DOCSLIB.ORG

F-Box Protein RAE1 Regulates the Stability of the Aluminum-Resistance Transcription Factor STOP1 in Arabidopsis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
F-Box Protein RAE1 Regulates the Stability of the Aluminum-Resistance Transcription Factor STOP1 in Arabidopsis F-box protein RAE1 regulates the stability of the aluminum-resistance transcription factor STOP1 in Arabidopsis Yang Zhanga,b,1, Jie Zhanga,1, Jinliang Guoa,b,1, Fanglin Zhoua, Somesh Singha, Xuan Xub, Qi Xiec, Zhongbao Yangd, and Chao-Feng Huanga,b,2 aNational Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, 200032 Shanghai, China; bCollege of Resources and Environmental Sciences, Nanjing Agricultural University, 210095 Nanjing, China; cState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China; and dKey Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, College of Life Science, Shandong University, 250100 Jinan, China Edited by Luis Herrera-Estrella, Center for Research and Advanced Studies, Irapuato, Mexico, and approved November 19, 2018 (received for review August 21, 2018) Aluminum (Al) toxicity is a major factor limiting crop production expression of STOP1-downstream Al-resistance genes, including on acid soils, which represent over 30% of the world’s arable land. AtALMT1, AtMATE, and ALS3, is induced by Al (8, 12). These Some plants have evolved mechanisms to detoxify Al. Arabidopsis, results suggest the possibility that STOP1 might be regulated by for example, secretes malate via the AtALMT1 transporter to che- Al at posttranscriptional or posttranslational levels. late and detoxify Al. The C2H2-type transcription factor STOP1 plays a Ubiquitin-mediated protein degradation is an important post- crucial role in Al resistance by inducing the expression of a set of translational mechanism that regulates numerous biological processes genes, including AtALMT1. Here, we identify andcharacterizeanF- (13). Ubiquitin conjugation is mediated through the sequential box protein-encoding gene regulation of Atalmt1 expression 1 (RAE1) action of three enzyme complexes: ubiquitin-activating (E1), ubiquitin- that regulates the level of STOP1. Mutation and overexpression of conjugating (E2), and ubiquitin ligase (E3) enzymes. The E3 li- RAE1 increases or decreases the expression of AtALMT1 and other gases are responsible for substrate recognition and ubiquitin STOP1-regulated genes, respectively. RAE1 interacts with and pro- transfer. Among various E3 families, the SKP1–CUL1–F-box (SCF) PLANT BIOLOGY motes the degradation of STOP1 via the ubiquitin-26S proteasome is the largest and best characterized and is composed of four major pathway, while Al stress promotes the accumulation of STOP1. We subunits: SKP1, Cullin1, RBX1, and an F-box protein (13, 14). find that STOP1 up-regulates RAE1 expression by directly binding to Cullin functions as a scaffold and interacts with SKP1 and RBX1 to the RAE1 promoter, thus forming a negative feedback loop between form a complex that generates the core ligase activity. F-box pro- STOP1 and RAE1. Our results demonstrate that RAE1 influences Al teins selectively interact with target proteins and deliver the targets resistance through the ubiquitination and degradation of STOP1. to the complex (15). The Arabidopsis genome contains nearly 700 genes that potentially encode F-box proteins (16). The F-box pro- aluminum toxicity | AtALMT1 | E3 ligase | low phosphate response | ubiquitination teins can be further divided into subgroups based on C-terminal protein-interaction domains. Members of the leucine-rich repeat – (LRR) subgroup are involved in the regulation of auxin, ethylene, pproximately 30 40% of the world arable land consists of jasmonate, and strigolactone hormone signaling (17–20), but no soils with a pH of 5.5 or lower (1). In these acidic soils, A roles in metal stress tolerance or signaling have been reported. aluminum (Al) is solubilized and becomes highly toxic to plants. Consequently, Al toxicity is a severe global problem for crops Significance growing on acid soils (2). To chelate and detoxify Al, some plants secrete organic acids, including malate, citrate, and oxalate (3–5). Arabidopsis plants, Aluminum (Al) toxicity is a major constraint of crop production for example, release both malate and citrate in response to Al on acid soils. Arabidopsis can secrete malate via the AtALMT1 stress, with malate being essential for Al detoxification (6–8). transporter to chelate and detoxify Al. The transcription factor The gene responsible for Al-activated secretion of malate in STOP1 is essentially required for Al resistance, mainly through roots, Al-activated malate transporter 1 (ALMT1), was first iden- the control of AtALMT1 expression. Here, we report an F-box tified in wheat and encodes an anion transporter/channel (9). protein RAE1 that regulates STOP1 stability. RAE1 interacts There are 12 ALMT members in Arabidopsis, and only AtALMT1 with STOP1 to promote STOP1 degradation via the ubiquitin- 26S proteasome pathway, whereas Al stress stabilizes STOP1. is indispensable for root malate secretion and Al detoxification Together, our results reveal an important role for RAE1 in the (7). Unlike TaALMT1, whose expression is largely constitutive and regulation of Al resistance. unaffected by Al stress (9), AtALMT1 expression is induced by Al in all Arabidopsis ecotypes (7). In addition to Al, plant hormones Author contributions: Y.Z., J.Z., J.G., and C.-F.H. designed research; Y.Z., J.Z., J.G., F.Z., S.S., and other stresses such as indole-3-acetic acid (IAA), abscisic acid and X.X. performed research; Q.X. and Z.Y. contributed new reagents/analytic tools; Y.Z., (ABA), low pH, and hydrogen peroxide trigger AtALMT1 tran- J.Z., J.G., and C.-F.H. analyzed data; and C.-F.H. wrote the paper. scription (10), which suggests that the regulation of AtALMT1 The authors declare no conflict of interest. expression is complex. The mechanisms that underlie the regula- This article is a PNAS Direct Submission. tion of AtALMT1 expression, however, are not fully understood. Published under the PNAS license. Through a forward genetic screen of mutants exhibiting in- Data deposition: The sequences reported in this paper have been deposited in the NCBI creased sensitivity to proton toxicity, a zinc-finger transcription Sequence Read Archive database (accession nos. SRR6781578 and SRR6781579). factor sensitive to proton rhizotoxicity 1 (STOP1) was identified 1Y.Z., J.Z., and J.G. contributed equally to this work. and found to be critical for both proton and Al tolerance (11). 2To whom correspondence should be addressed. Email: [email protected]. Mutation of STOP1 greatly suppresses AtALMT1 transcription (11), This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. demonstrating that STOP1 is a crucial regulator of AtALMT1 ex- 1073/pnas.1814426116/-/DCSupplemental. pression. STOP1 transcription is not affected by Al stress, but the Published online December 17, 2018. www.pnas.org/cgi/doi/10.1073/pnas.1814426116 PNAS | January 2, 2019 | vol. 116 | no. 1 | 319–327 Downloaded by guest on September 24, 2021 To gain insights into how AtALMT1 or STOP1 are modulated promoter to the uidA gene, which encodes β-glucuronidase at transcriptional or posttranscriptional levels, we conducted a (GUS) and selected a transgenic line that had a one-locus seg- forward genetic screen on an EMS-mutagenized population in regation pattern for GUS expression and introduced the trans- an AtALMT1 promoter-driven luciferase reporter (LUC) line. gene into the rae1-1 background by crossing. GUS staining Through this screen, we identified an F-box protein-encoding showed that GUS was expressed at higher levels in rae1-1 than in gene RAE1 that interacts with STOP1 to regulate its stability the WT in both the absence and presence of Al (SI Appendix, via the ubiquitin-26S proteasome pathway. Fig. S1 C and D). To determine whether rae1 mutations influence the expression Results of other Al-resistance genes, we analyzed the expression levels of Identification of Mutants with Altered AtALMT1 Expression. To AtMATE, ALS3, AtSTAR1, ALS1, and STOP1 in the WT and the identify components involved in the regulation of AtALMT1 rae1 mutants. The results showed that AtMATE and ALS3, two expression, we fused the AtALMT1 promoter to the luciferase additional target genes of STOP1 (Fig. 1 D and E) (8, 12), were reporter gene (pAtALMT1:LUC) and then introduced the con- also expressed at higher levels in the rae1 mutants than in the struct into the wild-type (WT) [Columbia-0 (Col-0)] seedlings. WT under both −Al and +Al conditions (Fig. 1 D and E). In We screened for single-copy transgenic lines displaying high lu- contrast, the expression levels of AtSTAR1 and ALS1, which are minescence and then performed thermal asymmetric interlaced not regulated by STOP1 (SI Appendix, Fig. S2 A and B) (12, 21), (TAIL)-PCR on these lines to pinpoint the location of the re- did not differ between the WT and the rae1 mutants (SI Ap- porter gene in the genome. With this procedure, we identified a pendix, Fig. S2 A and B). The expression of STOP1 was also not line in which the reporter gene was inserted in the intergenic affected in rae1 (SI Appendix, Fig. S2C). In addition, introduc- region between At4g23000 and At4g23010. We generated an tion of the stop1-3 mutation into the rae1-1 mutant background EMS-mutagenized library in the background of this transgenic fully suppressed the increased expression of LUC in the rae1-1 line for mutant screening. After screening ∼10,000 M2 lines, we mutant (SI Appendix, Fig. S1E). These results suggest that RAE1 finally identified 17 regulation of AtALMT1 expression (rae) mu- acts upstream of STOP1 to regulate the expression of Al- tants with altered luminescent signal. Two mutants with ex- resistance genes. tremely low luminescence had different mutations in the key Al- Because the expression of AtALMT1 was increased in rae1 resistance gene STOP1 (SI Appendix, Fig. S1A), which indicated mutants, we compared malate secretion between the WT and that our screening system was effective.
Load more

Recommended publications
  • UNIVERSITY of CALIFORNIA, SAN DIEGO Functional Analysis of Sall4
    UNIVERSITY OF CALIFORNIA, SAN DIEGO Functional analysis of Sall4 in modulating embryonic stem cell fate A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Molecular Pathology by Pei Jen A. Lee Committee in charge: Professor Steven Briggs, Chair Professor Geoff Rosenfeld, Co-Chair Professor Alexander Hoffmann Professor Randall Johnson Professor Mark Mercola 2009 Copyright Pei Jen A. Lee, 2009 All rights reserved. The dissertation of Pei Jen A. Lee is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ ______________________________________________________________ Co-Chair ______________________________________________________________ Chair University of California, San Diego 2009 iii Dedicated to my parents, my brother ,and my husband for their love and support iv Table of Contents Signature Page……………………………………………………………………….…iii Dedication…...…………………………………………………………………………..iv Table of Contents……………………………………………………………………….v List of Figures…………………………………………………………………………...vi List of Tables………………………………………………….………………………...ix Curriculum vitae…………………………………………………………………………x Acknowledgement………………………………………………….……….……..…...xi Abstract………………………………………………………………..…………….....xiii Chapter 1 Introduction ..…………………………………………………………………………….1 Chapter 2 Materials and Methods……………………………………………………………..…12
    [Show full text]
  • Viral Strategies to Arrest Host Mrna Nuclear Export
    Viruses 2013, 5, 1824-1849; doi:10.3390/v5071824 OPEN ACCESS viruses ISSN 1999-4915 www.mdpi.com/journal/viruses Review Nuclear Imprisonment: Viral Strategies to Arrest Host mRNA Nuclear Export Sharon K. Kuss *, Miguel A. Mata, Liang Zhang and Beatriz M. A. Fontoura Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; E-Mails: [email protected] (M.A.M.); [email protected] (L.Z.); [email protected] (B.M.A.F) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-214-633-2001; Fax: +1-214-648-5814. Received: 10 June 2013; in revised form: 27 June 2013 / Accepted: 11 July 2013 / Published: 18 July 2013 Abstract: Viruses possess many strategies to impair host cellular responses to infection. Nuclear export of host messenger RNAs (mRNA) that encode antiviral factors is critical for antiviral protein production and control of viral infections. Several viruses have evolved sophisticated strategies to inhibit nuclear export of host mRNAs, including targeting mRNA export factors and nucleoporins to compromise their roles in nucleo-cytoplasmic trafficking of cellular mRNA. Here, we present a review of research focused on suppression of host mRNA nuclear export by viruses, including influenza A virus and vesicular stomatitis virus, and the impact of this viral suppression on host antiviral responses. Keywords: virus; influenza virus; vesicular stomatitis virus; VSV; NS1; matrix protein; nuclear export; nucleo-cytoplasmic trafficking; mRNA export; NXF1; TAP; CRM1; Rae1 1. Introduction Nucleo-cytoplasmic trafficking of proteins and RNA is critical for proper cellular functions and survival.
    [Show full text]
  • BUB3 That Dissociates from BUB1 Activates Caspase-Independent Mitotic Death (CIMD)
    Cell Death and Differentiation (2010) 17, 1011–1024 & 2010 Macmillan Publishers Limited All rights reserved 1350-9047/10 $32.00 www.nature.com/cdd BUB3 that dissociates from BUB1 activates caspase-independent mitotic death (CIMD) Y Niikura1, H Ogi1, K Kikuchi1 and K Kitagawa*,1 The cell death mechanism that prevents aneuploidy caused by a failure of the spindle checkpoint has recently emerged as an important regulatory paradigm. We previously identified a new type of mitotic cell death, termed caspase-independent mitotic death (CIMD), which is induced during early mitosis by partial BUB1 (a spindle checkpoint protein) depletion and defects in kinetochore–microtubule attachment. In this study, we have shown that survived cells that escape CIMD have abnormal nuclei, and we have determined the molecular mechanism by which BUB1 depletion activates CIMD. The BUB3 protein (a BUB1 interactor and a spindle checkpoint protein) interacts with p73 (a homolog of p53), specifically in cells wherein CIMD occurs. The BUB3 protein that is freed from BUB1 associates with p73 on which Y99 is phosphorylated by c-Abl tyrosine kinase, resulting in the activation of CIMD. These results strongly support the hypothesis that CIMD is the cell death mechanism protecting cells from aneuploidy by inducing the death of cells prone to substantial chromosome missegregation. Cell Death and Differentiation (2010) 17, 1011–1024; doi:10.1038/cdd.2009.207; published online 8 January 2010 Aneuploidy – the presence of an abnormal number of of spindle checkpoint activity.20,21
    [Show full text]
  • Snapshot: the Nuclear Envelope II Andrea Rothballer and Ulrike Kutay Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
    SnapShot: The Nuclear Envelope II Andrea Rothballer and Ulrike Kutay Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland H. sapiens D. melanogaster C. elegans S. pombe S. cerevisiae Cytoplasmic filaments RanBP2 (Nup358) Nup358 CG11856 NPP-9 – – – Nup214 (CAN) DNup214 CG3820 NPP-14 Nup146 SPAC23D3.06c Nup159 Cytoplasmic ring and Nup88 Nup88 (Mbo) CG6819 – Nup82 SPBC13A2.02 Nup82 associated factors GLE1 GLE1 CG14749 – Gle1 SPBC31E1.05 Gle1 hCG1 (NUP2L1, NLP-1) tbd CG18789 – Amo1 SPBC15D4.10c Nup42 (Rip1) Nup98 Nup98 CG10198 Npp-10N Nup189N SPAC1486.05 Nup145N, Nup100, Nup116 Nup 98 complex RAE1 (GLE2) Rae1 CG9862 NPP-17 Rae1 SPBC16A3.05 Gle2 (Nup40) Nup160 Nup160 CG4738 NPP-6 Nup120 SPBC3B9.16c Nup120 Nup133 Nup133 CG6958 NPP-15 Nup132, Nup131 SPAC1805.04, Nup133 SPBP35G2.06c Nup107 Nup107 CG6743 NPP-5 Nup107 SPBC428.01c Nup84 Nup96 Nup96 CG10198 NPP-10C Nup189C SPAC1486.05 Nup145C Outer NPC scaffold Nup85 (PCNT1) Nup75 CG5733 NPP-2 Nup-85 SPBC17G9.04c Nup85 (Nup107-160 complex) Seh1 Nup44A CG8722 NPP-18 Seh1 SPAC15F9.02 Seh1 Sec13 Sec13 CG6773 Npp-20 Sec13 SPBC215.15 Sec13 Nup37 tbd CG11875 – tbd SPAC4F10.18 – Nup43 Nup43 CG7671 C09G9.2 – – – Centrin-21 tbd CG174931, CG318021 R08D7.51 Cdc311 SPCC1682.04 Cdc311 Nup205 tbd CG11943 NPP-3 Nup186 SPCC290.03c Nup192 Nup188 tbd CG8771 – Nup184 SPAP27G11.10c Nup188 Central NPC scaffold Nup155 Nup154 CG4579 NPP-8 tbd SPAC890.06 Nup170, Nup157 (Nup53-93 complex) Nup93 tbd CG7262 NPP-13 Nup97, Npp106 SPCC1620.11, Nic96 SPCC1739.14 Nup53(Nup35, MP44) tbd CG6540 NPP-19 Nup40 SPAC19E9.01c
    [Show full text]
  • RAE1 Ligands for the NKG2D Receptor Are Regulated by STING-Dependent DNA Sensor Pathways in Lymphoma
    Published OnlineFirst March 3, 2014; DOI: 10.1158/0008-5472.CAN-13-1703 Cancer Microenvironment and Immunology Research RAE1 Ligands for the NKG2D Receptor Are Regulated by STING-Dependent DNA Sensor Pathways in Lymphoma Adeline R. Lam1,2,NinaLeBert1,SamanthaS.W.Ho1,YuJ.Shen1,2, Melissa L.F. Tang1,GordonM.Xiong1, J. Ludovic Croxford1, Christine X. Koo1,2,3,4,KenJ.Ishii3,4,ShizuoAkira5,DavidH.Raulet6, and Stephan Gasser1,2 Abstract The immunoreceptor NKG2D originally identified in natural killer (NK) cells recognizes ligands that are upregulated on tumor cells. Expression of NKG2D ligands (NKG2DL) is induced by the DNA damage response (DDR), which is often activated constitutively in cancer cells, revealing them to NK cells as a mechanism of immunosurveillance. Here, we report that the induction of retinoic acid early transcript 1 (RAE1) ligands for NKG2D by the DDR relies on a STING-dependent DNA sensor pathway involving the effector molecules TBK1 and IRF3. Cytosolic DNA was detected in lymphoma cell lines that express RAE1 and its occurrence required activation of the DDR. Transfection of DNA into ligand-negative cells was sufficient to induce RAE1 expression. þ À Irf3 / ;Em-Myc mice expressed lower levels of RAE1 on tumor cells and showed a reduced survival rate compared þ þ with Irf3 / ;Em-Myc mice. Taken together, our results suggest that genomic damage in tumor cells leads to activation of STING-dependent DNA sensor pathways, thereby activating RAE1 and enabling tumor immuno- surveillance. Cancer Res; 74(8); 1–11. Ó2014 AACR. Introduction DNA damage and the constitutive expression of NKG2DLs in The NKG2D system is an arm of innate immune recognition, some tumor cell lines (6).
    [Show full text]
  • The DNA Sequence and Comparative Analysis of Human Chromosome 20
    articles The DNA sequence and comparative analysis of human chromosome 20 P. Deloukas, L. H. Matthews, J. Ashurst, J. Burton, J. G. R. Gilbert, M. Jones, G. Stavrides, J. P. Almeida, A. K. Babbage, C. L. Bagguley, J. Bailey, K. F. Barlow, K. N. Bates, L. M. Beard, D. M. Beare, O. P. Beasley, C. P. Bird, S. E. Blakey, A. M. Bridgeman, A. J. Brown, D. Buck, W. Burrill, A. P. Butler, C. Carder, N. P. Carter, J. C. Chapman, M. Clamp, G. Clark, L. N. Clark, S. Y. Clark, C. M. Clee, S. Clegg, V. E. Cobley, R. E. Collier, R. Connor, N. R. Corby, A. Coulson, G. J. Coville, R. Deadman, P. Dhami, M. Dunn, A. G. Ellington, J. A. Frankland, A. Fraser, L. French, P. Garner, D. V. Grafham, C. Grif®ths, M. N. D. Grif®ths, R. Gwilliam, R. E. Hall, S. Hammond, J. L. Harley, P. D. Heath, S. Ho, J. L. Holden, P. J. Howden, E. Huckle, A. R. Hunt, S. E. Hunt, K. Jekosch, C. M. Johnson, D. Johnson, M. P. Kay, A. M. Kimberley, A. King, A. Knights, G. K. Laird, S. Lawlor, M. H. Lehvaslaiho, M. Leversha, C. Lloyd, D. M. Lloyd, J. D. Lovell, V. L. Marsh, S. L. Martin, L. J. McConnachie, K. McLay, A. A. McMurray, S. Milne, D. Mistry, M. J. F. Moore, J. C. Mullikin, T. Nickerson, K. Oliver, A. Parker, R. Patel, T. A. V. Pearce, A. I. Peck, B. J. C. T. Phillimore, S. R. Prathalingam, R. W. Plumb, H. Ramsay, C. M.
    [Show full text]
  • RAE1 Mediated ZEB1 Expression Promotes Epithelial–Mesenchymal
    www.nature.com/scientificreports OPEN RAE1 mediated ZEB1 expression promotes epithelial–mesenchymal transition in breast cancer Received: 30 July 2018 Ji Hoon Oh1,2, Ji-Yeon Lee1, Sungsook Yu3, Yejin Cho3, Sumin Hur3, Ki Taek Nam3 & Accepted: 24 January 2019 Myoung Hee Kim 1,2 Published: xx xx xxxx Breast cancer metastasis accounts for most of the deaths from breast cancer. Since epithelial- mesenchymal transition (EMT) plays an important role in promoting metastasis of cancer, many mechanisms regarding EMT have been studied. We previously showed that Ribonucleic acid export 1 (RAE1) is dysregulated in breast cancer and its overexpression leads to aggressive breast cancer phenotypes by inducing EMT. Here, we evaluated the functional capacity of RAE1 in breast cancer metastasis by using a three-dimensional (3D) culture system and xenograft models. Furthermore, to investigate the mechanisms of RAE1-driven EMT, in vitro studies were carried out. The induction of EMT with RAE1-overexpression was confrmed under the 3D culture system and in vivo system. Importantly, RAE1 mediates upregulation of an EMT marker ZEB1, by binding to the promoter region of ZEB1. Knockdown of ZEB1 in RAE1-overexpressing cells suppressed invasive and migratory behaviors, accompanied by an increase in epithelial and a decrease in mesenchymal markers. Taken together, these data demonstrate that RAE1 contributes to breast cancer metastasis by regulating a key EMT-inducing factor ZEB1 expression, suggesting its potential as a therapeutic target. Breast cancer is one of the most commonly occurring cancers in women worldwide1. Te main reason for death of breast cancer patients is metastasis2. Te epithelial-mesenchymal transition (EMT), a process that is typically induced by interruption of intracellular tight junctions and loss of cell-cell contacts, is a key step in cancer metas- tasis1,3,4.
    [Show full text]
  • Exploring the Loci Responsible for Awn Development in Rice Through Comparative Analysis of All AA Genome Species
    plants Article Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species Kanako Bessho-Uehara 1,2, Yoshiyuki Yamagata 3 , Tomonori Takashi 4 , Takashi Makino 2, Hideshi Yasui 3, Atsushi Yoshimura 3 and Motoyuki Ashikari 1,* 1 Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan; [email protected] 2 Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan; [email protected] 3 Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; [email protected] (Y.Y.); [email protected] (H.Y.); [email protected] (A.Y.) 4 STAY GREEN Co., Ltd., 2-1-5 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-52-789-5202 Abstract: Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the Citation: Bessho-Uehara, K.; novel loci regulating awn development and understand the conservation of genes in other wild rice Yamagata, Y.; Takashi, T.; Makino, T.; relatives belonging to the AA genome group, we analyzed the chromosome segment substitution Yasui, H.; Yoshimura, A.; Ashikari, M.
    [Show full text]
  • A SARS-Cov-2 Protein Interaction Map Reveals Targets for Drug Repurposing
    Article A SARS-CoV-2 protein interaction map reveals targets for drug repurposing https://doi.org/10.1038/s41586-020-2286-9 A list of authors and affiliations appears at the end of the paper Received: 23 March 2020 Accepted: 22 April 2020 A newly described coronavirus named severe acute respiratory syndrome Published online: 30 April 2020 coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than Check for updates 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efcacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and eforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identifed the human proteins that physically associated with each of the SARS-CoV-2 proteins using afnity-purifcation mass spectrometry, identifying 332 high-confdence protein–protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors.
    [Show full text]
  • Variation in Protein Coding Genes Identifies Information Flow
    bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 1 1 2 3 4 5 Variation in protein coding genes identifies information flow as a contributor to 6 animal complexity 7 8 Jack Dean, Daniela Lopes Cardoso and Colin Sharpe* 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Institute of Biological and Biomedical Sciences 25 School of Biological Science 26 University of Portsmouth, 27 Portsmouth, UK 28 PO16 7YH 29 30 * Author for correspondence 31 [email protected] 32 33 Orcid numbers: 34 DLC: 0000-0003-2683-1745 35 CS: 0000-0002-5022-0840 36 37 38 39 40 41 42 43 44 45 46 47 48 49 Abstract bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 2 1 Across the metazoans there is a trend towards greater organismal complexity. How 2 complexity is generated, however, is uncertain. Since C.elegans and humans have 3 approximately the same number of genes, the explanation will depend on how genes are 4 used, rather than their absolute number.
    [Show full text]
  • New Activities of the Nuclear Pore Complexes
    cells Editorial New Activities of the Nuclear Pore Complexes Richard W. Wong 1,2,3 1 WPI-Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan; [email protected] 2 Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan 3 Cell-Bionomics Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan Abstract: Nuclear pore complexes (NPCs) at the surface of nuclear membranes play a critical role in regulating the transport of both small molecules and macromolecules between the cell nucleus and cytoplasm via their multilayered spiderweb-like central channel. During mitosis, nuclear envelope breakdown leads to the rapid disintegration of NPCs, allowing some NPC proteins to play crucial roles in the kinetochore structure, spindle bipolarity, and centrosome homeostasis. The aberrant functioning of nucleoporins (Nups) and NPCs has been associated with autoimmune diseases, viral infections, neurological diseases, cardiomyopathies, and cancers, especially leukemia. This Special Issue highlights several new contributions to the understanding of NPC proteostasis. Keywords: nuclear pore complex; nanomedicine; liquid–liquid phase separation; biomacromolecule; HS-AFM; nucleoporin; nanoimaging The nuclear pore complex (NPC) [1–3] is a nanoscale gatekeeper with a central, se- lective, cobweb-like barrier composed mainly of nucleoporins (Nups), which comprise intrinsically disordered (non-structured) regions (IDRs) with phenylalanine–glycine (FG) motifs (FG-Nups) [4–8]. A fully assembled NPC in vertebrates contains multiple copies of approximately 30 different Nups and has an estimated molecular mass of 120 MDa [9]. Citation: Wong, R.W. New Activities Despite our knowledge of the NPC structure, the molecular mechanisms underlying of the Nuclear Pore Complexes.
    [Show full text]
  • Chromatin Conformation Links Distal Target Genes to CKD Loci
    BASIC RESEARCH www.jasn.org Chromatin Conformation Links Distal Target Genes to CKD Loci Maarten M. Brandt,1 Claartje A. Meddens,2,3 Laura Louzao-Martinez,4 Noortje A.M. van den Dungen,5,6 Nico R. Lansu,2,3,6 Edward E.S. Nieuwenhuis,2 Dirk J. Duncker,1 Marianne C. Verhaar,4 Jaap A. Joles,4 Michal Mokry,2,3,6 and Caroline Cheng1,4 1Experimental Cardiology, Department of Cardiology, Thoraxcenter Erasmus University Medical Center, Rotterdam, The Netherlands; and 2Department of Pediatrics, Wilhelmina Children’s Hospital, 3Regenerative Medicine Center Utrecht, Department of Pediatrics, 4Department of Nephrology and Hypertension, Division of Internal Medicine and Dermatology, 5Department of Cardiology, Division Heart and Lungs, and 6Epigenomics Facility, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands ABSTRACT Genome-wide association studies (GWASs) have identified many genetic risk factors for CKD. However, linking common variants to genes that are causal for CKD etiology remains challenging. By adapting self-transcribing active regulatory region sequencing, we evaluated the effect of genetic variation on DNA regulatory elements (DREs). Variants in linkage with the CKD-associated single-nucleotide polymorphism rs11959928 were shown to affect DRE function, illustrating that genes regulated by DREs colocalizing with CKD-associated variation can be dysregulated and therefore, considered as CKD candidate genes. To identify target genes of these DREs, we used circular chro- mosome conformation capture (4C) sequencing on glomerular endothelial cells and renal tubular epithelial cells. Our 4C analyses revealed interactions of CKD-associated susceptibility regions with the transcriptional start sites of 304 target genes. Overlap with multiple databases confirmed that many of these target genes are involved in kidney homeostasis.
    [Show full text]