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The Membrane-Anchoring Region of the AcMNPV P74 Protein Is Expendable or Interchangeable with Homologs from Other Species. Viruses 2021; 13:v13122416. [PMID: 34960685 PMCID: PMC8704774 DOI: 10.3390/v13122416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/24/2022] Open
Abstract
Baculoviruses are insect pathogens that are characterized by assembling the viral dsDNA into two different enveloped virions during an infective cycle: occluded virions (ODVs; immersed in a protein matrix known as occlusion body) and budded virions (BVs). ODVs are responsible for the primary infection in midgut cells of susceptible larvae thanks to the per os infectivity factor (PIF) complex, composed of at least nine essential viral proteins. Among them, P74 is a crucial factor whose activity has been identified as virus-specific. In this work, the p74 gene from AcMNPV was pseudogenized using CRISPR/Cas9 technology and then complemented with wild-type alleles from SeMNPV and HearSNPV species, as well as chimeras combining the P74 amino and carboxyl domains. The results on Spodoptera exigua and Rachiplusia nu larvae showed that an amino terminal sector of P74 (lacking two potential transmembrane regions but possessing a putative nuclear export signal) is sufficient to restore the virus infectivity whether alone or fused to the P74 transmembrane regions of the other evaluated viral species. These results provide novel information about the functional role of P74 and delimit the region on which mutagenesis could be applied to enhance viral activity and, thus, produce better biopesticides.
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Pennemann FL, Mussabekova A, Urban C, Stukalov A, Andersen LL, Grass V, Lavacca TM, Holze C, Oubraham L, Benamrouche Y, Girardi E, Boulos RE, Hartmann R, Superti-Furga G, Habjan M, Imler JL, Meignin C, Pichlmair A. Cross-species analysis of viral nucleic acid interacting proteins identifies TAOKs as innate immune regulators. Nat Commun 2021; 12:7009. [PMID: 34853303 PMCID: PMC8636641 DOI: 10.1038/s41467-021-27192-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 11/02/2021] [Indexed: 12/11/2022] Open
Abstract
The cell intrinsic antiviral response of multicellular organisms developed over millions of years and critically relies on the ability to sense and eliminate viral nucleic acids. Here we use an affinity proteomics approach in evolutionary distant species (human, mouse and fly) to identify proteins that are conserved in their ability to associate with diverse viral nucleic acids. This approach shows a core of orthologous proteins targeting viral genetic material and species-specific interactions. Functional characterization of the influence of 181 candidates on replication of 6 distinct viruses in human cells and flies identifies 128 nucleic acid binding proteins with an impact on virus growth. We identify the family of TAO kinases (TAOK1, -2 and -3) as dsRNA-interacting antiviral proteins and show their requirement for type-I interferon induction. Depletion of TAO kinases in mammals or flies leads to an impaired response to virus infection characterized by a reduced induction of interferon stimulated genes in mammals and impaired expression of srg1 and diedel in flies. Overall, our study shows a larger set of proteins able to mediate the interaction between viral genetic material and host factors than anticipated so far, attesting to the ancestral roots of innate immunity and to the lineage-specific pressures exerted by viruses.
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Affiliation(s)
- Friederike L Pennemann
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Assel Mussabekova
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Christian Urban
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Alexey Stukalov
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Line Lykke Andersen
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Vincent Grass
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Teresa Maria Lavacca
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Cathleen Holze
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Lila Oubraham
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Yasmine Benamrouche
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Enrico Girardi
- CeMM - Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Rasha E Boulos
- Computer Science and Mathematics Department, School of Arts and Science, Lebanese American University, Byblos, Lebanon
| | - Rune Hartmann
- Aarhus University, Department of Molecular Biology and Genetics - Structural Biology, Aarhus, Denmark
| | - Giulio Superti-Furga
- CeMM - Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Matthias Habjan
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Jean-Luc Imler
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Carine Meignin
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Andreas Pichlmair
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany.
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany.
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany.
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Conserved E1B-55K SUMOylation in different human adenovirus species is a potent regulator of intracellular localization. J Virol 2021; 96:e0083821. [PMID: 34787461 DOI: 10.1128/jvi.00838-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Over the past decades, studies on the biology of human adenoviruses (HAdVs) mainly focused on the HAdV prototype species C type 5 (HAdV-C5) and revealed fundamental molecular insights into mechanisms of viral replication and viral cell transformation. Recently, other HAdV species are gaining more and more attention in the field. Reports on large E1B proteins (E1B-55K) from different HAdV species showed that these multifactorial proteins possess strikingly different features along with highly conserved functions. In this work, we identified potential SUMO-conjugation motifs (SCMs) in E1B-55K proteins from HAdV species A to F. Mutational inactivation of these SCMs demonstrated that HAdV E1B-55K proteins are SUMOylated at a single lysine residue that is highly conserved among HAdV species B to E. Moreover, we provide evidence that E1B-55K SUMOylation is a potent regulator of intracellular localization and p53-mediated transcription in most HAdV species. We also identified a lysine residue at position 101 (K101), which is unique to HAdV-C5 E1B-55K and specifically regulates its SUMOylation and nucleo-cytoplasmic shuttling. Our findings reveal important new aspects on HAdV E1B-55K proteins and suggest that different E1B-55K species possess conserved SCMs while their SUMOylation has divergent cellular effects during infection. Importance E1B-55K is a multifunctional adenoviral protein and its functions are highly regulated by SUMOylation. Although functional consequences of SUMOylated HAdV-C5 E1B-55K are well studied, we lack information on the effects of SUMOylation on homologous E1B-55K proteins from other HAdV species. Here, we show that SUMOylation is a conserved post-translational modification in most of the E1B-55K proteins, similar to what we know about HAdV-C5 E1B-55K. Moreover, we identify subcellular localization and regulation of p53-dependent transcription as highly conserved SUMOylation-regulated E1B-55K functions. Thus, our results highlight how HAdV proteins might have evolved in different HAdV species with conserved domains involved in virus replication and differing alternative functions and interactions with the host cell machinery. Future research will link these differences and similarities to the diverse pathogenicity and organ tropism of the different HAdV species.
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Wang Y, Wang G, Bai J, Zhang Y, Wang Y, Wen S, Li L, Yang Z, Hong N. A novel Actinidia cytorhabdovirus characterized using genomic and viral protein interaction features. MOLECULAR PLANT PATHOLOGY 2021; 22:1271-1287. [PMID: 34288324 PMCID: PMC8435229 DOI: 10.1111/mpp.13110] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
A novel cytorhabdovirus, tentatively named Actinidia virus D (AcVD), was identified from kiwifruit (Actinidia chinensis) in China using high-throughput sequencing technology. The genome of AcVD consists of 13,589 nucleotides and is organized into seven open reading frames (ORFs) in its antisense strand, coding for proteins in the order N-P-P3-M-G-P6-L. The ORFs were flanked by a 3' leader sequence and a 5' trailer sequence and are separated by conserved intergenic junctions. The genome sequence of AcVD was 44.6%-51.5% identical to those of reported cytorhabdoviruses. The proteins encoded by AcVD shared the highest sequence identities, ranging from 27.3% (P6) to 44.5% (L), with the respective proteins encoded by reported cytorhabdoviruses. Phylogenetic analysis revealed that AcVD clustered together with the cytorhabdovirus Wuhan insect virus 4. The subcellular locations of the viral proteins N, P, P3, M, G, and P6 in epidermal cells of Nicotiana benthamiana leaves were determined. The M protein of AcVD uniquely formed filament structures and was associated with microtubules. Bimolecular fluorescence complementation assays showed that three proteins, N, P, and M, self-interact, protein N plays a role in the formation of cytoplasm viroplasm, and protein M recruits N, P, P3, and G to microtubules. In addition, numerous paired proteins interact in the nucleus. This study presents the first evidence of a cytorhabdovirus infecting kiwifruit plants and full location and interaction maps to gain insight into viral protein functions.
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Affiliation(s)
- Yanxiang Wang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Guoping Wang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Jianyu Bai
- Laboratory of Fruit Trees DiseaseInstitute of Economic ForestryXinjiang Academy of Forestry SciencesUrumqiChina
| | - Yongle Zhang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ying Wang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Shaohua Wen
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Liu Li
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Zuokun Yang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ni Hong
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
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55
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Harrison AR, David CT, Rawlinson SM, Moseley GW. The Ebola Virus Interferon Antagonist VP24 Undergoes Active Nucleocytoplasmic Trafficking. Viruses 2021; 13:v13081650. [PMID: 34452514 PMCID: PMC8402725 DOI: 10.3390/v13081650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/25/2022] Open
Abstract
Viral interferon (IFN) antagonist proteins mediate evasion of IFN-mediated innate immunity and are often multifunctional, with distinct roles in viral replication. The Ebola virus IFN antagonist VP24 mediates nucleocapsid assembly, and inhibits IFN-activated signaling by preventing nuclear import of STAT1 via competitive binding to nuclear import receptors (karyopherins). Proteins of many viruses, including viruses with cytoplasmic replication cycles, interact with nuclear trafficking machinery to undergo nucleocytoplasmic transport, with key roles in pathogenesis; however, despite established karyopherin interaction, potential nuclear trafficking of VP24 has not been investigated. We find that inhibition of nuclear export pathways or overexpression of VP24-binding karyopherin results in nuclear localization of VP24. Molecular mapping indicates that cytoplasmic localization of VP24 depends on a CRM1-dependent nuclear export sequence at the VP24 C-terminus. Nuclear export is not required for STAT1 antagonism, consistent with competitive karyopherin binding being the principal antagonistic mechanism, while export mediates return of nuclear VP24 to the cytoplasm where replication/nucleocapsid assembly occurs.
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56
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Wang Y, Wang T, Liu L. The rice VCS1 is identified as a molecular tool to mark and visualize the vegetative cell of pollen. PLANT SIGNALING & BEHAVIOR 2021; 16:1924502. [PMID: 33982648 PMCID: PMC8244767 DOI: 10.1080/15592324.2021.1924502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/25/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Cell-type-specific markers are valuable tools to reveal developmental processes underlying cell differentiation during plant reproduction. Here we report the pollen vegetative cell marker gene VCS1 (Vegetative Cell Specific 1) of rice (Oryza sativa japonica). VCS1 was expressed specifically in late pollen and was predicted to encode a small FAF domain-containing protein of 205 amino acid residues (aa). The expression of reporter fusion proteins showed that VCS1 was exclusively targeted to the vegetative nucleus of pollen. Upon pollen germination, VCS1 lost vegetative nucleus localization, and appeared diffused in the vegetative cytoplasm of pollen grain but not in the pollen tube. T-DNA insertional mutation which disrupted the carboxyl-terminal 21 aa of VCS1 did not affect plant vegetative growth and pollen development, while destruction of VCS1 by CRISPR/Cas9 only moderately affect pollen viability. VCS1 is evolutionally conserved in monocots but appeared absent in dicotyledons. This study reveals a molecular tool for visualizing the vegetative cell of rice and possible other monocots, which has potential values in the genetic engineering of male-sterile lines.
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Affiliation(s)
- Yanli Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Tai Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Lingtong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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57
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Kashyap T, Murray J, Walker CJ, Chang H, Tamir S, Hou B, Shacham S, Kauffman MG, Tripp RA, Landesman Y. Selinexor, a novel selective inhibitor of nuclear export, reduces SARS-CoV-2 infection and protects the respiratory system in vivo. Antiviral Res 2021; 192:105115. [PMID: 34157321 PMCID: PMC8213878 DOI: 10.1016/j.antiviral.2021.105115] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023]
Abstract
The novel coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the recent global pandemic. The nuclear export protein (XPO1) has a direct role in the export of SARS-CoV proteins including ORF3b, ORF9b, and nucleocapsid. Inhibition of XPO1 induces anti-inflammatory, anti-viral, and antioxidant pathways. Selinexor is an FDA-approved XPO1 inhibitor. Through bioinformatics analysis, we predicted nuclear export sequences in the ACE-2 protein and confirmed by in vitro testing that inhibition of XPO1 with selinexor induces nuclear localization of ACE-2. Administration of selinexor inhibited viral infection prophylactically as well as therapeutically in vitro. In a ferret model of COVID-19, selinexor treatment reduced viral load in the lungs and protected against tissue damage in the nasal turbinates and lungs in vivo. Our studies demonstrated that selinexor downregulated the pro-inflammatory cytokines IL-1β, IL-6, IL-10, IFN-γ, TNF-α, and GMCSF, commonly associated with the cytokine storm observed in COVID-19 patients. Our findings indicate that nuclear export is critical for SARS-CoV-2 infection and for COVID-19 pathology and suggest that inhibition of XPO1 by selinexor could be a viable anti-viral treatment option.
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Affiliation(s)
| | - Jackelyn Murray
- University of Georgia College of Veterinary Medicine, Athens, GA, USA
| | | | - Hua Chang
- Karyopharm Therapeutics, Newton, MA, USA
| | | | - Bing Hou
- Antengene Corporation Co., Ltd., Shaoxing, PR China
| | | | | | - Ralph A Tripp
- University of Georgia College of Veterinary Medicine, Athens, GA, USA
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Duek P, Mary C, Zahn-Zabal M, Bairoch A, Lane L. Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students. Database (Oxford) 2021; 2021:baab046. [PMID: 34318869 PMCID: PMC8317215 DOI: 10.1093/database/baab046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022]
Abstract
About 10% of human proteins have no annotated function in protein knowledge bases. A workflow to generate hypotheses for the function of these uncharacterized proteins has been developed, based on predicted and experimental information on protein properties, interactions, tissular expression, subcellular localization, conservation in other organisms, as well as phenotypic data in mutant model organisms. This workflow has been applied to seven uncharacterized human proteins (C6orf118, C7orf25, CXorf58, RSRP1, SMLR1, TMEM53 and TMEM232) in the frame of a course-based undergraduate research experience named Functionathon organized at the University of Geneva to teach undergraduate students how to use biological databases and bioinformatics tools and interpret the results. C6orf118, CXorf58 and TMEM232 were proposed to be involved in cilia-related functions; TMEM53 and SMLR1 were proposed to be involved in lipid metabolism and C7orf25 and RSRP1 were proposed to be involved in RNA metabolism and gene expression. Experimental strategies to test these hypotheses were also discussed. The results of this manual data mining study may contribute to the project recently launched by the Human Proteome Organization (HUPO) Human Proteome Project aiming to fill gaps in the functional annotation of human proteins. Database URL: http://www.nextprot.org.
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Affiliation(s)
- Paula Duek
- CALIPHO group, SIB Swiss Institute of Bioinformatics
- Department of microbiology and molecular medicine, Faculty of medicine, University of Geneva, Geneva, Switzerland
| | - Camille Mary
- Department of microbiology and molecular medicine, Faculty of medicine, University of Geneva, Geneva, Switzerland
| | | | - Amos Bairoch
- CALIPHO group, SIB Swiss Institute of Bioinformatics
- Department of microbiology and molecular medicine, Faculty of medicine, University of Geneva, Geneva, Switzerland
| | - Lydie Lane
- CALIPHO group, SIB Swiss Institute of Bioinformatics
- Department of microbiology and molecular medicine, Faculty of medicine, University of Geneva, Geneva, Switzerland
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Li J, Guo Y, Deng Y, Hu L, Li B, Deng S, Zhong J, Xie L, Shi S, Hong X, Zheng X, Cai M, Li M. Subcellular Localization of Epstein-Barr Virus BLLF2 and Its Underlying Mechanisms. Front Microbiol 2021; 12:672192. [PMID: 34367081 PMCID: PMC8339435 DOI: 10.3389/fmicb.2021.672192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/24/2021] [Indexed: 11/13/2022] Open
Abstract
Epstein-Barr virus (EBV), the pathogen of several human malignancies, encodes many proteins required to be transported into the nucleus for viral DNA reproduction and nucleocapsids assembly in the lytic replication cycle. Here, fluorescence microscope, mutation analysis, interspecies heterokaryon assays, co-immunoprecipitation assay, RNA interference, and Western blot were performed to explore the nuclear import mechanism of EBV encoded BLLF2 protein. BLLF2 was shown to be a nucleocytoplasmic shuttling protein neither by a chromosomal region maintenance 1 (CRM1)- nor by a transporter associated with antigen processing (TAP)-dependent pathway. Yet, BLLF2's two functional nuclear localization signals (NLSs), NLS1 (16KRQALETVPHPQNRGR31) and NLS2 (44RRPRPPVAKRRRFPR58), were identified, whereas the predicted NES was nonfunctional. Finally, BLLF2 was proven to transport into the nucleus via a Ran-dependent and importin β1-dependent pathway. This mechanism may contribute to a more extensive insight into the assembly and synthesis of EBV virions in the nucleus, thus affording a new direction for the treatment of viruses.
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Affiliation(s)
- Jingjing Li
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Yingjie Guo
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Yangxi Deng
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Li Hu
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Bolin Li
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Shenyu Deng
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Jiayi Zhong
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Li Xie
- Centralab, Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Shaoxuan Shi
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Xuejun Hong
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Xuelong Zheng
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Mingsheng Cai
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Meili Li
- The Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
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Rawat K, Pal A, Banerjee S, Pal A, Mandal SC, Batabyal S. Ovine CD14- an Immune Response Gene Has a Role Against Gastrointestinal Nematode Haemonchus contortus-A Novel Report. Front Immunol 2021; 12:664877. [PMID: 34335567 PMCID: PMC8324245 DOI: 10.3389/fimmu.2021.664877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022] Open
Abstract
CD14 (also known as the monocyte differentiation antigen) is an important immune response gene known to be primarily responsible for innate immunity against bacterial pathogens, and as a pattern recognition receptor (PRR), binds with LPS (endotoxin), lipoproteins, and lipotechoic acid of bacteria. So far very limited work has been conducted in parasitic immunology. In the current study, we reported the role of CD14 in parasitic immunology in livestock species (sheep) for the first time. Ovine CD14 is characterized as a horse-shoe shaped bent solenoid with a hydrophobic amino-terminal pocket for CD14 along with domains. High mutation frequency was observed, out of total 41 mutations identified, 23 mutations were observed to be thermodynamically unstable and 11 mutations were deleterious in nature, causing major functional alteration of important domains of CD14, an indication of variations in individual susceptibility for sheep against Haemonchus contortus infestations. In silico studies with molecular docking reveal a role of immune response against Haemonchus contortus in sheep, which is later confirmed with experimental evidence through differential mRNA expression analysis for sheep, which revealed better expression of CD14 in Haemonchus contortus infected sheep compared to that of non-infected sheep. We confirmed the above findings with supportive evidence through haematological and biochemical analyses. Phylogenetic analysis was conducted to assess the evolutionary relationship with respect to humans and it was observed that sheep may well be used as model organisms due to better genetic closeness compared to that of mice.
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Affiliation(s)
- Kavita Rawat
- Department of BioChemistry, West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Aruna Pal
- Department of LFC, West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Samiddha Banerjee
- Department of Animal Science, Visva Bharati University, Bolpur, India
| | - Abantika Pal
- Department of Computer Science, Indian Institute of Technology, Kharagpur, India
| | - Subhas Chandra Mandal
- Department of Parasitology, West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Subhasis Batabyal
- Department of BioChemistry, West Bengal University of Animal and Fishery Sciences, Kolkata, India
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Aksnes I, Braaen S, Markussen T, Åkesson CP, Villoing S, Rimstad E. Genetically modified attenuated salmonid alphavirus: A potential strategy for immunization of Atlantic salmon. JOURNAL OF FISH DISEASES 2021; 44:923-937. [PMID: 33591590 DOI: 10.1111/jfd.13352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Pancreas disease (PD) is a serious challenge in European salmonid aquaculture caused by salmonid alphavirus (SAV). In this study, we report the effect of immunization of Atlantic salmon with three attenuated infectious SAV3 strains with targeted mutations in a glycosylation site of the envelope E2 protein and/or in a nuclear localization signal in the capsid protein. In a pilot experiment, it was shown that the mutated viral strains replicated in fish, transmitted to naïve cohabitants and that the transmission had not altered the sequences. In the main experiment, the fish were immunized with the strains and challenged with SAV3 eight weeks after immunization. Immunization resulted in infection both in injected fish and 2 weeks later in the cohabitant fish, followed by a persistent but declining load of the mutated virus variants in the hearts. The immunized fish developed clinical signs and pathology consistent with PD prior to challenge. However, fish injected with the virus mutated in both E2 and capsid showed little clinical signs and had higher average weight gain than the groups immunized with the single mutated variants. The SAV strain used for challenge was not detected in the immunized fish indicating that these fish were protected against superinfection with SAV during the 12 weeks of the experiment.
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Affiliation(s)
- Ida Aksnes
- Department of Paraclinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Stine Braaen
- Department of Paraclinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Turhan Markussen
- Department of Paraclinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
| | | | | | - Espen Rimstad
- Department of Paraclinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
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SRPassing Co-translational Targeting: The Role of the Signal Recognition Particle in Protein Targeting and mRNA Protection. Int J Mol Sci 2021; 22:ijms22126284. [PMID: 34208095 PMCID: PMC8230904 DOI: 10.3390/ijms22126284] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 01/13/2023] Open
Abstract
Signal recognition particle (SRP) is an RNA and protein complex that exists in all domains of life. It consists of one protein and one noncoding RNA in some bacteria. It is more complex in eukaryotes and consists of six proteins and one noncoding RNA in mammals. In the eukaryotic cytoplasm, SRP co-translationally targets proteins to the endoplasmic reticulum and prevents misfolding and aggregation of the secretory proteins in the cytoplasm. It was demonstrated recently that SRP also possesses an earlier unknown function, the protection of mRNAs of secretory proteins from degradation. In this review, we analyze the progress in studies of SRPs from different organisms, SRP biogenesis, its structure, and function in protein targeting and mRNA protection.
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63
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Anami S, Yamashino T, Suzuki R, Nakai K, Sato K, Wu B, Ryo M, Sugita M, Aoki S. Red light-regulated interaction of Per-Arnt-Sim histidine kinases with partner histidine-containing phosphotransfer proteins in Physcomitrium patens. Genes Cells 2021; 26:698-713. [PMID: 34086383 DOI: 10.1111/gtc.12878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 05/24/2021] [Accepted: 06/02/2021] [Indexed: 11/29/2022]
Abstract
Multi-step phosphorelay (MSP) is a broadly distributed signaling system in organisms. In MSP, histidine kinases (HKs) receive various environmental signals and transmit them by autophosphorylation followed by phosphotransfer to partner histidine-containing phosphotransfer proteins (HPts). Previously, we reported that Per-Arnt-Sim (PAS) domain-containing HK1 (PHK1) and PHK2 of the moss Physcomitrium (Physcomitrella) patens repressed red light-induced protonema branching, a critical step in the moss life cycle. In plants, PHK homolog-encoding genes are conserved only in early-diverging lineages such as bryophytes and lycophytes. PHKs-mediated signaling machineries attract attention especially from an evolutionary viewpoint, but they remain uninvestigated. Here, we studied the P. patens PHKs focusing on their subcellular patterns of localization and interaction with HPts. Yeast two-hybrid analysis, a localization assay with a green fluorescent protein, and a bimolecular fluorescence complementation analysis together showed that PHKs are localized and interact with partner HPts mostly in the nucleus, as unprecedented features for plant HKs. Additionally, red light triggered the interactions between PHKs and HPts in the cytoplasm, and light co-repressed the expression of PHK1 and PHK2 as well as genes encoding their partner HPts. Our results emphasize the uniqueness of PHKs-mediated signaling machineries, and functional implications of this uniqueness are discussed.
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Affiliation(s)
- Shu Anami
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | | | - Ryo Suzuki
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Kota Nakai
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Kensuke Sato
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Bowen Wu
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Masashi Ryo
- Graduate School of Information Science, Nagoya University, Nagoya, Japan
| | - Mamoru Sugita
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Setsuyuki Aoki
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
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64
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Kaspar S, Oertlin C, Szczepanowska K, Kukat A, Senft K, Lucas C, Brodesser S, Hatzoglou M, Larsson O, Topisirovic I, Trifunovic A. Adaptation to mitochondrial stress requires CHOP-directed tuning of ISR. SCIENCE ADVANCES 2021; 7:eabf0971. [PMID: 34039602 PMCID: PMC8153728 DOI: 10.1126/sciadv.abf0971] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
In response to disturbed mitochondrial gene expression and protein synthesis, an adaptive transcriptional response sharing a signature of the integrated stress response (ISR) is activated. We report an intricate interplay between three transcription factors regulating the mitochondrial stress response: CHOP, C/EBPβ, and ATF4. We show that CHOP acts as a rheostat that attenuates prolonged ISR, prevents unfavorable metabolic alterations, and postpones the onset of mitochondrial cardiomyopathy. Upon mitochondrial dysfunction, CHOP interaction with C/EBPβ is needed to adjust ATF4 levels, thus preventing overactivation of the ATF4-regulated transcriptional program. Failure of this interaction switches ISR from an acute to a chronic state, leading to early respiratory chain deficiency, energy crisis, and premature death. Therefore, contrary to its previously proposed role as a transcriptional activator of mitochondrial unfolded protein response, our results highlight a role of CHOP in the fine-tuning of mitochondrial ISR in mammals.
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Affiliation(s)
- Sophie Kaspar
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Medical Faculty, University of Cologne, D-50931 Cologne, Germany
- Institute for Mitochondrial Diseases and Ageing, Medical Faculty and Center for Molecular Medicine Cologne (CMMC) , University of Cologne, D-50931 Cologne, Germany
| | - Christian Oertlin
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Karolina Szczepanowska
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Medical Faculty, University of Cologne, D-50931 Cologne, Germany
- Institute for Mitochondrial Diseases and Ageing, Medical Faculty and Center for Molecular Medicine Cologne (CMMC) , University of Cologne, D-50931 Cologne, Germany
| | - Alexandra Kukat
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Medical Faculty, University of Cologne, D-50931 Cologne, Germany
- Institute for Mitochondrial Diseases and Ageing, Medical Faculty and Center for Molecular Medicine Cologne (CMMC) , University of Cologne, D-50931 Cologne, Germany
| | - Katharina Senft
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Medical Faculty, University of Cologne, D-50931 Cologne, Germany
- Institute for Mitochondrial Diseases and Ageing, Medical Faculty and Center for Molecular Medicine Cologne (CMMC) , University of Cologne, D-50931 Cologne, Germany
| | - Christina Lucas
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Medical Faculty, University of Cologne, D-50931 Cologne, Germany
| | - Susanne Brodesser
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Medical Faculty, University of Cologne, D-50931 Cologne, Germany
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Ivan Topisirovic
- Lady Davis Institute, SMBD Jewish General Hospital, Gerald Bronfman Department of Oncology and Departments of Experimental Medicine and Biochemistry, McGill University, Montreal, Canada
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Medical Faculty, University of Cologne, D-50931 Cologne, Germany.
- Institute for Mitochondrial Diseases and Ageing, Medical Faculty and Center for Molecular Medicine Cologne (CMMC) , University of Cologne, D-50931 Cologne, Germany
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65
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Prescher N, Hänsch S, Knobbe-Thomsen CB, Stühler K, Poschmann G. The migration behavior of human glioblastoma cells is influenced by the redox-sensitive human macrophage capping protein CAPG. Free Radic Biol Med 2021; 167:81-93. [PMID: 33711419 DOI: 10.1016/j.freeradbiomed.2021.02.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/26/2022]
Abstract
The macrophage capping protein CAPG belongs to the gelsolin superfamily which modulates actin dynamics by capping the growing end of actin filaments in a Ca2+- and PIP2-dependent manner resulting in polymerization inhibition of actin filaments. In the last years, additional functions for CAPG in transcription regulation were described and higher CAPG amounts have been linked to increased invasiveness and migration behavior in different human tumor entities like e.g. glioblastoma. Nevertheless, there is a lack of knowledge how additional functions of CAPG are regulated. As CAPG contains several cysteine residues which may be accessible to oxidation we were especially interested to investigate how alterations in the cysteine oxidation state may influence the function, localization, and regulation of CAPG. In the present study, we provide strong evidence that CAPG is a redox-sensitive protein and identified two cysteines: C282 and C290 as reversibly oxidized in glioblastoma cell lines. Whereas no evidence could be found that the canonical actin capping function of CAPG is redox-regulated, our results point to a novel role of the identified cysteines in the regulation of cell migration. Along with this, we found a localization shift out of the nucleus of CAPG and RAVER1, a potential interaction partner identified in our study which might explain the observed altered cell migration properties. The newly identified redox sensitive cysteines of CAPG could perspectively be considered as new targets for controlling tumor invasive properties.
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Affiliation(s)
- Nina Prescher
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Sebastian Hänsch
- Department of Biology, Center for Advanced Imaging (CAi), Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Christiane B Knobbe-Thomsen
- Department of Neuropathology, Heinrich-Heine University Düsseldorf and University Hospital, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Kai Stühler
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; Molecular Proteomics Laboratory, Biomedical Research Centre (BMFZ), Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Gereon Poschmann
- Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany.
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66
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Ding B, Sepehrimanesh M. Nucleocytoplasmic Transport: Regulatory Mechanisms and the Implications in Neurodegeneration. Int J Mol Sci 2021; 22:4165. [PMID: 33920577 PMCID: PMC8072611 DOI: 10.3390/ijms22084165] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleocytoplasmic transport (NCT) across the nuclear envelope is precisely regulated in eukaryotic cells, and it plays critical roles in maintenance of cellular homeostasis. Accumulating evidence has demonstrated that dysregulations of NCT are implicated in aging and age-related neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Alzheimer's disease (AD), and Huntington disease (HD). This is an emerging research field. The molecular mechanisms underlying impaired NCT and the pathogenesis leading to neurodegeneration are not clear. In this review, we comprehensively described the components of NCT machinery, including nuclear envelope (NE), nuclear pore complex (NPC), importins and exportins, RanGTPase and its regulators, and the regulatory mechanisms of nuclear transport of both protein and transcript cargos. Additionally, we discussed the possible molecular mechanisms of impaired NCT underlying aging and neurodegenerative diseases, such as ALS/FTD, HD, and AD.
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Affiliation(s)
- Baojin Ding
- Department of Biology, University of Louisiana at Lafayette, 410 East Saint Mary Boulevard, Lafayette, LA 70503, USA;
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Zhong R, Kandasamy MK, Ye ZH. XND1 Regulates Secondary Wall Deposition in Xylem Vessels through the Inhibition of VND Functions. PLANT & CELL PHYSIOLOGY 2021; 62:53-65. [PMID: 33764471 DOI: 10.1093/pcp/pcaa140] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/23/2020] [Indexed: 06/12/2023]
Abstract
Secondary wall deposition in xylem vessels is activated by Vascular-Related NAC Domain proteins (VNDs) that belong to a group of secondary wall NAC (SWN) transcription factors. By contrast, Xylem NAC Domain1 (XND1) negatively regulates secondary wall deposition in xylem vessels when overexpressed. The mechanism by which XND1 exerts its functions remains elusive. We employed the promoter of the fiber-specific Secondary Wall-Associated NAC Domain1 (SND1) gene to ectopically express XND1 in fiber cells to investigate its mechanism of action on secondary wall deposition. Ectopic expression of XND1 in fiber cells severely diminished their secondary wall deposition and drastically reduced the expression of SWN-regulated downstream transcription factors and secondary wall biosynthetic genes but not that of the SWN genes themselves. Transactivation analyses revealed that XND1 specifically inhibited SWN-activated expression of these downstream genes but not their MYB46-activated expression. Both the NAC domain and the C-terminus of XND1 were required for its inhibitory function and its NAC domain interacted with the DNA-binding domains of SWNs. XND1 was shown to be localized in the cytoplasm and the nucleus and its co-expression with VND6 resulted in the cytoplasmic sequestration of VND6. Furthermore, the C-terminus of XND1 was indispensable for the XND1-mediated cytoplasmic retention of VND6 and its fusion to VND6 was able to direct VND6 to the cytoplasm and render it unable to activate the gene expression. Since the XND1 gene is specifically expressed in xylem cells, these results indicate that XND1 acts through inhibiting VND functions to negatively regulate secondary wall deposition in xylem vessels.
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Affiliation(s)
- Ruiqin Zhong
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | | | - Zheng-Hua Ye
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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68
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Yehia L, Liu D, Fu S, Iyer P, Eng C. Non-canonical role of wild-type SEC23B in the cellular stress response pathway. Cell Death Dis 2021; 12:304. [PMID: 33753724 PMCID: PMC7985502 DOI: 10.1038/s41419-021-03589-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 11/21/2022]
Abstract
While germline recessive loss-of-function mutations in SEC23B in humans cause a rare form of anaemia, heterozygous change-of-function mutations result in increased predisposition to cancer. SEC23B encodes SEC23 homologue B, a component of coat protein complex II (COPII), which canonically transports proteins from the endoplasmic reticulum (ER) to the Golgi. Despite the association of SEC23B with anaemia and cancer, the precise pathophysiology of these phenotypic outcomes remains unknown. Recently, we reported that mutant SEC23B has non-canonical COPII-independent function, particularly within the ER stress and ribosome biogenesis pathways, and that may contribute to the pathobiology of cancer predisposition. In this study, we hypothesized that wild-type SEC23B has a baseline function within such cellular stress response pathways, with the mutant protein reflecting exaggerated effects. Here, we show that the wild-type SEC23B protein localizes to the nucleus in addition to classical distribution at the ER/Golgi interface and identify multiple putative nuclear localization and export signals regulating nuclear-cytoplasmic transport. Unexpectedly, we show that, independently of COPII, wild-type SEC23B can also localize to cell nucleoli under proteasome inhibition conditions, with distinct distribution patterns compared to mutant cells. Unbiased proteomic analyses through mass spectrometry further revealed that wild-type SEC23B interacts with a subset of nuclear proteins, in addition to central proteins in the ER stress, protein ubiquitination, and EIF2 signalling pathways. We validate the genotype-specific differential SEC23B-UBA52 (ribosomal protein RPL40) interaction. Finally, utilizing patient-derived lymphoblastoid cell lines harbouring either wild-type or mutant SEC23B, we show that SEC23B levels increase in response to ER stress, further corroborating its role as a cellular stress response sensor and/or effector. Overall, these observations suggest that SEC23B, irrespective of mutation status, has unexplored roles in the cellular stress response pathway, with implications relevant to cancer and beyond that, CDAII and normal cell biology.
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Affiliation(s)
- Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Darren Liu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA
| | - Shuai Fu
- Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Pranav Iyer
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA.
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
- Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA.
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69
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Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins. Int J Mol Sci 2021; 22:ijms22052647. [PMID: 33808029 PMCID: PMC7961639 DOI: 10.3390/ijms22052647] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Abstract
Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and functions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share similarities with transcriptional regulators and have positively charged electrostatic patches, which may indicate that they have previously unanticipated nucleic acid binding properties. Intrinsic dynamics analysis of Lim domains suggest that only Lim1 has similar internal dynamics properties, unlike Lim2/3. Furthermore, we analyzed protein expression and mutational frequency in various malignancies, as well as mapped protein-protein interaction networks they are involved in. Overall, our comprehensive bioinformatic analysis suggests that these proteins may play important roles in mediating protein-protein and protein-nucleic acid interactions.
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70
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Shaikhqasem A, Schmitt K, Valerius O, Ficner R. Crystal structure of human CRM1, covalently modified by 2-mercaptoethanol on Cys528, in complex with RanGTP. Acta Crystallogr F Struct Biol Commun 2021; 77:70-78. [PMID: 33682791 PMCID: PMC7938638 DOI: 10.1107/s2053230x2100203x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/21/2021] [Indexed: 11/23/2022] Open
Abstract
CRM1 is a nuclear export receptor that has been intensively targeted over the last decade for the development of antitumor and antiviral drugs. Structural analysis of several inhibitor compounds bound to CRM1 revealed that their mechanism of action relies on the covalent modification of a critical cysteine residue (Cys528 in the human receptor) located in the nuclear export signal-binding cleft. This study presents the crystal structure of human CRM1, covalently modified by 2-mercaptoethanol on Cys528, in complex with RanGTP at 2.58 Å resolution. The results demonstrate that buffer components can interfere with the characterization of cysteine-dependent inhibitor compounds.
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Affiliation(s)
- Alaa Shaikhqasem
- Department for Molecular Structural Biology, Georg-August-Universität Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Kerstin Schmitt
- Department of Molecular Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstrasse 8, 37077 Göttingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstrasse 8, 37077 Göttingen, Germany
| | - Ralf Ficner
- Department for Molecular Structural Biology, Georg-August-Universität Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
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71
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Analysis of Fox genes in Schmidtea mediterranea reveals new families and a conserved role of Smed-foxO in controlling cell death. Sci Rep 2021; 11:2947. [PMID: 33536473 PMCID: PMC7859237 DOI: 10.1038/s41598-020-80627-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/18/2020] [Indexed: 01/30/2023] Open
Abstract
The forkhead box (Fox) genes encode transcription factors that control several key aspects of development. Present in the ancestor of all eukaryotes, Fox genes underwent several duplications followed by loss and diversification events that gave rise to the current 25 families. However, few Fox members have been identified from the Lophotrochozoa clade, and specifically from planarians, which are a unique model for understanding development, due to the striking plasticity of the adult. The aim of this study was to identify and perform evolutionary and functional studies of the Fox genes of lophotrochozoan species and, specifically, of the planarian Schmidtea mediterranea. Generating a pipeline for identifying Forkhead domains and using phylogenetics allowed us the phylogenetic reconstruction of Fox genes. We corrected the annotation for misannotated genes and uncovered a new family, the QD, present in all metazoans. According to the new phylogeny, the 27 Fox genes found in Schmidtea mediterranea were classified into 12 families. In Platyhelminthes, family losses were accompanied by extensive gene diversification and the appearance of specific families, the A(P) and N(P). Among the newly identified planarian Fox genes, we found a single copy of foxO, which shows an evolutionary conserved role in controlling cell death.
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Mokdadi M, Abdelkrim YZ, Banroques J, Huvelle E, Oualha R, Yeter-Alat H, Guizani I, Barhoumi M, Tanner NK. The In Silico Identification of Potential Members of the Ded1/DDX3 Subfamily of DEAD-Box RNA Helicases from the Protozoan Parasite Leishmania infantum and Their Analyses in Yeast. Genes (Basel) 2021; 12:genes12020212. [PMID: 33535521 PMCID: PMC7912733 DOI: 10.3390/genes12020212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
DEAD-box RNA helicases are ubiquitous proteins found in all kingdoms of life and that are associated with all processes involving RNA. Their central roles in biology make these proteins potential targets for therapeutic or prophylactic drugs. The Ded1/DDX3 subfamily of DEAD-box proteins is of particular interest because of their important role(s) in translation. In this paper, we identified and aligned the protein sequences of 28 different DEAD-box proteins from the kinetoplast-protozoan parasite Leishmania infantum, which is the cause of the visceral form of leishmaniasis that is often lethal if left untreated, and compared them with the consensus sequence derived from DEAD-box proteins in general, and from the Ded1/DDX3 subfamily in particular, from a wide variety of other organisms. We identified three potential homologs of the Ded1/DDX3 subfamily and the equivalent proteins from the related protozoan parasite Trypanosoma brucei, which is the causative agent of sleeping sickness. We subsequently tested these proteins for their ability to complement a yeast strain deleted for the essential DED1 gene. We found that the DEAD-box proteins from Trypanosomatids are highly divergent from other eukaryotes, and consequently they are suitable targets for protein-specific drugs.
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Affiliation(s)
- Molka Mokdadi
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
- Institut National des Sciences Appliquées et Technologies, Université de Carthage, CEDEX, Tunis 1080, Tunisia
| | - Yosser Zina Abdelkrim
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Josette Banroques
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Emmeline Huvelle
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Rafeh Oualha
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Hilal Yeter-Alat
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Mourad Barhoumi
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
- Correspondence: (M.B.); (N.K.T.); Tel.: +216-71 843 755 (ext. 544) (M.B.); +33-1-58-41-52-37 (N.K.T.); Fax: +216-71-791-833 (M.B.); +33-1-58-41-50-25 (N.K.T.)
| | - N. Kyle Tanner
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
- Correspondence: (M.B.); (N.K.T.); Tel.: +216-71 843 755 (ext. 544) (M.B.); +33-1-58-41-52-37 (N.K.T.); Fax: +216-71-791-833 (M.B.); +33-1-58-41-50-25 (N.K.T.)
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73
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Zhang CF, Wang HM, Wu A, Li Y, Tian XL. FHA domain of AGGF1 is essential for its nucleocytoplasmic transport and angiogenesis. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1884-1894. [PMID: 33471274 DOI: 10.1007/s11427-020-1844-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/11/2020] [Indexed: 12/21/2022]
Abstract
Angiogenic factor with G-patch and FHA domains 1 (AGGF1) exhibits a dynamic distribution from the nucleus to the cytoplasm in endothelial cells during angiogenesis, but the biological significance and underlying mechanism of this nucleocytoplasmic transport remains unknown. Here, we demonstrate that the dynamic distribution is essential for AGGF1 to execute its angiogenic function. To search the structural bases for this nucleocytoplasmic transport, we characterized three potential nuclear localization regions, one potential nuclear export region, forkhead-associated (FHA), and G-patch domains to determine their effects on nucleocytoplasmic transport and angiogenesis, and we show that AGGF1 remains intact during the dynamic subcellular distribution and the region from 260 to 288 amino acids acts as a signal for its nuclear localization. The distribution of AGGF1 in cytoplasm needs both FHA domain and 14-3-3α/β. Binding of AGGF1 via FHA domain to 14-3-3α/β is required to complete the transport. Thus, we for the first time established structural bases for the nucleocytoplasmic transport of AGGF1 and revealed that the FHA domain of AGGF1 is essential for its nucleocytoplasmic transport and angiogenesis.
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Affiliation(s)
- Cui-Fang Zhang
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Han-Ming Wang
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Andong Wu
- Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 330031, China
| | - Yang Li
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Xiao-Li Tian
- Department of Human Population Genetics, Institute of Molecular Medicine, Peking University, Beijing, 100871, China. .,Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 330031, China.
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74
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Walker JS, Hing ZA, Harrington B, Baumhardt J, Ozer HG, Lehman A, Giacopelli B, Beaver L, Williams K, Skinner JN, Cempre CB, Sun Q, Shacham S, Stromberg BR, Summers MK, Abruzzo LV, Rassenti L, Kipps TJ, Parikh S, Kay NE, Rogers KA, Woyach JA, Coppola V, Chook YM, Oakes C, Byrd JC, Lapalombella R. Recurrent XPO1 mutations alter pathogenesis of chronic lymphocytic leukemia. J Hematol Oncol 2021; 14:17. [PMID: 33451349 PMCID: PMC7809770 DOI: 10.1186/s13045-021-01032-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 01/01/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Exportin 1 (XPO1/CRM1) is a key mediator of nuclear export with relevance to multiple cancers, including chronic lymphocytic leukemia (CLL). Whole exome sequencing has identified hot-spot somatic XPO1 point mutations which we found to disrupt highly conserved biophysical interactions in the NES-binding groove, conferring novel cargo-binding abilities and forcing cellular mis-localization of critical regulators. However, the pathogenic role played by change-in-function XPO1 mutations in CLL is not fully understood. METHODS We performed a large, multi-center retrospective analysis of CLL cases (N = 1286) to correlate nonsynonymous mutations in XPO1 (predominantly E571K or E571G; n = 72) with genetic and epigenetic features contributing to the overall outcomes in these patients. We then established a mouse model with over-expression of wildtype (wt) or mutant (E571K or E571G) XPO1 restricted to the B cell compartment (Eµ-XPO1). Eµ-XPO1 mice were then crossed with the Eµ-TCL1 CLL mouse model. Lastly, we determined crystal structures of XPO1 (wt or E571K) bound to several selective inhibitors of nuclear export (SINE) molecules (KPT-185, KPT-330/Selinexor, and KPT-8602/Eltanexor). RESULTS We report that nonsynonymous mutations in XPO1 associate with high risk genetic and epigenetic features and accelerated CLL progression. Using the newly-generated Eµ-XPO1 mouse model, we found that constitutive B-cell over-expression of wt or mutant XPO1 could affect development of a CLL-like disease in aged mice. Furthermore, concurrent B-cell expression of XPO1 with E571K or E571G mutations and TCL1 accelerated the rate of leukemogenesis relative to that of Eµ-TCL1 mice. Lastly, crystal structures of E571 or E571K-XPO1 bound to SINEs, including Selinexor, are highly similar, suggesting that the activity of this class of compounds will not be affected by XPO1 mutations at E571 in patients with CLL. CONCLUSIONS These findings indicate that mutations in XPO1 at E571 can drive leukemogenesis by priming the pre-neoplastic lymphocytes for acquisition of additional genetic and epigenetic abnormalities that collectively result in neoplastic transformation.
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Affiliation(s)
- Janek S Walker
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA
| | - Zachary A Hing
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA
| | - Bonnie Harrington
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Jordan Baumhardt
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hatice Gulcin Ozer
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Amy Lehman
- Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Brian Giacopelli
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA
| | - Larry Beaver
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA
| | - Katie Williams
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA
| | - Jordan N Skinner
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA
| | - Casey B Cempre
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA
| | - Qingxiang Sun
- Department of Pathology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | | | - Benjamin R Stromberg
- Department of Radiation Oncology, Arthur G James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, OH, USA
| | - Matthew K Summers
- Department of Radiation Oncology, Arthur G James Comprehensive Cancer Center and Richard L. Solove Research Institute, The Ohio State University, Columbus, OH, USA
| | - Lynne V Abruzzo
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Laura Rassenti
- Department of Medicine, Division of Hematology, University of California-San Diego School of Medicine, San Diego, CA, USA
| | - Thomas J Kipps
- Department of Medicine, Division of Hematology, University of California-San Diego School of Medicine, San Diego, CA, USA
| | - Sameer Parikh
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Neil E Kay
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kerry A Rogers
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA
| | - Jennifer A Woyach
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH, USA
- Genetically Engineered Mouse Modeling Core, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, OH, USA
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Christopher Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA
| | - John C Byrd
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA
- Division of Medicinal Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Rosa Lapalombella
- Division of Hematology, Department of Internal Medicine, The Ohio State University, 460 OSUCCC, 410 West 12th Avenue, Columbus, OH, 43210, USA.
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JAK3 Is Expressed in the Nucleus of Malignant T Cells in Cutaneous T Cell Lymphoma (CTCL). Cancers (Basel) 2021; 13:cancers13020280. [PMID: 33466582 PMCID: PMC7828698 DOI: 10.3390/cancers13020280] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/19/2020] [Accepted: 01/11/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary JAK3 plays an important role in the pathogenesis of cutaneous T cell lymphoma. JAK3 belongs to the Janus kinase family of receptor-associated tyrosine kinases located in cytoplasm adjacent to the plasma membrane. In this study, we show that JAK3 can also be ectopically expressed in the nucleus in CTCL cell lines and primary cells from CTCL patients. Importantly, JAK3 interacts with the nuclear protein RNA polymerase II and phosphorylates Histone H3. Thus, our data provide first evidence for nuclear expression of JAK3 and interactions with key nuclear proteins in malignant T cells suggesting a novel non-canonical role in CTCL. Abstract Perturbation in JAK-STAT signaling has been reported in the pathogenesis of cutaneous T cell lymphoma (CTCL). JAK3 is predominantly associated with the intra-cytoplasmic part of IL-2Rγc located in the plasma membrane of hematopoietic cells. Here we demonstrate that JAK3 is also ectopically expressed in the nucleus of malignant T cells. We detected nuclear JAK3 in various CTCL cell lines and primary malignant T cells from patients with Sézary syndrome, a leukemic variant of CTCL. Nuclear localization of JAK3 was independent of its kinase activity whereas STAT3 had a modest effect on nuclear JAK3 expression. Moreover, JAK3 nuclear localization was only weakly affected by blockage of nuclear export. An inhibitor of the nuclear export protein CRM1, Leptomycin B, induced an increased expression of SOCS3 in the nucleus, but only a weak increase in nuclear JAK3. Importantly, immunoprecipitation experiments indicated that JAK3 interacts with the nuclear protein POLR2A, the catalytic subunit of RNA Polymerase II. Kinase assays showed tyrosine phosphorylation of recombinant human Histone H3 by JAK3 in vitro—an effect which was blocked by the JAK inhibitor (Tofacitinib citrate). In conclusion, we provide the first evidence of nuclear localization of JAK3 in malignant T cells. Our findings suggest that JAK3 may have a cytokine-receptor independent function in the nucleus of malignant T cells, and thus a novel non-canonical role in CTCL.
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Zhang X, Ameer FS, Azhar G, Wei JY. Alternative Splicing Increases Sirtuin Gene Family Diversity and Modulates Their Subcellular Localization and Function. Int J Mol Sci 2021; 22:ijms22020473. [PMID: 33418837 PMCID: PMC7824890 DOI: 10.3390/ijms22020473] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing generates multiple distinct isoforms that increase transcriptome and proteome diversity. There are seven sirtuin genes in humans, each consists of multiple exons that are likely to undergo alternative splicing. Our aim was to characterize the effect of alternative splicing on the sirtuin genes. Here, we report the identification of 23 human sirtuin isoforms, most of which were not previously reported. Five of the sirtuin genes had more than one isoform, whereas sirtuin-6 had nine isoforms. Exon skipping was the main event. Most of the sirtuin isoforms were deficient in parts of the protein domains, including the catalytic domain, the N- or C-terminus, nuclear localization signal or mitochondrial targeting signal. The domain loss caused potential structural changes. Three SIRT1 isoforms had a differential effect on the mitochondrial oxygen consumption rate. Age-related changes in the expression of SIRT1 isoforms were observed in the human heart in fetus, adults, and very old individuals. We also identified 15 sirtuin isoforms in mice. Our data indicate that alternative splicing increases sirtuin gene diversity and may modulate subcellular localization and function, thereby adding complexity to the gene regulation of mitochondrial respiration, metabolism, and cardiac function during maturation and aging.
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Li K, Wong C, Cheng C, Cheng S, Li M, Mansveld S, Bergsma A, Huang T, van Eijk MJT, Lam H. GmDNJ1, a type-I heat shock protein 40 (HSP40), is responsible for both Growth and heat tolerance in soybean. PLANT DIRECT 2021; 5:e00298. [PMID: 33532690 PMCID: PMC7833466 DOI: 10.1002/pld3.298] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/26/2020] [Accepted: 12/02/2020] [Indexed: 05/24/2023]
Abstract
Global warming poses severe threats to agricultural production, including soybean. One of the major mechanisms for organisms to combat heat stress is through heat shock proteins (HSPs) that stabilize protein structures at above-optimum temperatures, by assisting in the folding of nascent, misfolded, or unfolded proteins. The HSP40 subgroups, or the J-domain proteins, functions as co-chaperones. They capture proteins that require folding or refolding and pass them on to HSP70 for processing. In this study, we have identified a type-I HSP40 gene in soybean, GmDNJ1, with high basal expression under normal growth conditions and also highly inducible under abiotic stresses, especially heat. Gmdnj1-knockout mutants had diminished growth in normal conditions, and when under heat stress, exhibited more severe browning, reduced chlorophyll contents, higher reactive oxygen species (ROS) contents, and higher induction of heat stress-responsive transcription factors and ROS-scavenging enzyme-encoding genes. Under both normal and heat-stress conditions, the mutant lines accumulated more aggregated proteins involved in protein catabolism, sugar metabolism, and membrane transportation, in both roots and leaves. In summary, GmDNJ1 plays crucial roles in the overall plant growth and heat tolerance in soybean, probably through the surveillance of misfolded proteins for refolding to maintain the full capacity of cellular functions.
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Affiliation(s)
- Kwan‐Pok Li
- School of Life Sciences and Center for Soybean Research of the State Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SAR
| | - Cheuk‐Hon Wong
- School of Life Sciences and Center for Soybean Research of the State Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SAR
| | - Chun‐Chiu Cheng
- School of Life Sciences and Center for Soybean Research of the State Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SAR
| | - Sau‐Shan Cheng
- School of Life Sciences and Center for Soybean Research of the State Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SAR
| | - Man‐Wah Li
- School of Life Sciences and Center for Soybean Research of the State Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SAR
| | | | | | | | | | - Hon‐Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SAR
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Molecular characterization of EhAK6, an endonuclease V domain-containing aurora kinase protein from Entamoeba histolytica: Protein-protein interaction, docking and functional aspect. CURRENT RESEARCH IN BIOTECHNOLOGY 2021. [DOI: 10.1016/j.crbiot.2021.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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79
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Sankunny M, Eng C. Identification of nuclear export signal in KLLN suggests potential role in proteasomal degradation in cancer cells. Oncotarget 2020; 11:4625-4636. [PMID: 33400740 PMCID: PMC7747863 DOI: 10.18632/oncotarget.27833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/20/2020] [Indexed: 11/25/2022] Open
Abstract
Germline and somatic promoter hypermethylation of KLLN has been found in diverse heritable and sporadic cancers, respectively. KLLN has many identified tumor suppressor functions, and when first reported, was thought to be exclusively nuclear. Here, we report on KLLN localization in both the nucleus and cytoplasm and the identification of a putative nuclear export signal (NES) sequence. KLLN overexpression in colon and breast cancer cells showed both nuclear and cytoplasmic presence. Inhibition of the CRM1 export pathway increased nuclear sequestration of KLLN, confirming the prediction of an NES sequence. Point mutations introduced in the predicted NES sequence decreased the strength of the NES and increased the nuclear sequestration of KLLN. Contrary to expectations, the transcription regulation and cellular proliferation functions of KLLN were unaffected by increased KLLN nuclear sequestration. Instead, increased nuclear KLLN correlated with increased nuclear sequestration of TRIM25 and decreased inhibitory phosphorylation of MDM2. Computational analysis of The Cancer Genome Atlas (TCGA) dataset showed positive correlation among KLLN, TRIM25 and MDM2 expression; pathway analysis of the common genes downstream of these three genes revealed protein degradation as one of the top canonical pathways. Together, our observations suggest that CRM1 pathway-based nuclear export of KLLN may impact proteasomal degradation.
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Affiliation(s)
- Madhav Sankunny
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Center for Personalized Genetic Healthcare, Cleveland Clinic Community Care and Population Health, Cleveland, Ohio 44195, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA.,Germline High Risk Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio 44106, USA
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80
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The Role of Protein Disorder in Nuclear Transport and in Its Subversion by Viruses. Cells 2020; 9:cells9122654. [PMID: 33321790 PMCID: PMC7764567 DOI: 10.3390/cells9122654] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
The transport of host proteins into and out of the nucleus is key to host function. However, nuclear transport is restricted by nuclear pores that perforate the nuclear envelope. Protein intrinsic disorder is an inherent feature of this selective transport barrier and is also a feature of the nuclear transport receptors that facilitate the active nuclear transport of cargo, and the nuclear transport signals on the cargo itself. Furthermore, intrinsic disorder is an inherent feature of viral proteins and viral strategies to disrupt host nucleocytoplasmic transport to benefit their replication. In this review, we highlight the role that intrinsic disorder plays in the nuclear transport of host and viral proteins. We also describe viral subversion mechanisms of the host nuclear transport machinery in which intrinsic disorder is a feature. Finally, we discuss nuclear import and export as therapeutic targets for viral infectious disease.
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81
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Imai K, Nakai K. Tools for the Recognition of Sorting Signals and the Prediction of Subcellular Localization of Proteins From Their Amino Acid Sequences. Front Genet 2020; 11:607812. [PMID: 33324450 PMCID: PMC7723863 DOI: 10.3389/fgene.2020.607812] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
At the time of translation, nascent proteins are thought to be sorted into their final subcellular localization sites, based on the part of their amino acid sequences (i.e., sorting or targeting signals). Thus, it is interesting to computationally recognize these signals from the amino acid sequences of any given proteins and to predict their final subcellular localization with such information, supplemented with additional information (e.g., k-mer frequency). This field has a long history and many prediction tools have been released. Even in this era of proteomic atlas at the single-cell level, researchers continue to develop new algorithms, aiming at accessing the impact of disease-causing mutations/cell type-specific alternative splicing, for example. In this article, we overview the entire field and discuss its future direction.
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Affiliation(s)
- Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Kenta Nakai
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Multiple wheat genomes reveal global variation in modern breeding. Nature 2020; 588:277-283. [PMID: 33239791 PMCID: PMC7759465 DOI: 10.1038/s41586-020-2961-x] [Citation(s) in RCA: 387] [Impact Index Per Article: 96.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/09/2020] [Indexed: 12/24/2022]
Abstract
Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars. Comparison of multiple genome assemblies from wheat reveals extensive diversity that results from the complex breeding history of wheat and provides a basis for further potential improvements to this important food crop.
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83
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Colozza G, De Robertis EM. Dact-4 is a Xenopus laevis Spemann organizer gene related to the Dapper/Frodo antagonist of β-catenin family of proteins. Gene Expr Patterns 2020; 38:119153. [PMID: 33186756 DOI: 10.1016/j.gep.2020.119153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/07/2020] [Accepted: 11/07/2020] [Indexed: 12/27/2022]
Abstract
Dact/Dapper/Frodo members belong to an evolutionarily conserved family of Dishevelled-binding proteins present in mammals, birds, amphibians and fishes that are involved in the regulation of Wnt and TGF-β signaling. In addition to the three established genes (Dact1-3) that compose the Dact family, a fourth paralogue group of related proteins has been recently identified and named Dact-4. Interestingly, Dact-4 is the most rapidly evolving gene of the entire family, as it displays very low homology with other Dact proteins and has lost key conserved domains. Dact-4 is not present in mammals, but weakly conserved homologs were found in reptiles and fishes. Recent RNAseq from our group identified new genes specifically expressed in the Xenopus laevis Spemann organizer. Among these, LOC100170590 mRNA encoded a protein sharing weak homology with a coelacanth Dact-like protein member. Here, by analyzing protein phylogeny and synteny, we show that this organizer gene corresponds to Dact-4. We report that Dact-4 is expressed in the Xenopus blastula pre-organizer region in addition to the gastrula organizer, as well as in placodes, eyes, neural tube, presomitic mesoderm and pronephros. Dact-4-Flag microinjection experiments suggest it is a nucleocytoplasmic protein, as are the other Dact paralogues.
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Affiliation(s)
- Gabriele Colozza
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095-1662, USA.
| | - Edward M De Robertis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095-1662, USA
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84
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Li J, Shi K, Xu T, Hu J, Li T, Li G, Chen K, Li D, Inoue K, Sui G. Mechanisms regulating DMTF1β/γ expression and their functional interplay with DMTF1α. Int J Oncol 2020; 58:20-32. [PMID: 33367929 PMCID: PMC7721083 DOI: 10.3892/ijo.2020.5146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/25/2020] [Indexed: 11/24/2022] Open
Abstract
The cyclin D binding myb-like transcription factor 1 (DMTF1), a haplo-insufficient tumor suppressor gene, has 3 alternatively spliced mRNA isoforms encoding DMTF1α, β and γ proteins. Previous studies have indicated a tumor suppressive role of DMTF1α and the oncogenic activity of DMTF1β, while the function of DMTF1γ remains largely undetermined. In the present study, the mechanisms regulating DMTF1 isoform expression were investigated and the functional interplay of DMTF1β and γ with DMTF1α was characterized. It was found that specific regions of DMTF1β and γ transcripts can impair their mRNA integrity or stability, and thus reduce protein expression levels. Additionally, DMTF1β and γ proteins exhibited a reduced stability compared to DMTF1α and all 3 DMTF1 isoforms were localized in the nuclei. Two basic residues, K52 and R53, in the DMTF1 isoforms determined their nuclear localization. Importantly, both DMTF1β and γ could associate with DMTF1α and antagonize its transactivation of the ARF promoter. Consistently, the ratios of both DMTF1β/α and γ/α were significantly associated with a poor prognoses of breast cancer patients, suggesting oncogenic roles of DMTF1β and γ isoforms in breast cancer development.
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Affiliation(s)
- Jialiang Li
- Key Laboratory of Saline‑Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang 150040, P.R. China
| | - Ke Shi
- Key Laboratory of Saline‑Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang 150040, P.R. China
| | - Tianqi Xu
- Key Laboratory of Saline‑Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang 150040, P.R. China
| | - Jingru Hu
- Key Laboratory of Saline‑Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang 150040, P.R. China
| | - Tianxin Li
- Key Laboratory of Saline‑Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang 150040, P.R. China
| | - Guangyue Li
- Key Laboratory of Saline‑Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang 150040, P.R. China
| | - Kuida Chen
- Key Laboratory of Saline‑Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang 150040, P.R. China
| | - Dangdang Li
- Key Laboratory of Saline‑Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang 150040, P.R. China
| | - Kazushi Inoue
- Department of Pathology and Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston‑Salem, NC 27157, USA
| | - Guangchao Sui
- Key Laboratory of Saline‑Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang 150040, P.R. China
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85
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Ma X, Huang X, Jiao Z, He L, Li Y, Ow DW. Overproduction of plant nuclear export signals enhances diamide tolerance in Schizosaccharomyces pombe. Biochem Biophys Res Commun 2020; 531:335-340. [PMID: 32800339 DOI: 10.1016/j.bbrc.2020.07.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 11/26/2022]
Abstract
The nuclear export signal (NES) endows a protein nuclear export ability. Surprisingly, our previous study shows that just the NES peptide of Schizosaccharomyces pombe Oxs1 (SpOxs1NES) can confer diamide tolerance by competing with transcription factor Pap1 for nuclear transport. This finding intrigued us to test the function of NESs from heterologous organisms. The Arabidopsis thaliana zinc finger transcription factor OXIDATIVE STRESS 2 (AtOXS2) is a nucleocytoplasmic shuttling protein and nearly all OXS2 members from maize and rice contain an NES. In this study, we find that the plant OXS2 members and their C-terminus (AT3 peptide) can confer diamide tolerance due to their NESs, and amino acids in non-conserved as well as conserved positions are necessary for the diamide tolerance. As in SpOxs1NES, the enhanced tolerance to diamide in fission yeast depends on Pap1. Like SpOxs1NES, OXS2 family NESs appear to compete for nuclear transport of the Pap1-like Arabidopsis protein bZIP10, as when overproduced in Arabidopsis protoplasts, bZIP10 is retained in the nucleus.
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Affiliation(s)
- Xiaoling Ma
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xing Huang
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhengli Jiao
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Lilong He
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yongqing Li
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - David W Ow
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
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86
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Napoli M, Li X, Ackerman HD, Deshpande AA, Barannikov I, Pisegna MA, Bedrosian I, Mitsch J, Quinlan P, Thompson A, Rajapakshe K, Coarfa C, Gunaratne PH, Marchion DC, Magliocco AM, Tsai KY, Flores ER. Pan-cancer analysis reveals TAp63-regulated oncogenic lncRNAs that promote cancer progression through AKT activation. Nat Commun 2020; 11:5156. [PMID: 33056990 PMCID: PMC7561725 DOI: 10.1038/s41467-020-18973-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/24/2020] [Indexed: 12/16/2022] Open
Abstract
The most frequent genetic alterations across multiple human cancers are mutations in TP53 and the activation of the PI3K/AKT pathway, two events crucial for cancer progression. Mutations in TP53 lead to the inhibition of the tumour and metastasis suppressor TAp63, a p53 family member. By performing a mouse-human cross species analysis between the TAp63 metastatic mammary adenocarcinoma mouse model and models of human breast cancer progression, we identified two TAp63-regulated oncogenic lncRNAs, TROLL-2 and TROLL-3. Further, using a pan-cancer analysis of human cancers and multiple mouse models of tumour progression, we revealed that these two lncRNAs induce the activation of AKT to promote cancer progression by regulating the nuclear to cytoplasmic translocation of their effector, WDR26, via the shuttling protein NOLC1. Our data provide preclinical rationale for the implementation of these lncRNAs and WDR26 as therapeutic targets for the treatment of human tumours dependent upon mutant TP53 and/or the PI3K/AKT pathway.
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Affiliation(s)
- Marco Napoli
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.,Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Xiaobo Li
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.,Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Hayley D Ackerman
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.,Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Avani A Deshpande
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.,Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Ivan Barannikov
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.,Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Marlese A Pisegna
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.,Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Isabelle Bedrosian
- Department of Surgical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jürgen Mitsch
- Advanced Data Analysis Centre, Nottingham, NG7 2RD, UK.,School of Computer Sciences University of Nottingham, Nottingham, NG7 2RD, UK
| | - Philip Quinlan
- Advanced Data Analysis Centre, Nottingham, NG7 2RD, UK.,School of Computer Sciences University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alastair Thompson
- Department of Surgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kimal Rajapakshe
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Preethi H Gunaratne
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77004, USA
| | - Douglas C Marchion
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Anthony M Magliocco
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Kenneth Y Tsai
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.,Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.,Department of Tumour Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Elsa R Flores
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA. .,Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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87
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Shen C, Yuan J. Genome-wide characterization and expression analysis of the heat shock transcription factor family in pumpkin (Cucurbita moschata). BMC PLANT BIOLOGY 2020; 20:471. [PMID: 33054710 PMCID: PMC7557022 DOI: 10.1186/s12870-020-02683-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/01/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND Crop quality and yield are affected by abiotic and biotic stresses, and heat shock transcription factors (Hsfs) are considered to play important roles in regulating plant tolerance under various stresses. To investigate the response of Cucurbita moschata to abiotic stress, we analyzed the genome of C. moschata. RESULTS In this research, a total of 36 C. moschata Hsf (CmHsf) members were identified and classified into three subfamilies (I, II, and III) according to their amino acid sequence identity. The Hsfs of the same subfamily usually exhibit a similar gene structure (intron-exon distribution) and conserved domains (DNA-binding and other functional domains). Chromosome localization analysis showed that the 36 CmHsfs were unevenly distributed on 18 of the 21 chromosomes (except for Cm_Chr00, Cm_Chr08 and Cm_Chr20), among which 18 genes formed 9 duplicated gene pairs that have undergone segmental duplication events. The Ka/Ks ratio showed that the duplicated CmHsfs have mainly experienced strong purifying selection. High-level synteny was observed between C. moschata and other Cucurbitaceae species. CONCLUSIONS The expression profile of CmHsfs in the roots, stems, cotyledons and true leaves revealed that the CmHsfs exhibit tissue specificity. The analysis of cis-acting elements and quantitative real-time polymerase chain reaction (qRT-PCR) revealed that some key CmHsfs were activated by cold stress, heat stress, hormones and salicylic acid. This study lays the foundation for revealing the role of CmHsfs in resistance to various stresses, which is of great significance for the selection of stress-tolerant C. moschata.
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Affiliation(s)
- Changwei Shen
- School of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Jingping Yuan
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China.
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, 453003, China.
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88
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Wei J, Zang S, Li C, Zhang X, Gao P, Qin Q. Grouper PKR activation inhibits red-spotted grouper nervous necrosis virus (RGNNV) replication in infected cells. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 111:103744. [PMID: 32442443 DOI: 10.1016/j.dci.2020.103744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/10/2020] [Accepted: 05/09/2020] [Indexed: 06/11/2023]
Abstract
The double-stranded RNA-activated protein kinase (PKR) is a Type I interferon (IFN) stimulated gene that has important biological and immunological functions. In viral infections, PKR inhibits or promotes viral replication. In the present study, PKR homologues of orange-spotted grouper (Epinephelus coioides) (EcPKR) were cloned and the involvement of EcPKR during Red-spotted grouper nervous necrosis virus (RGNNV) infection was investigated. EcPKR encodes a 621-amino acid polypeptide that is closely related to the equivalent protein in Larimichthys crocea. EcPKR encoded two dsRNA binding domains and a Serine/Threonine protein kinase domain. Quantitative real-time PCR (qRT-PCR) analysis indicated that EcPKR was present in all examined tissues, with higher expression in spleen, intestine and gill. When stimulated with poly(I:C), the expression of EcPKR in the grouper spleen was increased, with highest expression 12 h post stimulation. EcPKR concentration was significantly increased in RGNNV-infected cells, with highest expression at 36 h post stimulation. EcPKR is mainly present in the cytoplasm. Overexpression of EcPKR in grouper spleen (GS) cells inhibits the transcription of the RGNNV genes. Furthermore, our results show that EcPKR overexpression significantly enhances the immune response of interferon and the activation of interferon-beta (IFN-β), interferon stimulated response element (ISRE) and nuclear factor-kappa B (NF-κB). Taken together, these results are important for better understanding of the function of PKR in fish and reveal its involvement in host response to immune challenges in RGNNV.
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Affiliation(s)
- Jingguang Wei
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Shaoqing Zang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Qingdao, 266000, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China; CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Chen Li
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Xin Zhang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Pin Gao
- State Key Laboratory Breeding Base for Sustainable Exploitation of Tropical Biotic Resources, College of Marine Science, Hainan University, Haikou, 570228, China
| | - Qiwei Qin
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China.
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89
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Zhao L, Xia H, Huang J, Zheng Y, Liu C, Su J, Ping J. Features of Nuclear Export Signals of NS2 Protein of Influenza D Virus. Viruses 2020; 12:v12101100. [PMID: 33003329 PMCID: PMC7600798 DOI: 10.3390/v12101100] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 12/27/2022] Open
Abstract
Emerging influenza D viruses (IDVs), the newest member in the genus Orthomyxovirus family, which can infect and transmit in multiple mammalian species as its relatives the influenza A viruses (IAVs). Additional studies of biological characteristics of IDVs are needed; here, we studied the characteristics of IDV nonstructural protein 2 (NS2), which shares the lowest homology to known influenza proteins. First, we generated reassortant viruses via reverse genetics to analyze the segment compatibility and gene interchangeability between IAVs and IDVs. Next, we investigated the locations and exact sequences of nuclear export signals (NESs) of the IDV NS2 protein. Surprisingly, three separate NES regions were found to contribute to the nuclear export of an eGFP fusion protein. Alanine scanning mutagenesis identified critical amino acid residues within each NES, and co-immunoprecipitation experiments demonstrated that their nuclear export activities depend on the CRM1-mediated pathway, particularly for the third NES (136-146aa) of IDV NS2. Interestingly, the third NES was important for the interaction of NS2 protein with CRM1. The findings in this study contribute to the understanding of IDV NS2 protein’s role during nucleocytoplasmic transport of influenza viral ribonucleoprotein complexes (vRNPs) and will also facilitate the development of novel anti-influenza drugs targeting nuclear export signals of IDV NS2 protein.
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90
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Deveshwar P, Sharma S, Prusty A, Sinha N, Zargar SM, Karwal D, Parashar V, Singh S, Tyagi AK. Analysis of rice nuclear-localized seed-expressed proteins and their database (RSNP-DB). Sci Rep 2020; 10:15116. [PMID: 32934280 PMCID: PMC7492263 DOI: 10.1038/s41598-020-70713-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/03/2020] [Indexed: 01/16/2023] Open
Abstract
Nuclear proteins are primarily regulatory factors governing gene expression. Multiple factors determine the localization of a protein in the nucleus. An upright identification of nuclear proteins is way far from accuracy. We have attempted to combine information from subcellular prediction tools, experimental evidence, and nuclear proteome data to identify a reliable list of seed-expressed nuclear proteins in rice. Depending upon the number of prediction tools calling a protein nuclear, we could sort 19,441 seed expressed proteins into five categories. Of which, half of the seed-expressed proteins were called nuclear by at least one out of four prediction tools. Further, gene ontology (GO) enrichment and transcription factor composition analysis showed that 6116 seed-expressed proteins could be called nuclear with a greater assertion. Localization evidence from experimental data was available for 1360 proteins. Their analysis showed that a 92.04% accuracy of a nuclear call is valid for proteins predicted nuclear by at least three tools. Distribution of nuclear localization signals and nuclear export signals showed that the majority of category four members were nuclear resident proteins, whereas other categories have a low fraction of nuclear resident proteins and significantly higher constitution of shuttling proteins. We compiled all the above information for the seed-expressed genes in the form of a searchable database named Rice Seed Nuclear Protein DataBase (RSNP-DB) https://pmb.du.ac.in/rsnpdb. This information will be useful for comprehending the role of seed nuclear proteome in rice.
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Affiliation(s)
- Priyanka Deveshwar
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India
| | - Shivam Sharma
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India
| | - Ankita Prusty
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India
| | - Neha Sinha
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India
| | - Sajad Majeed Zargar
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India.,Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India
| | - Divya Karwal
- Institute of Informatics and Communications, University of Delhi, South Campus, New Delhi, India
| | - Vishal Parashar
- Institute of Informatics and Communications, University of Delhi, South Campus, New Delhi, India
| | - Sanjeev Singh
- Institute of Informatics and Communications, University of Delhi, South Campus, New Delhi, India
| | - Akhilesh Kumar Tyagi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India.
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91
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Alam T, Alazmi M, Naser R, Huser F, Momin AA, Astro V, Hong S, Walkiewicz KW, Canlas CG, Huser R, Ali AJ, Merzaban J, Adamo A, Jaremko M, Jaremko Ł, Bajic VB, Gao X, Arold ST. Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs. Bioinformatics 2020; 36:1121-1128. [PMID: 31584626 PMCID: PMC7703752 DOI: 10.1093/bioinformatics/btz703] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 09/03/2019] [Accepted: 09/28/2019] [Indexed: 01/08/2023] Open
Abstract
Motivation Leucine-aspartic acid (LD) motifs are short linear interaction motifs (SLiMs) that link paxillin family proteins to factors controlling cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. Results To enable a proteome-wide assessment of LD motifs, we developed an active learning based framework (LD motif finder; LDMF) that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome revealed a dozen new proteins containing LD motifs. We found that LD motif signalling evolved in unicellular eukaryotes more than 800 Myr ago, with paxillin and vinculin as core constituents, and nuclear export signal as a likely source of de novo LD motifs. We show that LD motif proteins form a functionally homogenous group, all being involved in cell morphogenesis and adhesion. This functional focus is recapitulated in cells by GFP-fused LD motifs, suggesting that it is intrinsic to the LD motif sequence, possibly through their effect on binding partners. Our approach elucidated the origin and dynamic adaptations of an ancestral SLiM, and can serve as a guide for the identification of other SLiMs for which only few representatives are known. Availability and implementation LDMF is freely available online at www.cbrc.kaust.edu.sa/ldmf; Source code is available at https://github.com/tanviralambd/LD/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tanvir Alam
- Computational Bioscience Research Center (CBRC), Division of Computer, Electrical and Mathematical Sciences & Engineering (CEMSE), Saudi Arabia
| | - Meshari Alazmi
- Computational Bioscience Research Center (CBRC), Division of Computer, Electrical and Mathematical Sciences & Engineering (CEMSE), Saudi Arabia
| | - Rayan Naser
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Saudi Arabia
| | - Franceline Huser
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Saudi Arabia
| | - Afaque A Momin
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Saudi Arabia
| | - Veronica Astro
- Division of Biological and Environmental Sciences and Engineering (BESE), Saudi Arabia
| | - SeungBeom Hong
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Saudi Arabia
| | - Katarzyna W Walkiewicz
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Saudi Arabia
| | | | - Raphaël Huser
- Division of Computer, Electrical and Mathematical Sciences & Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Amal J Ali
- Division of Biological and Environmental Sciences and Engineering (BESE), Saudi Arabia
| | - Jasmeen Merzaban
- Division of Biological and Environmental Sciences and Engineering (BESE), Saudi Arabia
| | - Antonio Adamo
- Division of Biological and Environmental Sciences and Engineering (BESE), Saudi Arabia
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), Saudi Arabia
| | - Łukasz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), Saudi Arabia
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), Division of Computer, Electrical and Mathematical Sciences & Engineering (CEMSE), Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Division of Computer, Electrical and Mathematical Sciences & Engineering (CEMSE), Saudi Arabia
| | - Stefan T Arold
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Sciences and Engineering (BESE), Saudi Arabia
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92
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Huerta M, Reyes L, García-Rivera G, Bañuelos C, Betanzos A, Díaz-Hernández M, Galindo A, Bolaños J, Cárdenas H, Azuara-Liceaga E, Chávez-Munguía B, Orozco E. A noncanonical GATA transcription factor of Entamoeba histolytica modulates genes involved in phagocytosis. Mol Microbiol 2020; 114:1019-1037. [PMID: 32808689 DOI: 10.1111/mmi.14592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022]
Abstract
In this paper, we explored the presence of GATA in Entamoeba histolytica and their function as regulators of phagocytosis-related genes. Bioinformatics analyses evidenced a single 579 bp sequence encoding for a protein (EhGATA), smaller than GATA factors of other organisms. EhGATA appeared phylogenetically close to Dictyostelium discoideum and Schistosoma mansoni GATA proteins. Its sequence predicts the presence of a zinc-finger DNA binding domain and an AT-Hook motif; it also has two nuclear localization signals. By transmission electron and confocal microscopy, anti-EhGATA antibodies revealed the protein in the cytoplasm and nucleus, and 65% of nuclear signal was in the heterochromatin. EhGATA recombinant protein and trophozoites nuclear extracts bound to GATA-DNA consensus sequence. By in silico scrutiny, 1,610 gene promoters containing GATA-binding sequences appeared, including Ehadh and Ehvps32 promoters, whose genes participate in phagocytosis. Chromatin immunoprecipitation assays showed that EhGATA interact with Ehadh and Ehvps32 promoters. In EhGATA-overexpressing trophozoites (NeoGATA), the Ehadh and Ehvps32 mRNAs amount was modified, strongly supporting that EhGATA could regulate their transcription. NeoGATA trophozoites exhibited rounded shapes, high proliferation rates, and diminished erythrophagocytosis. Our results provide new insights into the role of EhGATA as a noncanonical transcription factor, regulating genes associated with phagocytosis.
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Affiliation(s)
- Miriam Huerta
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Luz Reyes
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Cecilia Bañuelos
- Programa de Doctorado Transdisciplinario en Desarrollo Científico y Tecnológico para la Sociedad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Abigail Betanzos
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México.,Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Mitzi Díaz-Hernández
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Ausencio Galindo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Jeni Bolaños
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Helios Cárdenas
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Bibiana Chávez-Munguía
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
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93
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Siswanto FM, Oguro A, Arase S, Imaoka S. WDR23 regulates the expression of Nrf2-driven drug-metabolizing enzymes. Drug Metab Pharmacokinet 2020; 35:441-455. [PMID: 32839090 DOI: 10.1016/j.dmpk.2020.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/29/2020] [Accepted: 06/17/2020] [Indexed: 12/21/2022]
Abstract
Nrf2 plays a central role in the response to xenobiotics and oxidative stress. The activation of Nrf2 induces the expression of drug-metabolizing enzymes (DMEs) and is important for cytoprotection. Keap1 is a widely accepted proteasome-dependent regulator of Nrf2. Keap1 was reported to be absent in Caenorhabditis elegans, and the level of the Nrf2 ortholog SKN-1 was mainly regulated by WDR23. The WDR23 locus is highly conserved from C. elegans to humans. We investigated whether WDR23 regulates Nrf2 activity in mammalian cells, hepatocellular carcinoma cells (Hep3B) and human cervical carcinoma cells (HeLa). We found that WDR23 has two isoforms (1 and 2) and that knockdown of WDR23 was sufficient to stabilize Nrf2 and alter the expression of several DMEs. Keap1 knockdown resulted in higher Nrf2 levels than WDR23 knockdown, and their effects on DMEs differed. These results were consistent with Keap1 being a canonical regulator of Nrf2, and that WDR23 may assist in Nrf2 regulation. We confirmed that WDR23 physically interacted with Nrf2, suggesting that WDR23 directly regulates Nrf2-dependent DMEs. In immunostaining experiments, human WDR23 isoform 1 was localized to the cytoplasm, whereas isoform 2 mainly resided in the nucleus. Taken together, our results suggested WDR23 is a novel regulator of DME expression.
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Affiliation(s)
- Ferbian Milas Siswanto
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, 669-1337, Japan
| | - Ami Oguro
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, 669-1337, Japan; Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, 739-8521, Japan
| | - Saki Arase
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, 669-1337, Japan
| | - Susumu Imaoka
- Department of Biomedical Chemistry, School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, 669-1337, Japan.
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94
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Gomes JR, Lobo A, Nogueira R, Terceiro AF, Costelha S, Lopes IM, Magalhães A, Summavielle T, Saraiva MJ. Neuronal megalin mediates synaptic plasticity-a novel mechanism underlying intellectual disabilities in megalin gene pathologies. Brain Commun 2020; 2:fcaa135. [PMID: 33225275 PMCID: PMC7667529 DOI: 10.1093/braincomms/fcaa135] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 12/15/2022] Open
Abstract
Donnai-Barrow syndrome, a genetic disorder associated to LRP2 (low-density lipoprotein receptor 2/megalin) mutations, is characterized by unexplained neurological symptoms and intellectual deficits. Megalin is a multifunctional endocytic clearance cell-surface receptor, mostly described in epithelial cells. This receptor is also expressed in the CNS, mainly in neurons, being involved in neurite outgrowth and neuroprotective mechanisms. Yet, the mechanisms involved in the regulation of megalin in the CNS are poorly understood. Using transthyretin knockout mice, a megalin ligand, we found that transthyretin positively regulates neuronal megalin levels in different CNS areas, particularly in the hippocampus. Transthyretin is even able to rescue megalin downregulation in transthyretin knockout hippocampal neuronal cultures, in a positive feedback mechanism via megalin. Importantly, transthyretin activates a regulated intracellular proteolysis mechanism of neuronal megalin, producing an intracellular domain, which is translocated to the nucleus, unveiling megalin C-terminal as a potential transcription factor, able to regulate gene expression. We unveil that neuronal megalin reduction affects physiological neuronal activity, leading to decreased neurite number, length and branching, and increasing neuronal susceptibility to a toxic insult. Finally, we unravel a new unexpected role of megalin in synaptic plasticity, by promoting the formation and maturation of dendritic spines, and contributing for the establishment of active synapses, both in in vitro and in vivo hippocampal neurons. Moreover, these structural and synaptic roles of megalin impact on learning and memory mechanisms, since megalin heterozygous mice show hippocampal-related memory and learning deficits in several behaviour tests. Altogether, we unveil a complete novel role of megalin in the physiological neuronal activity, mainly in synaptic plasticity with impact in learning and memory. Importantly, we contribute to disclose the molecular mechanisms underlying the cognitive and intellectual disabilities related to megalin gene pathologies.
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Affiliation(s)
- João R Gomes
- Molecular Neurobiology Unit, IBMC- Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal.,I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Andrea Lobo
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,Addiction Biology Group, IBMC- Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal
| | - Renata Nogueira
- Molecular Neurobiology Unit, IBMC- Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal.,I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Ana F Terceiro
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,Addiction Biology Group, IBMC- Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal
| | - Susete Costelha
- Molecular Neurobiology Unit, IBMC- Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal.,I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Igor M Lopes
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,Addiction Biology Group, IBMC- Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal
| | - Ana Magalhães
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,Addiction Biology Group, IBMC- Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal
| | - Teresa Summavielle
- I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,Addiction Biology Group, IBMC- Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal
| | - Maria J Saraiva
- Molecular Neurobiology Unit, IBMC- Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal.,I3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
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95
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Xu JJ, Gao F, Wu JQ, Zheng H, Tong W, Cheng XF, Liu Y, Zhu H, Fu X, Jiang Y, Li L, Kong N, Li G, Tong G. Characterization of Nucleocytoplasmic Shuttling of Pseudorabies Virus Protein UL46. Front Vet Sci 2020; 7:484. [PMID: 32974393 PMCID: PMC7472561 DOI: 10.3389/fvets.2020.00484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023] Open
Abstract
Pseudorabies virus (PRV) is the etiological agent of Aujeszky's disease, which has caused severe economic loss in China since its re-emergence in 2011. UL46, a late gene of herpesvirus, codes for the abundant but non-essential viral phosphoproteins 11 and 12 (VP11/12). In this study, VP11/12 was found to localize inside both the nucleus and cytoplasm. The nuclear localization signal (NLS) of VP11/12 was identified as 3RRARGTRRASWKDASR18. Further research identified α5 and α7 to be the receptors for NLS and the chromosome region maintenance 1 (CRM1) to be the receptor for the nuclear export signal. Moreover, we found that PRV VP11/12 interacts with EP0 and the stimulator of interferon genes protein (STING), whereas the NLS of VP11/12 is the important part for VP11/12 to interact with UL48. To our knowledge, this is the first study to provide reliable evidence verifying the nuclear localization of VP11/12 and its role as an additional shuttling tegument protein for PRV. In addition, this is also the first study to elucidate the interactions between PRV VP11/12 and EP0 as well as between PRV VP11/12 and STING, while identifying the precise interaction sites of PRV VP11/12 and VP16.
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Affiliation(s)
- Jing-Jing Xu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Fei Gao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ji-Qiang Wu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xue-Fei Cheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yuting Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Haojie Zhu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xinling Fu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yifeng Jiang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Liwei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Guoxin Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.,Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.,Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
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96
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Kerman BE, Genoud S, Kurt Vatandaslar B, Denli AM, Georges Ghosh S, Xu X, Yeo GW, Aimone JB, Gage FH. Motoneuron expression profiling identifies an association between an axonal splice variant of HDGF-related protein 3 and peripheral myelination. J Biol Chem 2020; 295:12233-12246. [PMID: 32647008 PMCID: PMC7443494 DOI: 10.1074/jbc.ra120.014329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/27/2020] [Indexed: 11/06/2022] Open
Abstract
Disorders that disrupt myelin formation during development or in adulthood, such as multiple sclerosis and peripheral neuropathies, lead to severe pathologies, illustrating myelin's crucial role in normal neural functioning. However, although our understanding of glial biology is increasing, the signals that emanate from axons and regulate myelination remain largely unknown. To identify the core components of the myelination process, here we adopted a microarray analysis approach combined with laser-capture microdissection of spinal motoneurons during the myelinogenic phase of development. We identified neuronal genes whose expression was enriched during myelination and further investigated hepatoma-derived growth factor-related protein 3 (HRP3 or HDGFRP3). HRP3 was strongly expressed in the white matter fiber tracts of the peripheral (PNS) and central (CNS) nervous systems during myelination and remyelination in a cuprizone-induced demyelination model. The dynamic localization of HPR3 between axons and nuclei during myelination was consistent with its axonal localization during neuritogenesis. To study this phenomenon, we identified two splice variants encoded by the HRP3 gene: the canonical isoform HRP3-I and a newly recognized isoform, HRP3-II. HRP3-I remained solely in the nucleus, whereas HRP3-II displayed distinct axonal localization both before and during myelination. Interestingly, HRP3-II remained in the nuclei of unmyelinated neurons and glial cells, suggesting the existence of a molecular machinery that transfers it to and retains it in the axons of neurons fated for myelination. Overexpression of HRP3-II, but not of HRP3-I, increased Schwann cell numbers and myelination in PNS neuron-glia co-cultures. However, HRP3-II overexpression in CNS co-cultures did not alter myelination.
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Affiliation(s)
- Bilal Ersen Kerman
- Department of Histology and Embryology, Istanbul Medipol University International School of Medicine, Istanbul, Turkey; Regenerative and Restorative Medicine Research Center, Institute of Health Science, Department of Neuroscience, Istanbul Medipol University, Istanbul, Turkey; Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Stéphane Genoud
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, USA; Vifor Pharma, Villars-sur-Glâne, Switzerland
| | - Burcu Kurt Vatandaslar
- Regenerative and Restorative Medicine Research Center, Institute of Health Science, Department of Neuroscience, Istanbul Medipol University, Istanbul, Turkey; Institute of Health Science, Department of Neuroscience, Istanbul Medipol University, Istanbul, Turkey
| | - Ahmet Murat Denli
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Shereen Georges Ghosh
- Laboratory for Pediatric Brain Disease, University of California, San Diego, La Jolla, California, USA; Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Xiangdong Xu
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, California, USA
| | - James Bradley Aimone
- Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California, USA.
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97
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Sabino F, Madzharova E, Auf dem Keller U. Cell density-dependent proteolysis by HtrA1 induces translocation of zyxin to the nucleus and increased cell survival. Cell Death Dis 2020; 11:674. [PMID: 32826880 PMCID: PMC7442833 DOI: 10.1038/s41419-020-02883-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 01/01/2023]
Abstract
Proteases modulate critical processes in cutaneous tissue repair to orchestrate inflammation, cell proliferation and tissue remodeling. However, the functional consequences and implications in healing impairments of most cleavage events are not understood. Using iTRAQ-based Terminal Amine Isotopic Labeling of Substrates (TAILS) we had characterized proteolytic signatures in a porcine wound healing model and identified two neo-N termini derived from proteolytic cleavage of the focal adhesion protein and mechanotransducer zyxin. Here, we assign these proteolytic events to the activity of either caspase-1 or serine protease HtrA1 and analyze the biological relevance of the resultant zyxin truncations. By cellular expression of full-length and truncated zyxin proteins, we demonstrate nuclear translocation of a C-terminal zyxin fragment that could also be generated in vitro by HtrA1 cleavage and provide evidence for its anti-apoptotic activities, potentially by regulating the expression of modulators of cell proliferation, protein synthesis and genome stability. Targeted degradomics correlated endogenous generation of the same zyxin fragment with increased cell density in human primary dermal fibroblasts. Hence, this newly identified HtrA1-zyxin protease signaling axis might present a novel mechanism to transiently enhance cell survival in environments of increased cell density like in wound granulation tissue.
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Affiliation(s)
- Fabio Sabino
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Søltofts Plads, 2800, Kongens Lyngby, Denmark
- ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093, Zurich, Switzerland
| | - Elizabeta Madzharova
- ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093, Zurich, Switzerland
| | - Ulrich Auf dem Keller
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Søltofts Plads, 2800, Kongens Lyngby, Denmark.
- ETH Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093, Zurich, Switzerland.
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98
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Labrecque M, Marchand C, Archambault D. Characterization of Signal Sequences Determining the Nuclear/Nucleolar Import and Nuclear Export of the Caprine Arthritis-Encephalitis Virus Rev Protein. Viruses 2020; 12:v12080900. [PMID: 32824614 PMCID: PMC7471974 DOI: 10.3390/v12080900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022] Open
Abstract
Caprine arthritis-encephalitis virus (CAEV), a lentivirus, relies on the action of the Rev protein for its replication. The CAEV Rev fulfills its function by allowing the nuclear exportation of partially spliced or unspliced viral mRNAs. In this study, we characterized the nuclear and nucleolar localization signals (NLS and NoLS, respectively) and the nuclear export signal (NES) of the CAEV Rev protein. These signals are key actors in the nucleocytoplasmic shuttling of a lentiviral Rev protein. Several deletion and alanine substitution mutants were generated from a plasmid encoding the CAEV Rev wild-type protein that was fused to the enhanced green fluorescent protein (EGFP). Following cell transfection, images were captured by confocal microscopy and the fluorescence was quantified in the different cell compartments. The results showed that the NLS region is localized between amino acids (aa) 59 to 75, has a monopartite-like structure and is exclusively composed of arginine residues. The NoLS was found to be partially associated with the NLS. Finally, the CAEV Rev protein’s NES mapped between aa 89 to 101, with an aa spacing between the hydrophobic residues that was found to be unconventional as compared to that of other retroviral Rev/Rev-like proteins.
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Affiliation(s)
- Marlène Labrecque
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada
| | - Claude Marchand
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Denis Archambault
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Université de Montréal, Montréal, QC H3C 3J7, Canada
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99
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Han L, Liu K, Ma W, Jiang Y, Hou S, Tan Y, Yuan Q, Niu K, Fang X. Redesigning transcription factor Cre1 for alleviating carbon catabolite repression in Trichoderma reesei. Synth Syst Biotechnol 2020; 5:230-235. [PMID: 32695894 PMCID: PMC7365963 DOI: 10.1016/j.synbio.2020.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/17/2020] [Accepted: 07/04/2020] [Indexed: 12/14/2022] Open
Abstract
Carbon catabolite repression (CCR), which is mainly mediated by Cre1 and triggered by glucose, leads to a decrease in cellulase production in Trichoderma reesei. Many studies have focused on modifying Cre1 for alleviating CCR. Based on the homologous alignment of CreA from wild-type Penicillium oxalicum 114–2 (Po-0) and cellulase hyperproducer JUA10-1(Po-1), we constructed a C-terminus substitution strain—Po-2—with decreased transcriptional levels of cellulase and enhanced CCR. Results revealed that the C-terminal domain of CreAPo−1 plays an important role in alleviating CCR. Furthermore, we replaced the C-terminus of Cre1 with that of CreAPo−1 in T. reesei (Tr-0) and generated Tr-1. As a control, the C-terminus of Cre1 was truncated and Tr-2 was generated. The transcriptional profiles of these transformants revealed that the C-terminal chimera greatly improves cellulase transcription in the presence of glucose and thus upregulates cellulase in the presence of glucose and weakens CCR, consistent with truncating the C-terminus of Cre1 in Tr-0. Therefore, we propose constructing a C-terminal chimera as a new strategy to improve cellulase production and alleviate CCR in the presence of glucose.
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Affiliation(s)
- Lijuan Han
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Kuimei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.,Rongcheng Campus, Harbin University of Science and Technology, Weihai, 264300, China
| | - Wei Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Shaoli Hou
- Shandong Henglu Biological Technology Co., Ltd, Jinan, 250000, China
| | - Yinshuang Tan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Quanquan Yuan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Kangle Niu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.,Shandong Henglu Biological Technology Co., Ltd, Jinan, 250000, China
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100
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Expression patterns of activating transcription factor 5 (atf5a and atf5b) in zebrafish. Gene Expr Patterns 2020; 37:119126. [PMID: 32663618 DOI: 10.1016/j.gep.2020.119126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 11/20/2022]
Abstract
The Activating Transcription Factor 5 (ATF5) is a basic leucine-zipper (bZIP) transcription factor (TF) with proposed stress-protective, anti-apoptotic and oncogenic roles which were all established in cell systems. In whole animals, Atf5 function seems highly context dependent. Atf5 is strongly expressed in the rodent nose and mice knockout (KO) pups have defective olfactory sensory neurons (OSNs), smaller olfactory bulbs (OB), while adults are smell deficient. It was therefore proposed that Atf5 plays an important role in maturation and maintenance of OSNs. Atf5 expression was also described in murine liver and bones where it appears to promote differentiation of progenitor cells. By contrast in the rodent brain, Atf5 was first described as uniquely expressed in neuroprogenitors and thus, proposed to drive their proliferation and inhibit their differentiation. However, it was later also found in mature neurons stressing the need for additional work in whole animals. ATF5 is well conserved with two paralogs, atf5a and atf5b in zebrafish. Here, we present the expression patterns for both from 6 h (hpf) to 5day post-fertilization (dpf). We found early expression for both genes, and from 1dpf onwards overlapping expression patterns in the inner ear and the developing liver. In the brain, at 24hpf both atf5a and atf5b were expressed in the forebrain, midbrain, and hindbrain. However, from 2dpf and onwards we only detected atf5a expression namely in the olfactory bulbs, the mesencephalon, and the metencephalon. We further evidenced additional differential expression for atf5a in the sensory neurons of the olfactory organs, and for atf5b in the neuromasts, that form the superficial sensory organ called the lateral line (LL). Our results establish the basis for future functional analyses in this lower vertebrate.
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