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Ślusarz MJ. How kelch domain-containing protein 3 distinguishes between the C-end degron of herpesviral protein UL49.5 and its mutants - Insights from molecular dynamics. Bioorg Med Chem 2024; 109:117795. [PMID: 38878709 DOI: 10.1016/j.bmc.2024.117795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 05/13/2024] [Accepted: 06/07/2024] [Indexed: 06/30/2024]
Abstract
The C-terminal residues of proteins can function as degrons recognized by ubiquitin ligases for proteasomal degradation. Kelch domain-containing protein 3 (KLHDC3) is a substrate receptor for E3 ubiquitin ligase (Cullin2-RING ligase) that targets the C-terminal degrons. UL49.5 is 96 amino-acid type 1 transmembrane protein from bovine herpesvirus 1. Herpesviruses have evolved highly effective strategies to evade the antiviral immune response. One of these strategies is inhibition of the antigen processing and presentation pathway by MHC I, thereby reducing the presentation of the antigenic peptides on the surface of the infected cell. Recently, it has been demonstrated that UL49.5 triggers TAP degradation via recruiting the E3 ubiquitin ligase to TAP. Moreover, the mutagenesis revealed that the mutations within the UL49.5 C-degron sequence (93RGRG96) affect binding of UL49.5 to KLHDC3. In this work the molecular dynamics of KLHDC3 in complexes with the C-terminal decapeptide of the herpesviral protein UL4.95 and its three mutants has been employed to provide a framework for understanding molecular recognition of UL49.5 by KLHDC3. The findings of this study give insights into the interactions of the various degrons with KLHDC3. During the molecular dynamics, an active RGKG mutant adopts a conformation similar to that of the wild type decapeptide, whereas the conformations of two inactive mutants, KGRG and RGRD are significantly different. Both R93K and G96D mutations impair the interactions of the C-terminal glycine with KLHDC3. The findings of this study expand the existing knowledge about the mechanism of protein recognition by Cullin2-RING ligases thus contributing to the design of antiviral and anticancer drugs that can selectively promote or inhibit degradation of the proteins of interest.
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Affiliation(s)
- Magdalena J Ślusarz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
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2
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Abd-Hamid NA, Ismail I. An F-box Kelch repeat protein, PmFBK2, from Persicaria minor interacts with GID1b to modulate gibberellin signalling. JOURNAL OF PLANT PHYSIOLOGY 2024; 300:154299. [PMID: 38936241 DOI: 10.1016/j.jplph.2024.154299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
The F-box protein (FBP) family plays diverse functions in the plant kingdom, with the function of many members still unrevealed. In this study, a specific FBP called PmFBK2, containing Kelch repeats from Persicaria minor, was functionally investigated. Employing the yeast two-hybrid (Y2H) assay, PmFBK2 was found to interact with Skp1-like proteins from P. minor, suggesting its potential to form an E3 ubiquitin ligase, known as the SCF complex. Y2H and co-immunoprecipitation tests revealed that PmFBK2 interacts with full-length PmGID1b. The interaction marks the first documented binding between these two protein types, which have never been reported in other plants before, and they exhibited a negative effect on gibberellin (GA) signal transduction. The overexpression of PmFBK2 in the kmd3 mutant, a homolog from Arabidopsis, demonstrated the ability of PmFBK2 to restore the function of the mutated KMD3 gene. The function restoration was supported by morphophysiological and gene expression analyses, which exhibited patterns similar to the wild type (WT) compared to the kmd3 mutant. Interestingly, the overexpression of PmFBK2 or PmGID1b in Arabidopsis had opposite effects on rosette diameter, seed weight, and plant height. This study provides new insights into the complex GA signalling. It highlights the crucial roles of the interaction between FBP and the GA receptor (GID1b) in regulating GA responses. These findings have implications for developing strategies to enhance plant growth and yield by modulating GA signalling in crops.
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Affiliation(s)
- Nur-Athirah Abd-Hamid
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia; Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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3
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Giorgi FM, Pozzobon D, Di Meglio A, Mercatelli D. Genomic and transcriptomic analysis of the recent Mpox outbreak. Vaccine 2024; 42:1841-1849. [PMID: 38311533 DOI: 10.1016/j.vaccine.2023.12.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 02/06/2024]
Abstract
The Mpox (formerly named Monkeypox) virus is the etiological cause of a recent multi-country outbreak, with thousands of distinct cases detected outside the endemic areas of Africa as of December 2023. In this article, we analyze the sequences of full genomes of Mpox virus from Europe and compare them with all available Mpox sequences of historical relevance, annotated by year and geographic origin, as well as related Cowpox and Variola (smallpox) virus sequences. Our results show that the recent outbreak is most likely originating from the West African clade of Mpox, with >99 % sequence identity with sequences derived from historical and recent cases, dating from 1971 to 2017. We analyze specific mutations occurring in viral proteins between the current outbreak, previous Mpox and Cowpox sequences, and the historical Variola virus. Genome-wide sequence analysis of the recent outbreak and other Mpox/Cowpox/Variola viruses shows a very high conservation, with 97.9 % (protein-based) and 97.8 % (nucleotide-based) sequence identity. We identified significant correlation in human transcriptional responses as well, with a conserved immune pathway response induced in human cell cultures by the three families of Pox virus. The similarities identified between the major strains of Pox viruses, as well as within the Mpox clades, both at the genomic and transcriptomic levels, provide a molecular basis for the observed efficacy of Variola vaccines in other Poxviruses.
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Affiliation(s)
- Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
| | - Daniele Pozzobon
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Antonio Di Meglio
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
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McAllaster MR, Bhushan J, Balce DR, Orvedahl A, Park A, Hwang S, Sullender ME, Sibley LD, Virgin HW. Autophagy gene-dependent intracellular immunity triggered by interferon-γ. mBio 2023; 14:e0233223. [PMID: 37905813 PMCID: PMC10746157 DOI: 10.1128/mbio.02332-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 11/02/2023] Open
Abstract
Genes required for the lysosomal degradation pathway of autophagy play key roles in topologically distinct and physiologically important cellular processes. Some functions of ATG genes are independent of their role in degradative autophagy. One of the first described of these ATG gene-dependent, but degradative autophagy independent, processes is the requirement for a subset of ATG genes in interferon-γ (IFNγ)-induced inhibition of norovirus and Toxoplasma gondii replication. Herein, we identified additional genes that are required for, or that negatively regulate, this innate immune effector pathway. Enzymes in the UFMylation pathway negatively regulated IFNγ-induced inhibition of norovirus replication via effects of Ern1. IFNγ-induced inhibition of norovirus replication required Gate-16 (also termed GabarapL2), Wipi2b, Atg9a, Cul3, and Klhl9 but not Becn1 (encoding Beclin 1), Atg14, Uvrag, or Sqstm1. The phosphatidylinositol-3-phosphate and ATG16L1-binding domains of WIPI2B, as well as the ATG5-binding domain of ATG16L1, were required for IFNγ-induced inhibition of norovirus replication. Other members of the Cul3, Atg8, and Wipi2 gene families were not required, demonstrating exquisite specificity within these gene families for participation in IFNγ action. The generality of some aspects of this mechanism was demonstrated by a role for GATE-16 and WIPI2 in IFNγ-induced control of Toxoplasma gondii infection in human cells. These studies further delineate the genes and mechanisms of an ATG gene-dependent programmable form of cytokine-induced innate intracellular immunity. IMPORTANCE Interferon-γ (IFNγ) is a critical mediator of cell-intrinsic immunity to intracellular pathogens. Understanding the complex cellular mechanisms supporting robust interferon-γ-induced host defenses could aid in developing new therapeutics to treat infections. Here, we examined the impact of autophagy genes in the interferon-γ-induced host response. We demonstrate that genes within the autophagy pathway including Wipi2, Atg9, and Gate-16, as well as ubiquitin ligase complex genes Cul3 and Klhl9 are required for IFNγ-induced inhibition of murine norovirus (norovirus hereinafter) replication in mouse cells. WIPI2 and GATE-16 were also required for IFNγ-mediated restriction of parasite growth within the Toxoplasma gondii parasitophorous vacuole in human cells. Furthermore, we found that perturbation of UFMylation pathway components led to more robust IFNγ-induced inhibition of norovirus via regulation of endoplasmic reticulum (ER) stress. Enhancing or inhibiting these dynamic cellular components could serve as a strategy to control intracellular pathogens and maintain an effective immune response.
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Affiliation(s)
- Michael R. McAllaster
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Vir Biotechnology, San Francisco, California, USA
| | - Jaya Bhushan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dale R. Balce
- Vir Biotechnology, San Francisco, California, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Anthony Orvedahl
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Arnold Park
- Vir Biotechnology, San Francisco, California, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Meagan E. Sullender
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Herbert W. Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
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Sharma S, Ali ME. How do the mutations in PfK13 protein promote anti-malarial drug resistance? J Biomol Struct Dyn 2023; 41:7329-7338. [PMID: 36153000 DOI: 10.1080/07391102.2022.2120539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/27/2022] [Indexed: 10/14/2022]
Abstract
Plasmodium falciparum develops resistance to artemisinin upon exposure to the anti-malarial drug. Various mutations in the Plasmodium falciparum Kelch13 (PfK13) protein such as Y493H, R539T, I543T and C580Y have been associated with anti-malarial drug resistance. These mutations impede the regular ubiquitination process that eventually invokes drug resistance. However, the relationship between the mutation and the mechanism of drug resistance has not yet been fully elucidated. The comparative protein dynamics are studied by performing the classical molecular dynamics (MD) simulations and subsequent analysis of the trajectories adopting root-mean-square fluctuations, the secondary-structure predictions and the dynamical cross-correlation matrix analysis tools. Here, we observed that the mutations in the Kelch-domain do not have any structural impact on the mutated site; however, it significantly alters the overall dynamics of the protein. The loop-region of the BTB-domain especially for Y493H and C580Y mutants is found to have the enhanced dynamical fluctuations. The enhanced fluctuations in the BTB-domain could affect the protein-protein (PfK13-Cullin) binding interactions in the ubiquitination process and eventually lead to anti-malarial drug resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shikha Sharma
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab, India
| | - Md Ehesan Ali
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab, India
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Chakraborty A, Mondal S, Mahajan S, Sharma VK. High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl. Heliyon 2023; 9:e18571. [PMID: 37576271 PMCID: PMC10412995 DOI: 10.1016/j.heliyon.2023.e18571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
An intriguing example of differential adaptability is the case of two Asian peafowl species, Pavo cristatus (blue peafowl) and Pavo muticus (green peafowl), where the former has a "Least Concern" conservation status and the latter is an "Endangered" species. To understand the genetic basis of this differential adaptability of the two peafowl species, a comparative analysis of these species is much needed to gain the genomic and evolutionary insights. Thus, we constructed a high-quality genome assembly of blue peafowl with an N50 value of 84.81 Mb (pseudochromosome-level assembly), and a high-confidence coding gene set to perform the genomic and evolutionary analyses of blue and green peafowls with 49 other avian species. The analyses revealed adaptive evolution of genes related to neuronal development, immunity, and skeletal muscle development in these peafowl species. Major genes related to axon guidance such as NEO1 and UNC5, semaphorin (SEMA), and ephrin receptor showed adaptive evolution in peafowl species. However, blue peafowl showed the presence of 42% more coding genes compared to the green peafowl along with a higher number of species-specific gene clusters, segmental duplicated genes and expanded gene families, and comparatively higher evolution in neuronal and developmental pathways. Blue peafowl also showed longer branch length compared to green peafowl in the species phylogenetic tree. These genomic insights obtained from the high-quality genome assembly of P. cristatus constructed in this study provide new clues on the superior adaptability of the blue peafowl over green peafowl despite having a recent species divergence time.
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Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - Samuel Mondal
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - Vineet K. Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
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7
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Han L, Chen Z, Sun L. Expression, purification, and microscopic characterization of the tumor suppressor KLHL6. Protein Expr Purif 2023:106318. [PMID: 37286065 DOI: 10.1016/j.pep.2023.106318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/22/2023] [Accepted: 06/04/2023] [Indexed: 06/09/2023]
Abstract
Kelch-like protein 6 (KLHL6) plays a critical role in preventing the development and survival of diffuse large B-cell lymphoma (DLBCL) through its involvement in the ubiquitin proteasome system. Specifically, KLHL6 binds to cullin3 (Cul3) and the substrate, facilitating the assembly of the E3 ligase responsible for substrate ubiquitination. It is imperative to investigate the precise function of KLHL6 by conducting a structural analysis of its interaction with Cul3. Here, we present the expression, purification, and characterization of the full-length KLHL6. Our findings demonstrate that the addition of a Sumo-tag significantly enhances the production of KLHL6, while also improving its stability and solubility. Moreover, through gel filtration and negative staining electron microscopy (EM), we observed that KLHL6 adopts a homomultimeric form in solution. Additionally, we found that the presence of Cul3NTD enhances the stability and homogeneity of KLHL6 by forming a complex. Consequently, the successful expression and purification of full-length KLHL6 serve as a foundation for further investigations into the structure and function of the KLHL6/Cullin3/Rbx1 substrate complex, as well as provide a potential strategy for studying other proteins within the KLHL family that possess similar characteristics.
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Affiliation(s)
- Lin Han
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Zhenguo Chen
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Lei Sun
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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8
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Brennan G, Stoian AMM, Yu H, Rahman MJ, Banerjee S, Stroup JN, Park C, Tazi L, Rothenburg S. Molecular Mechanisms of Poxvirus Evolution. mBio 2023; 14:e0152622. [PMID: 36515529 PMCID: PMC9973261 DOI: 10.1128/mbio.01526-22] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Poxviruses are often thought to evolve relatively slowly because they are double-stranded DNA pathogens with proofreading polymerases. However, poxviruses have highly adaptable genomes and can undergo relatively rapid genotypic and phenotypic change, as illustrated by the recent increase in human-to-human transmission of monkeypox virus. Advances in deep sequencing technologies have demonstrated standing nucleotide variation in poxvirus populations, which has been underappreciated. There is also an emerging understanding of the role genomic architectural changes play in shaping poxvirus evolution. These mechanisms include homologous and nonhomologous recombination, gene duplications, gene loss, and the acquisition of new genes through horizontal gene transfer. In this review, we discuss these evolutionary mechanisms and their potential roles for adaption to novel host species and modulating virulence.
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Affiliation(s)
- Greg Brennan
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Ana M. M. Stoian
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Huibin Yu
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - M. Julhasur Rahman
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Shefali Banerjee
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Jeannine N. Stroup
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Chorong Park
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Loubna Tazi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Stefan Rothenburg
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
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Corzo Leon DE, Scheynius A, MacCallum DM, Munro CA. Malassezia sympodialis Mala s 1 allergen is a potential KELCH protein that cross reacts with human skin. FEMS Yeast Res 2023; 23:foad028. [PMID: 37188635 PMCID: PMC10281499 DOI: 10.1093/femsyr/foad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/28/2023] [Accepted: 05/12/2023] [Indexed: 05/17/2023] Open
Abstract
Malassezia are the dominant commensal yeast species of the human skin microbiota and are associated with inflammatory skin diseases, such as atopic eczema (AE). The Mala s 1 allergen of Malassezia sympodialis is a β-propeller protein, inducing both IgE and T-cell reactivity in AE patients. We demonstrate by immuno-electron microscopy that Mala s 1 is mainly located in the M. sympodialis yeast cell wall. An anti-Mala s 1 antibody did not inhibit M. sympodialis growth suggesting Mala s 1 may not be an antifungal target. In silico analysis of the predicted Mala s 1 protein sequence identified a motif indicative of a KELCH protein, a subgroup of β-propeller proteins. To test the hypothesis that antibodies against Mala s 1 cross-react with human skin (KELCH) proteins we examined the binding of the anti-Mala s 1 antibody to human skin explants and visualized binding in the epidermal skin layer. Putative human targets recognized by the anti-Mala s 1 antibody were identified by immunoblotting and proteomics. We propose that Mala s 1 is a KELCH-like β-propeller protein with similarity to human skin proteins. Mala s 1 recognition may trigger cross-reactive responses that contribute to skin diseases associated with M. sympodialis.
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Affiliation(s)
- Dora E Corzo Leon
- School of Medicine, Medical Sciences & Nutrition University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Annika Scheynius
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs' Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden
| | - Donna M MacCallum
- School of Medicine, Medical Sciences & Nutrition University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Carol A Munro
- School of Medicine, Medical Sciences & Nutrition University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
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Yang L, Wang ZA, Geng R, Niu S, Zuo H, Weng S, He J, Xu X. A kelch motif-containing protein KLHDC2 regulates immune responses against Vibrio parahaemolyticus and white spot syndrome virus in Penaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2022; 127:187-194. [PMID: 35716970 DOI: 10.1016/j.fsi.2022.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/04/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
The kelch motif-containing proteins are widely present in organisms and known to be involved in various biological processes, but their roles in immunity remain unclear. In this study, a kelch motif-containing protein KLHDC2 was identified from Pacific white shrimp Penaeus vannamei and its immune function was investigated. The klhdc2 gene was widely expressed in shrimp tissues and its protein product was mainly present in the nucleus. Expression of klhdc2 was regulated by shrimp NF-κB family members Dorsal and Relish, and changed after immune stimulation. KLHDC2 could enhance the immune defense against Vibrio parahaemolyticus in shrimp but inhibit that against white spot syndrome virus (WSSV). Further analyses showed that KLHDC2 did not affect the phagocytosis of hemocytes but regulated the expression of a series of immune effector genes. KLHDC2 has a complex regulatory relationship with Dorsal and Relish, which may partly contribute to its positive role in antibacterial response by regulating humoral immunity. Moreover, the regulatory effect of KLHDC2 on WSSV ie1 gene contributed to its negative effect on antiviral response. Therefore, the current study enrichs the knowledge on the Kelch family and helps to learn more about the regulatory mechanism of shrimp immunity.
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Affiliation(s)
- Linwei Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Zi-Ang Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Ran Geng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Shengwen Niu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Hongliang Zuo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Jianguo He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China
| | - Xiaopeng Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, PR China.
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Abstract
The recovery of DNA from viromes is a major obstacle in the use of long-read sequencing to study their genomes. For this reason, the use of cellular metagenomes (>0.2-μm size range) emerges as an interesting complementary tool, since they contain large amounts of naturally amplified viral genomes from prelytic replication. We have applied second-generation (Illumina NextSeq; short reads) and third-generation (PacBio Sequel II; long reads) sequencing to compare the diversity and features of the viral community in a marine sample obtained from offshore waters of the western Mediterranean. We found that a major wedge of the expected marine viral diversity was directly recovered by the raw PacBio circular consensus sequencing (CCS) reads. More than 30,000 sequences were detected only in this data set, with no homologues in the long- and short-read assembly, and ca. 26,000 had no homologues in the large data set of the Global Ocean Virome 2 (GOV2), highlighting the information gap created by the assembly bias. At the level of complete viral genomes, the performance was similar in both approaches. However, the hybrid long- and short-read assembly provided the longest average length of the sequences and improved the host assignment. Although no novel major clades of viruses were found, there was an increase in the intraclade genomic diversity recovered by long reads that produced an enriched assessment of the real diversity and allowed the discovery of novel genes with biotechnological potential (e.g., endolysin genes). IMPORTANCE We explored the vast genetic diversity of environmental viruses by using a combination of cellular metagenome (as opposed to virome) sequencing using high-fidelity long-read sequences (in this case, PacBio CCS). This approach resulted in the recovery of a representative sample of the viral population, and it performed better (more phage contigs, larger average contig size) than Illumina sequencing applied to the same sample. By this approach, the many biases of assembly are avoided, as the CCS reads recovers (typically around 5 kb) complete genes and even operons, resulting in a better discovery of the viral gene diversity based on viral marker proteins. Thus, biotechnologically promising genes, such as endolysin genes, can be very efficiently searched with this approach. In addition, hybrid assembly produces more complete and longer contigs, which is particularly important for studying little-known viral groups such as the nucleocytoplasmic large DNA viruses (NCLDV).
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Tang R, Dong H, He L, Li P, Shi Y, Yang Q, Jia X, Li XQ. Genome-wide identification, evolutionary and functional analyses of KFB family members in potato. BMC PLANT BIOLOGY 2022; 22:226. [PMID: 35501691 PMCID: PMC9063267 DOI: 10.1186/s12870-022-03611-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Kelch repeat F-box (KFB) proteins play vital roles in the regulation of multitudinous biochemical and physiological processes in plants, including growth and development, stress response and secondary metabolism. Multiple KFBs have been characterized in various plant species, but the family members and functions have not been systematically identified and analyzed in potato. RESULTS Genome and transcriptome analyses of StKFB gene family were conducted to dissect the structure, evolution and function of the StKFBs in Solanum tuberosum L. Totally, 44 StKFB members were identified and were classified into 5 groups. The chromosomal localization analysis showed that the 44 StKFB genes were located on 12 chromosomes of potato. Among these genes, two pairs of genes (StKFB15/16 and StKFB40/41) were predicted to be tandemly duplicated genes, and one pair of genes (StKFB15/29) was segmentally duplicated genes. The syntenic analysis showed that the KFBs in potato were closely related to the KFBs in tomato and pepper. Expression profiles of the StKFBs in 13 different tissues and in potato plants with different treatments uncovered distinct spatial expression patterns of these genes and their potential roles in response to various stresses, respectively. Multiple StKFB genes were differentially expressed in yellow- (cultivar 'Jin-16'), red- (cultivar 'Red rose-2') and purple-fleshed (cultivar 'Xisen-8') potato tubers, suggesting that they may play important roles in the regulation of anthocyanin biosynthesis in potato. CONCLUSIONS This study reports the structure, evolution and expression characteristics of the KFB family in potato. These findings pave the way for further investigation of functional mechanisms of StKFBs, and also provide candidate genes for potato genetic improvement.
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Affiliation(s)
- Ruimin Tang
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Haitao Dong
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Liheng He
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Peng Li
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Yuanrui Shi
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Qing Yang
- College of life sciences, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Xiaoyun Jia
- College of life sciences, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Xiu-Qing Li
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick E3B 4Z7 Canada
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Yuan H, Wang Q, Zeng X, He P, Xu W, Guo H, Liu Y, Lin Y. Clinical and molecular analysis of four unrelated Chinese families with pathogenic KLHL40 variants causing nemaline myopathy 8. Orphanet J Rare Dis 2022; 17:149. [PMID: 35379254 PMCID: PMC8981653 DOI: 10.1186/s13023-022-02306-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/23/2022] [Indexed: 11/15/2022] Open
Abstract
Background Homozygous or compound heterozygous variants in the KLHL40 gene cause nemaline myopathy 8 (NEM8), a severe autosomal recessive muscle disorder characterized by prenatal polyhydramnios, fetal akinesia or hypokinesia, joint contractures, fractures, respiratory failure and dysphagia. Currently, 46 individuals with NEM8 have been described in the literature, and 30 variants in KLHL40 have been identified.
Results Here, we reported five individuals from four unrelated Chinese families who presented common features of nemaline myopathy and infrequent clinical characteristics. Whole-exome sequencing (WES) was used to identify the causative gene. WES identified a recurrent missense variant c.1516A>C (p.Thr506Pro) and a novel frameshift variant c.543del (p.Ser182Profs*17) in KLHL40 in patient 1, a nonsense variant c.602G>A (p.Trp201*) and a missense variant c.1516A>C (p.Thr506Pro) in KLHL40 in patient 2, and homozygous variant c.1516A>C (p.Thr506Pro) in KLHL40 in patient 3 and both siblings (patients 4 and 5), all of which were confirmed by Sanger sequencing. Next, we estimated the incidence of this disorder in the southern and northern Chinese population to be 4.59/106 and 2.95/106, respectively, based on the cumulative allele frequency of pathogenic variants in internal database. Conclusion The results of our study expand the mutation spectrum of KLHL40 and enrich our understanding of the clinical characteristics of NEM8. Genetic counseling was provided for the four families involved in this study. Given the severity and the relatively high incidence of this condition, we strongly suggest that KLHL40 be incorporated into a carrier screening panel for the Chinese population. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02306-9.
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Ganguly RK, Al-Helal MA, Chakraborty SK. Role of bioactive xenobiotics towards reproductive potential of Odontotermes longignathus through in silico study: An amalgamation of ecoinformatics and ecotechnological insights of termite mounds from a tropical forest, India. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 232:113275. [PMID: 35131584 DOI: 10.1016/j.ecoenv.2022.113275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/09/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
The present research study has evaluated the roles of different naturally occurring compounds in termite mounds of Odontotermes longignathus (GenBank Id: MZ542727.1) which facilitate to promote higher population growth of termites and subsequent biodegradation. The study has also monitored the change in physicochemical parameters along with the trend of biodegradation of complex organic carbon-based compounds like lignin, polysaccharides etc. and nitrogenous compounds from two different types of termite mounds such as developing (T1) and developed (T2) mounds. The GC MS profiling of mound samples have revealed the occurrence of different humic acids like organic materials in both T1 and T2 mound samples. Both the termite mounds have demonstrated a high population density as T1 (23.67 ± 1.56) individuals and T2 (43.51 ± 2.36) individuals per 0.1 kg of mound materials. Such observations have prompted to undertake molecular docking experiments which revealed that different molecules interact at low binding affinity with hormone receptors involved in moulting, spermatogenesis and oogenesis of termite like Adamantane carboxylate (EcR: -7.6 Kcal/mol; BTB-KLHL10: -6.2 Kcal/mol; USP-LBD: -7.3 Kcal/mol; VgR: -6.8 Kcal/mol), Benzene dicarboxylic acid (EcR: -5.5 Kcal/mol; BTB-KLHL10: -5.1 Kcal/mol; USP-LBD: -5.4 Kcal/mol; VgR: -5.6 Kcal/mol), Hexadecanol (EcR: -6.0 Kcal/mol; BTB-KLHL10: -4.4 Kcal/mol; USP-LBD: -6.9 Kcal/mol; VgR: -6.0 Kcal/mol), oxirane (EcR: -5.3 Kcal/mol; BTB-KLHL10: -4.9 Kcal/mol; USP-LBD: -5.2 Kcal/mol; VgR: -5.3 Kcal/mol) and tocopherol (EcR: -8.0 Kcal/mol; BTB-KLHL10: -5.4 Kcal/mol; USP-LBD: -7.6 Kcal/mol; VgR: -7.0 Kcal/mol). Such spontaneous ligand binding phenomenon coupled with high population density of termites have established the significance of different bioactive xenobiotics in achieving high reproductive potential of termites which in turn facilitate the process of biodegradation and enhance the nutrient enrichment in the soils of tropical deciduous forest.
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Affiliation(s)
- Ram Kumar Ganguly
- Department of Zoology, Vidyasagar university, Midnapore 721102, West Bengal, India.
| | - Md Abdullah Al-Helal
- Department of Zoology, Vidyasagar university, Midnapore 721102, West Bengal, India
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Senkevich TG, Yutin N, Wolf YI, Koonin EV, Moss B. Ancient Gene Capture and Recent Gene Loss Shape the Evolution of Orthopoxvirus-Host Interaction Genes. mBio 2021; 12:e0149521. [PMID: 34253028 PMCID: PMC8406176 DOI: 10.1128/mbio.01495-21] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 01/27/2023] Open
Abstract
The survival of viruses depends on their ability to resist host defenses and, of all animal virus families, the poxviruses have the most antidefense genes. Orthopoxviruses (ORPV), a genus within the subfamily Chordopoxvirinae, infect diverse mammals and include one of the most devastating human pathogens, the now eradicated smallpox virus. ORPV encode ∼200 genes, of which roughly half are directly involved in virus genome replication and expression as well as virion morphogenesis. The remaining ∼100 "accessory" genes are responsible for virus-host interactions, particularly counter-defense of innate immunity. Complete sequences are currently available for several hundred ORPV genomes isolated from a variety of mammalian hosts, providing a rich resource for comparative genomics and reconstruction of ORPV evolution. To identify the provenance and evolutionary trends of the ORPV accessory genes, we constructed clusters including the orthologs of these genes from all chordopoxviruses. Most of the accessory genes were captured in three major waves early in chordopoxvirus evolution, prior to the divergence of ORPV and the sister genus Centapoxvirus from their common ancestor. The capture of these genes from the host was followed by extensive gene duplication, yielding several paralogous gene families. In addition, nine genes were gained during the evolution of ORPV themselves. In contrast, nearly every accessory gene was lost, some on multiple, independent occasions in numerous lineages of ORPV, so that no ORPV retains them all. A variety of functional interactions could be inferred from examination of pairs of ORPV accessory genes that were either often or rarely lost concurrently. IMPORTANCE Orthopoxviruses (ORPV) include smallpox (variola) virus, one of the most devastating human pathogens, and vaccinia virus, comprising the vaccine used for smallpox eradication. Among roughly 200 ORPV genes, about half are essential for genome replication and expression as well as virion morphogenesis, whereas the remaining half consists of accessory genes counteracting the host immune response. We reannotated the accessory genes of ORPV, predicting the functions of uncharacterized genes, and reconstructed the history of their gain and loss during the evolution of ORPV. Most of the accessory genes were acquired in three major waves antedating the origin of ORPV from chordopoxviruses. The evolution of ORPV themselves was dominated by gene loss, with numerous genes lost at the base of each major group of ORPV. Examination of pairs of ORPV accessory genes that were either often or rarely lost concurrently during ORPV evolution allows prediction of different types of functional interactions.
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Affiliation(s)
- Tatiana G. Senkevich
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Instutes of Health, Bethesda, Maryland, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Bernard Moss
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Instutes of Health, Bethesda, Maryland, USA
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Kashimoto R, Hisata K, Shinzato C, Satoh N, Shoguchi E. Expansion and Diversification of Fluorescent Protein Genes in Fifteen Acropora Species during the Evolution of Acroporid Corals. Genes (Basel) 2021; 12:genes12030397. [PMID: 33799612 PMCID: PMC8001845 DOI: 10.3390/genes12030397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022] Open
Abstract
In addition to a purple, non-fluorescent chromoprotein (ChrP), fluorescent proteins (FPs) account for the vivid colors of corals, which occur in green (GFP), cyan (CFP), and red (RFP) FPs. To understand the evolution of the coral FP gene family, we examined the genomes of 15 Acropora species and three confamilial taxa. This genome-wide survey identified 219 FP genes. Molecular phylogeny revealed that the 15 Acropora species each have 9–18 FP genes, whereas the other acroporids examined have only two, suggesting a pronounced expansion of the FP genes in the genus Acropora. The data estimates of FP gene duplication suggest that the last common ancestor of the Acropora species that survived in the period of high sea surface temperature (Paleogene period) has already gained 16 FP genes. Different evolutionary histories of lineage-specific duplication and loss were discovered among GFP/CFPs, RFPs, and ChrPs. Synteny analysis revealed core GFP/CFP, RFP, and ChrP gene clusters, in which a tandem duplication of the FP genes was evident. The expansion and diversification of Acropora FPs may have contributed to the present-day richness of this genus.
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Affiliation(s)
- Rio Kashimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.H.); (N.S.); (E.S.)
- Correspondence:
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.H.); (N.S.); (E.S.)
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan;
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.H.); (N.S.); (E.S.)
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; (K.H.); (N.S.); (E.S.)
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Qu Y, Wang J, Huang P, Liu X, Lu J, Lin FC. PoRal2 Is Involved in Appressorium Formation and Virulence via Pmk1 MAPK Pathways in the Rice Blast Fungus Pyricularia oryzae. FRONTIERS IN PLANT SCIENCE 2021; 12:702368. [PMID: 34589096 PMCID: PMC8473790 DOI: 10.3389/fpls.2021.702368] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/17/2021] [Indexed: 05/07/2023]
Abstract
Pyricularia oryzae is an important plant pathogenic fungus that can severely damage rice and wheat crops, leading to significant reductions in crop productivity. To penetrate into and invade tissues of its plant host, this fungus relies on an invasive structure known as an appressorium. Appressorium formation is rigorously regulated by the cAMP-PKA and Pmk1 MAPK pathways. Here, we identified PoRal2, a homologous protein of Schizosaccharomyces pombe Ral2, and characterized its roles in fungal development and virulence in P. oryzae. PoRal2 contains N-terminal kelch repeats and C-terminal BTB domains. PoRal2 is involved in sporulation, aerial hypha and conidiophore differentiation, appressorium formation, plant penetration, and virulence. During appressorium formation, ∆Poral2 mutants generate appressoria with long germ tubes on hydrophobic surfaces. ∆Poral2 mutants exhibited a defective response to exogenous cAMP and the activated RAS2 G18V on a hydrophilic surface, indicating impairment in the cAMP-PKA or Pmk1 MAPK signaling pathways. Deletion of PoRAL2 leads to lowered Pmk1 phosphorylation level in the mutant. Moreover, PoRal2 is found to interact with Scd1, Smo1, and Mst50, which are involved in activation of Pmk1. In addition, the expression levels of MPG1, WISH, and PDEH in the cAMP-PKA pathway, RAS2 in both the cAMP-PKA and Pmk1 MAPK pathways, and melanin biosynthesis genes (ALB1, BUF1, and RSY1) were significantly down-regulated in the ∆Poral2. Therefore, PoRal2 is involved in fungal development and virulence by its crosstalk in the cAMP-PKA and Pmk1 MAPK signaling pathways.
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Affiliation(s)
- Yingmin Qu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jing Wang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Pengyun Huang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaohong Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jianping Lu
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Jianping Lu,
| | - Fu-Cheng Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Fu-Cheng Lin,
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Kopacz A, Kloska D, Forman HJ, Jozkowicz A, Grochot-Przeczek A. Beyond repression of Nrf2: An update on Keap1. Free Radic Biol Med 2020; 157:63-74. [PMID: 32234331 PMCID: PMC7732858 DOI: 10.1016/j.freeradbiomed.2020.03.023] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/04/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022]
Abstract
Nrf2 (NFE2L2 - nuclear factor (erythroid-derived 2)-like 2) is a transcription factor, which is repressed by interaction with a redox-sensitive protein Keap1 (Kelch-like ECH-associated protein 1). Deregulation of Nrf2 transcriptional activity has been described in the pathogenesis of multiple diseases, and the Nrf2/Keap1 axis has emerged as a crucial modulator of cellular homeostasis. Whereas the significance of Nrf2 in the modulation of biological processes has been well established and broadly discussed in detail, the focus on Keap1 rarely goes beyond the regulation of Nrf2 activity and redox sensing. However, recent studies and scrutinized analysis of available data point to Keap1 as an intriguing and potent regulator of cellular function. This review aims to shed more light on Keap1 structure, interactome, regulation and non-canonical functions, thereby enhancing its significance in cell biology. We also intend to highlight the impact of balance between Keap1 and Nrf2 in the maintenance of cellular homeostasis.
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Affiliation(s)
- Aleksandra Kopacz
- Department of Medical Biotechnology, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Damian Kloska
- Department of Medical Biotechnology, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Henry Jay Forman
- Andrus Gerontology Center of the Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089-0191, USA
| | - Alicja Jozkowicz
- Department of Medical Biotechnology, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Anna Grochot-Przeczek
- Department of Medical Biotechnology, Faculty of Biochemistry Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland.
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Kong W, Gao M, Jin Y, Huang W, Huang Z, Xie Z. Prognostic model of patients with liver cancer based on tumor stem cell content and immune process. Aging (Albany NY) 2020; 12:16555-16578. [PMID: 32852285 PMCID: PMC7485734 DOI: 10.18632/aging.103832] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023]
Abstract
Globally, liver hepatocellular carcinoma (LIHC) has a high mortality and recurrence rate, leading to poor prognosis. The recurrence of LIHC is closely related to two aspects: degree of immune infiltration and content of tumor stem cells. Hence, this study aimed to used RNA-seq and clinical data of LIHC from The Cancer Genome Atlas, Estimation of Stromal and Immune cells in Malignant Tumours, mRNA stemness index score, and weighted gene correlation network analysis methods to find genes significantly linked to the aforementioned two aspects. Key genes and clinical factors were used as input. Lasso regression and multivariate Cox regression were conducted to build an effective prognostic model for patients with liver cancer. Finally, four key genes (KLHL30, PLN, LYVE1, and TIMD4) and four clinical factors (Asian, age, grade, and bilirubin) were included in the prognostic model, namely Immunity and Cancer-stem-cell Related Prognosis (ICRP) score. The ICRP score achieved a great performance in test set. The area under the curve value of the ICRP score in test set for 1, 3, and 5 years was 0.708, 0.723, and 0.765, respectively, which was better than that of other prognostic prediction methods for LIHC. The C-index evaluation method also reached the same conclusion.
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Affiliation(s)
- Weikaixin Kong
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, China
| | - Miaomiao Gao
- Peking University International Cancer Institute and Department of Pharmacology, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yuchen Jin
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, China
| | - Weiran Huang
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, China
| | - Zhuo Huang
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, China
| | - Zhengwei Xie
- Peking University International Cancer Institute and Department of Pharmacology, School of Basic Medical Sciences, Peking University, Beijing, China
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20
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Islinger M, Costello JL, Kors S, Soupene E, Levine TP, Kuypers FA, Schrader M. The diversity of ACBD proteins - From lipid binding to protein modulators and organelle tethers. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2020; 1867:118675. [PMID: 32044385 PMCID: PMC7057175 DOI: 10.1016/j.bbamcr.2020.118675] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/30/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022]
Abstract
Members of the large multigene family of acyl-CoA binding domain containing proteins (ACBDs) share a conserved motif required for binding of Coenzyme A esterified fatty acids of various chain length. These proteins are present in the three kingdoms of life, and despite their predicted roles in cellular lipid metabolism, knowledge about the precise functions of many ACBD proteins remains scarce. Interestingly, several ACBD proteins are now suggested to function at organelle contact sites, and are recognized as host interaction proteins for different pathogens including viruses and bacteria. Here, we present a thorough phylogenetic analysis of the ACBD family and discuss their structure and evolution. We summarize recent findings on the various functions of animal and fungal ACBDs with particular focus on peroxisomes, the role of ACBD proteins at organelle membranes, and their increasing recognition as targets for pathogens.
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Affiliation(s)
- Markus Islinger
- Institute of Neuroanatomy, Medical Faculty Manheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Joseph L Costello
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK
| | - Suzan Kors
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK
| | - Eric Soupene
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | | | - Frans A Kuypers
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK.
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21
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Samudrala SSK, North LM, Stamm KD, Earing MG, Frommelt MA, Willes R, Tripathi S, Dsouza NR, Zimmermann MT, Mahnke DK, Liang HL, Lund M, Lin C, Geddes GC, Mitchell ME, Tomita‐Mitchell A. Novel KLHL26 variant associated with a familial case of Ebstein's anomaly and left ventricular noncompaction. Mol Genet Genomic Med 2020; 8:e1152. [PMID: 31985165 PMCID: PMC7196453 DOI: 10.1002/mgg3.1152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/11/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Ebstein's anomaly (EA) is a rare congenital heart disease of the tricuspid valve and right ventricle. Patients with EA often manifest with left ventricular noncompaction (LVNC), a cardiomyopathy. Despite implication of cardiac sarcomere genes in some cases, very little is understood regarding the genetic etiology of EA/LVNC. Our study describes a multigenerational family with at least 10 of 17 members affected by EA/LVNC. METHODS We performed echocardiography on all family members and conducted exome sequencing of six individuals. After identifying candidate variants using two different bioinformatic strategies, we confirmed segregation with phenotype using Sanger sequencing. We investigated structural implications of candidate variants using protein prediction models. RESULTS Exome sequencing analysis of four affected and two unaffected members identified a novel, rare, and damaging coding variant in the Kelch-like family member 26 (KLHL26) gene located on chromosome 19 at position 237 of the protein (GRCh37). This variant region was confirmed by Sanger sequencing in the remaining family members. KLHL26 (c.709C > T p.R237C) segregates only with EA/LVNC-affected individuals (FBAT p < .05). Investigating structural implications of the candidate variant using protein prediction models suggested that the KLHL26 variant disrupts electrostatic interactions when binding to part of the ubiquitin proteasome, specifically Cullin3 (CUL3), a component of E3 ubiquitin ligase. CONCLUSION In this familial case of EA/LVNC, we have identified a candidate gene variant, KLHL26 (p.R237C), which may have an important role in ubiquitin-mediated protein degradation during cardiac development.
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Affiliation(s)
- Sai Suma K. Samudrala
- Department of Cell Biology, Neurobiology and AnatomyMedical College of WisconsinMilwaukeeWIUSA
| | - Lauren M. North
- Department of Otolaryngology and Communication SciencesMedical College of WisconsinMilwaukeeWIUSA
| | - Karl D. Stamm
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
| | - Michael G. Earing
- Department of PediatricsChildren’s Hospital of WisconsinMilwaukeeWIUSA
- Herma Heart InstituteChildren’s Hospital of WisconsinMilwaukeeWIUSA
| | - Michele A. Frommelt
- Department of PediatricsChildren’s Hospital of WisconsinMilwaukeeWIUSA
- Herma Heart InstituteChildren’s Hospital of WisconsinMilwaukeeWIUSA
| | - Richard Willes
- Department of PediatricsChildren’s Hospital of WisconsinMilwaukeeWIUSA
| | - Swarnendu Tripathi
- Bioinformatics Research and Developmental LabGenomic Sciences and Precision Medicine CenterMedical College of WisconsinMilwaukeeWIUSA
| | - Nikita R. Dsouza
- Bioinformatics Research and Developmental LabGenomic Sciences and Precision Medicine CenterMedical College of WisconsinMilwaukeeWIUSA
| | - Michael T. Zimmermann
- Bioinformatics Research and Developmental LabGenomic Sciences and Precision Medicine CenterMedical College of WisconsinMilwaukeeWIUSA
- Clinical and Translational Science InstituteMedical College of WisconsinMilwaukeeWIUSA
| | - Donna K. Mahnke
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
| | - Huan Ling Liang
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
| | - Michael Lund
- Department of Obstetrics and GynecologyMedical College of WisconsinMilwaukeeWIUSA
| | - Chien‐Wei Lin
- Division of BiostatisticsMedical College of WisconsinMilwaukeeWIUSA
| | | | - Michael E. Mitchell
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
- Herma Heart InstituteChildren’s Hospital of WisconsinMilwaukeeWIUSA
| | - Aoy Tomita‐Mitchell
- Department of SurgeryDivision of Cardiothoracic SurgeryMedical College of WisconsinMilwaukeeWIUSA
- Herma Heart InstituteChildren’s Hospital of WisconsinMilwaukeeWIUSA
- Department of Biomedical EngineeringMedical College of WisconsinMilwaukeeWIUSA
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22
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Abd-Hamid NA, Ahmad-Fauzi MI, Zainal Z, Ismail I. Diverse and dynamic roles of F-box proteins in plant biology. PLANTA 2020; 251:68. [PMID: 32072251 DOI: 10.1007/s00425-020-03356-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/05/2020] [Indexed: 05/23/2023]
Abstract
The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein degradation by the ubiquitin 26S-proteasome system (UPS). The UPS is an important system that generally keeps cellular events tightly regulated by purging misfolded or damaged proteins and selectively degrading important regulatory proteins. The specificity of this post-translational regulation is controlled by F-box proteins (FBPs) via selective recognition of a protein-protein interaction motif at the C-terminal domain. Hence, FBPs are pivotal proteins in determining the plant response in multiple scenarios. It is not surprising that the FBP family is one of the largest protein families in the plant kingdom. In this review, the roles of FBPs, specifically in plants, are compiled to provide insights into their involvement in secondary metabolites, plant stresses, phytohormone signalling, plant developmental processes and miRNA biogenesis.
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Affiliation(s)
- Nur-Athirah Abd-Hamid
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Muhammad-Izzat Ahmad-Fauzi
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Zamri Zainal
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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23
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Doonan LB, Hartigan A, Okamura B, Long PF. Stress-Free Evolution: The Nrf-Coordinated Oxidative Stress Response in Early Diverging Metazoans. Integr Comp Biol 2020; 59:799-810. [PMID: 31120488 DOI: 10.1093/icb/icz055] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Environmental stress from ultraviolet radiation, elevated temperatures or metal toxicity can lead to reactive oxygen species in cells, leading to oxidative DNA damage, premature aging, neurodegenerative diseases, and cancer. The transcription factor nuclear factor (erythroid-derived 2)-like 2 (Nrf2) activates many cytoprotective proteins within the nucleus to maintain homeostasis during oxidative stress. In vertebrates, Nrf2 levels are regulated by the Kelch-family protein Keap1 (Kelch-like ECH-associated protein 1) in the absence of stress according to a canonical redox control pathway. Little, however, is known about the redox control pathway used in early diverging metazoans. Our study examines the presence of known oxidative stress regulatory elements within non-bilaterian metazoans including free living and parasitic cnidarians, ctenophores, placozoans, and sponges. Cnidarians, with their pivotal position as the sister phylum to bilaterians, play an important role in understanding the evolutionary history of response to oxidative stress. Through comparative genomic and transcriptomic analysis our results show that Nrf homologs evolved early in metazoans, whereas Keap1 appeared later in the last common ancestor of cnidarians and bilaterians. However, key Nrf-Keap1 interacting domains are not conserved within the cnidarian lineage, suggesting this important pathway evolved with the radiation of bilaterians. Several known downstream Nrf targets are present in cnidarians suggesting that cnidarian Nrf plays an important role in oxidative stress response even in the absence of Keap1. Comparative analyses of key oxidative stress sensing and response proteins in early diverging metazoans thus provide important insights into the molecular basis of how these lineages interact with their environment and suggest a shared evolutionary history of regulatory pathways. Exploration of these pathways may prove important for the study of cancer therapeutics and broader research in oxidative stress, senescence, and the functional responses of early diverging metazoans to environmental change.
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Affiliation(s)
- Liam B Doonan
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - Ashlie Hartigan
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK.,Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Beth Okamura
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Paul F Long
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
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24
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Hedberg-Oldfors C, Abramsson A, Osborn DPS, Danielsson O, Fazlinezhad A, Nilipour Y, Hübbert L, Nennesmo I, Visuttijai K, Bharj J, Petropoulou E, Shoreim A, Vona B, Ahangari N, López MD, Doosti M, Banote RK, Maroofian R, Edling M, Taherpour M, Zetterberg H, Karimiani EG, Oldfors A, Jamshidi Y. Cardiomyopathy with lethal arrhythmias associated with inactivation of KLHL24. Hum Mol Genet 2020; 28:1919-1929. [PMID: 30715372 PMCID: PMC6812045 DOI: 10.1093/hmg/ddz032] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/26/2019] [Accepted: 01/28/2019] [Indexed: 12/18/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiovascular disorder, yet the genetic cause of up to 50% of cases remains unknown. Here, we show that mutations in KLHL24 cause HCM in humans. Using genome-wide linkage analysis and exome sequencing, we identified homozygous mutations in KLHL24 in two consanguineous families with HCM. Of the 11 young affected adults identified, 3 died suddenly and 1 had a cardiac transplant due to heart failure. KLHL24 is a member of the Kelch-like protein family, which acts as substrate-specific adaptors to Cullin E3 ubiquitin ligases. Endomyocardial and skeletal muscle biopsies from affected individuals of both families demonstrated characteristic alterations, including accumulation of desmin intermediate filaments. Knock-down of the zebrafish homologue klhl24a results in heart defects similar to that described for other HCM-linked genes providing additional support for KLHL24 as a HCM-associated gene. Our findings reveal a crucial role for KLHL24 in cardiac development and function.
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Affiliation(s)
- Carola Hedberg-Oldfors
- Department of Pathology and Genetics, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Alexandra Abramsson
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Daniel P S Osborn
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's University of London, Cranmer Terrace, London, UK
| | - Olof Danielsson
- Department of Neurology, and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Afsoon Fazlinezhad
- Razavi Cancer Research Center, Razavi Hospital, Imam Reza International University, Mashhad, Iran
| | - Yalda Nilipour
- Pediatric Pathology Research Center, Research Institute for Children Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Laila Hübbert
- Department of Medical and Health Sciences, Linköping University, Linköping, Sweden
| | - Inger Nennesmo
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - Kittichate Visuttijai
- Department of Pathology and Genetics, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Jaipreet Bharj
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's University of London, Cranmer Terrace, London, UK
| | - Evmorfia Petropoulou
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's University of London, Cranmer Terrace, London, UK
| | - Azza Shoreim
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's University of London, Cranmer Terrace, London, UK
| | - Barbara Vona
- Institute of Human Genetics, Julius Maximilians University of Würzburg, Würzburg, Germany
| | - Najmeh Ahangari
- Department of Modern Sciences and Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Marcela Dávila López
- Bioinformatics Core Facilities, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Rakesh Kumar Banote
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Reza Maroofian
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's University of London, Cranmer Terrace, London, UK
| | - Malin Edling
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Mehdi Taherpour
- Razavi Cancer Research Center, Razavi Hospital, Imam Reza International University, Mashhad, Iran
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 1PJ, UK
| | - Ehsan Ghayoor Karimiani
- Razavi Cancer Research Center, Razavi Hospital, Imam Reza International University, Mashhad, Iran.,Innovative Medical Research Center, Faculty of Medicine, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Anders Oldfors
- Department of Pathology and Genetics, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Yalda Jamshidi
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's University of London, Cranmer Terrace, London, UK
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25
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Lu L, Liu H, Wu Y, Yan G. Development and Characterization of Near-Isogenic Lines Revealing Candidate Genes for a Major 7AL QTL Responsible for Heat Tolerance in Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:1316. [PMID: 32983205 PMCID: PMC7485290 DOI: 10.3389/fpls.2020.01316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/11/2020] [Indexed: 05/22/2023]
Abstract
Wheat is one of the most important food crops in the world, but as a cool-season crop, it is more prone to heat stress, which severely affects crop production and grain quality. Heat tolerance in wheat is a quantitative trait, and the genes underlying reported quantitative trait loci (QTL) have rarely been identified. Near-isogenic lines (NILs) with a common genetic background but differing at a particular locus could turn quantitative traits into a Mendelian factor; therefore, they are suitable material for identifying candidate genes for targeted locus/loci. In this study, we developed and characterized NILs from two populations Cascades × Tevere and Cascades × W156 targeting a major 7AL QTL responsible for heat tolerance. Molecular marker screening and phenotyping for SPAD chlorophyll content and grain-yield-related traits confirmed four pairs of wheat NILs that contrasted for heat-stress responses. Genotyping the NILs using a 90K Infinium iSelect SNP array revealed five single nucleotide polymorphism (SNP) markers within the QTL interval that were distinguishable between the isolines. Seven candidate genes linked to the SNPs were identified as related to heat tolerance, and involved in important processes and pathways in response to heat stress. The confirmed multiple pairs of NILs and identified candidate genes in this study are valuable resources and information for further fine-mapping to clone major genes for heat tolerance.
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Affiliation(s)
- Lu Lu
- Faculty of Science, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hui Liu
- Faculty of Science, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Hui Liu, ; Guijun Yan,
| | - Yu Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guijun Yan
- Faculty of Science, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Hui Liu, ; Guijun Yan,
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26
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Kang ZX, Wei XJ, Miao J, Gao YL, Wang ZY, Yu XF. A family with nemaline myopathy type 6 caused by hseterozygous mutation (c.1222C>T) in the KBTBD13 gene in China: A case report. Neuropathology 2019; 40:104-108. [PMID: 31828823 DOI: 10.1111/neup.12610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 12/01/2022]
Abstract
Nemaline myopathy (NEM) is a congenital myopathy that typically presents with proximal muscle weakness and hypotonia. To date, 13 genes have been associated with NEM. The Kelch repeat and BTB domain-containing protein 13 (KBTBD13) gene (KBTBD13)-related NEM is a rarely reported condition, and not a single case has been reported in Asia. Here, we report the case of a mother and daughter in China with NEM caused by a mutation (c.1222C>T) in KBTBD13. Their shared clinical phenotype is symmetrical muscle weakness in the arms and legs with childhood onset. Muscle magnetic resonance imaging showed the unique replacement mode of muscle with fibro-fatty tissue. Histopathological examination revealed the presence of fibers containing rod-shaped structures in the cytoplasm or under the sarcolemma. DNA sequencing analysis detected a heterozygous mutation (c.1222C>T) in KBTBD13 in this family. A founder effect for the variant may exist in the Low Countries of Belgium and the Netherlands, and the mutation may be a hotspot mutation in Europe, as it has not been reported in Asia. Our case study expands the spectrum of KBTBD13-related NEM.
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Affiliation(s)
- Zhi-Xia Kang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Xiao-Jing Wei
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Jing Miao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Yan-Lu Gao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Zi-Yi Wang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Xue-Fan Yu
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
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27
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Kim H, Yu SI, Jung SH, Lee BH, Suh MC. The F-Box Protein SAGL1 and ECERIFERUM3 Regulate Cuticular Wax Biosynthesis in Response to Changes in Humidity in Arabidopsis. THE PLANT CELL 2019; 31:2223-2240. [PMID: 31320482 PMCID: PMC6751119 DOI: 10.1105/tpc.19.00152] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/04/2019] [Accepted: 07/12/2019] [Indexed: 05/21/2023]
Abstract
Cuticular waxes, which cover the aboveground parts of land plants, are essential for plant survival in terrestrial environments. However, little is known about the regulatory mechanisms underlying cuticular wax biosynthesis in response to changes in ambient humidity. Here, we report that the Arabidopsis (Arabidopsis thaliana) Kelch repeat F-box protein SMALL AND GLOSSY LEAVES1 (SAGL1) mediates proteasome-dependent degradation of ECERIFERUM3 (CER3), a biosynthetic enzyme involved in the production of very long chain alkanes (the major components of wax), thereby negatively regulating cuticular wax biosynthesis. Disruption of SAGL1 led to severe growth retardation, enhanced drought tolerance, and increased wax accumulation in stems, leaves, and roots. Cytoplasmic SAGL1 physically interacts with CER3 and targets it for degradation. β‑glucuronidase (GUS) expression was observed in the roots of pSAGL1:GUS plants but was barely detected in aerial organs. High humidity-induced GUS activity and SAGL1 transcript levels were reduced in response to abscisic acid treatment and water deficit. SAGL1 levels increase under high humidity, and the stability of this protein is regulated by the 26S proteasome. These findings indicate that the SAGL1-CER3 module negatively regulates cuticular wax biosynthesis in Arabidopsis in response to changes to humidity, and they highlight the importance of permeable cuticle formation in terrestrial plants under high humidity conditions.
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Affiliation(s)
- Hyojin Kim
- Department of Life Science, Sogang University, Seoul 04107, Republic of Korea
| | - Si-In Yu
- Department of Life Science, Sogang University, Seoul 04107, Republic of Korea
| | - Seh Hui Jung
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Byeong-Ha Lee
- Department of Life Science, Sogang University, Seoul 04107, Republic of Korea
| | - Mi Chung Suh
- Department of Life Science, Sogang University, Seoul 04107, Republic of Korea
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28
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Coppée R, Jeffares DC, Miteva MA, Sabbagh A, Clain J. Comparative structural and evolutionary analyses predict functional sites in the artemisinin resistance malaria protein K13. Sci Rep 2019; 9:10675. [PMID: 31337835 PMCID: PMC6650413 DOI: 10.1038/s41598-019-47034-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/03/2019] [Indexed: 01/31/2023] Open
Abstract
Numerous mutations in the Plasmodium falciparum Kelch13 (K13) protein confer resistance to artemisinin derivatives, the current front-line antimalarial drugs. K13 is an essential protein that contains BTB and Kelch-repeat propeller (KREP) domains usually found in E3 ubiquitin ligase complexes that target substrate protein(s) for ubiquitin-dependent degradation. K13 is thought to bind substrate proteins, but its functional/interaction sites and the structural alterations associated with artemisinin resistance mutations remain unknown. Here, we screened for the most evolutionarily conserved sites in the protein structure of K13 as indicators of structural and/or functional constraints. We inferred structure-dependent substitution rates at each amino acid site of the highly conserved K13 protein during the evolution of Apicomplexa parasites. We found two solvent-exposed patches of extraordinarily conserved sites likely involved in protein-protein interactions, one in BTB and the other one in KREP. The conserved patch in K13 KREP overlaps with a shallow pocket that displays a differential electrostatic surface potential, relative to neighboring sites, and that is rich in serine and arginine residues. Comparative structural and evolutionary analyses revealed that these properties were also found in the functionally-validated shallow pocket of other KREPs including that of the cancer-related KEAP1 protein. Finally, molecular dynamics simulations carried out on PfK13 R539T and C580Y artemisinin resistance mutant structures revealed some local structural destabilization of KREP but not in its shallow pocket. These findings open new avenues of research on one of the most enigmatic malaria proteins with the utmost clinical importance.
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Affiliation(s)
- Romain Coppée
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France
| | - Daniel C Jeffares
- Department of Biology and York Biomedical Research Institute, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Maria A Miteva
- Université de Paris, Inserm U1268 MCTR, CiTCom UMR 8038 CNRS, Paris, France
| | - Audrey Sabbagh
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France.
| | - Jérôme Clain
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France. .,Centre National de Référence du Paludisme, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, F-75018 Paris, France.
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29
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Li J, Hu J, Xiang D, Ji B, Xu S, Shi L, Zhao S. KLHL3 single-nucleotide polymorphism is associated with essential hypertension in Chinese Han population. Medicine (Baltimore) 2019; 98:e15766. [PMID: 31096542 PMCID: PMC6531237 DOI: 10.1097/md.0000000000015766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Hypertension, including secondary and essential hypertension (EH) variants, is a multifactorial disease, affecting more than one billion people worldwide. Secondary hypertension results from mutations in the putative gene KLHL3 (Kelch-like protein 3); however, it has not been reported whether the KLHL3 gene polymorphisms are associated with EH. Here, we investigated the association between KLHL3 (rs2301708 and rs7444370) polymorphisms and EH in the Chinese Han population.This case-control study included 522 subjects-260 patients with EH and 262 normotensive controls matched for age, gender, body mass index (BMI), hemoglobin A1c (HbA1c), total cholesterol (TC), triglyceride (TG), and levels of Na, K, and Cl. The distribution of functional rs2301708 and rs7444370 polymorphisms within the KLHL3 gene was assessed through polymerase chain reaction (PCR) and restriction-fragment length polymorphism (RFLP).There was no significant difference in allelic and genotypic frequencies of KLHL3 rs2301708 between the EH and normotensive groups; however, the rs7444370 T allele and CT genotype in females was significantly associated with a protective effect against EH (P = .001, P = .002; P = .019, P = .052), and the haplotype CT of rs2301708 and rs7444370 among females in the EH group was less than in the normotensive group (P = .000; P = .007).The KLHL3 rs7444370 variant could be a protective factor in the pathogenesis of females' EH.
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Affiliation(s)
- Jin Li
- School of Bioscience and Bioengineering, South China University of Technology
- Department of Pharmacy, Guangzhou United Family Hospital
| | | | | | - Bo Ji
- Department of Pharmacy, Guangzhou General Hospital of Guangzhou Military Command, Guangzhou, China
| | - Suowen Xu
- Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester, Rochester, NY, USA
| | - Lei Shi
- Department of Pharmacy, Guangzhou General Hospital of Guangzhou Military Command, Guangzhou, China
| | - Shujin Zhao
- School of Bioscience and Bioengineering, South China University of Technology
- Department of Pharmacy, Guangzhou General Hospital of Guangzhou Military Command, Guangzhou, China
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30
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Gao C, Pallett MA, Croll TI, Smith GL, Graham SC. Molecular basis of cullin-3 (Cul3) ubiquitin ligase subversion by vaccinia virus protein A55. J Biol Chem 2019; 294:6416-6429. [PMID: 30819806 PMCID: PMC6484134 DOI: 10.1074/jbc.ra118.006561] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 02/26/2019] [Indexed: 12/22/2022] Open
Abstract
BTB-Kelch proteins are substrate-specific adaptors for cullin-3 (Cul3) RING-box-based E3 ubiquitin ligases, mediating protein ubiquitylation for subsequent proteasomal degradation. Vaccinia virus encodes three BTB-Kelch proteins: A55, C2, and F3. Viruses lacking A55 or C2 have altered cytopathic effects in cultured cells and altered pathology in vivo Previous studies have shown that the ectromelia virus orthologue of A55 interacts with Cul3 in cells. We report that the N-terminal BTB-BACK (BB) domain of A55 binds directly to the Cul3 N-terminal domain (Cul3-NTD), forming a 2:2 complex in solution. We solved the structure of an A55BB/Cul3-NTD complex from anisotropic crystals diffracting to 2.3/3.7 Å resolution in the best/worst direction, revealing that the overall interaction and binding interface closely resemble the structures of cellular BTB/Cul3-NTD complexes, despite low sequence identity between A55 and cellular BTB domains. Surprisingly, despite this structural similarity, the affinity of Cul3-NTD for A55BB was stronger than for cellular BTB proteins. Glutamate substitution of the A55 residue Ile-48, adjacent to the canonical φX(D/E) Cul3-binding motif, reduced affinity of A55BB for Cul3-NTD by at least 2 orders of magnitude. Moreover, Ile-48 and the φX(D/E) motif are conserved in A55 orthologues from other poxviruses, but not in the vaccinia virus proteins C2 or F3. The high-affinity interaction between A55BB and Cul3-NTD suggests that, in addition to directing the Cul3-RING E3 ligase complex to degrade cellular/viral target proteins that are normally unaffected, A55 may also sequester Cul3 from cellular adaptor proteins, thereby protecting substrates of these cellular adaptors from ubiquitylation and degradation.
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Affiliation(s)
- Chen Gao
- From the Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP and
| | - Mitchell A Pallett
- From the Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP and
| | - Tristan I Croll
- the Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge CB2 0XY, United Kingdom
| | - Geoffrey L Smith
- From the Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP and
| | - Stephen C Graham
- From the Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP and
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31
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Hudson AM, Mannix KM, Gerdes JA, Kottemann MC, Cooley L. Targeted substrate degradation by Kelch controls the actin cytoskeleton during ring canal expansion. Development 2019; 146:dev.169219. [PMID: 30559276 DOI: 10.1242/dev.169219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/27/2018] [Indexed: 11/20/2022]
Abstract
During Drosophila oogenesis, specialized actin-based structures called ring canals form and expand to accommodate growth of the oocyte. Previous work demonstrated that Kelch and Cullin 3 function together in a Cullin 3-RING ubiquitin ligase complex (CRL3Kelch) to organize the ring canal cytoskeleton, presumably by targeting a substrate for proteolysis. Here, we use tandem affinity purification followed by mass spectrometry to identify HtsRC as the CRL3Kelch ring canal substrate. CRISPR-mediated mutagenesis of HtsRC revealed its requirement in the recruitment of the ring canal F-actin cytoskeleton. We present genetic evidence consistent with HtsRC being the CRL3Kelch substrate, as well as biochemical evidence indicating that HtsRC is ubiquitylated and degraded by the proteasome. Finally, we identify a short sequence motif in HtsRC that is necessary for Kelch binding. These findings uncover an unusual mechanism during development wherein a specialized cytoskeletal structure is regulated and remodeled by the ubiquitin-proteasome system.
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Affiliation(s)
- Andrew M Hudson
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Katelynn M Mannix
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Julianne A Gerdes
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Molly C Kottemann
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lynn Cooley
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA .,Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA
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32
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Yu SI, Kim H, Yun DJ, Suh MC, Lee BH. Post-translational and transcriptional regulation of phenylpropanoid biosynthesis pathway by Kelch repeat F-box protein SAGL1. PLANT MOLECULAR BIOLOGY 2019; 99:135-148. [PMID: 30542810 DOI: 10.1007/s11103-018-0808-8] [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: 11/05/2018] [Accepted: 12/05/2018] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE A Kelch repeat F-box containing protein, SMALL AND GLOSSY LEAVES1 (SAGL1) regulates phenylpropanoid biosynthesis as a post-translational regulator for PAL1 (phenylalanine ammonia-lyase) and an indirect transcriptional regulator for ANTHOCYANIDIN SYNTHASE. Phenylpropanoid biosynthesis in plants produces diverse aromatic metabolites with important biological functions. Phenylalanine ammonia-lyase (PAL) catalyzes the first step in phenylpropanoid biosynthesis by converting L-phenylalanine to trans-cinnamic acid. Here, we report that SMALL AND GLOSSY LEAVES1 (SAGL1), a Kelch repeat F-box protein, interacts with PAL1 protein for proteasome-mediated degradation to regulate phenylpropanoid biosynthesis in Arabidopsis. Mutations in SAGL1 caused high accumulation of anthocyanins and lignin derived from the phenylpropanoid biosynthesis pathway. We found that PAL enzyme activity increased in SAGL1-defective mutants, sagl1, but decreased in SAGL1-overexpressing Arabidopsis (SAGL1OE) without changes in the transcript levels of PAL genes, suggesting protein-level regulation by SAGL1. Indeed, the levels of PAL1-GFP fusion protein were reduced when both SAGL1 and PAL1-GFP were transiently co-expressed in leaves of Nicotiana benthamiana. In addition, bimolecular fluorescence complementation analysis suggested an interaction between SAGL1 and PAL1. We also found that the transcript levels of ANTHOCYANIDIN SYNTHASE (ANS) increased in the sagl1 mutants but decreased in SAGL1OE. Our results suggest that SAGL1 regulates phenylpropanoid biosynthesis post-translationally at PAL1 and transcriptionally at ANS.
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Affiliation(s)
- Si-In Yu
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Hyojin Kim
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Mi Chung Suh
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Byeong-Ha Lee
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea.
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Woraratanadharm T, Kmosek S, Banuett F. UmTea1, a Kelch and BAR domain-containing protein, acts at the cell cortex to regulate cell morphogenesis in the dimorphic fungus Ustilago maydis. Fungal Genet Biol 2018; 121:10-28. [PMID: 30205200 DOI: 10.1016/j.fgb.2018.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/10/2018] [Accepted: 09/07/2018] [Indexed: 10/28/2022]
Abstract
The spatial organization of a cell is crucial for distribution of cell components and for cell morphogenesis in all organisms. Ustilago maydis, a basidiomycete fungus, has a yeast-like and a filamentous form. The former buds once per cell cycle at one of the cell poles, and can use the same site repeatedly or choose a new site at the same pole or opposite pole. The filamentous form consists of a long apical cell with short septate basal compartments lacking cytoplasm. It grows at the apex and can reverse growth forming a new growth zone at the basal end. We are interested in understanding how these different morphologies are generated. Here we present identification and characterization of U. maydis Tea1, a homologue of the fission yeast cell end marker Tea1. We demonstrate that UmTea1, a Kelch domain protein, interacts with itself and is an important determinant of the site of polarized growth: tea1 mutants bud simultaneously from both cell poles and form bifurcate buds. UmTea1 also regulates septum positioning, cell wall deposition, cell and neck width, coordination of nuclear division and cell separation, and localization of sterol-rich membrane domains. Some of these functions are shared with UmTea4, another cell end marker. We show that Tea1::GFP localizes to sites of polarized or potential polarized growth and to the septation site in the yeast-like form. Additionally, localization of Tea1::GFP as rings along the filament suggests that the filament undergoes septation. We hypothesize that Tea1 may act as a scaffold for the assembly of proteins that determine the site of polarized growth.
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Affiliation(s)
- Tad Woraratanadharm
- Department of Biological Sciences, California State University, 1250 Bellflower Boulevard, Long Beach, CA 90840, United States
| | - Stephanie Kmosek
- Department of Biological Sciences, California State University, 1250 Bellflower Boulevard, Long Beach, CA 90840, United States
| | - Flora Banuett
- Department of Biological Sciences, California State University, 1250 Bellflower Boulevard, Long Beach, CA 90840, United States.
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Shukla A, Chatterjee A, Kondabagil K. The number of genes encoding repeat domain-containing proteins positively correlates with genome size in amoebal giant viruses. Virus Evol 2018; 4:vex039. [PMID: 29308275 PMCID: PMC5753266 DOI: 10.1093/ve/vex039] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Curiously, in viruses, the virion volume appears to be predominantly driven by genome length rather than the number of proteins it encodes or geometric constraints. With their large genome and giant particle size, amoebal viruses (AVs) are ideally suited to study the relationship between genome and virion size and explore the role of genome plasticity in their evolutionary success. Different genomic regions of AVs exhibit distinct genealogies. Although the vertically transferred core genes and their functions are universally conserved across the nucleocytoplasmic large DNA virus (NCLDV) families and are essential for their replication, the horizontally acquired genes are variable across families and are lineage-specific. When compared with other giant virus families, we observed a near–linear increase in the number of genes encoding repeat domain-containing proteins (RDCPs) with the increase in the genome size of AVs. From what is known about the functions of RDCPs in bacteria and eukaryotes and their prevalence in the AV genomes, we envisage important roles for RDCPs in the life cycle of AVs, their genome expansion, and plasticity. This observation also supports the evolution of AVs from a smaller viral ancestor by the acquisition of diverse gene families from the environment including RDCPs that might have helped in host adaption.
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Affiliation(s)
- Avi Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Anirvan Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
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Worton LE, Shi YC, Smith EJ, Barry SC, Gonda TJ, Whitehead JP, Gardiner EM. Ectodermal-Neural Cortex 1 Isoforms Have Contrasting Effects on MC3T3-E1 Osteoblast Mineralization and Gene Expression. J Cell Biochem 2017; 118:2141-2150. [PMID: 27996212 DOI: 10.1002/jcb.25851] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/19/2016] [Indexed: 01/01/2023]
Abstract
The importance of Wnt pathway signaling in development of bone has been well established. Here we investigated the role of a known Wnt target, ENC1 (ectodermal-neural cortex 1; NRP/B), in osteoblast differentiation. Enc1 expression was detected in mouse osteoblasts, chondrocytes, and osteocytes by in situ hybridization, and osteoblastic expression was verified in differentiating primary cultures and MC3T3-E1 pre-osteoblast cells, with 57 kDa and 67 kDa ENC1 protein isoforms detected throughout differentiation. Induced knockdown of both ENC1 isoforms reduced alkaline phosphatase staining and virtually abolished MC3T3-E1 mineralization. At culture confluence, Alpl (alkaline phosphatase liver/bone/kidney) expression was markedly reduced compared with control cells, and there was significant and coordinated alteration of other genes involved in cellular phosphate biochemistry. In contrast, with 67 kDa-selective knockdown mineralized nodule formation was enhanced and there was a two-fold increase in Alpl expression at confluence. There was enhanced expression of Wnt/β-catenin target genes with knockdown of both isoforms at this time-point and a five-fold increase in Frzb (Frizzled related protein) with 67 kDa-selective knockdown at mineralization, indicating possible ENC1 interactions with Wnt signaling in osteoblasts. These results are the first to demonstrate a role for ENC1 in the control of osteoblast differentiation. Additionally, the contrasting mineralization phenotypes and transcriptional patterns seen with coordinate knockdown of both ENC1 isoforms vs selective knockdown of 67 kDa ENC1 suggest opposing roles for the isoforms in regulation of osteoblastic differentiation, through effects on Alpl expression and phosphate cellular biochemistry. This study is the first to report differential roles for the ENC1 isoforms in any cell lineage. J. Cell. Biochem. 118: 2141-2150, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Leah E Worton
- The University of Queensland, Brisbane, Queensland, Australia.,Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington
| | - Yan-Chuan Shi
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,Faculty of Medicine, University of New South Wales, New South Wales, Australia
| | - Elisabeth J Smith
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Simon C Barry
- The University of Adelaide, Adelaide, South Australia, Australia
| | - Thomas J Gonda
- The University of Queensland, Brisbane, Queensland, Australia
| | | | - Edith M Gardiner
- The University of Queensland, Brisbane, Queensland, Australia.,Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington
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He Y, Maier K, Leppert J, Hausser I, Schwieger-Briel A, Weibel L, Theiler M, Kiritsi D, Busch H, Boerries M, Hannula-Jouppi K, Heikkilä H, Tasanen K, Castiglia D, Zambruno G, Has C. Monoallelic Mutations in the Translation Initiation Codon of KLHL24 Cause Skin Fragility. Am J Hum Genet 2016; 99:1395-1404. [PMID: 27889062 DOI: 10.1016/j.ajhg.2016.11.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/07/2016] [Indexed: 11/28/2022] Open
Abstract
The genetic basis of epidermolysis bullosa, a group of genetic disorders characterized by the mechanically induced formation of skin blisters, is largely known, but a number of cases still remain genetically unsolved. Here, we used whole-exome and targeted sequencing to identify monoallelic mutations, c.1A>G and c.2T>C, in the translation initiation codon of the gene encoding kelch-like protein 24 (KLHL24) in 14 individuals with a distinct skin-fragility phenotype and skin cleavage within basal keratinocytes. Remarkably, mutation c.1A>G occurred de novo and was recurrent in families originating from different countries. The striking similarities of the clinical features of the affected individuals point to a unique and very specific pathomechanism. We showed that mutations in the translation initiation codon of KLHL24 lead to the usage of a downstream translation initiation site with the same reading frame and formation of a truncated polypeptide. The pathobiology was examined in keratinocytes and fibroblasts of the affected individuals and via expression of mutant KLHL24, and we found mutant KLHL24 to be associated with abnormalities of intermediate filaments in keratinocytes and fibroblasts. In particular, KLHL24 mutations were associated with irregular and fragmented keratin 14. Recombinant overexpression of normal KLHL24 promoted keratin 14 degradation, whereas mutant KLHL24 showed less activity than the normal molecule. These findings identify KLHL24 mutations as a cause of skin fragility and identify a role for KLHL24 in maintaining the balance between intermediate filament stability and degradation required for skin integrity.
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Affiliation(s)
- Yinghong He
- Department of Dermatology, University Medical Center Freiburg, Freiburg 79104, Germany
| | - Kristin Maier
- Department of Dermatology, University Medical Center Freiburg, Freiburg 79104, Germany
| | - Juna Leppert
- Department of Dermatology, University Medical Center Freiburg, Freiburg 79104, Germany
| | - Ingrid Hausser
- Department of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Agnes Schwieger-Briel
- Department of Paediatric Dermatology, University Children's Hospital Zurich, Zurich 8091, Switzerland; Department of Dermatology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Lisa Weibel
- Department of Paediatric Dermatology, University Children's Hospital Zurich, Zurich 8091, Switzerland; Department of Dermatology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Martin Theiler
- Department of Paediatric Dermatology, University Children's Hospital Zurich, Zurich 8091, Switzerland; Department of Dermatology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Dimitra Kiritsi
- Department of Dermatology, University Medical Center Freiburg, Freiburg 79104, Germany
| | - Hauke Busch
- Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg 79104, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Comprehensive Cancer Center Freiburg, Freiburg 79106, Germany
| | - Melanie Boerries
- Systems Biology of the Cellular Microenvironment Group, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg 79104, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Comprehensive Cancer Center Freiburg, Freiburg 79106, Germany
| | - Katariina Hannula-Jouppi
- Department of Dermatology and Allergology, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland; Folkhälsan Institute of Genetics, University of Helsinki, Helsinki 00014, Finland
| | - Hannele Heikkilä
- Department of Dermatology and Allergology, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland
| | - Kaisa Tasanen
- Department of Dermatology, PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu 90014, Finland
| | - Daniele Castiglia
- Laboratory of Molecular and Cell Biology, Istituto Dermopatico dell'Immacolata, Istituto di Ricovero e Cura a Carattere Scientifico, Rome 00167, Italy
| | - Giovanna Zambruno
- Genetic and Rare Diseases Research Area, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome 00165, Italy
| | - Cristina Has
- Department of Dermatology, University Medical Center Freiburg, Freiburg 79104, Germany.
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Duru V, Witkowski B, Ménard D. Plasmodium falciparum Resistance to Artemisinin Derivatives and Piperaquine: A Major Challenge for Malaria Elimination in Cambodia. Am J Trop Med Hyg 2016; 95:1228-1238. [PMID: 27928074 DOI: 10.4269/ajtmh.16-0234] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 09/12/2016] [Indexed: 12/30/2022] Open
Abstract
Artemisinin-based combination therapies (ACTs) are the cornerstone of current strategies for fighting malaria. Over the last decade, ACTs have played a major role in decreasing malaria burden. However, this progress is being jeopardized by the emergence of artemisinin-resistant Plasmodium falciparum parasites. Artemisinin resistance was first detected in western Cambodia in 2008 and has since been observed in neighboring countries in southeast Asia. The problem of antimalarial drug resistance has recently worsened in Cambodia, with reports of parasites resistant to piperaquine, the latest generation of partner drug used in combination with dihydroartemisinin, leading to worrying rates of clinical treatment failure. The monitoring and the comprehension of both types of resistance are crucial to prevent the spread of multidrug-resistant parasites outside southeast Asia, and particularly to Africa, where the public health consequences would be catastrophic. To this end, new tools are required for studying the biological and molecular mechanisms underlying resistance to antimalarial drugs and for monitoring the geographic distribution of the resistant parasites. In this review, we detail the major advances in our understanding of resistance to artemisinin and piperaquine and define the challenges that the malaria community will have to face in the coming years.
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Affiliation(s)
- Valentine Duru
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Benoit Witkowski
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Didier Ménard
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia.
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38
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Mild clinical presentation in KLHL40-related nemaline myopathy (NEM 8). Neuromuscul Disord 2016; 26:712-716. [DOI: 10.1016/j.nmd.2016.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 07/01/2016] [Accepted: 07/25/2016] [Indexed: 11/22/2022]
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Structural mapping of Kelch13 mutations associated with artemisinin resistance in malaria. ACTA ACUST UNITED AC 2016; 17:51-6. [DOI: 10.1007/s10969-016-9205-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
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Chen HY, Liu CC, Chen RH. Cul3-KLHL20 ubiquitin ligase: physiological functions, stress responses, and disease implications. Cell Div 2016; 11:5. [PMID: 27042198 PMCID: PMC4818519 DOI: 10.1186/s13008-016-0017-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 03/16/2016] [Indexed: 01/01/2023] Open
Abstract
Cullin-RING ubiquitin ligases are the largest Ubiquitin ligase family in eukaryotes and are multi-protein complexes. In these complexes, the Cullin protein serves as a scaffold to connect two functional modules of the ligases, the catalytic subunit and substrate-binding subunit. KLHL20 is a substrate-binding subunit of Cullin3 (Cul3) ubiquitin ligase. Recent studies have identified a number of substrates of KLHL20-based ubiquitin ligase. Through ubiquitination of these substrates, KLHL20 elicits diverse cellular functions, some of which are associated with human diseases. Furthermore, the functions, subcellular localizations, and expression of KLHL20 are regulated by several physiological and stressed signals, which allow KLHL20 to preferentially act on certain substrates to response to these signals. Here, we provide a summary of the functions and regulations of KLHL20 in several physiological processes and stress responses and its disease implications.
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Affiliation(s)
- Hsin-Yi Chen
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Chin-Chih Liu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan ; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan ; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
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Lambrughi M, Lucchini M, Pignataro M, Sola M, Bortolotti CA. The dynamics of the β-propeller domain in Kelch protein KLHL40 changes upon nemaline myopathy-associated mutation. RSC Adv 2016. [DOI: 10.1039/c6ra06312h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The nemaline myopathy-associated E528K mutation in the KLHL40 alters the communication between the Kelch propeller blades.
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Affiliation(s)
- Matteo Lambrughi
- Department of Life Sciences
- University of Modena and Reggio Emilia
- Modena
- Italy
| | - Matteo Lucchini
- Department of Life Sciences
- University of Modena and Reggio Emilia
- Modena
- Italy
| | - Marcello Pignataro
- Department of Chemical and Geological Sciences
- University of Modena and Reggio Emilia
- Modena
- Italy
| | - Marco Sola
- Department of Life Sciences
- University of Modena and Reggio Emilia
- Modena
- Italy
| | - Carlo Augusto Bortolotti
- Department of Life Sciences
- University of Modena and Reggio Emilia
- Modena
- Italy
- CNR-Nano Institute of Nanoscience
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Johnson-Kerner BL, Garcia Diaz A, Ekins S, Wichterle H. Kelch Domain of Gigaxonin Interacts with Intermediate Filament Proteins Affected in Giant Axonal Neuropathy. PLoS One 2015; 10:e0140157. [PMID: 26460568 PMCID: PMC4604155 DOI: 10.1371/journal.pone.0140157] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/22/2015] [Indexed: 11/18/2022] Open
Abstract
Patients with giant axonal neuropathy (GAN) show progressive loss of motor and sensory function starting in childhood and typically live for less than 30 years. GAN is caused by autosomal recessive mutations leading to low levels of gigaxonin (GIG), a ubiquitously-expressed BTB/Kelch cytoplasmic protein believed to be an E3 ligase substrate adaptor. GAN pathology is characterized by aggregates of intermediate filaments (IFs) in multiple tissues. To delineate the molecular pathway between GIG deficiency and IF pathology, we undertook a proteomic screen to identify the normal binding partners of GIG. Prominent among them were several classes of IFs, including the neurofilament subunits whose accumulation leads to the axonal swellings for which GAN is named. We showed these interactions were dependent on the Kelch domain of GIG. Furthermore, we identified the E3 ligase MYCBP2 and the heat shock proteins HSP90AA1/AB1 as interactors with the BTB domain that may result in the ubiquitination and subsequent degradation of intermediate filaments. Our open-ended proteomic screen provides support to GIG’s role as an adaptor protein, linking IF proteins through its Kelch domain to the ubiquitin pathway proteins via its BTB domain, and points to future approaches for reversing the phenotype in human patients.
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Affiliation(s)
- Bethany L. Johnson-Kerner
- Project A.L.S./Jenifer Estess Laboratory for Stem Cell Research, New York, New York, United States of America
- Center for Motor Neuron Biology and Disease, Columbia University Medical Center, New York, New York, United States of America
- Departments of Pathology and Cell Biology, Neurology, and Neuroscience, Columbia University Medical Center, New York, New York, United States of America
- Columbia Stem Cell Initiative, Columbia University Medical Center, New York, New York, United States of America
| | - Alejandro Garcia Diaz
- Project A.L.S./Jenifer Estess Laboratory for Stem Cell Research, New York, New York, United States of America
- Center for Motor Neuron Biology and Disease, Columbia University Medical Center, New York, New York, United States of America
| | - Sean Ekins
- Collaborations in Chemistry, Fuquay-Varina, North Carolina, United States of America
| | - Hynek Wichterle
- Project A.L.S./Jenifer Estess Laboratory for Stem Cell Research, New York, New York, United States of America
- Center for Motor Neuron Biology and Disease, Columbia University Medical Center, New York, New York, United States of America
- Departments of Pathology and Cell Biology, Neurology, and Neuroscience, Columbia University Medical Center, New York, New York, United States of America
- Columbia Stem Cell Initiative, Columbia University Medical Center, New York, New York, United States of America
- * E-mail:
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Dorr C, Janik C, Weg M, Been RA, Bader J, Kang R, Ng B, Foran L, Landman SR, O'Sullivan MG, Steinbach M, Sarver AL, Silverstein KAT, Largaespada DA, Starr TK. Transposon Mutagenesis Screen Identifies Potential Lung Cancer Drivers and CUL3 as a Tumor Suppressor. Mol Cancer Res 2015; 13:1238-47. [PMID: 25995385 PMCID: PMC4543426 DOI: 10.1158/1541-7786.mcr-14-0674-t] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 04/30/2015] [Indexed: 02/06/2023]
Abstract
UNLABELLED Non-small cell lung cancers (NSCLC) harbor thousands of passenger events that hide genetic drivers. Even highly recurrent events in NSCLC, such as mutations in PTEN, EGFR, KRAS, and ALK, are detected, at most, in only 30% of patients. Thus, many unidentified low-penetrant events are causing a significant portion of lung cancers. To detect low-penetrance drivers of NSCLC, a forward genetic screen was performed in mice using the Sleeping Beauty (SB) DNA transposon as a random mutagen to generate lung tumors in a Pten-deficient background. SB mutations coupled with Pten deficiency were sufficient to produce lung tumors in 29% of mice. Pten deficiency alone, without SB mutations, resulted in lung tumors in 11% of mice, whereas the rate in control mice was approximately 3%. In addition, thyroid cancer and other carcinomas, as well as the presence of bronchiolar and alveolar epithelialization, in mice deficient for Pten were also identified. Analysis of common transposon insertion sites identified 76 candidate cancer driver genes. These genes are frequently dysregulated in human lung cancers and implicate several signaling pathways. Cullin3 (Cul3), a member of a ubiquitin ligase complex that plays a role in the oxidative stress response pathway, was identified in the screen and evidence demonstrates that Cul3 functions as a tumor suppressor. IMPLICATIONS This study identifies many novel candidate genetic drivers of lung cancer and demonstrates that CUL3 acts as a tumor suppressor by regulating oxidative stress.
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Affiliation(s)
- Casey Dorr
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. Minneapolis Medical Research Foundation, Minneapolis, Minnesota
| | - Callie Janik
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota
| | - Madison Weg
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota
| | - Raha A Been
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. Department of Comparative and Molecular Biosciences, University of Minnesota, St. Paul, Minnesota
| | - Justin Bader
- Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Ryan Kang
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota
| | - Brandon Ng
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota
| | - Lindsey Foran
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota
| | - Sean R Landman
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota
| | - M Gerard O'Sullivan
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota. Comparative Pathology Shared Resource, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Michael Steinbach
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Aaron L Sarver
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota
| | | | - David A Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. Department of Genetic, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota
| | - Timothy K Starr
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. Department of Genetic, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota.
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44
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Klhl31 attenuates β-catenin dependent Wnt signaling and regulates embryo myogenesis. Dev Biol 2015; 402:61-71. [DOI: 10.1016/j.ydbio.2015.02.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 02/16/2015] [Accepted: 02/17/2015] [Indexed: 11/19/2022]
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Heuchert A, Abduselam N, Zeynudin A, Eshetu T, Löscher T, Wieser A, Pritsch M, Berens-Riha N. Molecular markers of anti-malarial drug resistance in southwest Ethiopia over time: regional surveillance from 2006 to 2013. Malar J 2015; 14:208. [PMID: 25986047 PMCID: PMC4490604 DOI: 10.1186/s12936-015-0723-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 05/05/2015] [Indexed: 01/29/2023] Open
Abstract
Background Drug resistance is one of the main reasons of anti-malarial treatment failures and impedes malaria containment strategies. As single nucleotide polymorphisms (SNPs) have been found to correlate with anti-malarial drug resistance, the surveillance strategy includes continuous monitoring of known molecular markers and detection of new mutation patterns. With the introduction of artemisinin-based combination therapy, selection of specific patterns has been observed worldwide. Methods From March to June 2013, whole blood was collected on filter paper from microscopically malaria positive patients in Jimma zone (District), southwestern Ethiopia. Plasmodium falciparum, Plasmodium vivax and mixed infections were included. SNPs were investigated by conventional or real-time PCR, restriction fragment length pattern analysis or sequencing. Results were compared to molecular patterns from Ethiopian isolates in 2004, 2006 and 2008/9. Results Plasmodium falciparum, P. vivax, and mixed infections were molecularly confirmed in 177, 80, and 14 samples, respectively. In P. falciparum, mutations in the pfcrt, pfmdr 1and pfATP 6 (SERCA) gene were investigated. Whereas the mutation in the pfcrt gene at codon 76 K was still found in 95.6 % of all samples, the pfmdr 1 86 T mutation fell to 1.2 % (2/163) in 2013 compared to 9 % in 2008/9 and 86 % in 2006 (P <0.001). The pfmdr 1 184 F mutation dominated with 100.0 % (172/172) in 2013. Sequencing of the recently reported PF3D7_1343700 kelch propeller domain showed no mutation at codon 476. First sequencing data of the pvmdr 1 gene from Jimma region revealed a prevalence of the mutations 976 F and 1076 L in 72.7 % (16/23) and 100.0 % (19/19) of the isolates, respectively. Conclusion Since the introduction of artemether-lumefantrine (AL) in Jimma, Ethiopia, in 2006, the prevalence of certain SNPs associated with AL use has increased. Markers for chloroquine resistance in P. vivax were highly frequent. Continuous molecular and clinical surveillance are of paramount importance. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0723-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Heuchert
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Leopoldstrasse 5, 80802, Munich, Germany.
| | - Nuredin Abduselam
- Department of Laboratory Sciences and Pathology, Jimma University, Jimma for Infection Research (DZIF) at LMU, Munich, Germany.
| | - Ahmed Zeynudin
- Department of Laboratory Sciences and Pathology, Jimma University, Jimma for Infection Research (DZIF) at LMU, Munich, Germany.
| | - Teferi Eshetu
- Department of Laboratory Sciences and Pathology, Jimma University, Jimma for Infection Research (DZIF) at LMU, Munich, Germany.
| | - Thomas Löscher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Leopoldstrasse 5, 80802, Munich, Germany.
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Leopoldstrasse 5, 80802, Munich, Germany. .,Department of Laboratory Sciences and Pathology, Jimma University, Jimma for Infection Research (DZIF) at LMU, Munich, Germany. .,German Center for Infection Research (DZIF), Partner site Munich, Munich, Germany. .,Max von Pettenkofer-Institute of Hygiene and Medical Microbiology, Munich, Germany.
| | - Michael Pritsch
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Leopoldstrasse 5, 80802, Munich, Germany. .,German Center for Infection Research (DZIF), Partner site Munich, Munich, Germany.
| | - Nicole Berens-Riha
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Leopoldstrasse 5, 80802, Munich, Germany.
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Gong W, Gohla RM, Bowlin KM, Koyano-Nakagawa N, Garry DJ, Shi X. Kelch Repeat and BTB Domain Containing Protein 5 (Kbtbd5) Regulates Skeletal Muscle Myogenesis through the E2F1-DP1 Complex. J Biol Chem 2015; 290:15350-61. [PMID: 25940086 DOI: 10.1074/jbc.m114.629956] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Indexed: 01/14/2023] Open
Abstract
We have previously isolated a muscle-specific Kelch gene, Kelch repeat and BTB domain containing protein 5 (Kbtbd5)/Kelch-like protein 40 (Klhl40). In this report, we identified DP1 as a direct interacting factor for Kbtbd5 using a yeast two-hybrid screen and in vitro binding assays. Our studies demonstrate that Kbtbd5 interacts and regulates the cytoplasmic localization of DP1. GST pulldown assays demonstrate that the dimerization domain of DP1 interacts with all three of the Kbtbd5 domains. We further show that Kbtbd5 promotes the ubiquitination and degradation of DP1, thereby inhibiting E2F1-DP1 activity. To investigate the in vivo function of Kbtbd5, we used gene disruption technology and engineered Kbtbd5 null mice. Targeted deletion of Kbtbd5 resulted in postnatal lethality. Histological studies reveal that the Kbtbd5 null mice have smaller muscle fibers, a disorganized sarcomeric structure, increased extracellular matrix, and decreased numbers of mitochondria compared with wild-type controls. RNA sequencing and quantitative PCR analyses demonstrate the up-regulation of E2F1 target apoptotic genes (Bnip3 and p53inp1) in Kbtbd5 null skeletal muscle. Consistent with these observations, the cellular apoptosis in Kbtbd5 null mice was increased. Breeding of Kbtbd5 null mouse into the E2F1 null background rescues the lethal phenotype of the Kbtbd5 null mice but not the growth defect. The expression of Bnip3 and p53inp1 in Kbtbd5 mutant skeletal muscle are also restored to control levels in the E2F1 null background. In summary, our studies demonstrate that Kbtbd5 regulates skeletal muscle myogenesis through the regulation of E2F1-DP1 activity.
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Affiliation(s)
- Wuming Gong
- From the Lillehei Heart Institute, University of Minnesota-Twin Cities, Minneapolis Minnesota 55455
| | - Rachel M Gohla
- From the Lillehei Heart Institute, University of Minnesota-Twin Cities, Minneapolis Minnesota 55455
| | - Kathy M Bowlin
- From the Lillehei Heart Institute, University of Minnesota-Twin Cities, Minneapolis Minnesota 55455
| | - Naoko Koyano-Nakagawa
- From the Lillehei Heart Institute, University of Minnesota-Twin Cities, Minneapolis Minnesota 55455
| | - Daniel J Garry
- From the Lillehei Heart Institute, University of Minnesota-Twin Cities, Minneapolis Minnesota 55455
| | - Xiaozhong Shi
- From the Lillehei Heart Institute, University of Minnesota-Twin Cities, Minneapolis Minnesota 55455
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Kumar S, Kumari R, Pandey R. New insight-guided approaches to detect, cure, prevent and eliminate malaria. PROTOPLASMA 2015; 252:717-753. [PMID: 25323622 DOI: 10.1007/s00709-014-0697-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 09/01/2014] [Indexed: 06/04/2023]
Abstract
New challenges posed by the development of resistance against artemisinin-based combination therapies (ACTs) as well as previous first-line therapies, and the continuing absence of vaccine, have given impetus to research in all areas of malaria control. This review portrays the ongoing progress in several directions of malaria research. The variants of RTS,S and apical membrane antigen 1 (AMA1) are being developed and test adapted as multicomponent and multistage malaria control vaccines, while many other vaccine candidates and methodologies to produce antigens are under experimentation. To track and prevent the spread of artemisinin resistance from Southeast Asia to other parts of the world, rolling circle-enhanced enzyme activity detection (REEAD), a time- and cost-effective malaria diagnosis in field conditions, and a DNA marker associated with artemisinin resistance have become available. Novel mosquito repellents and mosquito trapping and killing techniques much more effective than the prevalent ones are undergoing field testing. Mosquito lines stably infected with their symbiotic wild-type or genetically engineered bacteria that kill sympatric malaria parasites are being constructed and field tested for stopping malaria transmission. A complementary approach being pursued is the addition of ivermectin-like drug molecules to ACTs to cure malaria and kill mosquitoes. Experiments are in progress to eradicate malaria mosquito by making it genetically male sterile. High-throughput screening procedures are being developed and used to discover molecules that possess long in vivo half life and are active against liver and blood stages for the fast cure of malaria symptoms caused by simple or relapsing and drug-sensitive and drug-resistant types of varied malaria parasites, can stop gametocytogenesis and sporogony and could be given in one dose. Target-based antimalarial drug designing has begun. Some of the putative next-generation antimalarials that possess in their scaffold structure several of the desired properties of malaria cure and control are exemplified by OZ439, NITD609, ELQ300 and tafenoquine that are already undergoing clinical trials, and decoquinate, usnic acid, torin-2, ferroquine, WEHI-916, MMV396749 and benzothiophene-type N-myristoyltransferase (NMT) inhibitors, which are candidates for future clinical usage. Among these, NITD609, ELQ300, decoquinate, usnic acid, torin-2 and NMT inhibitors not only cure simple malaria and are prophylactic against simple malaria, but they also cure relapsing malaria.
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Affiliation(s)
- Sushil Kumar
- SKA Institution for Research, Education and Development (SKAIRED), 4/11 SarvPriya Vihar, New Delhi, 110016, India,
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Zhang X, Gou M, Guo C, Yang H, Liu CJ. Down-regulation of Kelch domain-containing F-box protein in Arabidopsis enhances the production of (poly)phenols and tolerance to ultraviolet radiation. PLANT PHYSIOLOGY 2015; 167:337-50. [PMID: 25502410 PMCID: PMC4326750 DOI: 10.1104/pp.114.249136] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/12/2014] [Indexed: 05/17/2023]
Abstract
Phenylpropanoid biosynthesis in plants engenders myriad phenolics with diverse biological functions. Phenylalanine ammonia-lyase (PAL) is the first committed enzyme in the pathway, directing primary metabolic flux into a phenylpropanoid branch. Previously, we demonstrated that the Arabidopsis (Arabidopsis thaliana) Kelch domain-containing F-box proteins, AtKFB01, AtKFB20, and AtKFB50, function as the negative regulators controlling phenylpropanoid biosynthesis via mediating PAL's ubiquitination and subsequent degradation. Here, we reveal that Arabidopsis KFB39, a close homolog of AtKFB50, also interacts physically with PAL isozymes and modulates PAL stability and activity. Disturbing the expression of KFB39 reciprocally affects the accumulation/deposition of a set of phenylpropanoid end products, suggesting that KFB39 is an additional posttranslational regulator responsible for the turnover of PAL and negatively controlling phenylpropanoid biosynthesis. Furthermore, we discover that exposure of Arabidopsis to ultraviolet (UV)-B radiation suppresses the expression of all four KFB genes while inducing the transcription of PAL isogenes; these data suggest that Arabidopsis consolidates both transcriptional and posttranslational regulation mechanisms to maximize its responses to UV light stress. Simultaneous down-regulation of all four identified KFBs significantly enhances the production of (poly)phenols and the plant's tolerance to UV irradiation. This study offers a biotechnological approach for engineering the production of useful phenolic chemicals and for increasing a plant's resistance to environmental stress.
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Affiliation(s)
- Xuebin Zhang
- Biological, Environmental, and Climate Sciences Department, Brookhaven National Laboratory, Upton, New York 11973 (X.Z., M.G., H.Y., C.-J.L.);College of Art and Science, Shanxi Agriculture University, Taigu, Shanxi 030801, People's Republic of China (C.G.); andBiochemistry and Cell Biology Department, Stony Brook University, Stony Brook, New York 11972 (H.Y.)
| | - Mingyue Gou
- Biological, Environmental, and Climate Sciences Department, Brookhaven National Laboratory, Upton, New York 11973 (X.Z., M.G., H.Y., C.-J.L.);College of Art and Science, Shanxi Agriculture University, Taigu, Shanxi 030801, People's Republic of China (C.G.); andBiochemistry and Cell Biology Department, Stony Brook University, Stony Brook, New York 11972 (H.Y.)
| | - Chunrong Guo
- Biological, Environmental, and Climate Sciences Department, Brookhaven National Laboratory, Upton, New York 11973 (X.Z., M.G., H.Y., C.-J.L.);College of Art and Science, Shanxi Agriculture University, Taigu, Shanxi 030801, People's Republic of China (C.G.); andBiochemistry and Cell Biology Department, Stony Brook University, Stony Brook, New York 11972 (H.Y.)
| | - Huijun Yang
- Biological, Environmental, and Climate Sciences Department, Brookhaven National Laboratory, Upton, New York 11973 (X.Z., M.G., H.Y., C.-J.L.);College of Art and Science, Shanxi Agriculture University, Taigu, Shanxi 030801, People's Republic of China (C.G.); andBiochemistry and Cell Biology Department, Stony Brook University, Stony Brook, New York 11972 (H.Y.)
| | - Chang-Jun Liu
- Biological, Environmental, and Climate Sciences Department, Brookhaven National Laboratory, Upton, New York 11973 (X.Z., M.G., H.Y., C.-J.L.);College of Art and Science, Shanxi Agriculture University, Taigu, Shanxi 030801, People's Republic of China (C.G.); andBiochemistry and Cell Biology Department, Stony Brook University, Stony Brook, New York 11972 (H.Y.)
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Perissinotti PP, Ethington EA, Almazan E, Martínez-Hernández E, Kalil J, Koob MD, Piedras-Rentería ES. Calcium current homeostasis and synaptic deficits in hippocampal neurons from Kelch-like 1 knockout mice. Front Cell Neurosci 2015; 8:444. [PMID: 25610372 PMCID: PMC4285801 DOI: 10.3389/fncel.2014.00444] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/10/2014] [Indexed: 11/30/2022] Open
Abstract
Kelch-like 1 (KLHL1) is a neuronal actin-binding protein that modulates voltage-gated CaV2.1 (P/Q-type) and CaV3.2 (α1H T-type) calcium channels; KLHL1 knockdown experiments (KD) cause down-regulation of both channel types and altered synaptic properties in cultured rat hippocampal neurons (Perissinotti et al., 2014). Here, we studied the effect of ablation of KLHL1 on calcium channel function and synaptic properties in cultured hippocampal neurons from KLHL1 knockout (KO) mice. Western blot data showed the P/Q-type channel α1A subunit was less abundant in KO hippocampus compared to wildtype (WT); and P/Q-type calcium currents were smaller in KO neurons than WT during early days in vitro, although this decrease was compensated for at late stages by increases in L-type calcium current. In contrast, T-type currents did not change in culture. However, biophysical properties and western blot analysis revealed a differential contribution of T-type channel isoforms in the KO, with CaV3.2 α1H subunit being down-regulated and CaV3.1 α1G up-regulated. Synapsin I levels were also reduced in the KO hippocampus and cultured neurons displayed a concomitant reduction in synapsin I puncta and decreased miniature excitatory postsynaptic current (mEPSC) frequency. In summary, genetic ablation of the calcium channel modulator resulted in compensatory mechanisms to maintain calcium current homeostasis in hippocampal KO neurons; however, synaptic alterations resulted in a reduction of excitatory synapse number, causing an imbalance of the excitatory-inhibitory synaptic input ratio favoring inhibition.
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Affiliation(s)
- Paula P Perissinotti
- Department of Cell and Molecular Physiology, Loyola University Chicago, Stritch School of Medicine Maywood, IL, USA
| | - Elizabeth A Ethington
- Department of Cell and Molecular Physiology, Loyola University Chicago, Stritch School of Medicine Maywood, IL, USA
| | - Erik Almazan
- Department of Cell and Molecular Physiology, Loyola University Chicago, Stritch School of Medicine Maywood, IL, USA
| | - Elizabeth Martínez-Hernández
- Department of Cell and Molecular Physiology, Loyola University Chicago, Stritch School of Medicine Maywood, IL, USA
| | - Jennifer Kalil
- Department of Cell and Molecular Physiology, Loyola University Chicago, Stritch School of Medicine Maywood, IL, USA
| | - Michael D Koob
- Department of Laboratory Medicine and Pathology, Institute for Translational Neuroscience, University of Minnesota Minneapolis, MN, USA
| | - Erika S Piedras-Rentería
- Department of Cell and Molecular Physiology, Loyola University Chicago, Stritch School of Medicine Maywood, IL, USA ; Neuroscience Institute, Loyola University Chicago, Stritch School of Medicine Maywood, IL, USA
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50
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Naeem ul Hassan M, Zainal Z, Ismail I. Plant kelch containing F-box proteins: structure, evolution and functions. RSC Adv 2015. [DOI: 10.1039/c5ra01875g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Kelch repeat containing F-box proteins; a review on the progress of the research on these plant specific signalling proteins.
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Affiliation(s)
- M. Naeem ul Hassan
- School of Bioscience and Biotechnology
- Faculty of Science and Technology
- University Kebangsaan Malaysia
- Bangi, 43600
- Malaysia
| | - Zamri Zainal
- School of Bioscience and Biotechnology
- Faculty of Science and Technology
- University Kebangsaan Malaysia
- Bangi, 43600
- Malaysia
| | - Ismanizan Ismail
- School of Bioscience and Biotechnology
- Faculty of Science and Technology
- University Kebangsaan Malaysia
- Bangi, 43600
- Malaysia
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