Satoshi Naito
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View article: Ribosome stalling-induced <i>NIP5;1</i> mRNA decay triggers ARGONAUTE1-dependent transcription downregulation
Ribosome stalling-induced <i>NIP5;1</i> mRNA decay triggers ARGONAUTE1-dependent transcription downregulation Open
In eukaryotes, messenger RNA (mRNA) accumulation is regulated through the levels of transcription, processing, and degradation. Here, we uncover the multi-level regulatory mechanism governing the expression of NIP5;1, a boron (B) diffusion…
View article: Compensatory mechanisms underlying arginine vasopressin regulation in transient polyuria during pregnancy
Compensatory mechanisms underlying arginine vasopressin regulation in transient polyuria during pregnancy Open
Transient polyuria during pregnancy is reportedly caused by increased arginine vasopressin (AVP) degradation due to vasopressinase produced by the placenta. The mechanism underlying transient polyuria during pregnancy has not been establis…
View article: Phylogeny-linked occurrence of ribosome stalling on the mRNAs of Arabidopsis unfolded protein response factor <i>bZIP60</i> orthologs in divergent plant species
Phylogeny-linked occurrence of ribosome stalling on the mRNAs of Arabidopsis unfolded protein response factor <i>bZIP60</i> orthologs in divergent plant species Open
The bZIP60, XBP1 and HAC1 mRNAs encode transcription factors that mediate the unfolded protein response (UPR) in plants, animals and yeasts, respectively. Upon UPR, these mRNAs undergo unconventional cytoplasmic splicing on the endoplasmic…
View article: Upstream open reading frame-mediated upregulation of ANAC082 expression in response to nucleolar stress in Arabidopsis
Upstream open reading frame-mediated upregulation of ANAC082 expression in response to nucleolar stress in Arabidopsis Open
Perturbations in ribosome biogenesis cause a type of cellular stress called nucleolar or ribosomal stress, which triggers adaptive responses in both animal and plant cells. The Arabidopsis ANAC082 transcription factor has been identified a…
View article: The conserved upstream ORF of the Arabidopsis<i>ANAC082</i>gene mediates translational upregulation in response to nucleolar stress
The conserved upstream ORF of the Arabidopsis<i>ANAC082</i>gene mediates translational upregulation in response to nucleolar stress Open
Perturbations in ribosome biogenesis cause a type of cellular stress called nucleolar or ribosomal stress, which triggers adaptive responses in both animal and plant cells. The Arabidopsis ANAC082 transcription factor has been identified a…
View article: Translational Landscape of a C4 Plant, <i>Sorghum bicolor</i>, Under Normal and Sulfur-Deficient Conditions
Translational Landscape of a C4 Plant, <i>Sorghum bicolor</i>, Under Normal and Sulfur-Deficient Conditions Open
Recent accumulation of genomic and transcriptomic information has facilitated genetic studies. Increasing evidence has demonstrated that translation is an important regulatory step, and the transcriptome does not necessarily reflect the pr…
View article: Global analysis of boron‐induced ribosome stalling reveals its effects on translation termination and unique regulation by AUG‐stops in Arabidopsis shoots
Global analysis of boron‐induced ribosome stalling reveals its effects on translation termination and unique regulation by AUG‐stops in Arabidopsis shoots Open
SUMMARY We previously reported that ribosome stalling at AUG‐stop sequences in the 5′‐untranslated region plays a critical role in regulating the expression of Arabidopsis thaliana NIP5;1 , which encodes a boron uptake transporter, in resp…
View article: Genome-wide identification of Arabidopsis non-AUG-initiated upstream ORFs with evolutionarily conserved regulatory sequences that control protein expression levels
Genome-wide identification of Arabidopsis non-AUG-initiated upstream ORFs with evolutionarily conserved regulatory sequences that control protein expression levels Open
Upstream open reading frames (uORFs) are short ORFs found in the 5′-UTRs of many eukaryotic transcripts and can influence the translation of protein-coding main ORFs (mORFs). Recent genome-wide ribosome profiling studies have revealed that…
View article: Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes
Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes Open
Upstream open reading frames (uORFs) are present in the 5′-untranslated regions of many eukaryotic mRNAs, and some peptides encoded by these regions play important regulatory roles in controlling main ORF (mORF) translation. We previously …
View article: Additional file 1 of Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA
Additional file 1 of Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA Open
Additional file 1 : Supplementary Table S1. CPuORFs extracted from A. thaliana, O. sativa, S. lycopersicum, P. trichocarpa and V. vinifera.
View article: Additional file 2 of Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA
Additional file 2 of Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA Open
Additional file 2 : Supplementary Table S2. Taxonomic range of sequence conservation of the CPuORFs.
View article: Additional file 3 of Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA
Additional file 3 of Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA Open
Additional file 3 : Supplementary Table S3. Multiple CPuORF sequence alignments.
View article: Reverse genetics-based biochemical studies of the ribosomal exit tunnel constriction region in eukaryotic ribosome stalling: spatial allocation of the regulatory nascent peptide at the constriction
Reverse genetics-based biochemical studies of the ribosomal exit tunnel constriction region in eukaryotic ribosome stalling: spatial allocation of the regulatory nascent peptide at the constriction Open
A number of regulatory nascent peptides have been shown to regulate gene expression by causing programmed ribosome stalling during translation. Nascent peptide emerges from the ribosome through the exit tunnel, and one-third of the way alo…
View article: Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes
Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes Open
Upstream open reading frames (uORFs) are present in the 5’-untranslated regions of many eukaryotic mRNAs, and some peptides encoded by these regions play important regulatory roles in controlling main ORF (mORF) translation. We previously …
View article: Polar Localization of the Borate Exporter BOR1 Requires AP2-Dependent Endocytosis
Polar Localization of the Borate Exporter BOR1 Requires AP2-Dependent Endocytosis Open
Boron (B) is an essential element in plants but is toxic when it accumulates to high levels. In root cells of Arabidopsis (Arabidopsis thaliana), the borate exporter BOR1 is polarly localized in the plasma membrane toward the stele side fo…
View article: Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA
Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA Open
Background Upstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of do…
View article: Boron-Dependent Translational Suppression of the Borate Exporter <i>BOR1</i> Contributes to the Avoidance of Boron Toxicity
Boron-Dependent Translational Suppression of the Borate Exporter <i>BOR1</i> Contributes to the Avoidance of Boron Toxicity Open
Boron (B) is an essential element for plants; however, as high B concentrations are toxic, B transport must be tightly regulated. BOR1 is a borate exporter in Arabidopsis (Arabidopsis thaliana) that facilitates B translocation into shoots …
View article: Identification of Arabidopsis thaliana upstream open reading frames encoding peptide sequences that cause ribosomal arrest
Identification of Arabidopsis thaliana upstream open reading frames encoding peptide sequences that cause ribosomal arrest Open
Specific sequences of certain nascent peptides cause programmed ribosomal arrest during mRNA translation to control gene expression. In eukaryotes, most known regulatory arrest peptides are encoded by upstream open reading frames (uORFs) p…
View article: Co-ordinated Regulations of mRNA Synthesis and Decay during Cold Acclimation in Arabidopsis Cells
Co-ordinated Regulations of mRNA Synthesis and Decay during Cold Acclimation in Arabidopsis Cells Open
Plants possess a cold acclimation system to acquire freezing tolerance through pre-exposure to non-freezing low temperatures. The transcriptional cascade of C-repeat-binding factors (CBFs)/dehydration response element-binding factors (DREB…
View article: Sucrose sensing through nascent peptide‐meditated ribosome stalling at the stop codon of <i>Arabidopsis <scp>bZIP</scp>11 </i><scp>uORF</scp>2
Sucrose sensing through nascent peptide‐meditated ribosome stalling at the stop codon of <i>Arabidopsis <span>bZIP</span>11 </i><span>uORF</span>2 Open
Arabidopsis bZIP 11 is a transcription factor that modulates amino acid metabolism under high‐sucrose conditions. Expression of bZIP 11 is downregulated in a sucrose‐dependent manner during translation. Previous in vivo studies have identi…
View article: Polar Localization of the NIP5;1 Boric Acid Channel Is Maintained by Endocytosis and Facilitates Boron Transport in Arabidopsis Roots
Polar Localization of the NIP5;1 Boric Acid Channel Is Maintained by Endocytosis and Facilitates Boron Transport in Arabidopsis Roots Open
Boron uptake in Arabidopsis thaliana is mediated by nodulin 26-like intrinsic protein 5;1 (NIP5;1), a boric acid channel that is located preferentially on the soil side of the plasma membrane in root cells. However, the mechanism underlyin…
View article: The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation
The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation Open
Upstream open reading frames (uORFs) are often translated ahead of the main ORF of a gene and regulate gene expression, sometimes in a condition-dependent manner, but such a role for the minimum uORF (hereafter referred to as AUG-stop) in …
View article: DRP1-Dependent Endocytosis is Essential for Polar Localization and Boron-Induced Degradation of the Borate Transporter BOR1 in<i>Arabidopsis thaliana</i>
DRP1-Dependent Endocytosis is Essential for Polar Localization and Boron-Induced Degradation of the Borate Transporter BOR1 in<i>Arabidopsis thaliana</i> Open
Boron (B) is essential for plants but toxic in excess. The borate efflux transporter BOR1 is expressed in various root cells and localized to the inner/stele-side domain of the plasma membrane (PM) under low-B conditions. BOR1 is rapidly d…
View article: Tolerance to Excess-Boron Conditions Acquired by Stabilization of a BOR1 Variant with Weak Polarity in Arabidopsis
Tolerance to Excess-Boron Conditions Acquired by Stabilization of a BOR1 Variant with Weak Polarity in Arabidopsis Open
Boron (B) is a metalloid that is essential for plant growth but is toxic when present in excess. Arabidopsis BOR1 is a borate exporter, facilitating B translocation from root to shoot under limited-B conditions. BOR1 shows stele side polar…
View article: Evolutionary Divergence of Plant Borate Exporters and Critical Amino Acid Residues for the Polar Localization and Boron-Dependent Vacuolar Sorting of AtBOR1
Evolutionary Divergence of Plant Borate Exporters and Critical Amino Acid Residues for the Polar Localization and Boron-Dependent Vacuolar Sorting of AtBOR1 Open
Boron (B) is an essential micronutrient for plants but is toxic when accumulated in excess. The plant BOR family encodes plasma membrane-localized borate exporters (BORs) that control translocation and homeostasis of B under a wide range o…
View article: Identification of novel <i>Arabidopsis thaliana</i> upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner
Identification of novel <i>Arabidopsis thaliana</i> upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner Open
Upstream open reading frames (uORFs) are often found in the 5′-leader regions of eukaryotic mRNAs and can negatively modulate the translational efficiency of the downstream main ORF. Although the effects of most uORFs are thought to be ind…