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Loss-of-Function Variants in PPP1R12A: From Isolated Sex Reversal to Holoprosencephaly Spectrum and Urogenital Malformations. Am J Hum Genet 2020; 106:121-128. [PMID: 31883643 DOI: 10.1016/j.ajhg.2019.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/04/2019] [Indexed: 02/01/2023] Open
Abstract
In two independent ongoing next-generation sequencing projects for individuals with holoprosencephaly and individuals with disorders of sex development, and through international research collaboration, we identified twelve individuals with de novo loss-of-function (LoF) variants in protein phosphatase 1, regulatory subunit 12a (PPP1R12A), an important developmental gene involved in cell migration, adhesion, and morphogenesis. This gene has not been previously reported in association with human disease, and it has intolerance to LoF as illustrated by a very low observed-to-expected ratio of LoF variants in gnomAD. Of the twelve individuals, midline brain malformations were found in five, urogenital anomalies in nine, and a combination of both phenotypes in two. Other congenital anomalies identified included omphalocele, jejunal, and ileal atresia with aberrant mesenteric blood supply, and syndactyly. Six individuals had stop gain variants, five had a deletion or duplication resulting in a frameshift, and one had a canonical splice acceptor site loss. Murine and human in situ hybridization and immunostaining revealed PPP1R12A expression in the prosencephalic neural folds and protein localization in the lower urinary tract at critical periods for forebrain division and urogenital development. Based on these clinical and molecular findings, we propose the association of PPP1R12A pathogenic variants with a congenital malformations syndrome affecting the embryogenesis of the brain and genitourinary systems and including disorders of sex development.
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202
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Le Goff S, Keçeli BN, Jeřábková H, Heckmann S, Rutten T, Cotterell S, Schubert V, Roitinger E, Mechtler K, Franklin FCH, Tatout C, Houben A, Geelen D, Probst AV, Lermontova I. The H3 histone chaperone NASP SIM3 escorts CenH3 in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:71-86. [PMID: 31463991 DOI: 10.1111/tpj.14518] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/16/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Centromeres define the chromosomal position where kinetochores form to link the chromosome to microtubules during mitosis and meiosis. Centromere identity is determined by incorporation of a specific histone H3 variant termed CenH3. As for other histones, escort and deposition of CenH3 must be ensured by histone chaperones, which handle the non-nucleosomal CenH3 pool and replenish CenH3 chromatin in dividing cells. Here, we show that the Arabidopsis orthologue of the mammalian NUCLEAR AUTOANTIGENIC SPERM PROTEIN (NASP) and Schizosaccharomyces pombe histone chaperone Sim3 is a soluble nuclear protein that binds the histone variant CenH3 and affects its abundance at the centromeres. NASPSIM3 is co-expressed with Arabidopsis CenH3 in dividing cells and binds directly to both the N-terminal tail and the histone fold domain of non-nucleosomal CenH3. Reduced NASPSIM3 expression negatively affects CenH3 deposition, identifying NASPSIM3 as a CenH3 histone chaperone.
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Affiliation(s)
- Samuel Le Goff
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Burcu Nur Keçeli
- Department of Plants and Crops, Unit HortiCell, Faculty of Bioscience Engineering, Ghent University, Coupure links, 653, 9000, Ghent, Belgium
| | - Hana Jeřábková
- The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78 371, Olomouc, Czech Republic
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Sylviane Cotterell
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Elisabeth Roitinger
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, 1030, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, 1030, Austria
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, 1030, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, 1030, Austria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, 1030, Austria
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, 1030, Austria
| | | | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
| | - Danny Geelen
- Department of Plants and Crops, Unit HortiCell, Faculty of Bioscience Engineering, Ghent University, Coupure links, 653, 9000, Ghent, Belgium
| | - Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D-06466, Seeland, Germany
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
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203
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DNA Modification Readers and Writers and Their Interplay. J Mol Biol 2019:S0022-2836(19)30718-1. [PMID: 31866298 DOI: 10.1016/j.jmb.2019.12.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/28/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022]
Abstract
Genomic DNA is modified in a postreplicative manner and several modifications, the enzymes responsible for their deposition as well as proteins that read these modifications, have been described. Here, we focus on the impact of DNA modifications on the DNA helix and review the writers and readers of cytosine modifications and how they interplay to shape genome composition, stability, and function.
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204
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Neckles C, Boer RE, Aboreden N, Cross AM, Walker RL, Kim BH, Kim S, Schneekloth JS, Caplen NJ. HNRNPH1-dependent splicing of a fusion oncogene reveals a targetable RNA G-quadruplex interaction. RNA (NEW YORK, N.Y.) 2019; 25:1731-1750. [PMID: 31511320 PMCID: PMC6859848 DOI: 10.1261/rna.072454.119] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/08/2019] [Indexed: 05/05/2023]
Abstract
The primary oncogenic event in ∼85% of Ewing sarcomas is a chromosomal translocation that generates a fusion oncogene encoding an aberrant transcription factor. The exact genomic breakpoints within the translocated genes, EWSR1 and FLI1, vary; however, in EWSR1, breakpoints typically occur within introns 7 or 8. We previously found that in Ewing sarcoma cells harboring EWSR1 intron 8 breakpoints, the RNA-binding protein HNRNPH1 facilitates a splicing event that excludes EWSR1 exon 8 from the EWS-FLI1 pre-mRNA to generate an in-frame mRNA. Here, we show that the processing of distinct EWS-FLI1 pre-mRNAs by HNRNPH1, but not other homologous family members, resembles alternative splicing of transcript variants of EWSR1 We demonstrate that HNRNPH1 recruitment is driven by guanine-rich sequences within EWSR1 exon 8 that have the potential to fold into RNA G-quadruplex structures. Critically, we demonstrate that an RNA mimetic of one of these G-quadruplexes modulates HNRNPH1 binding and induces a decrease in the growth of an EWSR1 exon 8 fusion-positive Ewing sarcoma cell line. Finally, we show that EWSR1 exon 8 fusion-positive cell lines are more sensitive to treatment with the pan-quadruplex binding molecule, pyridostatin (PDS), than EWSR1 exon 8 fusion-negative lines. Also, the treatment of EWSR1 exon 8 fusion-positive cells with PDS decreases EWS-FLI1 transcriptional activity, reversing the transcriptional deregulation driven by EWS-FLI1. Our findings illustrate that modulation of the alternative splicing of EWS-FLI1 pre-mRNA is a novel strategy for future therapeutics against the EWSR1 exon 8 containing fusion oncogenes present in a third of Ewing sarcoma.
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Affiliation(s)
- Carla Neckles
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Robert E Boer
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Nicholas Aboreden
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Allison M Cross
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Robert L Walker
- Molecular Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Bong-Hyun Kim
- CCR Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702, USA
| | - Suntae Kim
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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205
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Buonocore F, Clifford-Mobley O, King TFJ, Striglioni N, Man E, Suntharalingham JP, del Valle I, Lin L, Lagos CF, Rumsby G, Conway GS, Achermann JC. Next-Generation Sequencing Reveals Novel Genetic Variants (SRY, DMRT1, NR5A1, DHH, DHX37) in Adults With 46,XY DSD. J Endocr Soc 2019; 3:2341-2360. [PMID: 31745530 PMCID: PMC6855215 DOI: 10.1210/js.2019-00306] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 10/04/2019] [Indexed: 12/11/2022] Open
Abstract
CONTEXT The genetic basis of human sex development is slowly being elucidated, and >40 different genetic causes of differences (or disorders) of sex development (DSDs) have now been reported. However, reaching a specific diagnosis using traditional approaches can be difficult, especially in adults where limited biochemical data may be available. OBJECTIVE We used a targeted next-generation sequencing approach to analyze known and candidate genes for DSDs in individuals with no specific molecular diagnosis. PARTICIPANTS AND DESIGN We studied 52 adult 46,XY women attending a single-center adult service, who were part of a larger cohort of 400 individuals. Classic conditions such as17β-hydroxysteroid dehydrogenase deficiency type 3, 5α-reductase deficiency type 2, and androgen insensitivity syndrome were excluded. The study cohort had broad working diagnoses of complete gonadal dysgenesis (CGD) (n = 27) and partially virilized 46,XY DSD (pvDSD) (n = 25), a group that included partial gonadal dysgenesis and those with a broad "partial androgen insensitivity syndrome" label. Targeted sequencing of 180 genes was undertaken. RESULTS Overall, a likely genetic cause was found in 16 of 52 (30.8%) individuals (22.2% CGD, 40.0% pvDSD). Pathogenic variants were found in sex-determining region Y (SRY; n = 3), doublesex and mab-3-related transcription factor 1 (DMRT1; n = 1), NR5A1/steroidogenic factor-1 (SF-1) (n = 1), and desert hedgehog (DHH; n = 1) in the CGD group, and in NR5A1 (n = 5), DHH (n = 1), and DEAH-box helicase 37 (DHX37; n = 4) in the pvDSD group. CONCLUSIONS Reaching a specific diagnosis can have clinical implications and provides insight into the role of these proteins in sex development. Next-generation sequencing approaches are invaluable, especially in adult populations or where diagnostic biochemistry is not possible.
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Affiliation(s)
- Federica Buonocore
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | | | - Tom F J King
- Reproductive Medicine Unit, University College London Hospitals, London, United Kingdom
| | - Niccolò Striglioni
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Elim Man
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Jenifer P Suntharalingham
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Ignacio del Valle
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Lin Lin
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Carlos F Lagos
- Chemical Biology and Drug Discovery Laboratory, Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Gill Rumsby
- Clinical Biochemistry, University College London Hospitals, London, United Kingdom
| | - Gerard S Conway
- Reproductive Medicine Unit, University College London Hospitals, London, United Kingdom
| | - John C Achermann
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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206
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Hammond MJ, Wang T, Cummins SF. Characterisation of early metazoan secretion through associated signal peptidase complex subunits, prohormone convertases and carboxypeptidases of the marine sponge (Amphimedon queenslandica). PLoS One 2019; 14:e0225227. [PMID: 31714927 PMCID: PMC6850559 DOI: 10.1371/journal.pone.0225227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/30/2019] [Indexed: 01/31/2023] Open
Abstract
Efficient communication between cells requires the ability to process precursor proteins into their mature and biologically active forms, prior to secretion into the extracellular space. Eukaryotic cells achieve this via a suite of enzymes that involve a signal peptidase complex, prohormone convertases and carboxypeptidases. Using genome and transcriptome data of the demosponge Amphimedon queenslandica, a universal ancestor to metazoan multicellularity, we endeavour to bridge the evolution of precursor processing machinery from single-celled eukaryotic ancestors through to the complex multicellular organisms that compromise Metazoa. The precursor processing repertoire as defined in this study of A. queenslandica consists of 3 defined signal peptidase subunits, 6 prohormone convertases and 1 carboxypeptidase, with 2 putative duplicates identified for signal peptidase complex subunits. Analysis of their gene expression levels throughout the sponge development enabled us to predict levels of activity. Some A. queenslandica precursor processing components belong to established functional clades while others were identified as having novel, yet to be discovered roles. These findings have clarified the presence of precursor processing machinery in the poriferans, showing the necessary machinery for the removal of precursor sequences, a critical post-translational modification required by multicellular organisms, and further sets a foundation towards understanding the molecular mechanism for ancient protein processing.
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Affiliation(s)
- Michael J. Hammond
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore Dc, Queensland, Australia
| | - Tianfang Wang
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore Dc, Queensland, Australia
| | - Scott F. Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore Dc, Queensland, Australia
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207
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The Novel Serine/Threonine Protein Kinase LmjF.22.0810 from Leishmania major may be Involved in the Resistance to Drugs such as Paromomycin. Biomolecules 2019; 9:biom9110723. [PMID: 31718000 PMCID: PMC6920834 DOI: 10.3390/biom9110723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 12/13/2022] Open
Abstract
The identification and clarification of the mechanisms of action of drugs used against leishmaniasis may improve their administration regimens and prevent the development of resistant strains. Herein, for the first time, we describe the structure of the putatively essential Ser/Thr kinase LmjF.22.0810 from Leishmania major. Molecular dynamics simulations were performed to assess the stability of the kinase model. The analysis of its sequence and structure revealed two druggable sites on the protein. Furthermore, in silico docking of small molecules showed that aminoglycosides preferentially bind to the phosphorylation site of the protein. Given that transgenic LmjF.22.0810-overexpressing parasites displayed less sensitivity to aminoglycosides such as paromomycin, our predicted models support the idea that the mechanism of drug resistance observed in those transgenic parasites is the tight binding of such compounds to LmjF.22.0810 associated with its overexpression. These results may be helpful to understand the complex machinery of drug response in Leishmania.
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208
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Identification of candidate ATP-binding cassette transporter gene family members in Diaphorina citri (Hemiptera: Psyllidae) via adult tissues transcriptome analysis. Sci Rep 2019; 9:15842. [PMID: 31676883 PMCID: PMC6825165 DOI: 10.1038/s41598-019-52402-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 10/15/2019] [Indexed: 12/12/2022] Open
Abstract
The ATP-binding cassette (ABC) transporters exist in all living organisms and play major roles in various biological functions by transporting a wide variety of substrates across membranes. The functions of ABC transporters in drug resistance have been extensively studied in vertebrates; however, they are rarely characterized in agricultural pests. The Asian citrus psyllid, Diaphorina citri, is one of the most damaging pests of the Citrus genus because of its transmission of Huanglongbing, also known as Yellow Dragon disease. In this study, the next-generation sequencing technique was applied to research the ABC transporters of D. citri. Fifty-three ABC transporter genes were found in the RNA-Seq data, and among these ABC transporters, 4, 4, 5, 2, 1, 4, 18 and 15 ABC proteins belonged to the ABCA-ABCH subfamilies, respectively. Different expression profiles of 52 genes between imidacloprid-resistant and imidacloprid-susceptible strains were studied by qRT-PCR; 5 ABCGs and 4 ABCHs were significantly upregulated in the imidacloprid-resistant strain. In addition, five of the nine upregulated genes were widely expressed in adult tissues in spatial expression analysis. The results suggest that these genes may play key roles in this phenotype. In general, this study contributed to our current understanding of D. citri resistance to insecticides.
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209
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Novel 5-Nitrofuran-Activating Reductase in Escherichia coli. Antimicrob Agents Chemother 2019; 63:AAC.00868-19. [PMID: 31481448 DOI: 10.1128/aac.00868-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/28/2019] [Indexed: 02/07/2023] Open
Abstract
The global spread of multidrug-resistant enterobacteria warrants new strategies to combat these pathogens. One possible approach is the reconsideration of "old" antimicrobials, which remain effective after decades of use. Synthetic 5-nitrofurans such as furazolidone, nitrofurantoin, and nitrofurazone are such a class of antimicrobial drugs. Recent epidemiological data showed a very low prevalence of resistance to this antimicrobial class among clinical Escherichia coli isolates in various parts of the world, forecasting the increasing importance of its uses to battle antibiotic-resistant enterobacteria. However, although they have had a long history of clinical use, a detailed understanding of the 5-nitrofurans' mechanisms of action remains limited. Nitrofurans are known as prodrugs that are activated in E. coli by reduction catalyzed by two redundant nitroreductases, NfsA and NfsB. Furazolidone, nevertheless, retains relatively significant antibacterial activity in the nitroreductase-deficient ΔnfsA ΔnfsB E. coli strain, indicating the presence of additional activating enzymes and/or antibacterial activity of the unreduced form. Using genome sequencing, genetic, biochemical, and bioinformatic approaches, we discovered a novel 5-nitrofuran-activating enzyme, AhpF, in E. coli The discovery of a new nitrofuran-reducing enzyme opens new avenues for overcoming 5-nitrofuran resistance, such as designing nitrofuran analogues with higher affinity for AhpF or screening for adjuvants that enhance AhpF expression.
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210
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Lin L, Wang Y, Liu L, Ying W, Wang W, Sun B, Sun J, Wang X. Clinical phenotype of a Chinese patient with RIPK1 deficiency due to novel mutation. Genes Dis 2019; 7:122-127. [PMID: 32181283 PMCID: PMC7063410 DOI: 10.1016/j.gendis.2019.10.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023] Open
Abstract
Accumulating evidence indicates that RIPK1 is associated with inflammation and apoptotic. RIPK1 deficiency leads to proinflammatory signaling impaired. However, only few patients with homozygous loss-of-function mutation in RIPK1 gene had been reported until now. Here, we report a Chinese combined immunodeficiency patient. He had recurrent infection, diarrhea after 3 months old. Immune function indicated that T, B and NK cells decreased significantly but immunoglobulins approximately remained normal. Whole-exome sequencing indicated that he had novel compound heterozygous mutations (c.998 C > A from his mother and c.1934 C > T from his father) in RIPK1 gene, which were confirmed by Sanger sequencing. Our study reports novel mutations in RIPK1 gene and new phenotype of patient with RIPK1 deficiency.
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Affiliation(s)
- Li Lin
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Ying Wang
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Luyao Liu
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Wenjing Ying
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Wenjie Wang
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Bijun Sun
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Jinqiao Sun
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Xiaochuan Wang
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, 201102, China
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211
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Zhao Z, Li T, Peng X, Wu K, Yang S. Identification and Characterization of Tomato SWI3-Like Proteins: Overexpression of SlSWIC Increases the Leaf Size in Transgenic Arabidopsis. Int J Mol Sci 2019; 20:ijms20205121. [PMID: 31623074 PMCID: PMC6829904 DOI: 10.3390/ijms20205121] [Citation(s) in RCA: 5] [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: 09/12/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 02/06/2023] Open
Abstract
As the subunits of the SWI/SNF (mating-type switching (SWI) and sucrose nonfermenting (SNF)) chromatin-remodeling complexes (CRCs), Swi3-like proteins are crucial to chromatin remodeling in yeast and human. Growing evidence indicate that AtSWI3s are also essential for development and response to hormones in Arabidopsis. Nevertheless, the biological functions of Swi3-like proteins in tomato (Solanum lycopersicum) have not been investigated. Here we identified four Swi3-like proteins from tomato, namely SlSWI3A, SlSWI3B, SlSWI3C, and SlSWI3D. Subcellular localization analysis revealed that all SlSWI3s are localized in the nucleus. The expression patterns showed that all SlSWI3s are ubiquitously expressed in all tissues and organs, and SlSWI3A and SlSWI3B can be induced by cold treatment. In addition, we found that SlSWI3B can form homodimers with itself and heterodimers with SlSWI3A and SlSWI3C. SlSWI3B can also interact with SlRIN and SlCHR8, two proteins involved in tomato reproductive development. Overexpression of SlSWI3C increased the leaf size in transgenic Arabidopsis with increased expression of GROWTH REGULATING FACTORs, such as GRF3, GRF5, and GRF6. Taken together, our results indicate that SlSWI3s may play important roles in tomato growth and development.
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Affiliation(s)
- Zhongyi Zhao
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610064, China.
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- College of Life Sciences, China West Normal University, Nanchong 637002, China.
| | - Tao Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510650, China.
| | - Xiuling Peng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China.
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan.
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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212
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Greenlip Abalone ( Haliotis laevigata) Genome and Protein Analysis Provides Insights into Maturation and Spawning. G3-GENES GENOMES GENETICS 2019; 9:3067-3078. [PMID: 31413154 PMCID: PMC6778792 DOI: 10.1534/g3.119.400388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Wild abalone (Family Haliotidae) populations have been severely affected by commercial fishing, poaching, anthropogenic pollution, environment and climate changes. These issues have stimulated an increase in aquaculture production; however production growth has been slow due to a lack of genetic knowledge and resources. We have sequenced a draft genome for the commercially important temperate Australian ‘greenlip’ abalone (Haliotis laevigata, Donovan 1808) and generated 11 tissue transcriptomes from a female adult abalone. Phylogenetic analysis of the greenlip abalone with reference to the Pacific abalone (Haliotis discus hannai) indicates that these abalone species diverged approximately 71 million years ago. This study presents an in-depth analysis into the features of reproductive dysfunction, where we provide the putative biochemical messenger components (neuropeptides) that may regulate reproduction including gonad maturation and spawning. Indeed, we isolate the egg-laying hormone neuropeptide and under trial conditions induce spawning at 80% efficiency. Altogether, we provide a solid platform for further studies aimed at stimulating advances in abalone aquaculture production. The H. laevigata genome and resources are made available to the public on the abalone ‘omics website, http://abalonedb.org.
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Rahfeld P, Wardman JF, Mehr K, Huff D, Morgan-Lang C, Chen HM, Hallam SJ, Withers SG. Prospecting for microbial α- N-acetylgalactosaminidases yields a new class of GH31 O-glycanase. J Biol Chem 2019; 294:16400-16415. [PMID: 31530641 DOI: 10.1074/jbc.ra119.010628] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/16/2019] [Indexed: 12/18/2022] Open
Abstract
α-Linked GalNAc (α-GalNAc) is most notably found at the nonreducing terminus of the blood type-determining A-antigen and as the initial point of attachment to the peptide backbone in mucin-type O-glycans. However, despite their ubiquity in saccharolytic microbe-rich environments such as the human gut, relatively few α-N-acetylgalactosaminidases are known. Here, to discover and characterize novel microbial enzymes that hydrolyze α-GalNAc, we screened small-insert libraries containing metagenomic DNA from the human gut microbiome. Using a simple fluorogenic glycoside substrate, we identified and characterized a glycoside hydrolase 109 (GH109) that is active on blood type A-antigen, along with a new subfamily of glycoside hydrolase 31 (GH31) that specifically cleaves the initial α-GalNAc from mucin-type O-glycans. This represents a new activity in this GH family and a potentially useful new enzyme class for analysis or modification of O-glycans on protein or cell surfaces.
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Affiliation(s)
- Peter Rahfeld
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada .,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jacob F Wardman
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, Vancouver, British Columbia V6T 1Z3, Canada
| | - Kevin Mehr
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Drew Huff
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Connor Morgan-Lang
- Department of Microbiology and Immunology, University of British Columbia, Life Sciences Centre, Vancouver, British Columbia V6T 1Z3, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
| | - Hong-Ming Chen
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Life Sciences Centre, Vancouver, British Columbia V6T 1Z3, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada .,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, Vancouver, British Columbia V6T 1Z3, Canada
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214
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Jing J, Wang B, Liu P. The Functional Role of SEC23 in Vesicle Transportation, Autophagy and Cancer. Int J Biol Sci 2019; 15:2419-2426. [PMID: 31595159 PMCID: PMC6775307 DOI: 10.7150/ijbs.37008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 08/01/2019] [Indexed: 02/06/2023] Open
Abstract
SEC23, the core component of the coat protein complex II (COPII), functions to transport newly synthesized proteins and lipids from the endoplasmic reticulum (ER) to the Golgi apparatus in cells for secretion. SEC23 protein has two isoforms (SEC23A and SEC23B) and their aberrant expression and mutations were reported to cause human diseases and oncogenesis, whereas SEC23A and SEC23B may have the opposite activity in human cancer, for a reason that remains unclear. This review summarizes recent research in SEC23, COPII-vesicle transportation, autophagy, and cancer.
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Affiliation(s)
- Jingchen Jing
- Center for Translational Medicine, The First Affiliated Hospital, Xi'an Jiaotong University.,The Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Bo Wang
- Center for Translational Medicine, The First Affiliated Hospital, Xi'an Jiaotong University.,The Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Peijun Liu
- Center for Translational Medicine, The First Affiliated Hospital, Xi'an Jiaotong University.,The Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
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215
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Lan H, Wu L, Sun R, Keller NP, Yang K, Ye L, He S, Zhang F, Wang S. The HosA Histone Deacetylase Regulates Aflatoxin Biosynthesis Through Direct Regulation of Aflatoxin Cluster Genes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1210-1228. [PMID: 30986121 DOI: 10.1094/mpmi-01-19-0033-r] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Histone deacetylases (HDACs) always function as corepressors and sometimes as coactivators in the regulation of fungal development and secondary metabolite production. However, the mechanism through which HDACs play positive roles in secondary metabolite production is still unknown. Here, classical HDAC enzymes were identified and analyzed in Aspergillus flavus, a fungus that produces one of the most carcinogenic secondary metabolites, aflatoxin B1 (AFB1). Characterization of the HDACs revealed that a class I family HDAC, HosA, played crucial roles in growth, reproduction, the oxidative stress response, AFB1 biosynthesis, and pathogenicity. To a lesser extent, a class II family HDAC, HdaA, was also involved in sclerotia formation and AFB1 biosynthesis. An in vitro analysis of HosA revealed that its HDAC activity was considerably diminished at nanomolar concentrations of trichostatin A. Notably, chromatin immunoprecipitation experiments indicated that HosA bound directly to AFB1 biosynthesis cluster genes to regulate their expression. Finally, we found that a transcriptional regulator, SinA, interacts with HosA to regulate fungal development and AFB1 biosynthesis. Overall, our results reveal a novel mechanism by which classical HDACs mediate the induction of secondary metabolite genes in fungi.
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Affiliation(s)
- Huahui Lan
- Fujian Key Laboratory of Pathogenic Fungi Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lianghuan Wu
- Fujian Key Laboratory of Pathogenic Fungi Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ruilin Sun
- Fujian Key Laboratory of Pathogenic Fungi Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Nancy P Keller
- Departments of Bacteriology, Medical Microbiology, and Immunology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Kunlong Yang
- Fujian Key Laboratory of Pathogenic Fungi Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liuqing Ye
- Fujian Key Laboratory of Pathogenic Fungi Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuibin He
- Fujian Key Laboratory of Pathogenic Fungi Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Feng Zhang
- Fujian Key Laboratory of Pathogenic Fungi Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shihua Wang
- Fujian Key Laboratory of Pathogenic Fungi Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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216
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Rolly NK, Lee SU, Imran QM, Hussain A, Mun BG, Kim KM, Yun BW. Nitrosative stress-mediated inhibition of OsDHODH1 gene expression suggests roots growth reduction in rice ( Oryza sativa L.). 3 Biotech 2019; 9:273. [PMID: 31245237 PMCID: PMC6581995 DOI: 10.1007/s13205-019-1800-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 06/06/2019] [Indexed: 12/11/2022] Open
Abstract
This study monitored the transcriptional response of OsDHODH1 under nitrosative stress conditions relative to the transcripts accumulations for the core mitochondrial cytochrome c oxidase1 (CcOX1) subunit, nuclear CcOX subunits 5b and 5c, two rice nitrate reductases (OsNIA1 and OsNIA2), and nitric oxide excess 1 (OsNOE1) genes. Our findings reveal that short-term exposure of rice seedlings to 1 mM SNP (Nitric oxide donor) applied exogenously for 1 h resulted in significant down-regulation of OsDHODH1 expression in all rice cultivars. In addition, the transcriptional patterns for the CcOX subunits, which are known to have a high affinity for nitric oxide, showed that the core catalytic subunit (OsCcOX1) and the nuclear subunit (OsCcOX5b) were up-regulated, while the nuclear subunit (OsCcOX5c) gene expression was suppressed. OsGSNOR1 expression was enhanced or decreased concomitant with a decrease or increase in SNO accumulation, particularly at the basal level. Moreover, high OsNIA1 expression was consistent with impaired root development, whereas low transcript accumulation matched a balanced root-growth pattern. This suggests that OsNIA1 expression would prevail over OsNIA2 expression under nitrosative stress response in rice. The level of malondialdehyde (MDA) content increased with the increase in SNP concentration, translating enhanced oxidative damage to the cell. We also observed increased catalase activity in response to 5 mM SNP suggesting that potential cross-talk exist between nitrosative and oxidative stress. These results collectively suggest a possible role of OsDHODH1 and OsCcOX5b role in plant root growth during nitrosative stress responses.
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Affiliation(s)
- Nkulu Kabange Rolly
- Laboratory of Plant Functional Genomics School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sang-Uk Lee
- Laboratory of Plant Functional Genomics School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Qari Muhammad Imran
- Laboratory of Plant Functional Genomics School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Adil Hussain
- Department of Agriculture, Abdul Wali Khan University, Mardan, Pakistan
| | - Bong-Gyu Mun
- Laboratory of Plant Functional Genomics School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Kyung-Min Kim
- Laboratory of Plant Molecular Breeding, School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Byung-Wook Yun
- Laboratory of Plant Functional Genomics School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
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217
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Cao S, Guo M, Wang C, Xu W, Shi T, Tong G, Zhen C, Cheng H, Yang C, Elsheery NI, Cheng Y. Genome-wide characterization of aspartic protease (AP) gene family in Populus trichocarpa and identification of the potential PtAPs involved in wood formation. BMC PLANT BIOLOGY 2019; 19:276. [PMID: 31234799 PMCID: PMC6591973 DOI: 10.1186/s12870-019-1865-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/03/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Aspartic protease (AP) is one of four large proteolytic enzyme families that are involved in plant growth and development. Little is known about the AP gene family in tree species, although it has been characterized in Arabidopsis, rice and grape. The AP genes that are involved in tree wood formation remain to be determined. RESULTS A total of 67 AP genes were identified in Populus trichocarpa (PtAP) and classified into three categories (A, B and C). Chromosome mapping analysis revealed that two-thirds of the PtAP genes were located in genome duplication blocks, indicating the expansion of the AP family by segmental duplications in Populus. The microarray data from the Populus eFP browser demonstrated that PtAP genes had diversified tissue expression patterns. Semi-qRT-PCR analysis further determined that more than 10 PtAPs were highly or preferentially expressed in the developing xylem. When the involvement of the PtAPs in wood formation became the focus, many SCW-related cis-elements were found in the promoters of these PtAPs. Based on PtAPpromoter::GUS techniques, the activities of PtAP66 promoters were observed only in fiber cells, not in the vessels of stems as the xylem and leaf veins developed in the transgenic Populus tree, and strong GUS signals were detected in interfascicular fiber cells, roots, anthers and sepals of PtAP17promoter::GUS transgenic plants. Intensive GUS activities in various secondary tissues implied that PtAP66 and PtAP17 could function in wood formation. In addition, most of the PtAP proteins were predicted to contain N- and (or) O-glycosylation sites, and the integration of PNGase F digestion and western blotting revealed that the PtAP17 and PtAP66 proteins were N-glycosylated in Populus. CONCLUSIONS Comprehensive characterization of the PtAP genes suggests their functional diversity during Populus growth and development. Our findings provide an overall understanding of the AP gene family in trees and establish a better foundation to further describe the roles of PtAPs in wood formation.
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Affiliation(s)
- Shenquan Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Mengjie Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Chong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Wenjing Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Tianyuan Shi
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Guimin Tong
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Cheng Zhen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Hao Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
| | | | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang China
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218
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Meng Q, Zhang J, Zhang H, Zhou G, Ni R, Zhao Y, Qin Q, Zou Z. Comparative analysis of C-type lectin domain proteins in the ghost moth, Thitarodes xiaojinensis (Lepidoptera: Hepialidae). INSECT SCIENCE 2019; 26:453-465. [PMID: 29274206 PMCID: PMC7379682 DOI: 10.1111/1744-7917.12564] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 11/03/2017] [Accepted: 11/19/2017] [Indexed: 05/24/2023]
Abstract
Insects have a large family of C-type lectins involved in cell adhesion, pathogen recognition and activation of immune responses. In this study, 32 transcripts encoding C-type lectin domain proteins (CTLDPs) were identified from the Thitarodes xiaojinensis transcriptome. According to their domain structures, six CTLDPs with one carbohydrate-recognition domain (CRD) were classified into the CTL-S subfamily. The other 23 CTLDPs with two CRDs were grouped into the immulectin (IML) subfamily. The remaining three with extra regulatory domains were sorted into the CTL-X subfamily. Phylogenetic analysis showed that CTL-S and CTL-X members from different insects could form orthologous groups. In contrast, no T. xiaojinensis IML orthologues were found in other insects. Remarkable lineage-specific expansion in this subfamily was observed reflecting that these CTLDPs, as important receptors, have evolved diversified members in response to a variety of microbes. Prediction of binding ligands revealed that T. xiaojinensis, a cold-adapted species, conserved the ability of CRDs to combine with Ca2+ to keep its receptors from freezing. Comparative analysis of induction of CTLDP genes after different immune challenges indicated that IMLs might play critical roles in immune defenses. This study examined T. xiaojinensis CTLDPs and provides a basis for further studies of their characteristics.
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Affiliation(s)
- Qian Meng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Ji‐Hong Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Huan Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Gui‐Ling Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Ruo‐Yao Ni
- College of Life SciencesHebei UniversityBaodingHebeiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yan‐Ni Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qi‐Lian Qin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Zhen Zou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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219
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Identification and Expression Analysis of Snf2 Family Proteins in Tomato ( Solanum lycopersicum). Int J Genomics 2019; 2019:5080935. [PMID: 31049349 PMCID: PMC6458923 DOI: 10.1155/2019/5080935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 12/18/2018] [Indexed: 02/03/2023] Open
Abstract
As part of chromatin-remodeling complexes (CRCs), sucrose nonfermenting 2 (Snf2) family proteins alter chromatin structure and nucleosome position by utilizing the energy of ATP, which allows other regulatory proteins to access DNA. Plant genomes encode a large number of Snf2 proteins, and some of them have been shown to be the key regulators at different developmental stages in Arabidopsis. Yet, little is known about the functions of Snf2 proteins in tomato (Solanum lycopersicum). In this study, 45 Snf2s were identified by the homologous search using representative sequences from yeast (S. cerevisiae), fruit fly (D. melanogaster), and Arabidopsis (A. thaliana) against the tomato genome annotation dataset. Tomato Snf2 proteins (also named SlCHRs) could be clustered into 6 groups and distributed on 11 chromosomes. All SlCHRs contained a helicase-C domain with about 80 amino acid residues and a SNF2-N domain with more variable amino acid residues. In addition, other conserved motifs were also identified in SlCHRs by using the MEME program. Expression profile analysis indicated that tomato Snf2 family genes displayed a wide range of expressions in different tissues and some of them were regulated by the environmental stimuli such as salicylic acid, abscisic acid, salt, and cold. Taken together, these results provide insights into the functions of SlCHRs in tomato.
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220
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Wang X, Guo Y, Wen C, Lv M, Gan N, Zhou H, Zhang A, Yang K. Molecular characterization of grass carp interleukin-6 receptor and the agonistic activity of its soluble form in head kidney leucocytes. FISH & SHELLFISH IMMUNOLOGY 2019; 86:1072-1080. [PMID: 30576778 DOI: 10.1016/j.fsi.2018.12.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/11/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
Interleukin (IL)-6 receptor (IL-6R) can specifically bind to IL-6 and the complex subsequently recruits a transmembrane signal transducer, gp130, to trigger the intracellular signal transduction. IL-6R exists in two forms, a transmembrane IL-6R and a soluble IL-6R (sIL-6R), leading to different signal transduction mechanisms as classic signaling and trans-signaling, respectively. There is now a general consensus that these two modes of signal transduction can mediate anti-inflammatory and pro-inflammatory activities of IL-6. The study on Il-6r is limited although Il-6 has been well studied in teleost. In the present study, a cDNA encoding grass carp Il-6r (gcIl-6r) was isolated. An in-silico analysis showed that gcIl-6r shared the same functional domains and conserved gene synteny at its loci with mouse homologue, and its amino acid sequence was conserved in fish species. A tissue distribution assay demonstrated that gcil6r mRNA was expressed with high levels in immune tissues including spleen and head kidney, and its expression was induced by LPS and Poly I:C in grass carp head kidney leucocytes (HKLs). An in vitro binding assay showed that recombinant soluble gcIl-6r (rgcsIl-6r) could specifically bind to recombinant gcIl-6 (rgcIl-6) protein. Moreover, rgcIl-6 stimulated suppressor of cytokine signaling 3 (socs3)'s mRNA expression in grass carp HKLs and it combined with rgcsIl-6r increased socs3 mRNA expression in CIK cells with gp130 but without Il-6r expression. In HKLs, rgcIl-6 stimulated the mRNA levels of both pro-inflammatory (tnfa and il1b) and anti-inflammatory (il10) cytokines, and rgcsIl-6r could augment these stimulatory effects of gcIl-6. Taken these data together, gcsIl-6r can mediate the immuno-regulatory functions of gcIl-6 and has an agonistic property in these actions of Il-6 in grass carp.
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Affiliation(s)
- Xinyan Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, PR China.
| | - Yafei Guo
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, PR China
| | - Chao Wen
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, PR China
| | - Mengyuan Lv
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, PR China
| | - Ning Gan
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, PR China
| | - Hong Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, PR China
| | - Anying Zhang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, PR China
| | - Kun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, PR China
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221
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Voltage-dependent calcium channels in the neurosecretory cells of cerebral ganglia of the mud crab, Scylla paramamosain. Neuroreport 2019; 29:1068-1074. [PMID: 29965872 DOI: 10.1097/wnr.0000000000001074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Voltage-dependent calcium channels (VDCCs) play a critical role in stimulus-secretion coupling in neurosecretory cells (NSCs). The crustacean cerebral ganglion plays a crucial role in neuromodulation and controls neuropeptide release. The present study used patch-clamp and Illumina sequencing techniques to investigate the potential features of VDCC in the cerebral ganglia of the mud crab (Scylla paramamosain). The electrophysiological characteristics of VDCC were analyzed in three types of NSCs with a patch clamp. The thresholds for activation of Ca channel current recorded from all the three types of NSCs were all above -40 mV, with peak amplitudes occurring around 0 mV. Therefore, it was concluded that the currents recorded in NSCs were mediated by high-voltage-activated Ca channels. Ca channel current densities in I type NSCs were significantly lower than those in II and III type NSCs. Four VDCC subunits derived from three transcripts were predicted from a transcriptome database of the cerebral ganglia. Among these transcripts, Cavα1, Cavβ, and Cavα2/δ were predicted to encode 1674, 554, and 776 amino acids, respectively, and they shared conservative domains with VDCC subunits in other species. Overall, these findings provide an important basis for further studies on the neuroendocrine mechanisms in crustaceans.
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222
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Li H, Ma L, Hu Z, Tu Y, Jiang C, Wu Q, Han J, Zeng B, He B. Heterologous expression of AoD9D enhances salt tolerance with increased accumulation of unsaturated fatty acid in transgenic Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2019; 46:231-239. [PMID: 30604237 DOI: 10.1007/s10295-018-02123-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/19/2018] [Indexed: 12/24/2022]
Abstract
Salt stress can trigger several physiological responses in microorganisms such as the increasing accumulation of unsaturated fatty acid, which was biosynthesized by delta-9 fatty acid desaturases (D9D) at the first step. In the present study, two D9D genes, designated AoD9D1 and AoD9D2, were isolated from Aspergillus oryzae. The expression analysis showed that AoD9D1 and AoD9D2 were upregulated under salt stress. To investigate the function of AoD9D, transgenic Saccharomyces cerevisiae strains that heterologously expressed AoD9D were exposed to salinity condition. These transgenic strains exhibited greater tolerance to salt stress than wild-type strains, and the heterologous expression of AoD9D increased the content in unsaturated fatty acids as compared to control cells. Moreover, AoD9D1 and AoD9D2 both contained fatty acid desaturase (FAD) and cytochrome b5-like Heme/Steroid-binding domains (Cyt-b5). S. cerevisiae separately transformed with the gene fragments coding for the FAD and Cyt-b5 domains in the AoD9D1 protein grew better and accumulated a higher concentration of unsaturated FAs than the control. Altogether, the heterologous expression of AoD9D enhanced the tolerance of transgenic S. cerevisiae to high salinity stress with increased accumulation of unsaturated fatty acid. The results provide some practical basis for the successful development of salt-tolerant fermentation microorganisms.
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Affiliation(s)
- Haoran Li
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Long Ma
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Zhihong Hu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Yayi Tu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Chunmiao Jiang
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Qinqin Wu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Jizhong Han
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-Vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, 330013, China.
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Gu Q, Yuan Q, Zhao D, Huang J, Hsiang T, Wei Y, Zheng L. Acetyl-coenzyme A synthetase gene ChAcs1 is essential for lipid metabolism, carbon utilization and virulence of the hemibiotrophic fungus Colletotrichum higginsianum. MOLECULAR PLANT PATHOLOGY 2019; 20:107-123. [PMID: 30136442 PMCID: PMC6430471 DOI: 10.1111/mpp.12743] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Acetyl-coenzyme A (acetyl-CoA) is a key molecule that participates in many biochemical reactions in amino acid, protein, carbohydrate and lipid metabolism. Here, we genetically dissected the distinct roles of two acetyl-CoA synthetase genes, ChAcs1 and ChAcs2, in the regulation of fermentation, lipid metabolism and virulence of the hemibiotrophic fungus Colletotrichum higginsianum. ChAcs1 and ChAcs2 are both highly expressed during appressorial development and the formation of primary hyphae, and are constitutively expressed in the cytoplasm throughout development. We found that C. higginsianum strains without ChAcs1 were non-viable in the presence of most non-fermentable carbon sources, including acetate, ethanol and acetaldehyde. Deletion of ChAcs1 also led to a decrease in lipid content of mycelia and delayed lipid mobilization in conidia to developing appressoria, which suggested that ChAcs1 contributes to lipid metabolism in C. higginsianum. Furthermore, a ChAcs1 deletion mutant was defective in the switch to invasive growth, which may have been directly responsible for its reduced virulence. Transcriptomic analysis and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) revealed that ChAcs1 can affect the expression of genes involved in virulence and carbon metabolism, and that plant defence genes are up-regulated, all demonstrated during infection by a ChAcs1 deletion mutant. In contrast, deletion of ChAcs2 only conferred a slight delay in lipid mobilization, although it was highly expressed in infection stages. Our studies provide evidence for ChAcs1 as a key regulator governing lipid metabolism, carbon source utilization and virulence of this hemibiotrophic fungus.
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Affiliation(s)
- Qiongnan Gu
- The Key Lab of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhan430070China
- Hubei Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Insect Pests and Weeds controlInstitute of Plant Protection and Soil ScienceWuhan430064China
| | - Qinfeng Yuan
- The Key Lab of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhan430070China
| | - Dian Zhao
- The Key Lab of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhan430070China
| | - Junbin Huang
- The Key Lab of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhan430070China
| | - Tom Hsiang
- School of Environmental SciencesUniversity of GuelphGuelphN1G 2W1Canada
| | - Yangdou Wei
- Department of BiologyUniversity of SaskatchewanSaskatoonS7N 5E2Canada
| | - Lu Zheng
- The Key Lab of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhan430070China
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224
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Structure-Based Classification Defines the Discrete Conformational Classes Adopted by the Arenaviral GP1. J Virol 2018; 93:JVI.01048-18. [PMID: 30305351 PMCID: PMC6288339 DOI: 10.1128/jvi.01048-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/28/2018] [Indexed: 02/08/2023] Open
Abstract
The genetically and geographically diverse group of viruses within the family Arenaviridae includes a number of zoonotic pathogens capable of causing fatal hemorrhagic fever. The multisubunit GPC glycoprotein spike complex displayed on the arenavirus envelope is a key determinant of species tropism and a primary target of the host humoral immune response. Here, we show that the receptor-binding GP1 subcomponent of the GPC spike from Old World but not New World arenaviruses adopts a distinct, pH-independent conformation in the absence of the cognate GP2. Our analysis provides a structure-based approach to understanding the discrete conformational classes sampled by these therapeutically important targets, informing strategies to develop arenaviral glycoprotein immunogens that resemble GPC as presented on the mature virion surface. The emergence of Old and New World arenaviruses from rodent reservoirs persistently threatens human health. The GP1 subunit of the envelope-displayed arenaviral glycoprotein spike complex (GPC) mediates host cell recognition and is an important determinant of cross-species transmission. Previous structural analyses of Old World arenaviral GP1 glycoproteins, alone and in complex with a cognate GP2 subunit, have revealed that GP1 adopts two distinct conformational states distinguished by differences in the orientations of helical regions of the molecule. Here, through comparative study of the GP1 glycoprotein architectures of Old World Loei River virus and New World Whitewater Arroyo virus, we show that these rearrangements are restricted to Old World arenaviruses and are not induced solely by the pH change that is associated with virus endosomal trafficking. Our structure-based phylogenetic analysis of arenaviral GP1s provides a blueprint for understanding the discrete structural classes adopted by these therapeutically important targets. IMPORTANCE The genetically and geographically diverse group of viruses within the family Arenaviridae includes a number of zoonotic pathogens capable of causing fatal hemorrhagic fever. The multisubunit GPC glycoprotein spike complex displayed on the arenavirus envelope is a key determinant of species tropism and a primary target of the host humoral immune response. Here, we show that the receptor-binding GP1 subcomponent of the GPC spike from Old World but not New World arenaviruses adopts a distinct, pH-independent conformation in the absence of the cognate GP2. Our analysis provides a structure-based approach to understanding the discrete conformational classes sampled by these therapeutically important targets, informing strategies to develop arenaviral glycoprotein immunogens that resemble GPC as presented on the mature virion surface.
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225
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Escobar-Hoyos L, Knorr K, Abdel-Wahab O. Aberrant RNA Splicing in Cancer. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2018; 3:167-185. [PMID: 32864546 DOI: 10.1146/annurev-cancerbio-030617-050407] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
RNA splicing, the enzymatic process of removing segments of premature RNA to produce mature RNA, is a key mediator of proteome diversity and regulator of gene expression. Increased systematic sequencing of the genome and transcriptome of cancers has identified a variety of means by which RNA splicing is altered in cancer relative to normal cells. These findings, in combination with the discovery of recurrent change-of-function mutations in splicing factors in a variety of cancers, suggest that alterations in splicing are drivers of tumorigenesis. Greater characterization of altered splicing in cancer parallels increasing efforts to pharmacologically perturb splicing and early-phase clinical development of small molecules that disrupt splicing in patients with cancer. Here we review recent studies of global changes in splicing in cancer, splicing regulation of mitogenic pathways critical in cancer transformation, and efforts to therapeutically target splicing in cancer.
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Affiliation(s)
- Luisa Escobar-Hoyos
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell Medical College, New York, NY 10065, USA.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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226
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Mir R, Sharma A, Pradhan SJ, Galande S. Regulation of Transcription Factor SP1 by the β-Catenin Destruction Complex Modulates Wnt Response. Mol Cell Biol 2018; 38:e00188-18. [PMID: 30181396 PMCID: PMC6206460 DOI: 10.1128/mcb.00188-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/22/2018] [Accepted: 08/28/2018] [Indexed: 01/05/2023] Open
Abstract
The ubiquitous transcription factor specificity protein 1 (SP1) is heavily modified posttranslationally. These modifications are critical for switching its functions and modulation of its transcriptional activity and DNA binding and stability. However, the mechanism governing the stability of SP1 by cellular signaling pathways is not well understood. Here, we provide biochemical and functional evidence that SP1 is an integral part of the Wnt signaling pathway. We identified a phosphodegron motif in SP1 that is specific to mammals. In the absence of Wnt signaling, glycogen synthase kinase 3β (GSK3β)-mediated phosphorylation and β-TrCP E3 ubiquitin ligase-mediated ubiquitination are required to induce SP1 degradation. When Wnt signaling is on, SP1 is stabilized in a β-catenin-dependent manner. SP1 directly interacts with β-catenin, and Wnt signaling induces the stabilization of SP1 by impeding its interaction with β-TrCP and axin1, components of the destruction complex. Wnt signaling suppresses ubiquitination and subsequent proteosomal degradation of SP1. Furthermore, SP1 regulates Wnt-dependent stability of β-catenin and their mutual stabilization is critical for target gene expression, suggesting a feedback mechanism. Upon stabilization, SP1 and β-catenin cooccupy the promoters of TCFL2/β-catenin target genes. Collectively, this study uncovers a direct link between SP1 and β-catenin in the Wnt signaling pathway.
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Affiliation(s)
- Rafeeq Mir
- Indian Institute of Science Education and Research, Pune, India
| | - Ankita Sharma
- Indian Institute of Science Education and Research, Pune, India
| | | | - Sanjeev Galande
- Indian Institute of Science Education and Research, Pune, India
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227
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Chu J, Chen Z. Molecular identification of histone acetyltransferases and deacetylases in lower plant Marchantia polymorpha. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:612-622. [PMID: 30336381 DOI: 10.1016/j.plaphy.2018.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/18/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
Histone is the core component of nucleosome and modification of amino acid residues on histone tails is one of the most pivotal epigenetic regulatory mechanisms. Histone acetylation or deacetylation is carried out by two groups of proteins: histone acetyltransferases (HATs) or histone deacetylases (HDACs), and has been proven to be tightly linked to regulation of gene expression in animals and vascular plants. The biological functions of HATs and HDACs in non-flowering plants remain largely unknown. We found that there are seven MpHAT genes and twelve MpHDAC genes present in the Marchantia genome, and the comprehensive protein sequence analysis of the HAT and HDAC families was introduced to investigate their potential functions. On the basis of the functional domain analysis, eight MpHATs and twelve MpHDACs contain the conserved functional domains as the defining feature of each family. Phylogenetic trees of all families of MpHATs and MpHDACs along with their homologs from different plant and green algae species were constructed to illustrate evolutionary relationship of HAT and HDAC proteins. We found both SIR2 family and RPD3/HDA1 superfamily possess lower plant-specific proteins indicating the potential unknown functions of HATs and HDACs in Marchantia and other lower plant or algae species. Subcellular localization prediction suggests that MpHATs and MpHDACs are likely functioning in various organelles. Expression analysis shows that all MpHAT and MpHDAC genes are expressed in all tissues with differences at the transcriptional level. In addition, their expression patterns were altered in response to various treatments with plant hormones and environmental stress. We concluded that all MpHATs and MpHDACs are functional proteins in Marchantia and involved in various signaling pathways. Marchantia could have developed a complex histone acetylation epigenetic mechanism to regulate growth and development, as well as responses to environment.
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Affiliation(s)
- Jiashu Chu
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore, 637616, Singapore
| | - Zhong Chen
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore, 637616, Singapore.
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228
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Zhang QB, Yu K, Liu Z, Wang D, Zhao Y, Yin S, Liu Z. Prediction of prkC-mediated protein serine/threonine phosphorylation sites for bacteria. PLoS One 2018; 13:e0203840. [PMID: 30278050 PMCID: PMC6168130 DOI: 10.1371/journal.pone.0203840] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/28/2018] [Indexed: 11/18/2022] Open
Abstract
As an abundant post-translational modification, reversible phosphorylation is critical for the dynamic regulation of various biological processes. prkC, a critical serine/threonine-protein kinase in bacteria, plays important roles in regulation of signaling transduction. Identification of prkC-specific phosphorylation sites is fundamental for understanding the molecular mechanism of phosphorylation-mediated signaling. However, experimental identification of substrates for prkC is time-consuming and labor-intensive, and computational methods for kinase-specific phosphorylation prediction in bacteria have yet to be developed. In this study, we manually curated the experimentally identified substrates and phosphorylation sites of prkC from the published literature. The analyses of the sequence preferences showed that the substrate recognition pattern for prkC might be miscellaneous, and a complex strategy should be employed to predict potential prkC-specific phosphorylation sites. To develop the predictor, the amino acid location feature extraction method and the support vector machine algorithm were employed, and the methods achieved promising performance. Through 10-fold cross validation, the predictor reached a sensitivity of 91.67% at the specificity of 95.12%. Then, we developed freely accessible software, which is provided at http://free.cancerbio.info/prkc/. Based on the predictor, hundreds of potential prkC-specific phosphorylation sites were annotated based on the known bacterial phosphorylation sites. prkC-PSP was the first predictor for prkC-specific phosphorylation sites, and its prediction performance was promising. We anticipated that these analyses and the predictor could be helpful for further studies of prkC-mediated phosphorylation.
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Affiliation(s)
- Qing-bin Zhang
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- * E-mail: (QbZ); (ZL)
| | - Kai Yu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zekun Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dawei Wang
- Department of Thoracic Surgery, China Meitan General Hospital, Beijing, China
| | - Yuanyuan Zhao
- School of Arts and Media, Hefei Normal University, Hefei, Anhui, China
| | - Sanjun Yin
- Healthtimegene Institute, Shenzhen, China
| | - Zexian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- * E-mail: (QbZ); (ZL)
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229
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Wei H, Lv M, Wen C, Zhang A, Yang K, Zhou H, Wang X. Identification of an intercellular cell adhesion molecule-1 homologue from grass carp: Evidence for its involvement in the immune cell adhesion in teleost. FISH & SHELLFISH IMMUNOLOGY 2018; 81:67-72. [PMID: 29981884 DOI: 10.1016/j.fsi.2018.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 06/08/2023]
Abstract
Intercellular cell adhesion molecule-1 (ICAM-1) is a single-chain transmembrane glycoprotein which plays key roles in transendothelial migration of leukocytes and interaction between antigen presenting cells and T cells. In teleost, information of cell adhesion-related molecules is still lacking. In this study, we identified a gene from grass carp sharing similar exon and intron organization with human ICAM-1. Cloning and in silico analysis of its homologues in zebrafish and other two cyprinid fishes, respectively demonstrated the existence of the gene in these fishes. Moreover, the molecular features of these genes in fishes were conserved compared with human ICAM-1. In grass carp, the transcripts of this gene were detected with high levels in heart and liver and its mRNA expression in headkidney leukocytes was induced by Il-1β. Overexpression of this molecule in COS-7 cells could increase the adhesion of the cells with grass carp peripheral blood lymphocytes (PBLs), and the adhesion was further enhanced by lipopolysaccharide stimulation on PBLs. Further studies revealed that the mRNA levels of lymphocyte function-associated antigen-1, a ligand for ICAM-1, were much higher in the PBLs adhering to the COS-7 cells with overexpressing this molecule than in the PBLs alone. These results collectively showed that the newly cloned cDNA encodes grass carp intercellular cell adhesion molecule-1 (Icam-1) and it can mediate the adhesion of PBLs. This provides functional evidence for the existence of Icam-1 in teleost and will facilitate investigation on the transendothelial migration of leukocytes in fish species.
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Affiliation(s)
- He Wei
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China; School of Biomedical Sciences, Chengdu Medical College, Chengdu, People's Republic of China
| | - Mengyuan Lv
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Chao Wen
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Anying Zhang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Kun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Hong Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Xinyan Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China.
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230
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Gunzelmann J, Rüthnick D, Lin TC, Zhang W, Neuner A, Jäkle U, Schiebel E. The microtubule polymerase Stu2 promotes oligomerization of the γ-TuSC for cytoplasmic microtubule nucleation. eLife 2018; 7:39932. [PMID: 30222109 PMCID: PMC6158006 DOI: 10.7554/elife.39932] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/14/2018] [Indexed: 12/25/2022] Open
Abstract
Stu2/XMAP215/ZYG-9/Dis1/Alp14/Msps/ch-TOG family members in association with with γ-tubulin complexes nucleate microtubules, but we know little about the interplay of these nucleation factors. Here, we show that the budding yeast Stu2 in complex with the γ-tubulin receptor Spc72 nucleates microtubules in vitro without the small γ-tubulin complex (γ-TuSC). Upon γ-TuSC addition, Stu2 facilitates Spc72–γ-TuSC interaction by binding to Spc72 and γ-TuSC. Stu2 together with Spc72–γ-TuSC increases microtubule nucleation in a process that is dependent on the TOG domains of Stu2. Importantly, these activities are also important for microtubule nucleation in vivo. Stu2 stabilizes Spc72–γ-TuSC at the minus end of cytoplasmic microtubules (cMTs) and an in vivo assay indicates that cMT nucleation requires the TOG domains of Stu2. Upon γ-tubulin depletion, we observed efficient cMT nucleation away from the spindle pole body (SPB), which was dependent on Stu2. Thus, γ-TuSC restricts cMT assembly to the SPB whereas Stu2 nucleates cMTs together with γ-TuSC and stabilizes γ-TuSC at the cMT minus end.
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Affiliation(s)
- Judith Gunzelmann
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Diana Rüthnick
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Tien-Chen Lin
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Wanlu Zhang
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Annett Neuner
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Ursula Jäkle
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
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231
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Zhang M, Chiang YH, Toruño TY, Lee D, Ma M, Liang X, Lal NK, Lemos M, Lu YJ, Ma S, Liu J, Day B, Dinesh-Kumar SP, Dehesh K, Dou D, Zhou JM, Coaker G. The MAP4 Kinase SIK1 Ensures Robust Extracellular ROS Burst and Antibacterial Immunity in Plants. Cell Host Microbe 2018; 24:379-391.e5. [PMID: 30212650 PMCID: PMC6279242 DOI: 10.1016/j.chom.2018.08.007] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 06/01/2018] [Accepted: 07/17/2018] [Indexed: 11/18/2022]
Abstract
Microbial patterns are recognized by cell-surface receptors to initiate pattern-triggered immunity (PTI) in plants. Receptor-like cytoplasmic kinases (RLCKs), such as BIK1, and calcium-dependent protein kinases (CPKs) are engaged during PTI to activate the NADPH oxidase RBOHD for reactive oxygen species (ROS) production. It is unknown whether protein kinases besides CPKs and RLCKs participate in RBOHD regulation. We screened mutants in all ten Arabidopsis MAP4 kinases (MAP4Ks) and identified the conserved MAP4K SIK1 as a positive regulator of PTI. sik1 mutants were compromised in their ability to elicit the ROS burst in response to microbial features and exhibited compromised PTI to bacterial infection. SIK1 directly interacts with, phosphorylates, and stabilizes BIK1 in a kinase activity-dependent manner. Furthermore, SIK1 directly interacts with and phosphorylates RBOHD upon flagellin perception. Thus, SIK1 positively regulates immunity by stabilizing BIK1 and activating RBOHD to promote the extracellular ROS burst.
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Affiliation(s)
- Meixiang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Yi-Hsuan Chiang
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Tania Y Toruño
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - DongHyuk Lee
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Miaomiao Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangxiu Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Neeraj K Lal
- Department of Plant Biology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Mark Lemos
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA; Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Yi-Ju Lu
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Shisong Ma
- Department of Plant Biology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Jun Liu
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Brad Day
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Katayoon Dehesh
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA; Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA.
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232
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Sheng Z, Xu Y, Wang S, Yuan Y, Huang T, Lu P. XPO1-mediated nuclear export of RNF146 protects from angiotensin II-induced endothelial cellular injury. Biochem Biophys Res Commun 2018; 503:1544-1549. [PMID: 30029878 DOI: 10.1016/j.bbrc.2018.07.077] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 01/03/2023]
Abstract
Endothelial cells death induced by angiotensin II (Ang II) plays a role in vascular injury. RNF146 is identified as a E3 ubiquitin ligase, which promotes cell survival under many types of stresses. However, the role of RNF146 in endothelial cellular injury is unknown. In human umbilical vein endothelial cells (HUVECs), Ang II treatment led to cell death by oxidative stress and promoted RNF146 to accumulate in nucleus in time dependent manner. Nuclear export signal was found in the RNF146's sequence. The interaction between RNF146 and XPO1 was further confirmed by co-immunoprecipitation. Inhibition of XPO1 with KPT-185 increased the level of RNF146 in nucleus. The expression of XPO1 was suppressed responding to Ang II treatment. Overexpression of XPO1 facilitated the nuclear shuttling of RNF146, which protected from Ang II-induced cell death. Moreover, overexpression of RNF146 in HUVECs reduced the cell death induced by Ang II, whereas inhibition of XPO1 abolished the protective effect of RNF146. Therefore, our data demonstrated that RNF146 was a protective factor against cell death induced by AngII in human endothelial cells, which was dependent on XPO1-mediated nuclear export.
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Affiliation(s)
- Zhiyong Sheng
- Intensive Care Unit, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Yun Xu
- Department of Emergency, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Shu Wang
- Intensive Care Unit, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Ying Yuan
- Intensive Care Unit, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Tieqiu Huang
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Peng Lu
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China.
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233
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Yehia L, Eng C. 65 YEARS OF THE DOUBLE HELIX: One gene, many endocrine and metabolic syndromes: PTEN-opathies and precision medicine. Endocr Relat Cancer 2018; 25:T121-T140. [PMID: 29792313 DOI: 10.1530/erc-18-0162] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/23/2018] [Indexed: 12/15/2022]
Abstract
An average of 10% of all cancers (range 1-40%) are caused by heritable mutations and over the years have become powerful models for precision medicine practice. Furthermore, such cancer predisposition genes for seemingly rare syndromes have turned out to help explain mechanisms of sporadic carcinogenesis and often inform normal development. The tumor suppressor PTEN encodes a ubiquitously expressed phosphatase that counteracts the PI3K/AKT/mTOR cascade - one of the most critical growth-promoting signaling pathways. Clinically, individuals with germline PTEN mutations have diverse phenotypes and fall under the umbrella term PTEN hamartoma tumor syndrome (PHTS). PHTS encompasses four clinically distinct allelic overgrowth syndromes, namely Cowden, Bannayan-Riley-Ruvalcaba, Proteus and Proteus-like syndromes. Relatedly, mutations in other genes encoding components of the PI3K/AKT/mTOR pathway downstream of PTEN also predispose patients to partially overlapping clinical manifestations, with similar effects as PTEN malfunction. We refer to these syndromes as 'PTEN-opathies.' As a tumor suppressor and key regulator of normal development, PTEN dysfunction can cause a spectrum of phenotypes including benign overgrowths, malignancies, metabolic and neurodevelopmental disorders. Relevant to clinical practice, the identification of PTEN mutations in patients not only establishes a PHTS molecular diagnosis, but also informs on more accurate cancer risk assessment and medical management of those patients and affected family members. Importantly, timely diagnosis is key, as early recognition allows for preventative measures such as high-risk screening and surveillance even prior to cancer onset. This review highlights the translational impact that the discovery of PTEN has had on the diagnosis, management and treatment of PHTS.
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Affiliation(s)
- Lamis Yehia
- Genomic Medicine InstituteLerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Charis Eng
- Genomic Medicine InstituteLerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Taussig Cancer InstituteCleveland Clinic, Cleveland, Ohio, USA
- Department of Genetics and Genome SciencesCase Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Germline High Risk Cancer Focus GroupCASE Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
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234
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Brennan P. drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics. F1000Res 2018; 7:1105. [PMID: 30210791 PMCID: PMC6107989 DOI: 10.12688/f1000research.14541.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/06/2018] [Indexed: 11/20/2022] Open
Abstract
Protein schematics are valuable for research, teaching and knowledge communication. However, the tools used to automate the process are challenging. The purpose of the drawProteins package is to enable the generation of schematics of proteins in an automated fashion that can integrate with the Bioconductor/R suite of tools for bioinformatics and statistical analysis. Using UniProt accession numbers, the package uses the UniProt API to get the features of the protein from the UniProt database. The features are assembled into a data frame and visualized using adaptations of the ggplot2 package. Visualizations can be customised in many ways including adding additional protein features information from other data frames, altering colors and protein names and adding extra layers using other ggplot2 functions. This can be completed within a script that makes the workflow reproducible and sharable.
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Affiliation(s)
- Paul Brennan
- Centre for Medical Education, School of Medicine, Cardiff University, Cardiff, Wales, UK
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235
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Lynch JH, Sa N, Saeheng S, Raffaelli N, Roje S. Characterization of a non-nudix pyrophosphatase points to interplay between flavin and NAD(H) homeostasis in Saccharomyces cerevisiae. PLoS One 2018; 13:e0198787. [PMID: 29902190 PMCID: PMC6002036 DOI: 10.1371/journal.pone.0198787] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/28/2018] [Indexed: 12/11/2022] Open
Abstract
The flavin cofactors FMN and FAD are required for a wide variety of biological processes, however, little is known about their metabolism. Here, we report the cloning and biochemical characterization of the Saccharomyces cerevisiae pyrophosphatase Fpy1p. Genetic and functional studies suggest that Fpy1p may play a key role in flavin metabolism and is the first-reported non-Nudix superfamily enzyme to display FAD pyrophosphatase activity. Characterization of mutant yeast strains found that deletion of fpy1 counteracts the adverse effects that are caused by deletion of flx1, a known mitochondrial FAD transporter. We show that Fpy1p is capable of hydrolyzing FAD, NAD(H), and ADP-ribose. The enzymatic activity of Fpy1p is dependent upon the presence of K+ and divalent metal cations, with similar kinetic parameters to those that have been reported for Nudix FAD pyrophosphatases. In addition, we report that the deletion of fpy1 intensifies the FMN-dependence of null mutants of the riboflavin kinase Fmn1p, demonstrate that fpy1 mutation abolishes the decreased fitness resulting from the deletion of the flx1 ORF, and offer a possible mechanism for the genetic interplay between fpy1, flx1 and fmn1.
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Affiliation(s)
- Joseph H. Lynch
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States of America
| | - Na Sa
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States of America
| | - Sompop Saeheng
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States of America
| | - Nadia Raffaelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States of America
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236
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Zhang MK, Tang J, Huang ZQ, Hu KD, Li YH, Han Z, Chen XY, Hu LY, Yao GF, Zhang H. Reduction of Aspergillus niger Virulence in Apple Fruits by Deletion of the Catalase Gene cpeB. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:5401-5409. [PMID: 29745230 DOI: 10.1021/acs.jafc.8b01841] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aspergillus niger, a common saprophytic fungus, causes rot in many fruits. We studied the role of a putative catalase-peroxidase-encoding gene, cpeB, in oxidative stress and virulence in fruit. The cpeB gene was deleted in A. niger by homologous recombination, and the Δ cpeB mutant showed decreased CAT activity compared with that of the wild type. The cpeB gene deletion caused increased sensitivity to H2O2 stress, and spore germination was significantly reduced; in addition, the reactive-oxygen-species (ROS) metabolites superoxide anions (·O2-), hydrogen peroxide (H2O2), and malondialdehyde (MDA) accumulated in the Δ cpeB mutant during H2O2 stress. Furthermore, ROS metabolism in A. niger infected apples was determined, and our results showed that the Δ cpeB mutant induced an attenuated response in apple fruit during the fruit-pathogen interaction; the cpeB gene deletion significantly reduced the development of lesions, suggesting that the cpeB gene in A. niger is essential for full virulence in apples.
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Affiliation(s)
- Meng-Ke Zhang
- School of Food Science and Engineering , Hefei University of Technology , Hefei 230009 , China
| | - Jun Tang
- Xuzhou Institute of Agricultural Sciences of the Xuhuai District of Jiangsu Province , Xuzhou 221131 , China
| | - Zhong-Qin Huang
- Xuzhou Institute of Agricultural Sciences of the Xuhuai District of Jiangsu Province , Xuzhou 221131 , China
| | - Kang-Di Hu
- School of Food Science and Engineering , Hefei University of Technology , Hefei 230009 , China
| | - Yan-Hong Li
- School of Food Science and Engineering , Hefei University of Technology , Hefei 230009 , China
| | - Zhuo Han
- School of Food Science and Engineering , Hefei University of Technology , Hefei 230009 , China
| | - Xiao-Yan Chen
- School of Food Science and Engineering , Hefei University of Technology , Hefei 230009 , China
| | - Lan-Ying Hu
- School of Food Science and Engineering , Hefei University of Technology , Hefei 230009 , China
| | - Gai-Fang Yao
- School of Food Science and Engineering , Hefei University of Technology , Hefei 230009 , China
| | - Hua Zhang
- School of Food Science and Engineering , Hefei University of Technology , Hefei 230009 , China
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237
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Zhang JS, Li XJ, Yang L, Li WW, Wang Q. Expression pattern and functional analysis of the two RING box protein RBX in spermatogenesis of Chinese mitten crab Eriocheir sinensis. Gene 2018; 668:237-245. [PMID: 29775751 DOI: 10.1016/j.gene.2018.05.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/05/2018] [Accepted: 05/08/2018] [Indexed: 11/27/2022]
Abstract
Studies in E. sinensis have shown that ubiquitination mediated by Cullin-RING E3 ligases (CRLs) plays important roles in spermatogenesis. In other species, CRLs are also essential in cell cycle progression, DNA replication, signal transduction, gene transcription, and development. The catalytic RING component, the RING box protein, is an important part of CRLs. However, there have been few studies on CRLs in crustaceans. In this study, we cloned two RING box protein genes from the Chinese mitten crab, Eriocheir sinensis, termed Es-RBX1 and Es-RBX2 The full length Es-RBX1 cDNA comprises 741 nucleotides, and encodes a protein of 124 amino acid residues, whereas the Es-RBX2 cDNA comprises 1325 nucleotides, and encodes a protein of 110 amino acid residues. Bioinformatics analysis showed that the domains and structure of the RBX proteins have been highly conserved during evolution. Quantitative real-time polymerase chain reaction and western blotting showed that Es-RBX1 is highly expressed in the testis, particularly during the spermatocyte stage, whereas Es-RBX2 did not show specific expression in the male reproductive system. Furthermore, Es-RBX1 is mainly distributed in the nucleus, and changed its location with the development of the nucleus. Co-immunoprecipitation showed that Es-RBX1 could bind Cullin4. These results suggested that Es-RBX1 plays a key role in spermatogenesis of E. sinensis though forming a complex with Cullin4.
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Affiliation(s)
- Jia-Shun Zhang
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Science, East China Normal University, Shanghai, China
| | - Xue-Jie Li
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Science, East China Normal University, Shanghai, China
| | - Lei Yang
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Science, East China Normal University, Shanghai, China
| | - Wei-Wei Li
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Science, East China Normal University, Shanghai, China
| | - Qun Wang
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Science, East China Normal University, Shanghai, China.
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238
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Chen J, Piao Y, Liu Y, Li X, Piao Z. Genome-wide identification and expression analysis of chitinase gene family in Brassica rapa reveals its role in clubroot resistance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:257-267. [PMID: 29576079 DOI: 10.1016/j.plantsci.2018.02.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 02/10/2018] [Accepted: 02/17/2018] [Indexed: 06/08/2023]
Abstract
Chitinases, a category of pathogenesis-related proteins, are responsible for catalyzing the hydrolysis of chitin into the N-acetyl-d-glucosamine. Therefore, chitinases are believed to function as a guardian against chitin-containing pathogens. Here, we examined the role of the Brassica rapa chitinase family genes in clubroot disease. A total of 33 chitinase genes were identified and grouped into five classes based on their conserved domain. They were distributed unevenly across eight chromosomes in B. rapa, and 31 of them contained few introns (≤2). In addition, the expression of these genes was organ-specific, and 14 genes were expressed differentially in response to Plasmodiophora brassicae challenge of clubroot-susceptible (CS NIL) and resistant (CR NIL) lines. Furthermore, reduced pathogen DNA content and clubroot symptoms were observed in the CS NILs after their treatment with chitin oligosaccharides 24 h prior to inoculation with P. brassicae. The findings indicate that chitinases play a crucial role in pathogen resistance of the host plants. The results offer an insight into the role of chitinase in B. rapa-P. brassicae interaction.
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Affiliation(s)
- Jingjing Chen
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; Life Science and Technology Institute, Yangtze Normal University, Chongqing 408100, China
| | - Yinglan Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Yiming Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaonan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China.
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China.
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239
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Huang T, Zhou Y, Zhang J, Cheng ASL, Yu J, To KF, Kang W. The physiological role of Motin family and its dysregulation in tumorigenesis. J Transl Med 2018; 16:98. [PMID: 29650031 PMCID: PMC5898069 DOI: 10.1186/s12967-018-1466-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/28/2018] [Indexed: 11/30/2022] Open
Abstract
Members in Motin family, or Angiomotins (AMOTs), are adaptor proteins that localize in the membranous, cytoplasmic or nuclear fraction in a cell context-dependent manner. They control the bioprocesses such as migration, tight junction formation, cell polarity, and angiogenesis. Emerging evidences have demonstrated that AMOTs participate in cancer initiation and progression. Many of the previous studies have focused on the involvement of AMOTs in Hippo-YAP1 pathway. However, it has been controversial for years that AMOTs serve as either positive or negative growth regulators in different cancer types because of the various cellular origins. The molecular mechanisms of these opposite roles of AMOTs remain elusive. This review comprehensively summarized how AMOTs function physiologically and how their dysregulation promotes or inhibits tumorigenesis. Better understanding the functional roles of AMOTs in cancers may lead to an improvement of clinical interventions as well as development of novel therapeutic strategies for cancer patients.
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Affiliation(s)
- Tingting Huang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China.,Institute of Digestive Disease, Partner State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China.,Li Ka Shing Institute of Health Science, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People's Republic of China
| | - Yuhang Zhou
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China.,Institute of Digestive Disease, Partner State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China.,Li Ka Shing Institute of Health Science, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China
| | - Jinglin Zhang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China.,Institute of Digestive Disease, Partner State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China.,Li Ka Shing Institute of Health Science, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China
| | - Alfred S L Cheng
- Institute of Digestive Disease, Partner State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People's Republic of China.,School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Jun Yu
- Institute of Digestive Disease, Partner State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People's Republic of China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Ka Fai To
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China. .,Institute of Digestive Disease, Partner State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China. .,Li Ka Shing Institute of Health Science, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People's Republic of China.
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China. .,Institute of Digestive Disease, Partner State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China. .,Li Ka Shing Institute of Health Science, Sir Y.K. Pao Cancer Center, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong, People's Republic of China. .,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People's Republic of China.
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240
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Halawani D, Gogonea V, DiDonato JA, Pipich V, Yao P, China A, Topbas C, Vasu K, Arif A, Hazen SL, Fox PL. Structural control of caspase-generated glutamyl-tRNA synthetase by appended noncatalytic WHEP domains. J Biol Chem 2018; 293:8843-8860. [PMID: 29643180 DOI: 10.1074/jbc.m117.807503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 03/26/2018] [Indexed: 02/02/2023] Open
Abstract
Aminoacyl-tRNA synthetases are ubiquitous, evolutionarily conserved enzymes catalyzing the conjugation of amino acids onto cognate tRNAs. During eukaryotic evolution, tRNA synthetases have been the targets of persistent structural modifications. These modifications can be additive, as in the evolutionary acquisition of noncatalytic domains, or subtractive, as in the generation of truncated variants through regulated mechanisms such as proteolytic processing, alternative splicing, or coding region polyadenylation. A unique variant is the human glutamyl-prolyl-tRNA synthetase (EPRS) consisting of two fused synthetases joined by a linker containing three copies of the WHEP domain (termed by its presence in tryptophanyl-, histidyl-, and glutamyl-prolyl-tRNA synthetases). Here, we identify site-selective proteolysis as a mechanism that severs the linkage between the EPRS synthetases in vitro and in vivo Caspase action targeted Asp-929 in the third WHEP domain, thereby separating the two synthetases. Using a neoepitope antibody directed against the newly exposed C terminus, we demonstrate EPRS cleavage at Asp-929 in vitro and in vivo Biochemical and biophysical characterizations of the N-terminally generated EPRS proteoform containing the glutamyl-tRNA synthetase and most of the linker, including two WHEP domains, combined with structural analysis by small-angle neutron scattering, revealed a role for the WHEP domains in modulating conformations of the catalytic core and GSH-S-transferase-C-terminal-like (GST-C) domain. WHEP-driven conformational rearrangement altered GST-C domain interactions and conferred distinct oligomeric states in solution. Collectively, our results reveal long-range conformational changes imposed by the WHEP domains and illustrate how noncatalytic domains can modulate the global structure of tRNA synthetases in complex eukaryotic systems.
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Affiliation(s)
- Dalia Halawani
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Valentin Gogonea
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and .,the Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115
| | - Joseph A DiDonato
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Vitaliy Pipich
- the Jülich Center for Neutron Science, Outstation at Maier-Leibnitz Zentrum, Forschungszentrum Jülich, GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany, and
| | - Peng Yao
- the Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester, Rochester, New York 14642
| | - Arnab China
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Celalettin Topbas
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and.,the Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115
| | - Kommireddy Vasu
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Abul Arif
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Stanley L Hazen
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and.,Center for Cardiovascular Diagnostics and Prevention, and Department of Cardiovascular Medicine, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Paul L Fox
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
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241
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Kitchen SA, Bourdelais AJ, Taylor AR. Interaction of a dinoflagellate neurotoxin with voltage-activated ion channels in a marine diatom. PeerJ 2018; 6:e4533. [PMID: 29632739 PMCID: PMC5888156 DOI: 10.7717/peerj.4533] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/05/2018] [Indexed: 01/04/2023] Open
Abstract
Background The potent neurotoxins produced by the harmful algal bloom species Karenia brevis are activators of sodium voltage-gated channels (VGC) in animals, resulting in altered channel kinetics and membrane hyperexcitability. Recent biophysical and genomic evidence supports widespread presence of homologous sodium (Na+) and calcium (Ca2+) permeable VGCs in unicellular algae, including marine phytoplankton. We therefore hypothesized that VGCs of these phytoplankton may be an allelopathic target for waterborne neurotoxins produced by K. brevis blooms that could lead to ion channel dysfunction and disruption of signaling in a similar manner to animal Na+ VGCs. Methods We examined the interaction of brevetoxin-3 (PbTx-3), a K. brevis neurotoxin, with the Na+/Ca2+ VGC of the non-toxic diatom Odontella sinensis using electrophysiology. Single electrode current- and voltage- clamp recordings from O. sinensis in the presence of PbTx-3 were used to examine the toxin’s effect on voltage gated Na+/Ca2+ currents. In silico analysis was used to identify the putative PbTx binding site in the diatoms. We identified Na+/Ca2+ VCG homologs from the transcriptomes and genomes of 12 diatoms, including three transcripts from O. sinensis and aligned them with site-5 of Na+ VGCs, previously identified as the PbTx binding site in animals. Results Up to 1 µM PbTx had no effect on diatom resting membrane potential or membrane excitability. The kinetics of fast inward Na+/Ca2+ currents that underlie diatom action potentials were also unaffected. However, the peak inward current was inhibited by 33%, delayed outward current was inhibited by 25%, and reversal potential of the currents shifted positive, indicating a change in permeability of the underlying channels. Sequence analysis showed a lack of conservation of the PbTx binding site in diatom VGC homologs, many of which share molecular features more similar to single-domain bacterial Na+/Ca2+ VGCs than the 4-domain eukaryote channels. Discussion Although membrane excitability and the kinetics of action potential currents were unaffected, the permeation of the channels underlying the diatom action potential was significantly altered in the presence of PbTx-3. However, at environmentally relevant concentrations the effects of PbTx- on diatom voltage activated currents and interference of cell signaling through this pathway may be limited. The relative insensitivity of phytoplankton VGCs may be due to divergence of site-5 (the putative PbTx binding site), and in some cases, such as O. sinensis, resistance to toxin effects may be because of evolutionary loss of the 4-domain eukaryote channel, while retaining a single domain bacterial-like VGC that can substitute in the generation of fast action potentials.
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Affiliation(s)
- Sheila A Kitchen
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
| | - Andrea J Bourdelais
- Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, United States of America
| | - Alison R Taylor
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
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242
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Chi CB, Tang Y, Zhang J, Dai YN, Abdalla M, Chen Y, Zhou CZ. Structural and Biochemical Insights into the Multiple Functions of Yeast Grx3. J Mol Biol 2018. [PMID: 29524511 DOI: 10.1016/j.jmb.2018.02.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The yeast Saccharomyces cerevisiae monothiol glutaredoxin Grx3 plays a key role in cellular defense against oxidative stress and more importantly, cooperates with BolA-like iron repressor of activation protein Fra2 to regulate the localization of the iron-sensing transcription factor Aft2. The interplay among Grx3, Fra2 and Aft2 responsible for the regulation of iron homeostasis has not been clearly described. Here we solved the crystal structures of the Trx domain (Grx3Trx) and Grx domain (Grx3Grx) of Grx3 in addition to the solution structure of Fra2. Structural analyses and activity assays indicated that the Trx domain also contributes to the glutathione S-transferase activity of Grx3, via an inter-domain disulfide bond between Cys37 and Cys176. NMR titration and pull-down assays combined with surface plasmon resonance experiments revealed that Fra2 could form a noncovalent heterodimer with Grx3 via an interface between the helix-turn-helix motif of Fra2 and the C-terminal segment of Grx3Grx, different from the previously identified covalent heterodimer mediated by Fe-S cluster. Comparative affinity assays indicated that the interaction between Fra2 and Aft2 is much stronger than that between Grx3 and Aft2, or Aft2 toward its target DNA. These structural and biochemical analyses enabled us to propose a model how Grx3 executes multiple functions to coordinate the regulation of Aft2-controlled iron metabolism.
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Affiliation(s)
- Chang-Biao Chi
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China
| | - YaJun Tang
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China.
| | - Jiahai Zhang
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China
| | - Ya-Nan Dai
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China
| | - Mohnad Abdalla
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China
| | - Yuxing Chen
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China
| | - Cong-Zhao Zhou
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China.
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Identification and expression analysis of the IPT and CKX gene families during axillary bud outgrowth in apple (Malus domestica Borkh.). Gene 2018; 651:106-117. [PMID: 29409851 DOI: 10.1016/j.gene.2018.01.101] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/16/2018] [Accepted: 01/31/2018] [Indexed: 12/30/2022]
Abstract
Cytokinins (CKs) play a crucial role in promoting axillary bud outgrowth and targeting the control of CK metabolism can be used to enhance branching in plants. CK levels are maintained mainly by CK biosynthesis (isopentenyl transferase, IPT) and degradation (dehydrogenase, CKX) genes in plants. A systematic study of the IPT and CKX gene families in apple, however, has not been conducted. In the present study, 12 MdIPTs and 12 MdCKXs were identified in the apple genome. Systematic phylogenetic, structural, and synteny analyses were performed. Expression analysis of these genes in different tissues was also assessed. MdIPT and MdCKX genes exhibit distinct expression patterns in different tissues. The response of MdIPT, MdCKX, and MdPIN1 genes to various treatments (6-BA, decapitation and Lovastatin, an inhibitor of CKs synthesis) that impact branching were also investigated. Results indicated that most of the MdIPT and MdCKX, and MdPIN1 genes were upregulated by 6-BA and decapitation treatment, but inhibited by Lovastatin, a compound that effectively suppresses axillary bud outgrowth induced by decapitation. These findings suggest that cytokinin biosynthesis is required for the activation of bud break and the export of auxin from buds in apple tree with intact primary shoot apex or decapitated apple tree. MdCKX8 and MdCKX10, however, exhibited little response to decapitation, but were significantly up-regulated by 6-BA and Lovastatin, a finding that warrants further investigation in order to understand their function in bud-outgrowth.
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244
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Wang L, Xue K, Wang Y, Niu L, Li L, Zhong T, Guo J, Feng J, Song T, Zhang H. Molecular and functional characterization of the adiponectin (AdipoQ) gene in goat skeletal muscle satellite cells. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:1088-1097. [PMID: 29381891 PMCID: PMC6043445 DOI: 10.5713/ajas.17.0407] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 01/30/2018] [Indexed: 01/21/2023]
Abstract
Objective It is commonly accepted that adiponectin binds to its two receptors to regulate fatty acid metabolism in adipocytes. To better understand their functions in the regulation of intramuscular adipogenesis in goats, we cloned the three genes (adiponectin [AdipoQ], adiponectin receptor 1 [AdipoR1], and AdipoR2) encoding these proteins and detected their mRNA distribution in different tissues. We also determined the role of AdipoQ in the adipogenic differentiation of goat skeletal muscle satellite cells (SMSCs). Methods SMSCs were isolated using 1 mg/mL Pronase E from the longissimus dorsi muscles of 3-day-old female Nanjiang brown goats. Adipogenic differentiation was induced in satellite cells by transferring the cells to Dulbecco’s modified Eagle’s medium supplemented with an isobutylmethylxanthine, dexamethasone and insulin cocktail. The pEGFP-N1-AD plasmid was transfected into SMSCs using Lipofectamine 2000. Expression of adiponectin in tissues and SMSCs was detected by quantitative polymerase chain reaction and immunocytochemical staining. Results The three genes were predominantly expressed in adipose and skeletal muscle tissues. According to fluorescence and immunocytochemical analyses, adiponectin protein expression was only observed in the cytoplasm, suggesting that adiponectin is localized to the cytoplasm of goat SMSCs. In SMSCs overexpressing the AdipoQ gene, adiponectin promoted SMSC differentiation into adipocytes and significantly (p<0.05) up-regulated expression of AdipoR2, acetyl-CoA carboxylase, fatty-acid synthase, and sterol regulatory element-binding protein-1, though expression of CCAAT/enhancer-binding protein-α, peroxisome proliferator-activated receptor γ, and AdipoR1 did not change significantly. Conclusion Adiponectin induced SMSC differentiation into adipocytes, indicating that adiponectin may promote intramuscular adipogenesis in goat SMSC.
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Affiliation(s)
- Linjie Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ke Xue
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lili Niu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tao Zhong
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiazhong Guo
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Feng
- Institute of Animal Science, Tibet Academy of Agricultural & Animal Husbandry Science, Lhasa, China
| | - Tianzeng Song
- Institute of Animal Science, Tibet Academy of Agricultural & Animal Husbandry Science, Lhasa, China
| | - Hongping Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
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245
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Wei M, Xu X, Li C. Identification and expression of CAMTA genes in Populus trichocarpa under biotic and abiotic stress. Sci Rep 2017; 7:17910. [PMID: 29263356 PMCID: PMC5738416 DOI: 10.1038/s41598-017-18219-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/07/2017] [Indexed: 12/16/2022] Open
Abstract
The calmodulin-binding transcription activators (CAMTAs) transcription factor family plays an important role in normal plant growth and development, as well as in biotic and abiotic stress resistance. In this study, we identified seven CAMTA genes across the whole genome of Populus trichocarpa and analyzed the expression patterns of PtCAMTAs in the root and leaf tissues. Promoter cis-element analysis indicated that most CAMTA genes contained stress- or phytohormone-related cis-elements. Quantitative real-time reverse transcription-PCR (qRT-PCR) indicated indicated that PtCAMTAs were induced by mannitol, NaCl, cold stress, pathogenic infection with A. alternata, and phytohormone treatments with abscisic acid, salicylic acid, and methyl jasmonate. We analyzed the expression of homologous genes between P. trichocarpa and P. ussuriensis and alternative splicing forms of PtCAMTA genes under cold stress. We also performed a network interaction analysis for PtCAMTA proteins to predict their interactions and associations. The results of the present study serve as a basis for future functional studies on the Populus CAMTA family.
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Affiliation(s)
- Ming Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Xuemei Xu
- Library of Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
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246
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Toh YK, Balakrishna AM, Manimekalai MSS, Chionh BB, Seetharaman RRC, Eisenhaber F, Eisenhaber B, Grüber G. Novel insights into the vancomycin-resistant Enterococcus faecalis (V583) alkylhydroperoxide reductase subunit F. Biochim Biophys Acta Gen Subj 2017; 1861:3201-3214. [DOI: 10.1016/j.bbagen.2017.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 10/18/2022]
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247
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Lyu Z, Lu Y. Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments. ISME JOURNAL 2017; 12:411-423. [PMID: 29135970 PMCID: PMC5776455 DOI: 10.1038/ismej.2017.173] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/31/2017] [Accepted: 08/09/2017] [Indexed: 11/09/2022]
Abstract
Methanogens have long been considered strictly anaerobic and oxygen-sensitive microorganisms, but their ability to survive oxygen stress has also been documented. Indeed, methanogens have been found in oxidative environments, and antioxidant genes have been detected in their genomes. How methanogens adapt to oxidative environments, however, remain poorly understood. Here, we systematically predicted and annotated antioxidant features from representative genomes across six well-established methanogen orders. Based on functional gene content involved in production of reactive oxygen species, Hierarchical Clustering analyses grouped methanogens into two distinct clusters, corresponding to the Class I and II methanogens, respectively. Comparative genomics suggested a systematic shift in metabolisms across the two classes, resulting in an enrichment of antioxidant features in the Class II. Moreover, meta-analysis of 16 S rRNA gene sequences obtained from EnvDB indicated that members of Class II were more frequently recovered from microaerophilic and even oxic environments than the Class I members. Phylogenomic analysis suggested that the Class I and II methanogens might have evolved before and around the Great Oxygenation Event, respectively. The enrichment of antioxidant features in the Class II methanogens may have played a key role in the adaption of this group to oxidative environments today and historically.
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Affiliation(s)
- Zhe Lyu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, PR China.,Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Yahai Lu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, PR China.,College of Urban and Environmental Sciences, Peking University, Beijing, PR China
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248
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Islam S, Rahman IA, Islam T, Ghosh A. Genome-wide identification and expression analysis of glutathione S-transferase gene family in tomato: Gaining an insight to their physiological and stress-specific roles. PLoS One 2017; 12:e0187504. [PMID: 29095889 PMCID: PMC5667761 DOI: 10.1371/journal.pone.0187504] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/21/2017] [Indexed: 01/18/2023] Open
Abstract
Glutathione S-transferase (GST) refers to one of the major detoxifying enzymes that plays an important role in different abiotic and biotic stress modulation pathways of plant. The present study aimed to a comprehensive genome-wide functional characterization of GST genes and proteins in tomato (Solanum lycopersicum L.). The whole genome sequence analysis revealed the presence of 90 GST genes in tomato, the largest GST gene family reported till date. Eight segmental duplicated gene pairs might contribute significantly to the expansion of SlGST gene family. Based on phylogenetic analysis of tomato, rice, and Arabidopsis GST proteins, GST family members could be further divided into ten classes. Members of each orthologous class showed high conservancy among themselves. Tau and lambda are the major classes of tomato; while tau and phi are the major classes for rice and Arabidopsis. Chromosomal localization revealed highly uneven distribution of SlGST genes in 13 different chromosomes, where chromosome 9 possessed the highest number of genes. Based on publicly available microarray data, expression analysis of 30 available SlGST genes exhibited a differential pattern in all the analyzed tissues and developmental stages. Moreover, most of the members showed highly induced expression in response to multiple biotic and abiotic stress inducers that could be harmonized with the increase in total GST enzyme activity under several stress conditions. Activity of tomato GST could be enhanced further by using some positive modulators (safeners) that have been predicted through molecular docking of SlGSTU5 and ligands. Moreover, tomato GST proteins are predicted to interact with a lot of other glutathione synthesizing and utilizing enzymes such as glutathione peroxidase, glutathione reductase, glutathione synthetase and γ-glutamyltransferase. This comprehensive genome-wide analysis and expression profiling would provide a rational platform and possibility to explore the versatile role of GST genes in crop engineering.
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Affiliation(s)
- Shiful Islam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Iffat Ara Rahman
- Plant Breeding and Biotechnology Laboratory, Department of Botany, University of Dhaka, Dhaka, Bangladesh
| | - Tahmina Islam
- Plant Breeding and Biotechnology Laboratory, Department of Botany, University of Dhaka, Dhaka, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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Structural Transitions of the Conserved and Metastable Hantaviral Glycoprotein Envelope. J Virol 2017; 91:JVI.00378-17. [PMID: 28835498 PMCID: PMC5640846 DOI: 10.1128/jvi.00378-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/10/2017] [Indexed: 01/13/2023] Open
Abstract
Hantaviruses are zoonotic pathogens that cause severe hemorrhagic fever and pulmonary syndrome. The outer membrane of the hantavirus envelope displays a lattice of two glycoproteins, Gn and Gc, which orchestrate host cell recognition and entry. Here, we describe the crystal structure of the Gn glycoprotein ectodomain from the Asiatic Hantaan virus (HTNV), the most prevalent pathogenic hantavirus. Structural overlay analysis reveals that the HTNV Gn fold is highly similar to the Gn of Puumala virus (PUUV), a genetically and geographically distinct and less pathogenic hantavirus found predominantly in northeastern Europe, confirming that the hantaviral Gn fold is architecturally conserved across hantavirus clades. Interestingly, HTNV Gn crystallized at acidic pH, in a compact tetrameric configuration distinct from the organization at neutral pH. Analysis of the Gn, both in solution and in the context of the virion, confirms the pH-sensitive oligomeric nature of the glycoprotein, indicating that the hantaviral Gn undergoes structural transitions during host cell entry. These data allow us to present a structural model for how acidification during endocytic uptake of the virus triggers the dissociation of the metastable Gn-Gc lattice to enable insertion of the Gc-resident hydrophobic fusion loops into the host cell membrane. Together, these data reveal the dynamic plasticity of the structurally conserved hantaviral surface. IMPORTANCE Although outbreaks of Korean hemorrhagic fever were first recognized during the Korean War (1950 to 1953), it was not until 1978 that they were found to be caused by Hantaan virus (HTNV), the most prevalent pathogenic hantavirus. Here, we describe the crystal structure of HTNV envelope glycoprotein Gn, an integral component of the Gn-Gc glycoprotein spike complex responsible for host cell entry. HTNV Gn is structurally conserved with the Gn of a genetically and geographically distal hantavirus, Puumala virus, indicating that the observed α/β fold is well preserved across the Hantaviridae family. The combination of our crystal structure with solution state analysis of recombinant protein and electron cryo-microscopy of acidified hantavirus allows us to propose a model for endosome-induced reorganization of the hantaviral glycoprotein lattice. This provides a molecular-level rationale for the exposure of the hydrophobic fusion loops on the Gc, a process required for fusion of viral and cellular membranes.
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Comprehensive genome-wide analysis of Glutathione S-transferase gene family in potato (Solanum tuberosum L.) and their expression profiling in various anatomical tissues and perturbation conditions. Gene 2017; 639:149-162. [PMID: 28988961 DOI: 10.1016/j.gene.2017.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/29/2017] [Accepted: 10/05/2017] [Indexed: 12/20/2022]
Abstract
Glutathione S-transferases (GSTs) are ubiquitous enzymes which play versatile functions including cellular detoxification and stress tolerance. In this study, a comprehensive genome-wide identification of GST gene family was carried out in potato (Solanum tuberosum L.). The result demonstrated the presence of at least 90 GST genes in potato which is greater than any other reported species. According to the phylogenetic analyses of Arabidopsis, rice and potato GST members, GSTs could be subdivided into ten different classes and each class is found to be highly conserved. The largest class of potato GST family is tau with 66 members, followed by phi and lambda. The chromosomal localization analysis revealed the highly uneven distribution of StGST genes across the potato genome. Transcript profiling of 55 StGST genes showed the tissue-specific expression for most of the members. Moreover, expression of StGST genes were mainly repressed in response to abiotic stresses, while largely induced in response to biotic and hormonal elicitations. Further analysis of StGST gene's promoter identified the presence of various stress responsive cis-regulatory elements. Moreover, one of the highly stress responsive StGST members, StGSTU46, showed strong affinity towards flurazole with lowest binding energy of -7.6kcal/mol that could be used as antidote to protect crop against herbicides. These findings will facilitate the further functional and evolutionary characterization of GST genes in potato.
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