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Genome-Wide Identification and Expression Analysis of Auxin Response Factor (ARF) Gene Family in Longan (Dimocarpus longan L.).

Plants (Basel) 2020 Feb 8;9(2). Epub 2020 Feb 8.

College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Auxin response factor (ARF) is the key regulator involved in plant development. Despite their physiological importance identified in various woody plants, the functions of ARF genes in longan were still not clear. In this study, 17 longan ARF genes (DlARF) were identified using the reference longan genome data. Read More

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February 2020

The role of protein-protein interactions mediated by the PB1 domain of NLP transcription factors in nitrate-inducible gene expression.

BMC Plant Biol 2019 Feb 28;19(1):90. Epub 2019 Feb 28.

Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.

Background: NIN-LIKE PROTEIN (NLP) transcription factors are master regulators of nitrate-inducible gene expression in higher plants. NLP transcription factors contain a nitrate signal-responsive domain in the amino-terminal region, an RWP-RK-type DNA-binding domain in the middle, and a Phox and Bem1 (PB1) domain at the carboxy terminus. Although the PB1 domain of NLP transcription factors appears to mediate protein-protein interactions associated with nitrate-inducible gene expression in higher plants, its precise role in nitrate-inducible gene expression has not previously been characterized. Read More

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February 2019

Neuropathy-causing mutations in HSPB1 impair autophagy by disturbing the formation of SQSTM1/p62 bodies.

Autophagy 2019 06 31;15(6):1051-1068. Epub 2019 Jan 31.

a Peripheral Neuropathy Research Group , Institute Born Bunge and University of Antwerp , Antwerp , Belgium.

HSPB1 (heat shock protein family B [small] member 1) is a ubiquitously expressed molecular chaperone. Most mutations in HSPB1 cause axonal Charcot-Marie-Tooth neuropathy and/or distal hereditary motor neuropathy. In this study we show that mutations in HSPB1 lead to impairment of macroautophagic/autophagic flux. Read More

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A size-invariant bud-duration timer enables robustness in yeast cell size control.

PLoS One 2018 21;13(12):e0209301. Epub 2018 Dec 21.

Marine Biological Laboratory, Woods Hole, MA, United States of America.

Cell populations across nearly all forms of life generally maintain a characteristic cell type-dependent size, but how size control is achieved has been a long-standing question. The G1/S boundary of the cell cycle serves as a major point of size control, and mechanisms operating here restrict passage of cells to Start if they are too small. In contrast, it is less clear how size is regulated post-Start, during S/G2/M. Read More

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The transcription of atypical protein kinase C in hemocytes of the giant freshwater prawn, Macrobrachium rosenbergii, during the molt stage and injection of pathogen-associated compounds.

Fish Shellfish Immunol 2017 Oct 14;69:52-58. Epub 2017 Aug 14.

Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan, ROC. Electronic address:

Protein kinase C (PKC), which is involved in cell signaling pathways, comprises a family of serine/threonine kinases ubiquitously present in animals and its members are grouped on the basis of structural and activation characteristics into novel, classical, and atypical PKC forms. In this study, an atypical PKC of Macrobrachium rosenbergii, designated MraPKC, was successfully cloned, and its protein comprised structural domains similar to those of atypical PKC homologues, including the Phox and Bem1 (PB1) domain, a zinc finger phorbol-ester/DAG-type signature, protein kinase signatures, and a cAMP-dependent, cGMP-dependent, and PKC (AGC) kinase C-terminal domain. Phylogenetic analyses revealed a close evolutionary relationship between MraPKC and aPKCs of insects. Read More

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October 2017

Sec15 links bud site selection to polarised cell growth and exocytosis in Candida albicans.

Sci Rep 2016 05 26;6:26464. Epub 2016 May 26.

Institute of Health Sciences, Anhui University, Hefei 230601, China.

The exocyst plays a crucial role in the targeting of secretory vesicles to the plasma membrane during exocytosis. It has been shown to be involved in diverse cellular processes including yeast budding. However, the mechanism of the exocyst regulating yeast budding has not been fully elucidated. Read More

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Zeta Inhibitory Peptide Disrupts Electrostatic Interactions That Maintain Atypical Protein Kinase C in Its Active Conformation on the Scaffold p62.

J Biol Chem 2015 Sep 17;290(36):21845-56. Epub 2015 Jul 17.

From the Department of Pharmacology,

Atypical protein kinase C (aPKC) enzymes signal on protein scaffolds, yet how they are maintained in an active conformation on scaffolds is unclear. A myristoylated peptide based on the autoinhibitory pseudosubstrate fragment of the atypical PKCζ, zeta inhibitory peptide (ZIP), has been extensively used to inhibit aPKC activity; however, we have previously shown that ZIP does not inhibit the catalytic activity of aPKC isozymes in cells (Wu-Zhang, A. X. Read More

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September 2015

Endothelial cells in health and disease.

Antioxid Redox Signal 2015 May;22(14):1209-11

1 IUF-Leibniz Research Institute for Environmental Medicine , Duesseldorf, Germany .

According to the World Health Organization, from 2014, cardiovascular diseases (CVD) are the number one cause of death worldwide. One of the key players in maintaining proper cardiovascular function is the endothelium, the inner layer of all blood vessels. This monolayer of cells on one hand serves as a barrier between blood and the surrounding tissue and on the other hand regulates many aspects of vessel function. Read More

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Directed dimerization: an in vivo expression system for functional studies of type II phytochromes.

Plant J 2013 Sep 3;75(6):915-26. Epub 2013 Aug 3.

Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA.

Type II phytochromes (phy) in Arabidopsis form homodimers and heterodimers, resulting in a diverse collection of light-stable red/far-red (R/FR) sensing photoreceptors. We describe an in vivo protein engineering system and its use in characterizing the activities of these molecules. Using a phyB null mutant background, singly and doubly transgenic plants were generated that express fusion proteins containing the phyB-phyE N-terminal photosensory regions (NB-NE PSRs), a nuclear localization sequence, and small yeast protein domains that mediate either homodimerization or heterodimerization. Read More

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September 2013

Profilin is required for Ca2+ homeostasis and Ca2+-modulated bud formation in yeast.

Mol Genet Genomics 2013 Aug 26;288(7-8):317-28. Epub 2013 May 26.

Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Building FBS-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.

A cls5-1 mutant of Saccharomyces cerevisiae is specifically sensitive to high concentrations of Ca2+, with elevated intracellular calcium content and altered cell morphology in the presence of 100 mM Ca2+. To reveal the mechanisms of the Ca2+-sensitive phenotype, we investigated the gene responsible and its interacting network. We demonstrated that CLS5 is identical to PFY1, encoding profilin. Read More

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Cdc42p regulation of the yeast formin Bni1p mediated by the effector Gic2p.

Mol Biol Cell 2012 Oct 23;23(19):3814-26. Epub 2012 Aug 23.

Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.

Actin filaments are dynamically reorganized to accommodate ever-changing cellular needs for intracellular transport, morphogenesis, and migration. Formins, a major family of actin nucleators, are believed to function as direct effectors of Rho GTPases, such as the polarity regulator Cdc42p. However, the presence of extensive redundancy has made it difficult to assess the in vivo significance of the low-affinity Rho GTPase-formin interaction and specifically whether Cdc42p polarizes the actin cytoskeleton via direct formin binding. Read More

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October 2012

Cla4 kinase triggers destruction of the Rac1-GEF Cdc24 during polarized growth in Ustilago maydis.

Mol Biol Cell 2011 Sep 14;22(17):3253-62. Epub 2011 Jul 14.

Department of Biology, University of Marburg, 35032 Marburg, Germany.

Dimorphic switching from budding to filamentous growth is a characteristic feature of many pathogenic fungi. In the fungal model organism Ustilago maydis polarized growth is induced by the multiallelic b mating type locus and requires the Rho family GTPase Rac1. Here we show that mating type-induced polarized growth involves negative feedback regulation of the Rac1-specific guanine nucleotide exchange factor (GEF) Cdc24. Read More

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September 2011

NMR structure of the heterodimer of Bem1 and Cdc24 PB1 domains from Saccharomyces cerevisiae.

J Biochem 2009 Sep 18;146(3):317-25. Epub 2009 May 18.

Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita 12 Nishi 6, Kita-ku, Sapporo 060-0812, Japan.

Bem1 and Cdc24 of the budding yeast Saccharomyces cerevisiae interact with each other through PB1-PB1 heterodimer formation to regulate the establishment of cell polarity. Here we present the tertiary structure of the heterodimer of Bem1 and Cdc24 PB1 domains determined by NMR spectroscopy. To avoid ambiguity in the NMR spectral analysis, we first prepared a mutant of the Cdc24 PB1 domain that had truncated loops. Read More

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September 2009

Structure and function of the PB1 domain, a protein interaction module conserved in animals, fungi, amoebas, and plants.

Sci STKE 2007 Aug 28;2007(401):re6. Epub 2007 Aug 28.

Medical Institute of Bioregulation, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan.

Proteins containing the PB1 domain, a protein interaction module conserved in animals, fungi, amoebas, and plants, participate in diverse biological processes. The PB1 domains adopt a ubiquitin-like beta-grasp fold, containing two alpha helices and a mixed five-stranded beta sheet, and are classified into groups harboring an acidic OPCA motif (type I), the invariant lysine residue on the first beta strand (type II), or both (type I/II). The OPCA motif of a type I PB1 domain forms salt bridges with basic residues, especially the conserved lysine, of a type II PB1 domain, thereby mediating a specific PB1-PB1 heterodimerization, whereas additional contacts contribute to high affinity and specificity of the modular interaction. Read More

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A novel Cdc42-interacting domain of the yeast polarity establishment protein Bem1. Implications for modulation of mating pheromone signaling.

J Biol Chem 2007 Jan 7;282(1):29-38. Epub 2006 Nov 7.

Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Japan.

In Saccharomyces cerevisiae, the Rho-type small GTPase Cdc42 is activated by its guanine-nucleotide exchange factor Cdc24 to polarize the cell for budding and mating. A multidomain protein Bem1 interacts not only with Cdc42 but also with Cdc24 and the effectors of Cdc42, including the p21-activated kinase Ste20, to function as a scaffold for cell polarity establishment. Although Bem1 interacts with Cdc24 and Ste20 via its PB1 and the second SH3 domains (SH3b), respectively, it is unclear how Bem1 binds Cdc42. Read More

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January 2007

Bem1p is a positive regulator of the homotypic fusion of yeast vacuoles.

J Biol Chem 2006 Sep 19;281(37):27158-66. Epub 2006 Jul 19.

Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755-3844, USA.

Docked vacuoles are believed to undergo rapid lipid mixing during hemifusion and then a slow, rate-limiting completion of fusion and mixing of lumenal contents. Previous genomic analysis has suggested that Bem1p, a scaffold protein critical for cell polarity, may support vacuole fusion. We now report that bem1Delta strains have fragmented vacuoles (vps class B and C). Read More

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September 2006

Sequencing, expression, and functional analyses support the candidacy of Ncf2 in susceptibility to Salmonella typhimurium infection in wild-derived mice.

J Immunol 2006 Jun;176(11):6954-61

Department of Human Genetics, McGill University, Montreal, Quebec, Canada.

A recessive Salmonella Typhimurium susceptibility locus (immunity to Typhimurium (Ity3) was reported previously on distal mouse chromosome 1 using a cross between C57BL/6J and wild-derived MOLF/Ei mice. This quantitative trait locus is located in a genomic region spanning 84 Mb, rich in candidate genes for which a role in host resistance to Salmonella infection is either known or can be envisioned. In this study, we report the evaluation of neutrophil cytosolic factor 2 (Ncf2) as a candidate Salmonella susceptibility gene for Ity3. Read More

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The nucleotide exchange factor Cdc24p may be regulated by auto-inhibition.

EMBO J 2004 Mar 26;23(5):1051-62. Epub 2004 Feb 26.

Swiss Institute for Experimental Cancer Research (ISREC), Epalinges/VD, Switzerland.

Site-specific activation of the Rho-type GTPase Cdc42p by its guanine-nucleotide exchange factor (GEF) Cdc24p is critical for the establishment of cell polarity. Here we show that binding of Cdc24p to the small GTPase Rsr1p/Bud1p is required for its recruitment to the incipient bud site. Rsr1p/Bud1p binds to the CH-domain of Cdc24p, which is essential for its function in vivo. Read More

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Generation of conditional lethal Candida albicans mutants by inducible deletion of essential genes.

Mol Microbiol 2002 Oct;46(1):269-80

Institüt für Molekulare Infektionsbiologie, Universität Würzburg, Röntgenring 11, D-97070 Würzburg, Germany.

The yeast Candida albicans is the most important fungal pathogen of humans and a model organism for studying fungal virulence. Sequencing of the C. albicans genome will soon be completed, allowing systematic approaches to analyse gene function. Read More

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October 2002

Phosphorylation of the Cdc42 exchange factor Cdc24 by the PAK-like kinase Cla4 may regulate polarized growth in yeast.

Mol Cell 2000 Nov;6(5):1155-67

Swiss Institute for Experimental Cancer Research Chemin des Boveresses 155 1066 Epalinges, Vaud, Switzerland.

Rho-type GTPases control many cytoskeletal rearrangements, but their regulation remains poorly understood. Here, we show that in S. cerevisiae, activation of the CDK Cdc28-Cln2 at bud emergence triggers relocalization of Cdc24, the GEF for Cdc42, from the nucleus to the polarization site, where it is stably maintained by binding to the adaptor Bem1. Read More

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November 2000

Genetic interactions indicate a role for Mdg1p and the SH3 domain protein Bem1p in linking the G-protein mediated yeast pheromone signalling pathway to regulators of cell polarity.

Mol Gen Genet 1996 Oct;252(5):608-21

Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada.

The pheromone signal in the yeast Saccharomyces cerevisiae is transmitted by the beta and gamma subunits of the mating response G-protein. The STE20 gene, encoding a protein kinase required for pheromone signal transduction, has recently been identified in a genetic screen for high-gene-dosage suppressors of a partly defective G beta mutation. The same genetic screen identified BEM1, which encodes an SH3 domain protein required for polarized morphogenesis in response to pheromone, and a novel gene, designated MDG1 (multicopy suppressor of defective G-protein). Read More

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October 1996

Associations among PH and SH3 domain-containing proteins and Rho-type GTPases in Yeast.

J Cell Biol 1996 May;133(4):879-94

Department of Biology, Indiana University, Bloomington 47405, USA.

The src homology region 3 (SH3) domain-bearing protein Bem1p and the Rho-type GTPase Cdc42p are important for bud emergence in Saccharomyces cervisiae. Here, we present evidence that through its second SH3 domain, Bem1p binds to the structurally and functionally similar proteins Boi1p and Boi2p, each of which contain an SH3 and pleckstrin homology (PH) domain. Deletion of BOI1 and BO12 together leads to impaired morphogenesis and poor ability. Read More

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Yeast src homology region 3 domain-binding proteins involved in bud formation.

J Cell Biol 1996 May;133(4):865-78

Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan.

The yeast protein Bem1p, which bears two src homology region 3 (SH3) domains, is involved in cell polarization. A Rho-type GTPase, Rho3p, is involved in the maintenance of cell polarity for bud formation, and the rho3 defect is suppressed by a high dose of BEM1. Mutational analysis revealed that the second SH3 domain from the NH2 terminus (SH3-2) of Bem1p is important for the functions of Bem1p in bud formation and in the suppression of the rho3 defect. Read More

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Interactions between the ankyrin repeat-containing protein Akr1p and the pheromone response pathway in Saccharomyces cerevisiae.

Mol Cell Biol 1996 Jan;16(1):168-78

Department of Biology, Indiana University, Bloomington 47405, USA.

Akr1p, which contains six ankyrin repeats, was identified during a screen for mutations that displayed synthetic lethality with a mutant allele of the bud emergence gene BEM1. Cells from which AKR1 had been deleted were alive but misshapen at 30 degrees C and inviable at 37 degrees C. During a screen for mutants that required one or more copies of wild-type AKR1 for survival at 30 degrees C, we isolated mutations in GPA1, which encodes the G alpha subunit of the pheromone receptor-coupled G protein. Read More

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January 1996

Interactions among proteins involved in bud-site selection and bud-site assembly in Saccharomyces cerevisiae.

J Biol Chem 1995 Jan;270(2):626-30

Department of Pharmacology, Cornell University, Ithaca, New York 14850.

Bud formation in yeast involves the actions of the Ras-type GTPase Rsr1, which is required for the proper selection of the bud site, and the Rho-type GTPase Cdc42, which is necessary for the assembly of cytoskeletal structures at that site. The Cdc24 protein is required both for proper bud-site selection and bud-site assembly and has been recently shown to display guanine-nucleotide-exchange factor (GEF) activity toward Cdc42. Here, we demonstrate, using recombinant proteins, that Cdc24 can also bind directly to Rsr1. Read More

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January 1995

Interactions between the bud emergence proteins Bem1p and Bem2p and Rho-type GTPases in yeast.

J Cell Biol 1994 Dec;127(5):1395-406

Department of Biology, Indiana University, Bloomington 47405.

The SH3 domain-containing protein Bem1p is needed for normal bud emergence and mating projection formation, two processes that require asymmetric reorganizations of the cortical cytoskeleton in Saccharomyces cerevisiae. To identify proteins that functionally and/or physically interact with Bem1p, we screened for mutations that display synthetic lethality with a mutant allele of the BEM1 gene and for genes whose products display two-hybrid interactions with the Bem1 protein. CDC24, which is required for bud emergence and encodes a GEF (guanine-nucleotide exchange factor) for the essential Rho-type GTPase Cdc42p, was identified during both screens. Read More

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December 1994

Saccharomyces cerevisiae MATa mutant cells defective in pointed projection formation in response to alpha-factor at high concentrations.

Authors:
T Yorihuzi Y Ohsumi

Yeast 1994 May;10(5):579-94

Department of Biology, College of Arts and Sciences, University of Tokyo, Japan.

We have isolated Saccharomyces cerevisiae MATa mutant cells that do not form a pointed projection but elongate in response to alpha-factor at high concentrations. Complementation tests defined three genes, PPF1, PPF2, and PPF3 (for pointed projection formation), necessary for pointed projection formation. Allelism tests with genes known to be needed for projection formation revealed that PPF1 is identical to SPA2, while PPF2 and PPF3 are not allelic to SST2, STE2, SPA2, BEM1 or SLK1/SSP31/BCK1. Read More

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Identification of genes required for normal pheromone-induced cell polarization in Saccharomyces cerevisiae.

Genetics 1994 Apr;136(4):1287-96

Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.

In response to mating pheromones, cells of the yeast Saccharomyces cerevisiae adopt a polarized "shmoo" morphology, in which the cytoskeleton and proteins involved in mating are localized to a cell-surface projection. This polarization is presumed to reflect the oriented morphogenesis that occurs between mating partners to facilitate cell and nuclear fusion. To identify genes involved in pheromone-induced cell polarization, we have isolated mutants defective in mating to an enfeebled partner and studied a subset of these mutants. Read More

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Yeast BUD5, encoding a putative GDP-GTP exchange factor, is necessary for bud site selection and interacts with bud formation gene BEM1.

Cell 1991 Jun;65(7):1213-24

Department of Biochemistry and Biophysics, University of California, San Francisco 94143.

Cells of the yeast S. cerevisiae choose bud sites in an axial or bipolar spatial pattern depending on their cell type. We have identified a gene, BUD5, that resembles BUD1 and BUD2 in being required for both patterns; bud5- mutants also exhibit random budding in all cell types. Read More

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Use of a screen for synthetic lethal and multicopy suppressee mutants to identify two new genes involved in morphogenesis in Saccharomyces cerevisiae.

Mol Cell Biol 1991 Mar;11(3):1295-305

Department of Biology, University of Michigan, Ann Arbor 48109.

Genes CDC24 and CDC42 are required for the establishment of cell polarity and for bud formation in Saccharomyces cerevisiae. Temperature-sensitive (Ts-) mutations in either of these genes cause arrest as large, unbudded cells in which the nuclear cycle continues. MSB1 was identified previously as a multicopy suppressor of Ts- cdc24 and cdc42 mutations. Read More

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