Kenji Irie

• Doctor of Philosophy
• Professor (Full) at University of Tsukuba

Clb1 and Clb2 are functionally redundant B-type cyclins, and the clb1Δ clb2Δ double mutant is lethal. In normal mitotic growth, Clb2 plays the central role in the G2-M progression. We previously demonstrated that the RNA-binding protein Puf5 positively regulates CLB1 expression by downregulating expression of the repressor Ixr1. The decreased expre...

Gametogenesis in budding yeast involves a large-scale rearrangement of membrane traffic to allow the de novo formation of a membrane, called the prospore membrane (PSM). However, the mechanism underlying this event is not fully elucidated. Here, we show that the number of endoplasmic reticulum exit sites (ERES) per cell fluctuates and switches from...

Gametogenesis in budding yeast involves large-scale rearrangement of membrane traffic to allow de novo formation of a membrane, called the prospore membrane (PSM). However, the mechanism underlying this event is not fully elucidated. Here, we show that the number of endoplasmic reticulum exit sites (ERES) per cell fluctuates and switches from decre...

The spot assay of the budding yeast Saccharomyces cerevisiae is an experimental method that is used to evaluate the effect of genotypes, medium conditions, and environmental stresses on cell growth and survival. Automation of the spot assay experiments from preparing a dilution series to spotting to observing spots continuously has been implemented...

Puf5, a Puf-family RNA-binding protein, binds to 3´ untranslated region of target mRNAs and negatively regulates their expression in Saccharomyces cerevisiae. The puf5Δ mutant shows pleiotropic phenotypes including a weakened cell wall, a temperature-sensitive growth, and a shorter lifespan. To further analyze a role of Puf5 in cell growth, we sear...

RNA stability control contributes to the proper expression of gene products. Messenger RNAs (mRNAs) in eukaryotic cells possess a 5’ cap structure and the 3’ poly(A) tail which are important for mRNA stability and efficient translation. The Ccr4-Not complex is a major cytoplasmic deadenylase and functions in mRNA degradation. The CLB1-6 genes in Sa...

There are two major deadenylase complexes, Ccr4-Not and Pan2-Pan3, which shorten the 3′ poly(A) tail of mRNA and are conserved from yeast to human. We have previously shown that the Ccr4-mediated deadenylation plays the important role in gene expression regulation in the yeast stationary phase cell. In order to further understand the role of deaden...

Selective autophagy requires the autophagy receptor specifically localizing to the target for degradation. In the budding yeast, Atg39 and Atg40 function as an autophagy receptor for the endoplasmic reticulum (ER)-selective autophagy, referred to as ER-phagy. The expression level of the ATG39 gene is increased in response to ER stress and nitrogen...

Pbp1, the yeast ortholog of human Ataxin-2, was originally isolated as a poly(A) binding protein (Pab1)-binding protein. Pbp1 regulates the Pan2-Pan3 deadenylase complex, thereby modulating the mRNA stability and translation efficiency. However, the physiological significance of Pbp1 remains unclear since a yeast strain harboring PBP1 deletion grow...

eIF4E-binding proteins (4E-BPs) are translational repressors that compete with eIF4G for binding to eIF4E. Here we investigated the roles of yeast 4E-BPs, Eap1 and Caf20, in cell wall integrity pathway and gene expression. We found that eap1∆ mutation, but not caf20∆ mutation, showed synthetic growth defect with mutation in ROM2 gene encoding Rho1...

CCR4 and POP2 genes encode the catalytic subunit of the Ccr4‐Not complex involved in shortening mRNA poly(A) tail in Saccharomyces cerevisiae. The ccr4Δ and pop2∆ mutants exhibit pleiotropic phenotypes such as slow and temperature‐sensitive growth, aberrant expression of glucose repression genes, and abnormal cell wall synthesis. We previously foun...

Autophagy is a fundamental process responsible for degradation and recycling of intracellular contents. In the budding yeast, non-selective macroautophagy and microautophagy of the endoplasmic reticulum (ER) are caused by ER stress, the circumstance where aberrant proteins accumulate in the ER. The more recent study showed that protein aggregation...

The S. cerevisiae Pop2 protein is an exonuclease in the Ccr4-Not complex that is a conserved regulator of gene expression. Pop2 regulates gene expression post-transcriptionally by shortening the poly(A) tail of mRNA. A previous study has shown that Pop2 is phosphorylated at threonine 97 (T97) by Yak1 protein kinase in response to glucose limitation...

Strains used in this study. (DOCX)

Plasmids used in this study. (DOCX)

POP2 deletion induced the expression of stress response genes in YPD medium. (DOCX)

The PUF RNA‐binding protein Puf5 is involved in regulation of the cell wall integrity (CWI) pathway in yeast. Puf5 negatively regulates expression of LRG1 mRNA, encoding for a GTPase‐activating protein for Rho1 small GTPase. Here we further analyzed the effect of Puf5 on LRG1 expression, together with Ccr4 and Pop2 deadenylases, Dhh1 decapping acti...

Expression control of the protein phosphatase is critically involved in crosstalk and feedback of the cellular signaling. In the budding yeast ER stress response, multiple signaling pathways are activated and play key roles in adaptive reactions. However, it remains unclear how the expression level of the protein phosphatase is modulated during ER...

Sec2 activates Sec4 Rab GTPase as a guanine nucleotide exchange factor for the recruitment of downstream effectors to facilitate tethering and fusion of post-Golgi vesicles at the plasma membrane. During the meiosis and sporulation of budding yeast, post-Golgi vesicles are transported to and fused at the spindle pole body (SPB) to form a de novo me...

AMP-activated protein kinase (AMPK) is an evolutionarily conserved heterotrimeric kinase complex consisting of a catalytic subunit, α, and two regulatory subunits, β and γ. Previously, we demonstrated that Snf1, the Saccharomyces cerevisiae ortholog of AMPK, negatively regulates the unfolded protein response (UPR) pathway and the Hog1 MAP kinase pa...

Ccr4 is a major cytoplasmic deadenylase involved in mRNA poly(A) tail shortening in Saccharomyces cerevisiae. We have previously shown that Ccr4 negatively regulates expression of LRG1 mRNA encoding a GTPase-activating protein for the small GTPase Rho1, a component of cell wall integrity pathway, and deletion of LRG1 suppresses the temperature-sens...

Strains used in this study. (DOCX)

Plasmids used in this study. (DOCX)

References. (DOCX)

Post-transcriptional upregulation is an effective way to increase the expression of transgenes and thus maximize the yields of target chemicals from metabolically engineered organisms. Refractory elements in the 3′ untranslated region (UTR) that increase mRNA half-life might be available. In Saccharomyces cerevisiae, several terminator regions have...

Scd6, a yeast homologue of human RAP55, is a component of messenger ribonucleoproteins (mRNPs) that repress translation by binding to translation initiation factors, and also is a decapping activator along with the binding partners Edc3 and Dhh1. Herein, we report that Scd6 is a substrate of the intrinsic protein arginine methyltransferase, Hmt1, i...

Results of Yeast two-hybrid screening. (PDF)

Scd6 overexpression does not affect cell growth. Growth assays; Cells containing indicated plasmids were spotted onto SC medium lacking uracil (SC-Ura) and were incubated at 30°C. (TIF)

P-body formation is not affected by HMT1 discruption. Dcp2-GFP foci formation; Wild-type and hmt1 cells expressing Dcp2-GFP were grown to mid-log phase and resuspended into medium lacking glucose. (TIF)

Strains used in this study. (PDF)

Scd6 was not essential for general translation repression under glucose starvation conditions. Wild-type (WT) and scd6 dhh1 cells were grown in rich medium (+Dex) and were subjected to glucose deprivation (-Dex) and typical polysome profiles (OD254 traces) are presented. Small and large ribosomal subunits (40S and 60S, respectively), monosomes (80S...

Plasmids used in this study. (PDF)

No remarkable changes were observed for Scd6Flag associated proteins and RNAs in wild-type and hmt1 cells. (A) Colloidal Blue staining of Scd6Flag immunoprecipitates; Scd6Flag proteins from wild-type and hmt1 cells were immunoprecipitated using an anti-Flag antibody and were separated using SDS-PAGE gels followed by Colloidal blue staining. (B) Pur...

Ccr4, a component of the Ccr4-Not cytoplasmic deadenylase complex, is known to be required for the cell wall integrity (CWI) pathway in the budding yeast Saccharomyces cerevisiae. However, it is not fully understood how Ccr4 and other components of the Ccr4-Not complex regulate the CWI pathway. Previously, we showed that Ccr4 functions in the CWI p...

Author Summary All organisms are always exposed to several environmental stresses, including ultraviolet, heat, and chemical compounds. Therefore, every cell possesses defense mechanisms to maintain their survival under stressed conditions. Numerous studies have shown that a family of protein kinases plays a principal role in adaptive response to e...

The substantial merit of Cordyceps s.l. spp. in terms of medicinal benefits is largely appreciated. Nevertheless, only few studies have characterized and examined the clinical complications of the use of health tonics containing this species. Here, we epitypified C. formosana isolates that were collected and characterized as Ophiocordyceps formosan...

Degenerated primer sequences (Supporting Table 1) derived from the largest subunit of RNA polymerase II (RPB1), the second large subunit of RNA polymerase II (RPB2) and translation elongation factor-1α (EF1-α) genes were synthesized according to previous reports (30, 31, 32) and used for the molecular identifications of Cordyceps spp, (s. l.), incl...

The Saccharomyces cerevisiae Pbp1 [poly(A)-binding protein (Pab1)-binding protein] is believed to be involved in RNA metabolism and regulation of translation, since Pbp1 regulates a length of poly(A) tail and is involved in stress granule (SG) formation. However, a physiological function of Pbp1 remains unclear, since the pbp1Δ mutation has no obvi...

Nuclear factor-kappaB (NF-κB) is critical for the expression of multiple genes involved in inflammatory responses and cellular survival. NF-κB is normally sequestered in the cytoplasm through interaction with an inhibitor of NF-κB (IκB), but inflammatory stimulation induces proteasomal degradation of IκB, followed by NF-κB nuclear translocation. Th...

Sequence alignment of Brap2. Conserved sequences are highlighted in black. Asterisk indicates predicted neddylation sites on Brap2. (TIF)

Brap2 KR suppresses RelA/p65 translocation similar to Brap2 WT. HeLa cells were transfected with either Flag-Brap2 WT or Flag-Brap2 KR and stimulated with or without 5 ng/ml TNF-α for 30 min, and were subjected to immunocytochemistry using anti-Flag or anti-RelA/p65 antibodies. Bars, 10 µm. (TIF)

Nedd8 forms smear bands. HEK293 cells were transfected with either HA-Nedd8 or HA-Ub. Cell lysates were subjected to immunoprecipitation (IP) with HA antibody. The immunoprecipitants (IP) were subjected to immunoblot (IB) analyses with antibody to HA. (TIF)

Post-transcriptional regulation of gene expression by RNA-binding proteins has pivotal roles in many biological processes. We have shown that Stau1, a conserved RNA-binding protein, negatively regulates myogenesis in C2C12 myoblasts. However, its target mRNAs in regulation of myogenesis remain unknown. Here we describe that Stau1 positively regulat...

The Saccharomyces cerevisiae RNA-binding protein Khd1/Hek2 associates with hundreds of potential mRNA targets preferentially, including the mRNAs encoding proteins localized to the cell wall and plasma membrane. We have previously revealed that Khd1 positively regulates expression of MTL1 mRNA encoding a membrane sensor in the cell wall integrity (...

The smp3-1 mutant allele confers increased holding stability of heterologous plasmid, pSR1, and a temperature-sensitive growth defect which is remediable by the addition of 1 M sorbitol as the osmotic stabilizer. The smp3-1 allele contains two base substitutions; one is in the open reading frame and changed the 490th CAT (encoding Histidine) to TAT...

Khd1p (KH-domain protein 1) is a yeast RNA-binding protein highly homologous to mammalian hnRNP K. Khd1p associates with hundreds of potential mRNA targets including a bud-localized ASH1 mRNA and mRNAs encoding membrane-associated proteins such as Mid2p and Mtl1p. While Khd1p negatively regulates gene expression of Ash1p by translational repression...

Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a conserved RNA-binding protein that is involved in multiple processes of gene expression, including chromatin remodeling, transcription, RNA splicing, mRNA stability and translation, together with diverse groups of molecular partners. Here we identified a previously uncharacterized protein RNA...

The RNA-binding protein Khd1p (KH-domain protein 1) is required for efficient localization of ASH1 mRNA to the bud-tip, probably acting as a translational repressor during mRNA transport in yeast. Here, we have systematically examined Khd1p mRNA targets and colocalization with known bud-tip-localized mRNAs in vivo. Affinity purification and DNA mic...

Sequential expression of myogenic regulatory factors (MRFs) such as MyoD and myogenin drives myogenic differentiation. Besides transcriptional activation of MRFs, this process is also coordinated by post-transcriptional regulation; MyoD and myogenin mRNAs are stabilized by RNA-binding protein HuR. Stau1 is known to regulate mRNA stability in a comp...

Par-3 is a cell-polarity protein that regulates the formation of tight junctions (TJs) in epithelial cells, where claudin is a major cell-cell adhesion molecule (CAM). TJs are formed at the apical side of adherens junctions (AJs), where E-cadherin and nectin are major CAMs. We have revealed that nectin first forms cell-cell adhesions, and then recr...

Nectin is an immunoglobulin-like cell-cell adhesion molecule, which plays essential roles in the initial step of formation of adherens junctions and tight junctions. We demonstrate here the role of nectin-1 in the epidermis using nectin-1–/– mice. Newborn nectin-1–/– pups showed shiny and slightly reddish skin; the amount of loricrin, one of the di...

Seminiferous epithelia of the testes contain two types of intercellular junctions: Sertoli-Sertoli junctions and Sertoli-spermatid junctions. The former junctions are equipped with tight and adherens junctions while the latter junctions are not. Ca2+ -independent immunoglobulin-like cell-cell adhesion molecules, nectin-2 and nectin-3, asymmetricall...

Adherens junctions (AJs) and tight junctions (TJs) comprise a junctional complex which plays key roles not only in cell adhesion and polarization but also in regulation of cell movement and proliferation in epithelial cells. E-Cadherin and nectin are major cell-cell adhesion molecules (CAMs) at AJs, whereas claudin is a major CAM at TJs. We have sh...

The Ca2+-independent immunoglobulin-like molecule nectin first forms cell-cell adhesion and then assembles cadherin at nectin-based cell-cell adhesion sites, resulting in the formation of adherens junctions (AJs). Afadin is a nectin- and actin filament-binding protein that connects nectin to the actin cytoskeleton. Here, we studied the roles and mo...

Nectin is a Ca2+-independent Ig-like cell-cell adhesion molecule that forms homo- and hetero-trans-dimers (trans-interaction). Nectin first forms cell-cell adhesions and then recruits cadherin to the nectin-based cell-cell adhesion sites to form AJ cooperatively with cadherin. In addition, the trans-interaction of nectin and nectin induces the acti...

The formation of tight junctions (TJs) is dependent on the formation of adherens junctions (AJs) in MDCK cells. E-Cadherin and nectin are major cell-cell adhesion molecules (CAMs) at AJs, whereas claudin, occludin and junctional adhesion molecule (JAM) are major CAMs at TJs. When MDCK cells precultured at 2 microm Ca(2+) are cultured at 2 mm Ca(2+)...

Nectins are Ca2+-independent immunoglobulin-like cell-cell-adhesion molecules consisting of four members. Nectins homophilically and heterophilically trans-interact to form a variety of cell-cell junctions, including cadherin-based adherens junctions in epithelial cells and fibroblasts in culture, synaptic junctions in neurons, and Sertoli cell-spe...

Necl-5/Tage4/poliovirus receptor/CD155 is the poliovirus receptor and upregulated in rodent and human carcinoma. We have recently shown that mouse Necl-5 is upregulated by an oncogenic Ki-Ras (V12Ki-Ras) in NIH3T3 cells and enhances cell movement induced by growth factors, including platelet-derived growth factor and fibroblast growth factor (FGF),...

E-cadherin and nectins are major cell-cell adhesion molecules at adherens junctions (AJs) in epithelial cells. When Madin-Darby canine kidney (MDCK) cells stably expressing nectin-1 (nectin-1-MDCK cells) are cultured at normal Ca(2+), E-cadherin and nectin-1 are concentrated at the cell-cell contact sites. When these cells are cultured at low Ca(2+...

Nectins are Ca(2+)-independent immunoglobulin (Ig)-like cell-cell adhesion molecules (CAMs), which comprise a family consisting of four members. Each nectin homophilically and heterophilically trans-interacts and causes cell-cell adhesion. Biochemical, cell biological, and knockout mice studies have revealed that nectins play important roles in for...

Nectins, Ca(2+)-independent immunoglobulin (Ig)-like cell-cell adhesion molecules and cadherins, Ca(2+)-dependent cell-cell adhesion molecules, are associated through their respective cytoplasmic tail-binding proteins, afadin and catenins and play roles in formation of adherens junctions (AJs) in epithelial cells and fibroblasts. Nectin-like molecu...

Nectins, Ca(2+)-independent immunoglobulin-like cell adhesion molecules (CAMs), first form cell-cell adhesion where cadherins are recruited, forming adherens junctions (AJs) in epithelial cells and fibroblasts. In addition, nectins recruit claudins, occludin, and junctional adhesion molecules (JAMs) to the apical side of AJs, forming tight junction...

Afadin DIL domain-interacting protein (ADIP) is a novel protein that binds both afadin and alpha-actinin and localizes at adherens junctions, which are formed by nectins and cadherins, cell-cell adhesion molecules. Afadin is an actin filament (F-actin)-binding protein which connects nectins to the actin cytoskeleton. alpha-Actinin is another F-acti...

Nectins are Ca(2+)-independent immunoglobulin-like cell-cell adhesion molecules that are involved in formation of cadherin-based adherens junctions (AJs). The nectin-based cell-cell adhesion induces activation of Cdc42 and Rac small G proteins, which eventually enhances the formation of AJs through reorganization of the actin cytoskeleton. Although...

The human homologue of the Drosophila discs large tumor suppressor gene (hDlg) is a member of the membrane-associated guanylate kinase family with three PSD-95/Dlg/ZO-1 (PDZ) domains. hDlg has been shown to bind tumor suppressor proteins, adenomatous polyposis coli (APC) and protein tyrosine phosphatase and tensin homologue (PTEN), and several vira...

Cells of budding yeast give rise to mother and daughter cells, which differ in that only mother cells express the HO endonuclease gene and are thereby able to switch mating types. In this study, we identified the MKT1 gene as a positive regulator of HO expression. The MKT1 gene encodes a protein with two domains, XPG-N and XPG-I, which are conserve...

Vimentin-type intermediate filaments (IFs) play an important role in cytoskeletal organization and cell morphology. We identified here a novel protein associated with vimentin-type IFs and named it vimentin-type IF-associated coiled-coil protein (Vmac). Vmac consists of 171 amino acids with a calculated Mr of 18,844 and has a coiled-coil domain in...

Nectins are Ca(2+)-independent immunoglobulin-like cell-cell adhesion molecules which constitute a family of four members. Nectins homophilically and heterophilically trans-interact and cause cell-cell adhesion. This nectin-based cell-cell adhesion plays roles in the organization of adherens junctions in epithelial cells and fibroblasts and synapti...

Background: Two types of intercellular junctions, synaptic junctions (SJs) and puncta adherentia junctions (PAs), are observed at the synapses between the mossy fibre terminals and the dendrites of pyramidal cells in the CA3 area of the hippocampus. SJs are associated with active zones and postsynaptic densities (PSDs) where neurotransmission occu...

Nectins are a family of Ca(2+)-independent immunoglobulin-like cell-cell adhesion molecules consisting of four members, which homophilically and heterophilically trans-interact and cause cell-cell adhesion. Nectin-based cell-cell adhesion is involved in the formation of cadherin-based adherens junctions in epithelial cells and fibroblasts. The nect...

She4p/Dim1p, a member of the UNC-45/CRO1/She4p (UCS) domain-containing protein family, is required for endocytosis, polarization of actin cytoskeleton, and polarization of ASH1 mRNA in Saccharomyces cerevisiae. We show herein that She4p/Dim1p is involved in endocytosis and actin polarization through interactions with the type I myosins Myo3p and My...

Cadherins are key Ca(2+)-dependent cell-cell adhesion molecules at adherens junctions (AJs) in fibroblasts and epithelial cells, whereas claudins are key Ca(2+)-independent cell-cell adhesion molecules at tight junctions (TJs) in epithelial cells. The formation and maintenance of TJs are dependent on the formation and maintenance of AJs. Nectins ar...

Nectin and afadin constitute a novel intercellular adhesion system that organizes adherens junctions in cooperation with the cadherin-catenin system in epithelial cells. Nectin is a Ca(2+)-independent immunoglobulin-like adhesion molecule and afadin is an actin filament (F-actin)-binding protein that connects nectin to the actin cytoskeleton. At th...

Nectins are Ca2+-independent immunoglobulin-like cell-cell adhesion molecules which associate with cadherins to form adherens junctions (AJs) in epithelial cells and fibroblasts. Nectin-1 and -3 are members of the nectin family which most strongly trans-interact, causing cell-cell adhesion. The trans-interaction between nectin-1 and -3 induces the...

IQGAP1, a putative downstream target of the Rho family small G proteins, Cdc42 and Rac, localizes at adherens junctions (AJs) in epithelial cells. It has been suggested that IQGAP1 localizes at AJs through its binding to beta-catenin, and negatively regulates the E-cadherin-mediated cell-cell adhesion. Nectin is a Ca(2+)-independent, immunoglobulin...

Afadin is an actin filament (F-actin)-binding protein that is associated with the cytoplasmic tail of nectin, a Ca(2+)-independent immunoglobulin-like cell-cell adhesion molecule. Nectin and afadin strictly localize at cell-cell adherens junctions (AJs) undercoated with F-actin bundles and are involved in the formation of AJs in cooperation with E-...

Nectin is a Ca2+-independent immunoglobulin-like cell-cell adhesion molecule at the E-cadherin-based cell-cell adherens junctions (AJs), and comprises a family consisting of four members, nectin-1, -2, -3, and -4. Nectin and E-cadherin are associated with afadin and alpha-catenin, actin filament (F-actin)-binding proteins connecting respective adhe...

Nectin is a Ca(2+)-independent immunoglobulin-like cell-cell adhesion molecule implicated in the organization of the junctional complex comprised of E-cadherin-based adherens junctions and claudin-based tight junctions in epithelial cells. Scatter factor (SF)/hepatocyte growth factor (HGF) and 12-O-tetradecanoylphorbol-13-acetate (TPA), a tumor-pro...

Nectin is a Ca2+-independent immunoglobulin-like cell–cell adhesion molecule implicated in the organization of the junctional complex comprised of E-cadherin-based adherens junctions and claudin-based tight junctions in epithelial cells. Scatter factor (SF)/hepatocyte growth factor (HGF) and 12-O-tetradecanoylphorbol-13-acetate (TPA), a tumor-promo...

Junctional adhesion molecule (JAM) is a Ca2+-independent immunoglobulin-like cell-cell adhesion molecule which localizes at tight junctions (TJs). Claudin is a key cell-cell adhesion molecule that forms TJ strands at TJs. JAM is associated with claudin through their cytoplasmic tail-binding protein, ZO-1. JAM is furthermore associated with Par-3, a...

In polarized epithelial cells, cell-cell adhesion forms specialized membrane structures comprised of claudin-based tight junctions (TJs) and of E-cadherin-based adherens junctions (AJs). These structures are aligned from the apical to the basal side of the lateral membrane, but the mechanism of this organization remains unknown. Nectin is a Ca2+ in...

Actin-based cell-cell adherens junctions (AJs) are crucial not only for mechanical adhesion but also for cell morphogenesis and differentiation. While organization of homotypic AJs is attributed mostly to classic cadherins, the adhesive mechanism of heterotypic AJs in more complex tissues remains to be clarified. Nectin, a member of a family of imm...

Nectin is a Ca(2+)-independent immunoglobulin (Ig)-like cell-cell adhesion molecule that forms cell-cell adherens junctions cooperatively with E-cadherin in a variety of cells. Nectin has one transmembrane segment and three Ig-like loops in the extracellular region. The first Ig-like loop is essential for the trans-dimer formation of nectin of two...