their expression is controlled by circadian rhythm.
Inositol transporters (ITRs) are membrane proteins in the carbohydrate transporter super-family. ... more Inositol transporters (ITRs) are membrane proteins in the carbohydrate transporter super-family. We have characterized plant ITR-like coding regions from Mesembryanthemum and Arabidopsis by their expression in yeast strains deficient in myo-inositol (MI) biosynthesis and compromised in inositol uptake. Both AtITR1 and McITR1 were capable of complementing the uptake deficiency of the cells albeit at a lower efficiency when compared to
The molecular mechanism for meiotic entry remains largely elusive in flowering plants. Only Arabi... more The molecular mechanism for meiotic entry remains largely elusive in flowering plants. Only Arabidopsis SWI1/DYAD and maize AM1, both of which are the coiled-coil protein, are known to be required for the initiation of plant meiosis. The mechanism underlying the synchrony of male meiosis, characteristic to flowering plants, has also been unclear in the plant kingdom. In other eukaryotes, RNA-recognition-motif (RRM) proteins are known to play essential roles in germ-cell development and meiosis progression. Rice MEL2 protein discovered in this study shows partial similarity with human proline-rich RRM protein, deleted in Azoospermia-Associated Protein1 (DAZAP1), though MEL2 also possesses ankyrin repeats and a RING finger motif. Expression analyses of several cell-cycle markers revealed that, in mel2 mutant anthers, most germ cells failed to enter premeiotic S-phase and meiosis, and a part escaped from the defect and underwent meiosis with a significant delay or continued mitotic cycles. Immunofluorescent detection revealed that T7 peptide-tagged MEL2 localized at cytoplasmic perinuclear region of germ cells during premeiotic interphase in transgenic rice plants. This study is the first report of the plant RRM protein, which is required for regulating the premeiotic G1/S-phase transition of male and female germ cells and also establishing synchrony of male meiosis. This study will contribute to elucidation of similarities and diversities in reproduction system between plants and other species.
Post-transcriptional gene regulation by RNA recognition motif (RRM) proteins through binding to c... more Post-transcriptional gene regulation by RNA recognition motif (RRM) proteins through binding to cis-elements in the 3'-untranslated region (3'-UTR) is widely used in eukaryotes to complete various biological processes. Rice MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2) is the RRM protein that functions in the transition to meiosis in proper timing. The MEL2 RRM preferentially associated with the U-rich RNA consensus, UUAGUU[U/A][U/G][A/U/G]U, dependently on sequences and proportionally to MEL2 protein amounts in vitro. The consensus sequences were located in the putative looped structures of the RNA ligand. A genome-wide survey revealed a tendency of MEL2-binding consensus appearing in 3'-UTR of rice genes. Of 249 genes that conserved the consensus in their 3'-UTR, 13 genes spatiotemporally co-expressed with MEL2 in meiotic flowers, and included several genes whose function was supposed in meiosis; such as Replication protein A and OsMADS3. The proteome analysis revealed that the amounts of small ubiquitin-related modifier-like protein and eukaryotic translation initiation factor3-like protein were dramatically altered in mel2 mutant anthers. Taken together with transcriptome and gene ontology results, we propose that the rice MEL2 is involved in the translational regulation of key meiotic genes on 3'-UTRs to achieve the faithful transition of germ cells to meiosis.
Proceedings of The National Academy of Sciences, 2008
Histone modification in chromatin is one of the key control points in gene regulation in eukaryot... more Histone modification in chromatin is one of the key control points in gene regulation in eukaryotic cells. Protein complexes composed of histone acetyltransferase or deacetylase, WD40 repeat protein, and many other components have been implicated in this process. Here, we report the identification and functional characterization of HOS15, a WD40-repeat protein crucial for repression of genes associated with abiotic stress
Investigations of plant responses to abiotic stresses has recently been advanced by new technolog... more Investigations of plant responses to abiotic stresses has recently been advanced by new technologies that promise to move from the analysis of single factors to an integrative understanding of entire systems. We will discuss results from relevant new technologies. First, collections of mutants specifically generated to report altered response to, for example, ionic and osmotic imbalances or pathogen attack. Literally hundreds of such mutants have been characterized to some degree. For many genes that have been recognized in these mutant lines a clear relationship to a specific function in the stress response is difficult to assess. A picture emerges suggesting that any deviation from cellular homeostasis that is perceived by different signaling events leads to responses that are not necessarily specific to the particular stress. Instead, there seems to be an inbuilt element of noise that may serve in eliminating unspecific stress responses and focusing on a specific reaction sequenc...
Using a cDNA microarray containing 7943 ESTs, the behavior of the maize root transcriptome has be... more Using a cDNA microarray containing 7943 ESTs, the behavior of the maize root transcriptome has been monitored in a time course for 72 h after imposition of salinity stress (150 mM NaCI). Under these conditions, root sodium amounts increased faster than in leaves, and root potassium decreased significantly. Although the overall free amino acid concentration was not affected, amino acid composition was changed with proline and asparagine increasing. Microarray analysis identified 916 ESTs representing genes whose steady-state RNA levels were significantly altered at various time points, corresponding to 11% of the ESTs printed. The response of the transcriptome to sub-lethal salt stress was rapid and transient, leading to a burst of changes at the three-hour time point. The salt-regulated ESTs represented 472 tentatively unique genes (TUGs), which, based on functional category analysis, are involved in a broad range of cellular and biochemical activities, prominent amongst which were ...
We report the genome sequence of the nonseed vascular plant, Selaginella moellendorffii, and by c... more We report the genome sequence of the nonseed vascular plant, Selaginella moellendorffii, and by comparative genomics identify genes that likely played important roles in the early evolution of vascular plants and their subsequent evolution
Vascular plants appeared ~410 million years ago, then diverged into several lineages of which onl... more Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
ABSTRACT The common ice plant, Mesembryanthemum crystallinum L., is a eu-halophytic model species... more ABSTRACT The common ice plant, Mesembryanthemum crystallinum L., is a eu-halophytic model species with an environmental stress-initiated switch from C-3 photosynthesis to crassulacean acid metabolism (CAM). Phosphoenolpyruvate carboxylase activity in 6-week-old plants exposed to salt stress for 5 days was similar to 15-fold higher than before stress, indicating the salinity-dependent induction of the C-3 to CAM transition. Five plant protein phosphatase type 2C (PP2C) genes were cloned, representative of. ve of the 10 plant PP2C sub-families. We measured mRNA levels of these PP2Cs and of myo-inositol 1-phosphate synthase (Inps1) in 6-week-old plants before (C-3) and after (CAM) salt stress. Remarkably, four PP2C genes and Inps1 were expressed with a diurnal fluctuation in plants in C-3 mode. After salt-induced CAM induction, the six genes were expressed with more prominent fluctuations than before stress, suggesting that these PP2C genes may be involved in the diurnal regulation of protein phosphorylation in CAM. Under continuous light treatment the expression of two PP2C genes continued to fluctuate, indicating that their expression is controlled by circadian rhythm.
Inositol transporters (ITRs) are membrane proteins in the carbohydrate transporter super-family. ... more Inositol transporters (ITRs) are membrane proteins in the carbohydrate transporter super-family. We have characterized plant ITR-like coding regions from Mesembryanthemum and Arabidopsis by their expression in yeast strains deficient in myo-inositol (MI) biosynthesis and compromised in inositol uptake. Both AtITR1 and McITR1 were capable of complementing the uptake deficiency of the cells albeit at a lower efficiency when compared to
The molecular mechanism for meiotic entry remains largely elusive in flowering plants. Only Arabi... more The molecular mechanism for meiotic entry remains largely elusive in flowering plants. Only Arabidopsis SWI1/DYAD and maize AM1, both of which are the coiled-coil protein, are known to be required for the initiation of plant meiosis. The mechanism underlying the synchrony of male meiosis, characteristic to flowering plants, has also been unclear in the plant kingdom. In other eukaryotes, RNA-recognition-motif (RRM) proteins are known to play essential roles in germ-cell development and meiosis progression. Rice MEL2 protein discovered in this study shows partial similarity with human proline-rich RRM protein, deleted in Azoospermia-Associated Protein1 (DAZAP1), though MEL2 also possesses ankyrin repeats and a RING finger motif. Expression analyses of several cell-cycle markers revealed that, in mel2 mutant anthers, most germ cells failed to enter premeiotic S-phase and meiosis, and a part escaped from the defect and underwent meiosis with a significant delay or continued mitotic cycles. Immunofluorescent detection revealed that T7 peptide-tagged MEL2 localized at cytoplasmic perinuclear region of germ cells during premeiotic interphase in transgenic rice plants. This study is the first report of the plant RRM protein, which is required for regulating the premeiotic G1/S-phase transition of male and female germ cells and also establishing synchrony of male meiosis. This study will contribute to elucidation of similarities and diversities in reproduction system between plants and other species.
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Papers by Saori Miyazaki