1
|
Yang Y, Wu M, Pan Y, Hua Y, He X, Li X, Wang J, Gan X. WW domains form a folded type of nuclear localization signal to guide YAP1 nuclear import. J Cell Biol 2024; 223:e202308013. [PMID: 38488622 PMCID: PMC10942854 DOI: 10.1083/jcb.202308013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/31/2023] [Accepted: 02/23/2024] [Indexed: 03/18/2024] Open
Abstract
The nuclear translocation of YAP1 is significantly implicated in the proliferation, stemness, and metastasis of cancer cells. Although the molecular basis underlying YAP1 subcellular distribution has been extensively explored, it remains to be elucidated how the nuclear localization signal guides YAP1 to pass through the nuclear pore complex. Here, we define a globular type of nuclear localization signal composed of folded WW domains, named as WW-NLS. It directs YAP1 nuclear import through the heterodimeric nuclear transport receptors KPNA-KPNB1, bypassing the canonical nuclear localization signal that has been well documented in KPNA/KPNB1-mediated nuclear import. Strikingly, competitive interference with the function of the WW-NLS significantly attenuates YAP1 nuclear translocation and damages stemness gene activation and sphere formation in malignant breast cancer cells. Our findings elucidate a novel globular type of nuclear localization signal to facilitate nuclear entry of WW-containing proteins including YAP1.
Collapse
Affiliation(s)
- Yilin Yang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, PR China
| | - Mengxiao Wu
- Department of Biochemistry and Molecular Biology, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, PR China
| | - Yu Pan
- Department of Biochemistry and Molecular Biology, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, PR China
| | - Yue Hua
- Department of Biochemistry and Molecular Biology, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, PR China
| | - Xinyu He
- Department of Biochemistry and Molecular Biology, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, PR China
| | - Xinyang Li
- Department of Biochemistry and Molecular Biology, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, PR China
| | - Jiyong Wang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, PR China
| | - Xiaoqing Gan
- Department of Biochemistry and Molecular Biology, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, PR China
| |
Collapse
|
2
|
Zhang W, Wang H, Luo Z, Jian Y, Gong C, Wang H, Lin X, Liu M, Wang Y, Shao H. Hitchhiking of Cas9 with nucleus-localized proteins impairs its controllability and leads to efficient genome editing of NLS-free Cas9. Mol Ther 2024; 32:920-934. [PMID: 38341611 DOI: 10.1016/j.ymthe.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/09/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
CRISPR-Cas9 is the most commonly used genome-editing tool in eukaryotic cells. To modulate Cas9 entry into the nucleus to enable control of genome editing, we constructed a light-controlled CRISPR-Cas9 system to control exposure of the Cas9 protein nuclear localization signal (NLS). Although blue-light irradiation was found to effectively control the entry of Cas9 protein into the nucleus with confocal microscopy observation, effective gene editing occurred in controls with next-generation sequencing analysis. To further clarify this phenomenon, a CRISPR-Cas9 editing system without the NLS and a CRISPR-Cas9 editing system containing a nuclear export signal were also constructed. Interestingly, both Cas9 proteins could achieve effective editing of target sites with significantly reduced off-target effects. Thus, we speculated that other factors might mediate Cas9 entry into the nucleus. However, NLS-free Cas9 was found to produce effective target gene editing even following inhibition of cell mitosis to prevent nuclear import caused by nuclear membrane disassembly. Furthermore, multiple nucleus-localized proteins were found to interact with Cas9, which could mediate the "hitchhiking" of NLS-free Cas9 into the nucleus. These findings will inform future attempts to construct controllable gene-editing systems and provide new insights into the evolution of the nucleus and compatible protein functions.
Collapse
Affiliation(s)
- Wenfeng Zhang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China.
| | - Haozheng Wang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Zhongtao Luo
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Yingzhen Jian
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Chenyu Gong
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Hui Wang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Xinjian Lin
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Meilin Liu
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Yangmin Wang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China
| | - Hongwei Shao
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, P.R. China; Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, P.R. China.
| |
Collapse
|
3
|
Shrikondawar AN, Chennoju K, Ghosh DK, Ranjan A. Identification and characterization of nuclear localization signals in the circumsporozoite protein of Plasmodium falciparum. FEBS Lett 2024; 598:801-817. [PMID: 38369616 DOI: 10.1002/1873-3468.14829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/30/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
Secretory proteins of Plasmodium exhibit differential spatial and functional activity within the host cell nucleus. However, the nuclear localization signals (NLSs) for these proteins remain largely uncharacterized. In this study, we have identified and characterized two NLSs in the circumsporozoite protein of Plasmodium falciparum (Pf-CSP). Both NLSs in the Pf-CSP contain clusters of lysine and arginine residues essential for specific interactions with the conserved tryptophan and asparagine residues of importin-α, facilitating nuclear translocation of Pf-CSP. While the two NLSs of Pf-CSP function independently and are both crucial for nuclear localization, a single NLS of Pf-CSP leads to weak nuclear localization. These findings shed light on the mechanism of nuclear penetrability of secretory proteins of Plasmodium proteins.
Collapse
Affiliation(s)
- Akshaykumar Nanaji Shrikondawar
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Regional Centre for Biotechnology, Faridabad, India
| | - Kiranmai Chennoju
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | | | - Akash Ranjan
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| |
Collapse
|
4
|
Cross EM, Akbari N, Ghassabian H, Hoad M, Pavan S, Ariawan D, Donnelly CM, Lavezzo E, Petersen GF, Forwood JK, Alvisi G. A functional and structural comparative analysis of large tumor antigens reveals evolution of different importin α-dependent nuclear localization signals. Protein Sci 2024; 33:e4876. [PMID: 38108201 PMCID: PMC10807245 DOI: 10.1002/pro.4876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
Nucleocytoplasmic transport regulates the passage of proteins between the nucleus and cytoplasm. In the best characterized pathway, importin (IMP) α bridges cargoes bearing basic, classical nuclear localization signals (cNLSs) to IMPβ1, which mediates transport through the nuclear pore complex. IMPα recognizes three types of cNLSs via two binding sites: the major binding site accommodates monopartite cNLSs, the minor binding site recognizes atypical cNLSs, while bipartite cNLSs simultaneously interact with both major and minor sites. Despite the growing knowledge regarding IMPα-cNLS interactions, our understanding of the evolution of cNLSs is limited. We combined bioinformatic, biochemical, functional, and structural approaches to study this phenomenon, using polyomaviruses (PyVs) large tumor antigens (LTAs) as a model. We characterized functional cNLSs from all human (H)PyV LTAs, located between the LXCXE motif and origin binding domain. Surprisingly, the prototypical SV40 monopartite NLS is not well conserved; HPyV LTA NLSs are extremely heterogenous in terms of structural organization, IMPα isoform binding, and nuclear targeting abilities, thus influencing the nuclear accumulation properties of full-length proteins. While several LTAs possess bipartite cNLSs, merkel cell PyV contains a hybrid bipartite cNLS whose upstream stretch of basic amino acids can function as an atypical cNLS, specifically binding to the IMPα minor site upon deletion of the downstream amino acids after viral integration in the host genome. Therefore, duplication of a monopartite cNLS and subsequent accumulation of point mutations, optimizing interaction with distinct IMPα binding sites, led to the evolution of bipartite and atypical NLSs binding at the minor site.
Collapse
Affiliation(s)
- Emily M. Cross
- School of Dentistry and Medical SciencesCharles Sturt UniversityWagga WaggaAustralia
- Diamond Light SourceHarwell Science and Innovation CampusDidcotUnited Kingdom
| | - Nasim Akbari
- Department of Molecular MedicineUniversity of PadovaPadovaItaly
| | | | - Mikayla Hoad
- School of Dentistry and Medical SciencesCharles Sturt UniversityWagga WaggaAustralia
| | - Silvia Pavan
- Department of Molecular MedicineUniversity of PadovaPadovaItaly
| | - Daryl Ariawan
- Dementia Research CentreMacquarie UniversitySydneyAustralia
| | - Camilla M. Donnelly
- School of Dentistry and Medical SciencesCharles Sturt UniversityWagga WaggaAustralia
| | - Enrico Lavezzo
- Department of Molecular MedicineUniversity of PadovaPadovaItaly
| | | | - Jade K. Forwood
- School of Dentistry and Medical SciencesCharles Sturt UniversityWagga WaggaAustralia
- Gulbali InstituteCharles Sturt UniversityWagga WaggaAustralia
| | | |
Collapse
|
5
|
Moraes IR, de Oliveira HC, Fontes MRM. Structural basis of nuclear transport for NEIL DNA glycosylases mediated by importin-alpha. Biochim Biophys Acta Proteins Proteom 2024; 1872:140974. [PMID: 38065227 DOI: 10.1016/j.bbapap.2023.140974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/18/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024]
Abstract
NEIL glycosylases, including NEIL1, NEIL2, and NEIL3, play a crucial role in the base excision DNA repair pathway (BER). The classical importin pathway mediated by importin α/β and cargo proteins containing nuclear localization sequences (NLS) is the most common transport mechanism of DNA repair proteins to the nucleus. Previous studies have identified putative NLSs located at the C-terminus of NEIL3 and NEIL1. Crystallographic, bioinformatics, calorimetric (ITC), and fluorescence assays were used to investigate the interaction between NEIL1 and NEIL3 putative NLSs and importin-α (Impα). Our findings showed that NEIL3 contains a typical cNLS, with medium affinity for the major binding site of Impα. In contrast, crystallographic analysis of NEIL1 NLS revealed its binding to Impα, but with high B-factors and a lack of electron density at the linker region. ITC and fluorescence assays indicated no detectable affinity between NEIL1 NLS and Impα. These data suggest that NEIL1 NLS is a non-classical NLS with low affinity to Impα. Additionally, we compared the binding mode of NEIL3 and NEIL1 with Mus musculus Impα to human isoforms HsImpα1 and HsImpα3, which revealed interesting binding differences for HsImpα3 variant. NEIL3 is a classical medium affinity monopartite NLS, while NEIL1 is likely to be an unclassical low-affinity bipartite NLS. The base excision repair pathway is one of the primary systems involved in repairing DNA. Thus, understanding the mechanisms of nuclear transport of NEIL proteins is crucial for comprehending the role of these proteins in DNA repair and disease development.
Collapse
Affiliation(s)
- Ivan R Moraes
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Hamine C de Oliveira
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Marcos R M Fontes
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil; Instituto de Estudos Avançados do Mar (IEAMar), Universidade Estadual Paulista (UNESP), São Vicente, SP, Brazil.
| |
Collapse
|
6
|
Onodera W, Kawasaki K, Oishi M, Aoki S, Asahi T. Functional Divergence and Origin of the Vertebrate Praja Family. J Mol Evol 2024; 92:21-29. [PMID: 38158403 DOI: 10.1007/s00239-023-10150-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
The Praja family is an E3 ubiquitin ligase, promoting polyubiquitination and subsequent degradation of substrates. It comprises two paralogs, praja1 and praja2. Prior research suggests these paralogs have undergone functional divergence, with examples, such as their distinct roles in neurite outgrowth. However, the specific evolutionary trajectories of each paralog remain largely unexplored preventing mechanistic understanding of functional differences between paralogs. Here, we investigated the phylogeny and divergence of the vertebrate Praja family through molecular evolutionary analysis. Phylogenetic examination of the vertebrate praja revealed that praja1 and praja2 originated from the common ancestor of placentals via gene duplication, with praja1 evolving at twice the rate of praja2 shortly after the duplication. Moreover, a unique evolutionary trajectory for praja1 relative to other vertebrate Praja was indicated, as evidenced by principal component analysis on GC content, codon usage frequency, and amino acid composition. Subsequent motif/domain comparison revealed conserved N terminus and C terminus in praja1 and praja2, together with praja1-specific motifs, including nuclear localization signal and Ala-Gly-Ser repeats. The nuclear localization signal was demonstrated to be functional in human neuroblastoma SH-SY5Y cells using deletion mutant, while praja2 was exclusively expressed in the nucleus. These discoveries contribute to a more comprehensive understanding of the Praja family's phylogeny and suggest a functional divergence between praja1 and praja2. Specifically, the shift of praja1 into the nucleus implies the degradation of novel substrates located in the nucleus as an evolutionary consequence.
Collapse
Affiliation(s)
- Wataru Onodera
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-0056, Japan.
| | - Kotaro Kawasaki
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-0056, Japan
| | - Mizuho Oishi
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-0056, Japan
| | - Shiho Aoki
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-0056, Japan
| | - Toru Asahi
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-0056, Japan.
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda-Tsurumaki, Shinjuku, Tokyo, 162-0041, Japan.
| |
Collapse
|
7
|
Cross EM, Marin O, Ariawan D, Aragão D, Cozza G, Di Iorio E, Forwood JK, Alvisi G. Structural determinants of phosphorylation-dependent nuclear transport of HCMV DNA polymerase processivity factor UL44. FEBS Lett 2024; 598:199-209. [PMID: 38158756 DOI: 10.1002/1873-3468.14797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Human cytomegalovirus DNA polymerase processivity factor UL44 is transported into the nucleus by importin (IMP) α/β through a classical nuclear localization signal (NLS), and this region is susceptible to cdc2-mediated phosphorylation at position T427. Whilst phosphorylation within and close to the UL44 NLS regulates nuclear transport, the details remain elusive, due to the paucity of structural information regarding the role of negatively charged cargo phosphate groups. We addressed this issue by studying the effect of UL44 T427 phosphorylation on interaction with several IMPα isoforms by biochemical and structural approaches. Phosphorylation decreased UL44/IMPα affinity 10-fold, and a comparative structural analysis of UL44 NLS phosphorylated and non-phosphorylated peptides complexed with mouse IMPα2 revealed the structural rearrangements responsible for phosphorylation-dependent inhibition of UL44 nuclear import.
Collapse
Affiliation(s)
- Emily M Cross
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, Australia
- Diamond Light Source, Didcot, UK
| | - Oriano Marin
- Department of Biomedical Sciences, University of Padova, Italy
| | - Daryl Ariawan
- Dementia Research Centre, Macquarie University, Sydney, Australia
| | | | - Giorgio Cozza
- Department of Molecular Medicine, University of Padua, Italy
| | - Enzo Di Iorio
- Department of Molecular Medicine, University of Padua, Italy
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, Australia
| | | |
Collapse
|
8
|
Athukorala A, Donnelly CM, Pavan S, Nematollahzadeh S, Djossou VA, Nath B, Helbig KJ, Di Iorio E, McSharry BP, Alvisi G, Forwood JK, Sarker S. Structural and functional characterization of siadenovirus core protein VII nuclear localization demonstrates the existence of multiple nuclear transport pathways. J Gen Virol 2024; 105. [PMID: 38261399 DOI: 10.1099/jgv.0.001928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Adenovirus protein VII (pVII) plays a crucial role in the nuclear localization of genomic DNA following viral infection and contains nuclear localization signal (NLS) sequences for the importin (IMP)-mediated nuclear import pathway. However, functional analysis of pVII in adenoviruses to date has failed to fully determine the underlying mechanisms responsible for nuclear import of pVII. Therefore, in the present study, we extended our analysis by examining the nuclear trafficking of adenovirus pVII from a non-human species, psittacine siadenovirus F (PsSiAdV). We identified a putative classical (c)NLS at pVII residues 120-128 (120PGGFKRRRL128). Fluorescence polarization and electrophoretic mobility shift assays demonstrated direct, high-affinity interaction with both IMPα2 and IMPα3 but not IMPβ. Structural analysis of the pVII-NLS/IMPα2 complex confirmed a classical interaction, with the major binding site of IMPα occupied by K124 of pVII-NLS. Quantitative confocal laser scanning microscopy showed that PsSiAdV pVII-NLS can confer IMPα/β-dependent nuclear localization to GFP. PsSiAdV pVII also localized in the nucleus when expressed in the absence of other viral proteins. Importantly, in contrast to what has been reported for HAdV pVII, PsSiAdV pVII does not localize to the nucleolus. In addition, our study demonstrated that inhibition of the IMPα/β nuclear import pathway did not prevent PsSiAdV pVII nuclear targeting, indicating the existence of alternative pathways for nuclear localization, similar to what has been previously shown for human adenovirus pVII. Further examination of other potential NLS signals, characterization of alternative nuclear import pathways, and investigation of pVII nuclear targeting across different adenovirus species is recommended to fully elucidate the role of varying nuclear import pathways in the nuclear localization of pVII.
Collapse
Affiliation(s)
- Ajani Athukorala
- Department of Microbiology, Anatomy, Physiology, and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
| | - Camilla M Donnelly
- School of Dentistry and Medical Sciences, Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Silvia Pavan
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Sepehr Nematollahzadeh
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | | | - Babu Nath
- School of Dentistry and Medical Sciences, Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Karla J Helbig
- Department of Microbiology, Anatomy, Physiology, and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
| | - Enzo Di Iorio
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Brian P McSharry
- School of Dentistry and Medical Sciences, Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Gualtiero Alvisi
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Subir Sarker
- Department of Microbiology, Anatomy, Physiology, and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
- Biomedical Sciences & Molecular Biology, College of Public Health Medical, and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
| |
Collapse
|
9
|
Liu Y, Li K, Wenren M, Cheng W, Zhou X, Xu D, Chi C, Lü Z, Liu H. Identification, functional characterization and expression pattern of interferon-gamma (IFN-γ) and interferon-gamma receptor 1 (IFNGR1) in Nibea albiflora. Fish Shellfish Immunol 2024; 144:109274. [PMID: 38072135 DOI: 10.1016/j.fsi.2023.109274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/26/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
Interferon-gamma (IFN-γ) is an inflammatory cytokine that plays a crucial role in regulating both innate and cell-mediated immune responses by binding to a receptor complex made up of IFNGR1 and IFNGR2. In this study, the complete cDNA of IFN-γ and IFNGR1 from Nibea albiflora were cloned and functionally characterized (named NaIFN-γ and NaIFNGR1), whose complete cDNA sequences were 1593 bp and 2792 bp, encoding 201 and 399 amino acids, respectively. Multiple sequence alignment and phylogenetic analysis showed that the concluded amino acids sequences of NaIFN-γ and NaIFNGR1 shared high identity with their teleost orthologues including the IFN-γ signature and nuclear localization signal (NLS) motif in NaIFN-γ and FN Ⅲ domain in NaIFNGR1. Real-time PCR showed that NaIFN-γ and NaIFNGR1 constitutively expressed in all tested tissues, such as the head-kidney, spleen, liver, kidney, gill, muscle, blood, and intestine with the highest expression of NaIFN-γ and NaIFNGR1 appearing in the liver and gill, respectively. After experiencing stimulation with Polyinosinic-polycytidylic acid (Poly (I:C)), Vibrio alginolyticus (V. alginolyticus) or Vibrio parahaemolyticus (V. parahaemolyticus), NaIFN-γ and NaIFNGR1 mRNA were up-regulated with the time-dependent model. Due to the presence of a nuclear localization signal (NLS), the subcellular localization revealed that NaIFN-γ dispersed throughout the cytoplasm and nucleus. NaIFNGR1, as a member of Cytokine receptor family B, was primarily expressed on the cell membrane. When NaIFN-γ and NaIFNGR1 were co-transfected, their fluorescence signals overlapped on the membrane of HEK 293T cells indicating the potential interaction between IFN-γ and IFNGR1. The GST-pull-down results further showed that NaIFN-γ could directly interact with the extracellular region of NaIFNGR1, further confirming the affinity between IFN-γ and IFNGR1. Taken together, the results firstly demonstrated that the NaIFN-γ ligand-receptor system existed in N.albiflora and played a pivotal part in N.albiflora's immune response against pathogenic bacterial infections, which contributed to the better understanding of the role of IFN-γ in the immunomodulatory mechanisms of teleost.
Collapse
Affiliation(s)
- Yongxin Liu
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Kaihui Li
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Mingming Wenren
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Wei Cheng
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Xu Zhou
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Dongdong Xu
- Marine Fishery Institute of Zhejiang Province, Key Lab of Mariculture and Enhancement of Zhejiang Province, Zhoushan, 316100, China
| | - Changfeng Chi
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Zhenming Lü
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Huihui Liu
- National and Provincial Joint Laboratory of Exploration and Utilization of Marine Aquatic Genetic Resources, National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
| |
Collapse
|
10
|
Choleva L, Wang P, Liu H, Wood O, Lambertini L, Scott DK, Karakose E, Stewart AF. Structure-Function Analysis of p57KIP2 in the Human Pancreatic Beta Cell Reveals a Bipartite Nuclear Localization Signal. Endocrinology 2023; 165:bqad197. [PMID: 38151968 DOI: 10.1210/endocr/bqad197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/12/2023] [Accepted: 12/22/2023] [Indexed: 12/29/2023]
Abstract
Mutations in CDKN1C, encoding p57KIP2, a canonical cell cycle inhibitor, underlie multiple pediatric endocrine syndromes. Despite this central role in disease, little is known about the structure and function of p57KIP2 in the human pancreatic beta cell. Since p57KIP2 is predominantly nuclear in human beta cells, we hypothesized that disease-causing mutations in its nuclear localization sequence (NLS) may correlate with abnormal phenotypes. We prepared RIP1 insulin promoter-driven adenoviruses encoding deletions of multiple disease-associated but unexplored regions of p57KIP2 and performed a comprehensive structure-function analysis of CDKN1C/p57KIP2. Real-time polymerase chain reaction and immunoblot analyses confirmed p57KIP2 overexpression, construct size, and beta cell specificity. By immunocytochemistry, wild-type (WT) p57KIP2 displayed nuclear localization. In contrast, deletion of a putative NLS at amino acids 278-281 failed to access the nucleus. Unexpectedly, we identified a second downstream NLS at amino acids 312-316. Further analysis showed that each individual NLS is required for nuclear localization, but neither alone is sufficient. In summary, p57KIP2 contains a classical bipartite NLS characterized by 2 clusters of positively charged amino acids separated by a proline-rich linker region. Variants in the sequences encoding these 2 NLS sequences account for functional p57KIP2 loss and beta cell expansion seen in human disease.
Collapse
Affiliation(s)
- Lauryn Choleva
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peng Wang
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hongtao Liu
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Olivia Wood
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Luca Lambertini
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Donald K Scott
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Esra Karakose
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew F Stewart
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
11
|
Niinuma S, Wake Y, Nakagawa Y, Kaneko T. Importance of nuclear localization signal-fused Cas9 in the production of genome-edited mice via embryo electroporation. Biochem Biophys Res Commun 2023; 685:149140. [PMID: 37918326 DOI: 10.1016/j.bbrc.2023.149140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/09/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023]
Abstract
Previously, to generate genome-edited animals by introducing CRISPR-associated protein 9 (Cas9) into embryos, we developed the Technique for Animal Knockout system by Electroporation (TAKE). Additionally, by fluorescently labeling Cas9, we successfully visualized the Cas9 introduced into the pronuclei of embryos; however, whether Cas9 was introduced directly into the pronuclei by electric pulse or transferred from the cytoplasm by nuclear localization signal (NLS) remained unknown. Herein, we evaluated the localization of Cas9 with (Cas9-NLS) or without NLS (Cas9-noNLS) in mice embryos following electroporation by fusing them with GFP. Furthermore, we visually studied their effects on genome-editing rates in offspring by targeting tyrosinase gene. Fluorescence intensity in pronuclei of Cas9-NLS-electroporated embryos and genome-editing rates of offspring were significantly higher than those of Cas9-noNLS-electroporated embryos. Furthermore, fluorescence in Cas9-NLS-electroporated embryos in which pronuclei had not yet appeared 2.5 h after insemination was observed in the pronuclei of embryos appearing 3.5 h after electroporation. We demonstrated the effective transportation of Cas9 from the cytoplasm to pronuclei by the NLS following TAKE, which resulted in increased genome-editing rates in offspring. The TAKE along with fluorescently labeled nucleases can be used to verify nuclease delivery into individual embryos prior to embryo transfer for efficiently producing genome-edited animals.
Collapse
Affiliation(s)
- Sakura Niinuma
- Division of Science and Engineering, Graduate School of Arts and Science, Iwate University, Iwate, 020-8551, Japan
| | - Yui Wake
- Division of Science and Engineering, Graduate School of Arts and Science, Iwate University, Iwate, 020-8551, Japan
| | - Yuki Nakagawa
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Iwate, 020-8551, Japan
| | - Takehito Kaneko
- Division of Science and Engineering, Graduate School of Arts and Science, Iwate University, Iwate, 020-8551, Japan; Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Iwate, 020-8551, Japan.
| |
Collapse
|
12
|
Armour EM, Thomas CM, Greco G, Bhatnagar A, Elefant F. Experience-dependent Tip60 nucleocytoplasmic transport is regulated by its NLS/NES sequences for neuroplasticity gene control. Mol Cell Neurosci 2023; 127:103888. [PMID: 37598897 DOI: 10.1016/j.mcn.2023.103888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/22/2023] Open
Abstract
Nucleocytoplasmic transport (NCT) in neurons is critical for enabling proteins to enter the nucleus and regulate plasticity genes in response to environmental cues. Such experience-dependent (ED) neural plasticity is central for establishing memory formation and cognitive function and can influence the severity of neurodegenerative disorders like Alzheimer's disease (AD). ED neural plasticity is driven by histone acetylation (HA) mediated epigenetic mechanisms that regulate dynamic activity-dependent gene transcription profiles in response to neuronal stimulation. Yet, how histone acetyltransferases (HATs) respond to extracellular cues in the in vivo brain to drive HA-mediated activity-dependent gene control remains unclear. We previously demonstrated that extracellular stimulation of rat hippocampal neurons in vitro triggers Tip60 HAT nuclear import with concomitant synaptic gene induction. Here, we focus on investigating Tip60 HAT subcellular localization and NCT specifically in neuronal activity-dependent gene control by using the learning and memory mushroom body (MB) region of the Drosophila brain as a powerful in vivo cognitive model system. We used immunohistochemistry (IHC) to compare the subcellular localization of Tip60 HAT in the Drosophila brain under normal conditions and in response to stimulation of fly brain neurons in vivo either by genetically inducing potassium channels activation or by exposure to natural positive ED conditions. Furthermore, we found that both inducible and ED condition-mediated neural induction triggered Tip60 nuclear import with concomitant induction of previously identified Tip60 target genes and that Tip60 levels in both the nucleus and cytoplasm were significantly decreased in our well-characterized Drosophila AD model. Mutagenesis of a putative nuclear localization signal (NLS) sequence and nuclear export signal (NES) sequence that we identified in the Drosophila Tip60 protein revealed that both are functionally required for appropriate Tip60 subcellular localization. Our results support a model by which neuronal stimulation triggers Tip60 NCT via its NLS and NES sequences to promote induction of activity-dependent neuroplasticity gene transcription and that this process may be disrupted in AD.
Collapse
Affiliation(s)
- Ellen M Armour
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Christina M Thomas
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Gabrielle Greco
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Akanksha Bhatnagar
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Felice Elefant
- Department of Biology, Drexel University, Philadelphia, PA, United States of America.
| |
Collapse
|
13
|
Andrade-Salas A, Canela-Pérez I, Cevallos AM, López-Villaseñor I, Hernández R. Trypanosoma cruzi Fibrillarins: Two paralogous proteins with non-identical signals for nuclear transport. Biochem Biophys Res Commun 2023; 682:274-280. [PMID: 37832384 DOI: 10.1016/j.bbrc.2023.10.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/14/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023]
Abstract
Trypanosoma cruzi is a parasitic protozoa causative of Chagas disease. As part of our interest in studying the basic biology of this microorganism, this work reports our observations related to the characterization of motifs and structural domains present in two fibrillarin isoforms (TcFib1 and TcFib2) that were found to be necessary for the nuclear targeting of these nucleolar proteins. Previous characterization of these proteins indicated that they share 68.67% of identical amino acids and are both expressed as nucleolar proteins in T. cruzi epimastigotes. Using an approach based on the transfection of recombinant genes encoding fluorescent fibrillarin-EGFP fusion proteins, this study found evidence for the presence of 4 motifs or protein domains that help target these proteins to the nucleus: The GAR domain and carboxyl terminus in both TcFibs, as well as two lysines and a computationally predicted cNLS in TcFib1. As a distinctive feature, the GAR domain of TcFib2 proved to be essential for the nuclear localization of this protein paralog. Such a difference between TcFib1 and Tcfib2 nuclear localization signals can be explained as the presence of two partially related nuclear import pathways for the two fibrillarin homologues in this organism.
Collapse
Affiliation(s)
- Arturo Andrade-Salas
- Departamento de Biología Molecular y Biotecnología. Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510, México City, Mexico
| | - Israel Canela-Pérez
- Departamento de Biología Molecular y Biotecnología. Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510, México City, Mexico
| | - Ana María Cevallos
- Departamento de Biología Molecular y Biotecnología. Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510, México City, Mexico
| | - Imelda López-Villaseñor
- Departamento de Biología Molecular y Biotecnología. Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510, México City, Mexico
| | - Roberto Hernández
- Departamento de Biología Molecular y Biotecnología. Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510, México City, Mexico.
| |
Collapse
|
14
|
Haidar R, Shabo R, Moeser M, Luch A, Kugler J. The nuclear entry of the aryl hydrocarbon receptor (AHR) relies on the first nuclear localization signal and can be negatively regulated through IMPα/β specific inhibitors. Sci Rep 2023; 13:19668. [PMID: 37951956 PMCID: PMC10640566 DOI: 10.1038/s41598-023-47066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023] Open
Abstract
The human aryl hydrocarbon receptor (AHR) undergoes continuous shuttling between nucleus and cytoplasm. Binding to exogenous or endogenous ligands promotes its rapid nuclear import. The proposed mechanism for the ligand-dependent import is based on exposing the bipartite nuclear localisation signal (NLS) to members of the importin (IMP) superfamily. Among this, the molecular interactions involved in the basal import still need to be clarified. Utilizing fluorescently fused AHR variants, we recapitulated and characterized AHR localization and nucleo-cytoplasmic shuttling in living cells. Analysis of AHR variants carrying NLS point mutations demonstrated a mandatory role of first (13RKRRK17) and second (37KR-R40) NLS segments on the basal import of AHR. Further experiments indicated that ligand-induced import is mainly regulated through the first NLS, while the second NLS is supportive but not essential. Additionally, applying IMPα/β specific inhibitors, ivermectin (IVM) and importazole (IPZ), slowed down the ligand-induced import and, correspondingly, decreased the basal nuclear accumulation of the receptor. In conclusion, our data show that ligand-induced and basal nuclear entry of AHR rely on the same mechanism but are controlled uniquely by the two NLS components.
Collapse
Affiliation(s)
- Rashad Haidar
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany.
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - Reneh Shabo
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Marie Moeser
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Josephine Kugler
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| |
Collapse
|
15
|
Huybrechts Y, De Ridder R, Steenackers E, Devogelaer JP, Mortier G, Hendrickx G, Van Hul W. Genetic Screening of ZNF687 and PFN1 in a Paget's Disease of Bone Cohort Indicates an Important Role for the Nuclear Localization Signal of ZNF687. Calcif Tissue Int 2023; 113:552-557. [PMID: 37728743 DOI: 10.1007/s00223-023-01137-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023]
Abstract
Paget's disease of bone (PDB) is a common, late-onset bone disorder, characterized by focal increases of bone turnover that can result in bone lesions. Heterozygous pathogenic variants in the Sequestosome 1 (SQSTM1) gene are found to be the main genetic cause of PDB. More recently, PFN1 and ZNF687 have been identified as causal genes in patients with a severe, early-onset, polyostotic form of PDB, and an increased likelihood to develop giant cell tumors. In our study, we screened the coding regions of PFN1 and ZNF687 in a Belgian PDB cohort (n = 188). In the PFN1 gene, no variants could be identified, supporting the observation that variants in this gene are extremely rare in PDB. However, we identified 3 non-synonymous coding variants in ZNF687. Interestingly, two of these rare variants (p.Pro937His and p.Arg939Cys) were clustering in the nuclear localization signal of the encoded ZNF687 protein, also harboring the p.Pro937Arg variant, a previously reported disease-causing variant. In conclusion, our findings support the involvement of genetic variation in ZNF687 in the pathogenesis of classical PDB, thereby expanding its mutational spectrum.
Collapse
Affiliation(s)
- Yentl Huybrechts
- Center of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Raphaël De Ridder
- Center of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Ellen Steenackers
- Center of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Jean-Pierre Devogelaer
- Department of Rheumatology, Saint-Luc University Hospital, Université Catholique de Louvain, Brussels, Belgium
| | - Geert Mortier
- Laboratory for Skeletal Dysplasia Research, Department of Human Genetics, KU Leuven and University Hospital Leuven, Louvain, Belgium
| | - Gretl Hendrickx
- Laboratory for Skeletal Dysplasia Research, Department of Human Genetics, KU Leuven and University Hospital Leuven, Louvain, Belgium
| | - Wim Van Hul
- Center of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium.
| |
Collapse
|
16
|
Ali Z, Godoy-Corchuelo JM, Martins-Bach AB, Garcia-Toledo I, Fernández-Beltrán LC, Nair RR, Spring S, Nieman BJ, Jimenez-Coca I, Bains RS, Forrest H, Lerch JP, Miller KL, Fisher EMC, Cunningham TJ, Corrochano S. Mutation in the FUS nuclear localisation signal domain causes neurodevelopmental and systemic metabolic alterations. Dis Model Mech 2023; 16:dmm050200. [PMID: 37772684 PMCID: PMC10642611 DOI: 10.1242/dmm.050200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
Variants in the ubiquitously expressed DNA/RNA-binding protein FUS cause aggressive juvenile forms of amyotrophic lateral sclerosis (ALS). Most FUS mutation studies have focused on motor neuron degeneration; little is known about wider systemic or developmental effects. We studied pleiotropic phenotypes in a physiological knock-in mouse model carrying the pathogenic FUSDelta14 mutation in homozygosity. RNA sequencing of multiple organs aimed to identify pathways altered by the mutant protein in the systemic transcriptome, including metabolic tissues, given the link between ALS-frontotemporal dementia and altered metabolism. Few genes were commonly altered across all tissues, and most genes and pathways affected were generally tissue specific. Phenotypic assessment of mice revealed systemic metabolic alterations related to the pathway changes identified. Magnetic resonance imaging brain scans and histological characterisation revealed that homozygous FUSDelta14 brains were smaller than heterozygous and wild-type brains and displayed significant morphological alterations, including a thinner cortex, reduced neuronal number and increased gliosis, which correlated with early cognitive impairment and fatal seizures. These findings show that the disease aetiology of FUS variants can include both neurodevelopmental and systemic alterations.
Collapse
Affiliation(s)
- Zeinab Ali
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxfordshire OX11 ORD, UK
| | - Juan M. Godoy-Corchuelo
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
| | - Aurea B. Martins-Bach
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford OX3 9D, UK
| | - Irene Garcia-Toledo
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
| | - Luis C. Fernández-Beltrán
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
- Department of Medicine, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Remya R. Nair
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxfordshire OX11 ORD, UK
| | - Shoshana Spring
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M57 3H7, Canada
| | - Brian J. Nieman
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M57 3H7, Canada
| | - Irene Jimenez-Coca
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
| | - Rasneer S. Bains
- Mary Lyon Centre at MRC Harwell, Didcot, Oxfordshire OX11 ORD, UK
| | - Hamish Forrest
- Mary Lyon Centre at MRC Harwell, Didcot, Oxfordshire OX11 ORD, UK
| | - Jason P. Lerch
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford OX3 9D, UK
| | - Karla L. Miller
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford OX3 9D, UK
| | - Elizabeth M. C. Fisher
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Thomas J. Cunningham
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxfordshire OX11 ORD, UK
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, University College London, London W1W 7FF, UK
| | - Silvia Corrochano
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxfordshire OX11 ORD, UK
| |
Collapse
|
17
|
Lee J, Kwon YE, Edwards SD, Guim H, Jae Jeong K. Improved biocompatibility of dendrimer-based gene delivery by histidine-modified nuclear localization signals. Int J Pharm 2023; 644:123299. [PMID: 37558147 DOI: 10.1016/j.ijpharm.2023.123299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/29/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
Polyamidoamine (PAMAM) dendrimers have been explored as an alternative to polyethylenimine (PEI) as a gene delivery carrier because of their relatively low cytotoxicity and excellent biocompatibility. The transfection efficiency of PAMAM dendrimers can be improved by the addition of nuclear localization signal (NLS), a positively charged peptide sequence recognized by cargo proteins in the cytoplasm for nuclear transport. However, increased positive charges from NLS can cause damage to the cytoplasmic and mitochondrial membranes and lead to reactive oxygen species (ROS)-induced cytotoxicity. This negative effect of NLS can be negated without a significant reduction in transfection efficiency by adding histidine, an essential amino acid known as a natural antioxidant, to NLS. However, little is known about the exact mechanism by which histidine reduces cytotoxicity of NLS-modified dendrimers. In this study, we selected cystamine core PAMAM dendrimer generation 2 (cPG2) and conjugated it with NLS derived from Merkel cell polyomavirus large T antigen and histidine (n = 0-3) to improve transfection efficiency and reduce cytoxicity. NLS-modified cPG2 derivatives showed similar or higher transfection efficiency than PEI 25 kDa in NIH3T3 and human mesenchymal stem cells (hMSC). The cytotoxicity of NLS-modified cPG2 derivatives was substantially lower than PEI 25 kDa and was further reduced as the number of histidine in NLS increased. To understand the mechanism of cytoprotective effect of histidine-conjugated NLS, we examined ROS scavenging, hydroxyl radical generation and mitochondrial membrane potential as a function of the number of histidine in NLS. As the number of hisidine increased, cPG2 scavenged ROS more effectively as evidenced by the hydroxyl radical antioxidant capacity (HORAC) assay. This was consistent with the reduced intracellular hydroxyl radical concentration measured by 2',7'-dichlorodihydrofluorescein diacetate (DCFDA) assay in NIH3T3. Finally, fluorescence imaging with JC-1 confirmed that the mitochondrial membranes of NIH 3T3 were well-protected during the transfection when NLS contained histidine. These experimental results confirm the hypothesis that histidine residues scavenge ROS that is generated during the transfection process, preventing the excessive damage to mitochondrial membranes, leading to reduced cytotoxicity.
Collapse
Affiliation(s)
- Jeil Lee
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Yong-Eun Kwon
- Center for Scientific Instrumentation, Korea Basic Science Institute, 169-148 Gwahak-ro, Yuseong-gu, Daejeon 34133, Republic of Korea
| | - Seth D Edwards
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Hwanuk Guim
- Research Center for Materials Analysis, Korea Basic Science Institute, 169-148 Gwahak-ro, Yuseong-gu, Daejeon 34133, Republic of Korea
| | - Kyung Jae Jeong
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire 03824, United States.
| |
Collapse
|
18
|
Hyodo T, Honda A, Yamate S, Kubo Y, Komatsu M, Shiozaki K. Elucidation of the mechanism of nuclear localization of Mexican tetra Neu4 via bipartite nuclear localization signal and less conserved regions. Biochimie 2023; 212:123-134. [PMID: 37094779 DOI: 10.1016/j.biochi.2023.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/01/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
Nuclear sialoglycans are minor components in the nucleus, and their biological significance was not well understood. Recently, Nile tilapia Neu4 sialidase (OnNeu4) was identified and reported as the first nuclear sialidase in vertebrates. Although OnNeu4 possesses the nuclear localization signal (NLS) required for nuclear localization, other fish Neu4 sialidases, such as zebrafish and Japanese medaka, also possess NLS, but their subcellular localizations are not nucleus. To understand the nuclear localization mechanism of fish Neu4, we focused on Mexican tetra Neu4 (AmNeu4), which, unlike Neu4 in other fishes, has a bipartite NLS. AmNeu4 exhibited a wide range of optimal pH and substrate specificity, and its gene expression was specifically detected in the liver, spleen, and gut in adult fish. AmNeu4, like OnNeu4, exhibited nuclear localization, which was attenuated by importin inhibitor, and deletion of the bipartite NLS completely reduced the nuclear localization. In addition, the conjugation of the bipartite NLS of AmNeu4 made GFP show nuclear localization. To understand the mechanism of nuclear localization of AmNeu4 and OnNeu4, we compared fish Neu4 amino acid sequences and focused on the less conserved region of Neu4 sialidase (LCR). LCR-deletion mutants of AmNeu4 and OnNeu4 showed significantly reduced the nuclear localization. The LCR region in AmNeu4 and OnNeu4 possessed consecutive Ser/Thr. The Neu4 mutants in which consecutive Ser/Thr in LCR were changed to Ala or deleted significantly suppressed the nuclear localization. These results suggest that the nuclear localization of Neu4 in Nile tilapia and Mexican tetra may be regulated by NLS and LCR.
Collapse
Affiliation(s)
- Toshiki Hyodo
- Department of Food Life Sciences, Faculty of Fisheries, Kagoshima University, Kagoshima, Japan
| | - Akinobu Honda
- Course of Biological Science and Technology, The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan; Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Satsuki Yamate
- Department of Food Life Sciences, Faculty of Fisheries, Kagoshima University, Kagoshima, Japan
| | - Yurina Kubo
- Department of Food Life Sciences, Faculty of Fisheries, Kagoshima University, Kagoshima, Japan
| | - Masaharu Komatsu
- Department of Food Life Sciences, Faculty of Fisheries, Kagoshima University, Kagoshima, Japan; Course of Biological Science and Technology, The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Kazuhiro Shiozaki
- Department of Food Life Sciences, Faculty of Fisheries, Kagoshima University, Kagoshima, Japan; Course of Biological Science and Technology, The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.
| |
Collapse
|
19
|
Aoki M, Aoki-Ogata H, Bulut H, Hayashi H, Takamune N, Kishimoto N, Tanaka H, Higashi-Kuwata N, Hattori SI, Das D, Venkateswara Rao K, Iwama K, Davis DA, Hasegawa K, Murayama K, Yarchoan R, Ghosh AK, Pau AK, Machida S, Misumi S, Mitsuya H. GRL-142 binds to and impairs HIV-1 integrase nuclear localization signal and potently suppresses highly INSTI-resistant HIV-1 variants. Sci Adv 2023; 9:eadg2955. [PMID: 37436982 PMCID: PMC10337902 DOI: 10.1126/sciadv.adg2955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
Nuclear localization signal (NLS) of HIV-1 integrase (IN) is implicated in nuclear import of HIV-1 preintegration complex (PIC). Here, we established a multiclass drug-resistant HIV-1 variant (HIVKGD) by consecutively exposing an HIV-1 variant to various antiretroviral agents including IN strand transfer inhibitors (INSTIs). HIVKGD was extremely susceptible to a previously reported HIV-1 protease inhibitor, GRL-142, with IC50 of 130 femtomolar. When cells were exposed to HIVKGD IN-containing recombinant HIV in the presence of GRL-142, significant decrease of unintegrated 2-LTR circular cDNA was observed, suggesting that nuclear import of PIC was severely compromised by GRL-142. X-ray crystallographic analyses revealed that GRL-142 interacts with NLS's putative sequence (DQAEHLK) and sterically blocks the nuclear transport of GRL-142-bound HIVKGD's PIC. Highly INSTI-resistant HIV-1 variants isolated from heavily INSTI-experienced patients proved to be susceptible to GRL-142, suggesting that NLS-targeting agents would serve as salvage therapy agents for highly INSTI-resistant variant-harboring individuals. The data should offer a new modality to block HIV-1 infectivity and replication and shed light on developing NLS inhibitors for AIDS therapy.
Collapse
Affiliation(s)
- Manabu Aoki
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Medical Technology, Kumamoto Health Science University, Kumamoto, Japan
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Hiromi Aoki-Ogata
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Haydar Bulut
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hironori Hayashi
- Department of Intelligent Network for Infection Control, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of infectious Diseases, International Research Institute of Disaster Science, Tohoku University, Miyagi, Japan
| | - Nobutoki Takamune
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Naoki Kishimoto
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroki Tanaka
- Department of Structural Virology, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Shin-Ichiro Hattori
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Debananda Das
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Kazuya Iwama
- Department of Intelligent Network for Infection Control, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of infectious Diseases, International Research Institute of Disaster Science, Tohoku University, Miyagi, Japan
| | - David A Davis
- Viral Oncology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kazuya Hasegawa
- Structural Biology Division, Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Kazutaka Murayama
- Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Miyagi, Japan
| | - Robert Yarchoan
- Viral Oncology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arun K Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN, USA
| | - Alice K Pau
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shinichi Machida
- Department of Structural Virology, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Shogo Misumi
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroaki Mitsuya
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Division of Clinical Sciences, Kumamoto University Hospital, Kumamoto, Japan
| |
Collapse
|
20
|
Lee RS, Geronimo CL, Liu L, Twarowski JM, Malkova A, Zakian VA. Identification of the nuclear localization signal in the Saccharomyces cerevisiae Pif1 DNA helicase. PLoS Genet 2023; 19:e1010853. [PMID: 37486934 PMCID: PMC10399864 DOI: 10.1371/journal.pgen.1010853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/03/2023] [Accepted: 07/02/2023] [Indexed: 07/26/2023] Open
Abstract
Saccharomyces cerevisiae Pif1 is a multi-functional DNA helicase that plays diverse roles in the maintenance of the nuclear and mitochondrial genomes. Two isoforms of Pif1 are generated from a single open reading frame by the use of alternative translational start sites. The Mitochondrial Targeting Signal (MTS) of Pif1 is located between the two start sites, but a Nuclear Localization Signal (NLS) has not been identified. Here we used sequence and functional analysis to identify an NLS element. A mutant allele of PIF1 (pif1-NLSΔ) that lacks four basic amino acids (781KKRK784) in the carboxyl-terminal domain of the 859 amino acid Pif1 was expressed at wild type levels and retained wild type mitochondrial function. However, pif1-NLSΔ cells were defective in four tests for nuclear function: telomere length maintenance, Okazaki fragment processing, break-induced replication (BIR), and binding to nuclear target sites. Fusing the NLS from the simian virus 40 (SV40) T-antigen to the Pif1-NLSΔ protein reduced the nuclear defects of pif1-NLSΔ cells. Thus, four basic amino acids near the carboxyl end of Pif1 are required for the vast majority of nuclear Pif1 function. Our study also reveals phenotypic differences between the previously described loss of function pif1-m2 allele and three other pif1 mutant alleles generated in this work, which will be useful to study nuclear Pif1 functions.
Collapse
Affiliation(s)
- Rosemary S. Lee
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Carly L. Geronimo
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Liping Liu
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Jerzy M. Twarowski
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Virginia A. Zakian
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| |
Collapse
|
21
|
Liu S, Deng S, Li X, Chen J, Yuan Y, Zhao H, Zhou J, Wang J, Zhang H, Cheng D. Endosomal Escapable and Nuclear Localizing Cationic Polyaspartate-Based CRISPR Activation System for Preventing Respiratory Virus Infection by Specifically Inducing Interferon-λ. ACS Appl Mater Interfaces 2022; 14:55376-55391. [PMID: 36503225 DOI: 10.1021/acsami.2c16588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Global pandemics caused by viruses cause widespread panic and economic losses. The lack of specific antivirals and vaccines increases the spreading of viral diseases worldwide. Thus, alternative strategies are required to manage viral outbreaks. Here, we develop a CRISPR activation (CRISPRa) system based on polymeric carriers to prevent respiratory virus infection in a mouse model. A polyaspartate grafted with 2-(diisopropylamino) ethylamine (DIP) and nuclear localization signal peptides (NLS-MTAS fusion peptide) was complexed with plasmid DNA (pDNA) encoding dCas9-VPR and sgRNA targeting IFN-λ. The pH-sensitive DIP and NLS-MTAS groups were favor of endo-lysosomal escape and nuclear localization of pDNA, respectively. They synergistically improved gene transfection efficiency, resulting in significant reporter gene expression and IFN-λ upregulation in lung tissue. In vitro and in vivo prophylactic experiments showed that the non-viral CRISPRa system could prevent infection caused by H1N1 viruses with minimal inflammatory responses, presenting a promising prophylactic approach against respiratory virus infections.
Collapse
Affiliation(s)
- Shuang Liu
- Key Laboratory for Polymeric Composite & Functional Materials of Ministry of Education, School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou510275, PR China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510275, PR China
| | - Shaohui Deng
- Key Laboratory for Polymeric Composite & Functional Materials of Ministry of Education, School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou510275, PR China
| | - Xiaoxia Li
- Key Laboratory for Polymeric Composite & Functional Materials of Ministry of Education, School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou510275, PR China
| | - Jifeng Chen
- Key Laboratory for Polymeric Composite & Functional Materials of Ministry of Education, School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou510275, PR China
| | - Yaochang Yuan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510275, PR China
| | - Hanjun Zhao
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong999077, PR China
| | - Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong999077, PR China
| | - Jin Wang
- Department of Radiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou510630, PR China
| | - Hui Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510275, PR China
| | - Du Cheng
- Key Laboratory for Polymeric Composite & Functional Materials of Ministry of Education, School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou510275, PR China
| |
Collapse
|
22
|
Rizzuti B, Iovanna JL, Neira JL. Deciphering the Binding of the Nuclear Localization Sequence of Myc Protein to the Nuclear Carrier Importin α3. Int J Mol Sci 2022; 23:ijms232315333. [PMID: 36499669 PMCID: PMC9739371 DOI: 10.3390/ijms232315333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The oncoprotein Myc is a transcription factor regulating global gene expression and modulating cell proliferation, apoptosis, and metabolism. Myc has a nuclear localization sequence (NLS) comprising residues Pro320 to Asp328, to allow for nuclear translocation. We designed a peptide comprising such region and the flanking residues (Ala310-Asn339), NLS-Myc, to study, in vitro and in silico, the ability to bind importin α3 (Impα3) and its truncated species (ΔImpα3) depleted of the importin binding domain (IBB), by using fluorescence, circular dichroism (CD), biolayer interferometry (BLI), nuclear magnetic resonance (NMR), and molecular simulations. NLS-Myc interacted with both importin species, with affinity constants of ~0.5 µM (for Impα3) and ~60 nM (for ΔImpα3), as measured by BLI. The molecular simulations predicted that the anchoring of NLS-Myc took place in the major binding site of Impα3 for the NLS of cargo proteins. Besides clarifying the conformational behavior of the isolated NLS of Myc in solution, our results identified some unique properties in the binding of this localization sequence to the nuclear carrier Impα3, such as a difference in the kinetics of its release mechanism depending on the presence or absence of the IBB domain.
Collapse
Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
- Instituto de Biocomputación y Física de Sistemas Complejos–Unidad Mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Correspondence: (B.R.); (J.L.N.)
| | - Juan L. Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille Université, 13288 Marseille, France
| | - José L. Neira
- Instituto de Biocomputación y Física de Sistemas Complejos–Unidad Mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDIBE), Universidad Miguel Hernández, 03202 Elche, Spain
- Correspondence: (B.R.); (J.L.N.)
| |
Collapse
|
23
|
Walunj SB, Wang C, Wagstaff KM, Patankar S, Jans DA. Conservation of Importin α Function in Apicomplexans: Ivermectin and GW5074 Target Plasmodium falciparum Importin α and Inhibit Parasite Growth in Culture. Int J Mol Sci 2022; 23:ijms232213899. [PMID: 36430384 PMCID: PMC9695642 DOI: 10.3390/ijms232213899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Signal-dependent transport into and out of the nucleus mediated by members of the importin (IMP) superfamily of nuclear transporters is critical to the eukaryotic function and a point of therapeutic intervention with the potential to limit disease progression and pathogenic outcomes. Although the apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii both retain unique IMPα genes that are essential, a detailed analysis of their properties has not been performed. As a first step to validate apicomplexan IMPα as a target, we set out to compare the properties of P. falciparum and T. gondii IMPα (PfIMPα and TgIMPα, respectively) to those of mammalian IMPα, as exemplified by Mus musculus IMPα (MmIMPα). Close similarities were evident, with all three showing high-affinity binding to modular nuclear localisation signals (NLSs) from apicomplexans as well as Simian virus SV40 large tumour antigen (T-ag). PfIMPα and TgIMPα were also capable of binding to mammalian IMPβ1 (MmIMPβ1) with high affinity; strikingly, NLS binding by PfIMPα and TgIMPα could be inhibited by the mammalian IMPα targeting small molecules ivermectin and GW5074 through direct binding to PfIMPα and TgIMPα to perturb the α-helical structure. Importantly, GW5074 could be shown for the first time to resemble ivermectin in being able to limit growth of P. falciparum. The results confirm apicomplexan IMPα as a viable target for the development of therapeutics, with agents targeting it worthy of further consideration as an antimalarial.
Collapse
Affiliation(s)
- Sujata B. Walunj
- Molecular Parasitology Lab., Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
- Nuclear Signalling Lab., Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Monash, VIC 3800, Australia
| | - Chunxiao Wang
- Nuclear Signalling Lab., Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Monash, VIC 3800, Australia
| | - Kylie M. Wagstaff
- Nuclear Signalling Lab., Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Monash, VIC 3800, Australia
| | - Swati Patankar
- Molecular Parasitology Lab., Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - David A. Jans
- Nuclear Signalling Lab., Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Monash, VIC 3800, Australia
- Correspondence:
| |
Collapse
|
24
|
Huang C, Han Z, Evangelopoulos M, Mirkin CA. CRISPR Spherical Nucleic Acids. J Am Chem Soc 2022; 144:18756-18760. [PMID: 36201634 PMCID: PMC10430604 DOI: 10.1021/jacs.2c07913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of CRISPR/Cas9 systems in genome editing has been limited by the inability to efficiently deliver the key editing components to and across tissues and cell membranes, respectively. Spherical nucleic acids (SNAs) are nanostructures that provide privileged access to both but have yet to be explored as a means of facilitating gene editing. Herein, a new class of CRISPR SNAs are designed and evaluated in the context of genome editing. Specifically, Cas9 ProSNAs comprised of Cas9 cores densely modified with DNA on their exteriors and preloaded with single-guide RNA were synthesized and evaluated for their genome editing capabilities in the context of multiple cell lines. The radial orientation of the DNA on the Cas9 protein surface enhances cellular uptake, without the need for electroporation or transfection agents. In addition, the Cas9 proteins defining the cores of the ProSNAs were fused with GALA peptides on their N-termini and nuclear localization signals on their C-termini to facilitate endosomal escape and maximize nuclear localization and editing efficiency, respectively. These constructs were stable against protease digestion under conditions that fully degrade the Cas9 protein, when not transformed into an SNA, and used to achieve genome editing efficiency between 32 and 47%. Taken together, these novel constructs and advances point toward a way of significantly broadening the scope of use and impact of CRISPR-Cas9 genome editing systems.
Collapse
Affiliation(s)
- Chi Huang
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Zhenyu Han
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael Evangelopoulos
- Department of Biomedical Engineering and International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Chad A. Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208-3113, United States
- Department of Biomedical Engineering and International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208-3113, United States
| |
Collapse
|
25
|
Tang Q, Liu Y, Liu Y, Zhu F, Yu Q, Chen H, Chen L, Ma S, Xu H, Chen K, Li G. Bombyx mori Flap endonuclease 1 correlates with the repair of ultraviolet-induced DNA damage. J Insect Physiol 2022; 142:104424. [PMID: 35878701 DOI: 10.1016/j.jinsphys.2022.104424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Solar ultraviolet radiation (UV) can cause DNA damage in microorganisms. Flap endonuclease 1 (FEN1) is a structure-specific nuclease and plays important roles in DNA replication and repair. At present, the properties and functions of FEN1 have not been characterized in detail in invertebrates such as Bombyx mori. In this study, Bombyx mori FEN1 (BmFEN1) was expressed in E. coli, and was shown to have nuclease activity that nonspecifically cleaved DNA in vitro. However, inside the cell, BmFEN1 did not cleave DNA randomly. Truncated BmFEN1 missing the nuclear localization signal (346-380 aa) still had the nuclease activity, but was no longer precisely localized to the sites of UV-induced DNA damage. It was further found that BmFEN1 favored the faster repair of UV-damaged DNA. The present study will provide a reference for further understanding the functions of BmFEN1 and UV-induced DNA damage repair mechanisms in insects.
Collapse
Affiliation(s)
- Qi Tang
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Yue Liu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Yutong Liu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Feifei Zhu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Qian Yu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Huiqing Chen
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Liang Chen
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Shangshang Ma
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Huixin Xu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China.
| | - Guohui Li
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China.
| |
Collapse
|
26
|
Shinkado S, Saito H, Yamazaki M, Kotera S, Arazoe T, Arie T, Kamakura T. Genome editing using a versatile vector-based CRISPR/Cas9 system in Fusarium species. Sci Rep 2022; 12:16243. [PMID: 36171473 PMCID: PMC9519947 DOI: 10.1038/s41598-022-20697-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022] Open
Abstract
Fusarium species include important filamentous fungal pathogens that can infect plants, animals, and humans. Meanwhile, some nonpathogenic Fusarium species are promising biocontrol agents against plant pathogens. Here, we developed a genome editing technology using a vector-based CRISPR/Cas9 system for Fusarium oxysporum f. sp. lycopersici (Fol). This optimized CRISPR/Cas9 system, harboring an endogenous U6 small nuclear RNA promoter for the expression of single-guide RNA and an endogenous H2B nuclear localization signal for the localization of Cas9, enabled efficient targeted gene knock-out, including in the accessory chromosomal regions in Fol. We further demonstrated single crossover-mediated targeted base editing and endogenous gene tagging. This system was also applicable for genome editing in F. oxysporum f. sp. spinaciae and F. commune without any modifications, suggesting that this CRISPR/Cas9 vector has a potential application for a broad range of researches on other Fusarium species.
Collapse
Affiliation(s)
- Sota Shinkado
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Hiroki Saito
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-0054, Japan
- Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Masaya Yamazaki
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Shunsuke Kotera
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-0054, Japan
| | - Takayuki Arazoe
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
| | - Tsutomu Arie
- Faculty of Agriculture, Institute of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-0054, Japan.
| | - Takashi Kamakura
- Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
| |
Collapse
|
27
|
Somashekara SC, Muniyappa K. Dual targeting of Saccharomyces cerevisiae Pso2 to mitochondria and the nucleus, and its functional relevance in the repair of DNA interstrand crosslinks. G3 (Bethesda) 2022; 12:jkac066. [PMID: 35482533 PMCID: PMC9157068 DOI: 10.1093/g3journal/jkac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/15/2022] [Indexed: 11/12/2022]
Abstract
Repair of DNA interstrand crosslinks involves a functional interplay among different DNA surveillance and repair pathways. Previous work has shown that interstrand crosslink-inducing agents cause damage to Saccharomyces cerevisiae nuclear and mitochondrial DNA, and its pso2/snm1 mutants exhibit a petite phenotype followed by loss of mitochondrial DNA integrity and copy number. Complex as it is, the cause and underlying molecular mechanisms remains elusive. Here, by combining a wide range of approaches with in vitro and in vivo analyses, we interrogated the subcellular localization and function of Pso2. We found evidence that the nuclear-encoded Pso2 contains 1 mitochondrial targeting sequence and 2 nuclear localization signals (NLS1 and NLS2), although NLS1 resides within the mitochondrial targeting sequence. Further analysis revealed that Pso2 is a dual-localized interstrand crosslink repair protein; it can be imported into both nucleus and mitochondria and that genotoxic agents enhance its abundance in the latter. While mitochondrial targeting sequence is essential for mitochondrial Pso2 import, either NLS1 or NLS2 is sufficient for its nuclear import; this implies that the 2 nuclear localization signal motifs are functionally redundant. Ablation of mitochondrial targeting sequence abrogated mitochondrial Pso2 import, and concomitantly, raised its levels in the nucleus. Strikingly, mutational disruption of both nuclear localization signal motifs blocked the nuclear Pso2 import; at the same time, they enhanced its translocation into the mitochondria, consistent with the notion that the relationship between mitochondrial targeting sequence and nuclear localization signal motifs is competitive. However, the nuclease activity of import-deficient species of Pso2 was not impaired. The potential relevance of dual targeting of Pso2 into 2 DNA-bearing organelles is discussed.
Collapse
Affiliation(s)
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| |
Collapse
|
28
|
Liu HT, Zou YX, Zhu WJ, Sen-Liu, Zhang GH, Ma RR, Guo XY, Gao P. lncRNA THAP7-AS1, transcriptionally activated by SP1 and post-transcriptionally stabilized by METTL3-mediated m6A modification, exerts oncogenic properties by improving CUL4B entry into the nucleus. Cell Death Differ 2022; 29:627-641. [PMID: 34608273 PMCID: PMC8901790 DOI: 10.1038/s41418-021-00879-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 11/09/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are dysregulated in different cancer types, and thus have emerged as important regulators of the initiation and progression of human cancers. However, the biological functions and the underlying mechanisms responsible for their functions in gastric cancer (GC) remain poorly understood. Here, by lncRNA microarray, we identified 1414 differentially expressed lncRNAs, among which THAP7-AS1 was significantly upregulated in GC tissues compared with non-tumorous gastric tissues. High expression of THAP7-AS1 was correlated with positive lymph node metastasis and poorer prognosis. SP1, a transcription factor, could bind directly to the THAP7-AS1 promoter region and activate its transcription. Moreover, the m6A modification of THAP7-AS1 by METTL3 enhanced its expression depending on the "reader" protein IGF2BP1-dependent pathway. THAP7-AS1 promoted GC cell progression. Mechanistically, THAP7-AS1 interacted with the 1-50 Amino Acid Region (nuclear localization signal) of CUL4B through its 1-442 nt Sequence, and it promoted interaction between nuclear localization signal (NLS) and importin α1, and improved the CUL4B protein entry into the nucleus, repressing miR-22-3p and miR-320a expression by CUL4B-catalyzed H2AK119ub1 and the EZH2-mediated H3K27me3, subsequently activating PI3K/AKT signaling pathway to promote GC progression. Moreover, LV-sh-THAP7-AS1 treatment could suppress GC growth, invasion and metastasis, indicating that THAP7-AS1 may act as a promising molecular target for GC therapies. Taken together, our results show that THAP7-AS1, transcriptionally activated by SP1 and then modified by METTL3-mediated m6A, exerts oncogenic functions, by promoting interaction between NLS and importin α1 and then improving the CUL4B protein entry into the nucleus to repress the transcription of miR-22-3p and miR-320a.
Collapse
Affiliation(s)
- Hai-Ting Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, P.R. China
- Department of Pathology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, P.R. China
| | - Yong-Xin Zou
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, P.R. China
| | - Wen-Jie Zhu
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, P.R. China
| | - Sen-Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, P.R. China
| | - Guo-Hao Zhang
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, P.R. China
| | - Ran-Ran Ma
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, P.R. China
| | - Xiang-Yu Guo
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, P.R. China
| | - Peng Gao
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, P.R. China.
- Department of Pathology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, P.R. China.
| |
Collapse
|
29
|
Kalyvianaki K, Panagiotopoulos AA, Patentalaki M, Castanas E, Kampa M. Importins involved in the nuclear transportation of steroid hormone receptors: In silico and in vitro data. Front Endocrinol (Lausanne) 2022; 13:954629. [PMID: 36147566 PMCID: PMC9487861 DOI: 10.3389/fendo.2022.954629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
The nuclear receptor superfamily (NRS) consists of 48 receptors for lipophilic substances and is divided into 7 different subfamilies, with subfamily 3 comprising steroid hormone receptors. Several nuclear receptors usually bind their cognate ligands in the cytosol and the complex (mono- or dimerized) is transported to the nucleus, where it acts as a transcription initiating factor for a number of genes. The general structure of nuclear receptors consists of an N-terminal activating domain (A/B), important for the binding of activating or inhibitory co-factors, the DNA-binding domain (C), responsible for the association of the receptor-ligand-co-factor complex to the nucleus, the ligand-AF2 domain (E/F), where ligand binding occurs as well as that of ligand-dependent activating/inhibiting factors, and a flexible/non-structured domain (D), linking the DBD and LBD, called hinge region, on which a significant number of post-translational modifications occur. This hinge domain, for the sub-class of steroid receptors, is a non-structured domain and was reported as mainly responsible for the nuclear transport of steroid receptors, since it contains a specific amino acid sequence (Nuclear Localization Signal-NLS), recognized by importin α. In addition to the importin α/β complex, a number of other importins have been discovered and reported to be responsible for the nuclear transport of a number of significant proteins; however, the corresponding recognition sequences for these importins have not been identified. Recently, we have reported the identification of the NLS sequences for importins 4, 5 and 7. In this work, we provide in silico data, followed by experimental in vitro validation, showing that these alternative importins are responsible for the nuclear transportation of steroid hormone receptors such as ERα, AR and PR, and therefore they may consist of alternative targets for the pharmacological manipulation of steroid hormone actions. Moreover, we provide additional in silico data for the hinge region of steroid hormone receptors which is highly enriched with NLS sequences for importins 4, 5 and 7, in addition to the recognition NLS for importin α/β.
Collapse
|
30
|
Wang LY, Xiao SJ, Kunimoto H, Tokunaga K, Kojima H, Kimura M, Yamamoto T, Yamamoto N, Zhao H, Nishio K, Tani T, Nakajima K, Sunami K, Inoue A. Sequestration of RBM10 in Nuclear Bodies: Targeting Sequences and Biological Significance. Int J Mol Sci 2021; 22:ijms221910526. [PMID: 34638866 PMCID: PMC8508765 DOI: 10.3390/ijms221910526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/26/2022] Open
Abstract
RBM10 is an RNA-binding protein that regulates alternative splicing (AS). It localizes to the extra-nucleolar nucleoplasm and S1-1 nuclear bodies (NBs) in the nucleus. We investigated the biological significance of this localization in relation to its molecular function. Our analyses, employing deletion mutants, revealed that RBM10 possesses two S1-1 NB-targeting sequences (NBTSs), one in the KEKE motif region and another in the C2H2 Zn finger (ZnF). These NBTSs act synergistically to localize RBM10 to S1-1 NBs. The C2H2 ZnF not only acts as an NBTS, but is also essential for AS regulation by RBM10. Moreover, RBM10 does not participate in S1-1 NB formation, and without alterations of RBM10 protein levels, its NB-localization changes, increasing as cellular transcriptional activity declines, and vice versa. These results indicate that RBM10 is a transient component of S1-1 NBs and is sequestered in NBs via its NBTSs when cellular transcription decreases. We propose that the C2H2 ZnF exerts its NB-targeting activity when RBM10 is unbound by pre-mRNAs, and that NB-localization of RBM10 is a mechanism to control its AS activity in the nucleus.
Collapse
Affiliation(s)
- Ling-Yu Wang
- Department of Immunology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan; (L.-Y.W.); (S.-J.X.); (H.K.); (H.K.); (H.Z.); (K.N.)
- Department of Human Genetics, Guilin Medical University, Guilin 541004, China
| | - Sheng-Jun Xiao
- Department of Immunology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan; (L.-Y.W.); (S.-J.X.); (H.K.); (H.K.); (H.Z.); (K.N.)
- Department of Pathology, Guilin Medical University, Guilin 541004, China
| | - Hiroyuki Kunimoto
- Department of Immunology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan; (L.-Y.W.); (S.-J.X.); (H.K.); (H.K.); (H.Z.); (K.N.)
| | - Kazuaki Tokunaga
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan; (K.T.); (T.T.)
| | - Hirotada Kojima
- Department of Immunology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan; (L.-Y.W.); (S.-J.X.); (H.K.); (H.K.); (H.Z.); (K.N.)
| | - Masatsugu Kimura
- Radioisotope Center, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan;
| | - Takahiro Yamamoto
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan;
| | - Naoki Yamamoto
- Center for Basic Medical Research, and Graduate School of Pharmaceutical Sciences, International University of Health and Welfare, Ohtawara 324-8501, Japan;
- Laboratory of Neurobiology, Graduate School of Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Hong Zhao
- Department of Immunology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan; (L.-Y.W.); (S.-J.X.); (H.K.); (H.K.); (H.Z.); (K.N.)
| | - Koji Nishio
- Department of Anatomy and Neurosciences, Graduate School of Medicine, Nagoya University, Nagoya 466-8550, Japan;
| | - Tokio Tani
- Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan; (K.T.); (T.T.)
| | - Koichi Nakajima
- Department of Immunology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan; (L.-Y.W.); (S.-J.X.); (H.K.); (H.K.); (H.Z.); (K.N.)
| | - Kishiko Sunami
- Department of Otolaryngology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan;
| | - Akira Inoue
- Department of Immunology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan; (L.-Y.W.); (S.-J.X.); (H.K.); (H.K.); (H.Z.); (K.N.)
- Department of Otolaryngology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan;
- Correspondence:
| |
Collapse
|
31
|
Abstract
Understanding the trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high-quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. The receptor-binding domain of the spike protein and the region of the nucleocapsid protein associated with nuclear localization signals (NLS) are enriched with positively selected amino acid replacements. These replacements form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. Virus diversity within each geographic region has been steadily growing for the entirety of the pandemic, but analysis of the phylogenetic distances between pairs of regions reveals four distinct periods based on global partitioning of the tree and the emergence of key mutations. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. The NLS-associated variants across multiple partitions rose to global prominence in March to July, during a period of stasis in terms of interregional diversity. Finally, beginning in July 2020, multiple mutations, some of which have since been demonstrated to enable antibody evasion, began to emerge associated with ongoing regional diversification, which might be indicative of speciation.
Collapse
Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142;
- HHMI, Massachusetts Institute of Technology, Cambridge, MA 02139
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;
| |
Collapse
|
32
|
Hirota K, Matsuda-Imai N, Kiuchi T, Katsuma S. Characterization of nuclear localization signal in Ostrinia furnacalis Masculinizer protein. Arch Insect Biochem Physiol 2021; 106:e21768. [PMID: 33644912 DOI: 10.1002/arch.21768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/29/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Bombyx mori Masculinizer protein (BmMasc) is essential for both masculinization and dosage compensation in B. mori. We previously identified a bipartite nuclear localization signal (NLS) of BmMasc and two essential residues (lysine at 274 [K274] and arginine at 275 [R275]) implicated in its function. Sequence comparison showed the presence of putative NLSs in lepidopteran Masc proteins, but their functional properties and critical residues are unknown. Here we characterized a putative NLS of Ostrinia furnacalis Masc (OfMasc) using B. mori ovary-derived BmN-4 cell line. Deletion and alanine scanning mutagenesis revealed that a putative NLS is required for nuclear localization of OfMasc. However, mutations at both K227 and R228, which correspond to K274 and R275 of BmMasc, respectively, do not greatly abolish the NLS activity. Additional mutagenesis analysis revealed that triple mutations at K227, R228, and K240 almost completely inhibited OfMasc nuclear localization. These results suggest that lepidopteran Masc proteins possess a common functional NLS, but the critical residues for its activity are different. Moreover, we examined the masculinizing activity of OfMasc derivatives and found that nuclear localization is not required for the masculinizing activity of OfMasc. The results from our studies indicate that lepidopteran Masc proteins function in the cytoplasm to drive masculinizing cascade.
Collapse
Affiliation(s)
- Kanako Hirota
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Noriko Matsuda-Imai
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
33
|
Gonzalez A, Mannen T, Çağatay T, Fujiwara A, Matsumura H, Niesman AB, Brautigam CA, Chook YM, Yoshizawa T. Mechanism of karyopherin-β2 binding and nuclear import of ALS variants FUS(P525L) and FUS(R495X). Sci Rep 2021; 11:3754. [PMID: 33580145 PMCID: PMC7881136 DOI: 10.1038/s41598-021-83196-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/29/2021] [Indexed: 02/06/2023] Open
Abstract
Mutations in the RNA-binding protein FUS cause familial amyotropic lateral sclerosis (ALS). Several mutations that affect the proline-tyrosine nuclear localization signal (PY-NLS) of FUS cause severe juvenile ALS. FUS also undergoes liquid-liquid phase separation (LLPS) to accumulate in stress granules when cells are stressed. In unstressed cells, wild type FUS resides predominantly in the nucleus as it is imported by the importin Karyopherin-β2 (Kapβ2), which binds with high affinity to the C-terminal PY-NLS of FUS. Here, we analyze the interactions between two ALS-related variants FUS(P525L) and FUS(R495X) with importins, especially Kapβ2, since they are still partially localized to the nucleus despite their defective/missing PY-NLSs. The crystal structure of the Kapβ2·FUS(P525L)PY-NLS complex shows the mutant peptide making fewer contacts at the mutation site, explaining decreased affinity for Kapβ2. Biochemical analysis revealed that the truncated FUS(R495X) protein, although missing the PY-NLS, can still bind Kapβ2 and suppresses LLPS. FUS(R495X) uses its C-terminal tandem arginine-glycine-glycine regions, RGG2 and RGG3, to bind the PY-NLS binding site of Kapβ2 for nuclear localization in cells when arginine methylation is inhibited. These findings suggest the importance of the C-terminal RGG regions in nuclear import and LLPS regulation of ALS variants of FUS that carry defective PY-NLSs.
Collapse
Affiliation(s)
- Abner Gonzalez
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Taro Mannen
- College of Life Sciences, Ritsumeikan University, Shiga, Japan
| | - Tolga Çağatay
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ayano Fujiwara
- College of Life Sciences, Ritsumeikan University, Shiga, Japan
| | | | - Ashley B Niesman
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chad A Brautigam
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | | |
Collapse
|
34
|
Abstract
Correct cellular localization is essential for the function of many eukaryotic proteins and hence cell physiology. Here, we present a synthetic genetic device that allows the control of nuclear and cytosolic localization based on controlled alternative splicing in human cells. The device is based on the fact that an alternative 3' splice site is located within a TetR aptamer that in turn is positioned between the branch point and the canonical splice site. The novel splice site is only recognized when the TetR repressor is bound. Addition of doxycycline prevents TetR aptamer binding and leads to recognition of the canonical 3' splice site. It is thus possible to produce two independent splice isoforms. Since the terminal loop of the aptamer may be replaced with any sequence of choice, one of the two isoforms may be extended by the respective sequence of choice depending on the presence of doxycycline. In a proof-of-concept study, we fused a nuclear localization sequence to a cytosolic target protein, thus directing the protein into the nucleus. However, the system is not limited to the control of nuclear localization. In principle, any target sequence can be integrated into the aptamer, allowing not only the production of a variety of different isoforms on demand, but also to study the function of mislocalized proteins. Moreover, it also provides a valuable tool for investigating the mechanism of alternative splicing in human cells.
Collapse
Affiliation(s)
- Adam A Mol
- Department of Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Marc Vogel
- Department of Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| |
Collapse
|
35
|
Komorizono R, Sassa Y, Horie M, Makino A, Tomonaga K. Evolutionary Selection of the Nuclear Localization Signal in the Viral Nucleoprotein Leads to Host Adaptation of the Genus Orthobornavirus. Viruses 2020; 12:v12111291. [PMID: 33187187 PMCID: PMC7698282 DOI: 10.3390/v12111291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/23/2022] Open
Abstract
Adaptation of the viral life cycle to host cells is necessary for efficient viral infection and replication. This evolutionary process has contributed to the mechanism for determining the host range of viruses. Orthobornaviruses, members of the family Bornaviridae, are non-segmented, negative-strand RNA viruses, and several genotypes have been isolated from different vertebrate species. Previous studies revealed that some genotypes isolated from avian species can replicate in mammalian cell lines, suggesting the zoonotic potential of avian orthobornaviruses. However, the mechanism by which the host specificity of orthobornaviruses is determined has not yet been identified. In this study, we found that the infectivity of orthobornaviruses is not determined at the viral entry step, mediated by the viral glycoprotein and matrix protein. Furthermore, we demonstrated that the nuclear localization signal (NLS) sequence in the viral nucleoprotein (N) has evolved under natural selection and determines the host-specific viral polymerase activity. A chimeric mammalian orthobornavirus, which has the NLS sequence of avian orthobornavirus N, exhibited a reduced propagation efficiency in mammalian cells. Our findings indicated that nuclear transport of the viral N is a determinant of the host range of orthobornaviruses, providing insights into the evolution and host adaptation of orthobornaviruses.
Collapse
Affiliation(s)
- Ryo Komorizono
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; (R.K.); (M.H.)
- Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
| | - Yukiko Sassa
- Laboratory of Veterinary Infectious Disease, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan;
| | - Masayuki Horie
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; (R.K.); (M.H.)
- Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8507, Japan
| | - Akiko Makino
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; (R.K.); (M.H.)
- Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
- Correspondence: (A.M.); (K.T.)
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; (R.K.); (M.H.)
- Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
- Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Correspondence: (A.M.); (K.T.)
| |
Collapse
|
36
|
Adams MK, Banks CAS, Thornton JL, Kempf CG, Zhang Y, Miah S, Hao Y, Sardiu ME, Killer M, Hattem GL, Murray A, Katt ML, Florens L, Washburn MP. Differential Complex Formation via Paralogs in the Human Sin3 Protein Interaction Network. Mol Cell Proteomics 2020; 19:1468-1484. [PMID: 32467258 PMCID: PMC8143632 DOI: 10.1074/mcp.ra120.002078] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Indexed: 01/09/2023] Open
Abstract
Despite the continued analysis of HDAC inhibitors in clinical trials, the heterogeneous nature of the protein complexes they target limits our understanding of the beneficial and off-target effects associated with their application. Among the many HDAC protein complexes found within the cell, Sin3 complexes are conserved from yeast to humans and likely play important roles as regulators of transcriptional activity. The presence of two Sin3 paralogs in humans, SIN3A and SIN3B, may result in a heterogeneous population of Sin3 complexes and contributes to our poor understanding of the functional attributes of these complexes. Here, we profile the interaction networks of SIN3A and SIN3B to gain insight into complex composition and organization. In accordance with existing data, we show that Sin3 paralog identity influences complex composition. Additionally, chemical cross-linking MS identifies domains that mediate interactions between Sin3 proteins and binding partners. The characterization of rare SIN3B proteoforms provides additional evidence for the existence of conserved and divergent elements within human Sin3 proteins. Together, these findings shed light on both the shared and divergent properties of human Sin3 proteins and highlight the heterogeneous nature of the complexes they organize.
Collapse
Affiliation(s)
- Mark K Adams
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | | | - Janet L Thornton
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | | | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Sayem Miah
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Yan Hao
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Mihaela E Sardiu
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Maxime Killer
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Gaye L Hattem
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Alexis Murray
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Maria L Katt
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri, USA; Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA.
| |
Collapse
|
37
|
Abstract
Nucleocytoplasmic transport is tightly regulated by the nuclear pore complex (NPC). Among the thousands of molecules that cross the NPC, even very large (>15 nm) cargoes such as pathogens, mRNAs and pre-ribosomes can pass the NPC intact. For these cargoes, there is little quantitative understanding of the requirements for their nuclear import, especially the role of multivalent binding to transport receptors via nuclear localisation sequences (NLSs) and the effect of size on import efficiency. Here, we assayed nuclear import kinetics of 30 large cargo models based on four capsid-like particles in the size range of 17-36 nm, with tuneable numbers of up to 240 NLSs. We show that the requirements for nuclear transport can be recapitulated by a simple two-parameter biophysical model that correlates the import flux with the energetics of large cargo transport through the NPC. Together, our results reveal key molecular determinants of large cargo import in cells.
Collapse
Affiliation(s)
- Giulia Paci
- Biocentre, Johannes Gutenberg-University MainzMainzGermany
- Institute of Molecular BiologyMainzGermany
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Tiantian Zheng
- Department of Physics, University of TorontoTorontoCanada
| | - Joana Caria
- Biocentre, Johannes Gutenberg-University MainzMainzGermany
- Institute of Molecular BiologyMainzGermany
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Anton Zilman
- Department of Physics, University of TorontoTorontoCanada
- Institute for Biomaterials and Biomedical Engineering (IBBME), University of TorontoTorontoCanada
| | - Edward A Lemke
- Biocentre, Johannes Gutenberg-University MainzMainzGermany
- Institute of Molecular BiologyMainzGermany
- European Molecular Biology LaboratoryHeidelbergGermany
| |
Collapse
|
38
|
Sen Nkwe N, Daou S, Uriarte M, Gagnon J, Iannantuono NV, Barbour H, Yu H, Masclef L, Fernández E, Zamorano Cuervo N, Mashtalir N, Binan L, Sergeev M, Bélanger F, Drobetsky E, Milot E, Wurtele H, Costantino S, Affar EB. A potent nuclear export mechanism imposes USP16 cytoplasmic localization during interphase. J Cell Sci 2020; 133:jcs239236. [PMID: 32005696 DOI: 10.1242/jcs.239236] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/13/2020] [Indexed: 01/09/2023] Open
Abstract
USP16 (also known as UBP-M) has emerged as a histone H2AK119 deubiquitylase (DUB) implicated in the regulation of chromatin-associated processes and cell cycle progression. Despite this, available evidence suggests that this DUB is also present in the cytoplasm. How the nucleo-cytoplasmic transport of USP16, and hence its function, is regulated has remained elusive. Here, we show that USP16 is predominantly cytoplasmic in all cell cycle phases. We identified the nuclear export signal (NES) responsible for maintaining USP16 in the cytoplasm. We found that USP16 is only transiently retained in the nucleus following mitosis and then rapidly exported from this compartment. We also defined a non-canonical nuclear localization signal (NLS) sequence that plays a minimal role in directing USP16 into the nucleus. We further established that this DUB does not accumulate in the nucleus following DNA damage. Instead, only enforced nuclear localization of USP16 abolishes DNA double-strand break (DSB) repair, possibly due to unrestrained DUB activity. Thus, in contrast to the prevailing view, our data indicate that USP16 is actively excluded from the nucleus and that this DUB might indirectly regulate DSB repair.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Nadine Sen Nkwe
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - Salima Daou
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Maxime Uriarte
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - Jessica Gagnon
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Institute for Research in Immunology and Cancer, University of Montréal, Montréal, QC H3T 1J4, Canada
| | - Nicholas Victor Iannantuono
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Institute for Research in Immunology and Cancer, University of Montréal, Montréal, QC H3T 1J4, Canada
| | - Haithem Barbour
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - Helen Yu
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumor Research Centre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Louis Masclef
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - Erlinda Fernández
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - Natalia Zamorano Cuervo
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, QC H2X 0A9, Canada
| | - Nazar Mashtalir
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Loïc Binan
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Ophthalmology, University of Montréal, Montréal, Québec, Canada
| | - Mikhail Sergeev
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - François Bélanger
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
| | - Elliot Drobetsky
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - Eric Milot
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - Hugo Wurtele
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - Santiago Costantino
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Ophthalmology, University of Montréal, Montréal, Québec, Canada
| | - El Bachir Affar
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada
- Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| |
Collapse
|
39
|
Li H, Ying X, Shang L, Redfern B, Kypraios N, Xie X, Xu F, Wang S, Zhang J, Jian H, Yu H, Lv D. Heterologous Expression of CLIBASIA_03915/CLIBASIA_04250 by Tobacco Mosaic Virus Resulted in Phloem Necrosis in the Senescent Leaves of Nicotiana benthamiana. Int J Mol Sci 2020; 21:E1414. [PMID: 32093101 PMCID: PMC7073121 DOI: 10.3390/ijms21041414] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 02/15/2020] [Accepted: 02/17/2020] [Indexed: 12/02/2022] Open
Abstract
Huanglongbing (HLB), also known as citrus greening, is the most notorious citrus disease worldwide. Candidatus Liberibacter asiaticus (CaLas) is a phloem-restricted bacterium associated with HLB. Because there is no mutant library available, the pathogenesis of CaLas is obscure. In this study, we employed tobacco mosaic virus (TMV) to express two mature secretion proteins CLIBASIA_03915 (m03915) and CLIBASIA_04250 (m04250) in Nicotiana benthamiana (N. benthamiana). Phloem necrosis was observed in the senescent leaves of N. benthamiana that expressed the two low molecular weight proteins, while no phloem necrosis was observed in the plants that expressed the control, green fluorescent protein (GFP). Additionally, no phloem necrosis was observed in the senescent leaves of N. benthamiana that expressed the null mutation of m03915 and frameshifting m04250. The subcellular localizations of m03915 and m04250 were determined by fusion with GFP using confocal microscopy. The subcellular localization of m03915 was found to be as free GFP without a nuclear localization sequence (NLS). However, m04250 did have an NLS. Yeast two-hybrid (Y2H) was carried out to probe the citrus proteins interacting with m03915 and m04250. Six citrus proteins were found to interact with m03915. The identified proteins were involved in the metabolism of compounds, transcription, response to abiotic stress, ubiquitin-mediated protein degradation, etc. The prey of m04250 was involved in the processing of specific pre-mRNAs. Identification of new virulence factors of CaLas will give insight into the pathogenesis of CaLas, and therefore, it will eventually help develop the HLB-resistant citrus.
Collapse
Affiliation(s)
- Hui Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (H.L.); (L.S.); (H.J.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
| | - Xiaobao Ying
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, USA; (X.Y.); (B.R.); (N.K.)
| | - Lina Shang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (H.L.); (L.S.); (H.J.)
| | - Bryce Redfern
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, USA; (X.Y.); (B.R.); (N.K.)
| | - Nicholas Kypraios
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, USA; (X.Y.); (B.R.); (N.K.)
| | - Xuejun Xie
- Changzhou Institute of Technology, Changzhou 213032, China;
| | - FeiFei Xu
- Heilongjiang Academy of Agricultural Sciences, Harbin 10086, China (S.W.); (J.Z.); (H.Y.)
| | - Shaopeng Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin 10086, China (S.W.); (J.Z.); (H.Y.)
| | - Jinghua Zhang
- Heilongjiang Academy of Agricultural Sciences, Harbin 10086, China (S.W.); (J.Z.); (H.Y.)
| | - Hongju Jian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (H.L.); (L.S.); (H.J.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
| | - Hongtao Yu
- Heilongjiang Academy of Agricultural Sciences, Harbin 10086, China (S.W.); (J.Z.); (H.Y.)
| | - Dianqiu Lv
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (H.L.); (L.S.); (H.J.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
| |
Collapse
|
40
|
Mou C, Wang M, Pan S, Chen Z. Identification of Nuclear Localization Signals in the ORF2 Protein of Porcine Circovirus Type 3. Viruses 2019; 11:v11121086. [PMID: 31766638 PMCID: PMC6950156 DOI: 10.3390/v11121086] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 11/16/2022] Open
Abstract
Porcine circovirus type 3 (PCV3) contains two major open reading frames (ORFs) and the ORF2 gene encodes the major structural capsid protein. In this study, nuclear localization of ORF2 was demonstrated by fluorescence observation and subcellular fractionation assays in ORF2-transfected PK-15 cells. The subcellular localization of truncated ORF2 indicated that the 38 N-terminal amino acids were responsible for the nuclear localization of ORF2. The truncated and site-directed mutagenesis of this domain were constructed, and the results demonstrated that the basic amino acid residues at positions 8-32 were essential for the strict nuclear localization. The basic motifs 8RRR-R-RRR16 and 16RRRHRRR22 were further shown to be the key functional nucleolar localization signals that guide PCV3 ORF2 into nucleoli. Furthermore, sequence analysis showed that the amino acids of PCV3 nuclear localization signals were highly conserved. Overall, this study provides insight into the biological and functional characteristics of the PCV3 ORF2 protein.
Collapse
Affiliation(s)
- Chunxiao Mou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (C.M.); (S.P.)
| | - Minmin Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (C.M.); (S.P.)
| | - Shuonan Pan
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (C.M.); (S.P.)
| | - Zhenhai Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (C.M.); (S.P.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-182-5274-7459 or +86-514-8979-8271; Fax: 0514-8797-2218
| |
Collapse
|
41
|
Maio F, Arroyo-Mateos M, Bobay BG, Bejarano ER, Prins M, van den Burg HA. A Lysine Residue Essential for Geminivirus Replication Also Controls Nuclear Localization of the Tomato Yellow Leaf Curl Virus Rep Protein. J Virol 2019; 93:e01910-18. [PMID: 30842320 PMCID: PMC6498046 DOI: 10.1128/jvi.01910-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/20/2019] [Indexed: 02/07/2023] Open
Abstract
Geminiviruses are single-stranded DNA (ssDNA) viruses that infect a wide range of plants. To promote viral replication, geminiviruses manipulate the host cell cycle. The viral protein Rep is essential to reprogram the cell cycle and then initiate viral DNA replication by interacting with a plethora of nuclear host factors. Even though many protein domains of Rep have been characterized, little is known about its nuclear targeting. Here, we show that one conserved lysine in the N-terminal part of Rep is pivotal for nuclear localization of the Rep protein from Tomato yellow leaf curl virus (TYLCV), with two other lysines also contributing to its nuclear import. Previous work had identified that these residues are essential for Rep from Tomato golden mosaic virus (TGMV) to interact with the E2 SUMO-conjugating enzyme (SCE1). We here show that mutating these lysines leads to nuclear exclusion of TYLCV Rep without compromising its interaction with SCE1. Moreover, the ability of TYLCV Rep to promote viral DNA replication also depends on this highly conserved lysine independently of its role in nuclear import of Rep. Our data thus reveal that this lysine potentially has a broad role in geminivirus replication, but its role in nuclear import and SCE1 binding differs depending on the Rep protein examined.IMPORTANCE Nuclear activity of the replication initiator protein (Rep) of geminiviruses is essential for viral replication. We now define that one highly conserved lysine is important for nuclear import of Rep from three different begomoviruses. To our knowledge, this is the first time that nuclear localization has been mapped for any geminiviral Rep protein. Our data add another key function to this lysine residue, besides its roles in viral DNA replication and interaction with host factors, such as the SUMO E2-conjugating enzyme.
Collapse
Affiliation(s)
- Francesca Maio
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Manuel Arroyo-Mateos
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, Málaga, Spain
| | - Benjamin G Bobay
- Duke University NMR Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biochemistry, Duke University, Durham, North Carolina, USA
- Department of Radiology, Duke University, Durham, North Carolina, USA
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento Biología Celular, Genética y Fisiología, Universidad de Málaga, Campus Teatinos, Málaga, Spain
| | - Marcel Prins
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
- Keygene N.V., Wageningen, the Netherlands
| | - Harrold A van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
42
|
Cheng JH, Lai GH, Lien YY, Sun FC, Hsu SL, Chuang PC, Lee MS. Identification of nuclear localization signal and nuclear export signal of VP1 from the chicken anemia virus and effects on VP2 shuttling in cells. Virol J 2019; 16:45. [PMID: 30953524 PMCID: PMC6451244 DOI: 10.1186/s12985-019-1153-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 03/25/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND VP1 of the chicken anemia virus (CAV) is a structural protein that is required for virus encapsulation. VP1 proteins are present both in the nucleus and cytoplasm; however, the functional nuclear localization signal (NLS) and nuclear export signal (NES) of VP1 are still unknown. This study aimed to characterize the NLS and NES motifs of VP1 using bioinformatics methods and multiple-site fragment deletions, and investigate shuttling of VP2 from nucleus to cytoplasm by co-transfection with VP1. METHODS Two putative NLS motifs were predicted by the WoLF PSORT and NLStradamus programs from the amino acid sequence of VP1. Three NES motifs of VP1 were predicted by the NetNES 1.1 Server and ELM server programs. All mutants were created by multiple-site fragment deletion mutagenesis. VP1 and VP2 were co-expressed in cells using plasmid transfection. RESULTS A functional NLS motif was identified at amino acid residues 3 to 10 (RRARRPRG) of VP1. Critical amino acids 3 to 10 were significantly involved in nuclear import in cells and were evaluated using systematic deletion mutagenesis. Three NES motifs of VP1 were predicted by the NetNES 1.1 Server and ELM server programs. A functional NES was identified at amino acid residues 375 to 388 (ELDTNFFTLYVAQ). Leptomycin B (LMB) treatment demonstrated that VP1 export from nucleus to cytoplasm occurred through a chromosome region maintenance 1 (CRM1)-dependent pathway. With co-expression of VP1 and VP2 in cells, we observed that VP1 may transport VP2 from nucleus to cytoplasm. CONCLUSION Our data showed that VP1 of CAV contained functional NLS and NES motifs that modulated nuclear import and export through a CRM1-dependent pathway. Further, VP1 may play a role in the transport of VP2 from nucleus to cytoplasm.
Collapse
Affiliation(s)
- Jai-Hong Cheng
- Center for Shockwave Medicine and Tissue Engineering, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123 Tai-Pei Road, Niao Sung District, Kaohsiung, Taiwan 833
| | - Guan-Hua Lai
- Graduate Institute of Biotechnology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 40402 Taiwan
| | - Yi-Yang Lien
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Center of Animal Biologics, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Fang-Chun Sun
- Department of Bioresources, Da-Yeh University, Changhua, Taiwan
| | - Shan-Ling Hsu
- Department of Orthopedic Surgery, Center for Shockwave Medicine and Tissue Engineering, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine; Fooyin University, School of Nursing, Kaohsiung, Taiwan
| | - Pei-Chin Chuang
- Center for Shockwave Medicine and Tissue Engineering, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123 Tai-Pei Road, Niao Sung District, Kaohsiung, Taiwan 833
| | - Meng-Shiou Lee
- Department of Chinese Pharmaceutical Science and Chinese Medicine Resources, China Medical University, 91, Hsueh-Shih Road, Taichung, Taiwan
| |
Collapse
|
43
|
Venkatesan A, Fan JY, Bouyain S, Price JL. The Circadian tau Mutation in Casein Kinase 1 Is Part of a Larger Domain That Can Be Mutated to Shorten Circadian Period. Int J Mol Sci 2019; 20:E813. [PMID: 30769795 PMCID: PMC6412653 DOI: 10.3390/ijms20040813] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 01/31/2019] [Accepted: 02/11/2019] [Indexed: 01/21/2023] Open
Abstract
Drosophila Double-time (DBT) phosphorylates the circadian protein Period (PER). The period-altering mutation tau, identified in hamster casein kinase I (CKIε) and created in Drosophila DBT, has been shown to shorten the circadian period in flies, as it does in hamsters. Since CKI often phosphorylates downstream of previously phosphorylated residues and the tau amino acid binds a negatively charged ion in X-ray crystal structures, this amino acid has been suggested to contribute to a phosphate recognition site for the substrate. Alternatively, the tau amino acid may affect a nuclear localization signal (NLS) with which it interacts. We mutated the residues that were close to or part of the phosphate recognition site or NLS. Flies expressing DBT with mutations of amino acids close to or part of either of these motifs produced a shortening of period, suggesting that a domain, including the phosphate recognition site or the NLS, can be mutated to produce the short period phenotype. Mutation of residues affecting internally placed residues produced a longer period, suggesting that a specific domain on the surface of the kinase might generate an interaction with a substrate or regulator, with short periods produced when the interaction is disrupted.
Collapse
Affiliation(s)
- Anandakrishnan Venkatesan
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
| | - Jin-Yuan Fan
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
| | - Samuel Bouyain
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
| | - Jeffrey L Price
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
| |
Collapse
|
44
|
Lu QY, Yang L, Huang J, Zheng L, Sun X. Identification and subcellular location of an RNA silencing suppressor encoded by mulberry crinkle leaf virus. Virology 2019; 526:45-51. [PMID: 30342301 DOI: 10.1016/j.virol.2018.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 10/04/2018] [Accepted: 10/04/2018] [Indexed: 11/28/2022]
Abstract
Mulberry crinkle leaf virus (MCLV) is a novel geminivirus recently identified from the woody plant mulberry (Morus alba L.). Little is known about the functions of the proteins encoded by the MCLV genome. Here, all the MCLV-encoded proteins were examined for the ability to suppress gene silencing by an agroinfiltration assay in combination with northern blot analysis of green fluorescent protein (GFP) mRNA and western blot analysis. Of the six proteins, only one protein, V3, which has been predicted to play a role in viral movement, was found to suppress the gene silencing induced by a sense GFP gene in Nicotiana benthamiana 16c. The minimal amino acid sequence of V3 that maintains suppressor activity was also determined by constructing truncated mutants lacking different lengths of the amino acid sequences at the N- or C-terminus of the V3 protein. The results showed that the 94 N-terminal amino acid residues of V3 are sufficient to maintain V3 suppressor activity. In addition, the subcellular location of the V3 protein was investigated by confocal laser scanning microscopy after the expression of a V3-RFP fused protein in leaf epidermal cells of N. benthamiana. The results indicated that the V3 protein localized not only to the cytoplasm but also to the nucleus of N. benthamiana, implying that V3 can shuttle between the nucleus and the cytoplasm. Deletion mutant analysis indicated that a putative nuclear localization signal (NLS) between aa 118-134 might be responsible for the nuclear distribution of the V3 protein. Given the importance of RNA silencing in plant-virus interactions, the identification of a silencing suppressor of MCLV should be valuable in understanding the pathogenicity and molecular biology of this virus.
Collapse
Affiliation(s)
- Quan-You Lu
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu, China; Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu, China.
| | - Lei Yang
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu, China; Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu, China
| | - Jinshan Huang
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu, China; Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu, China
| | - Luping Zheng
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Xin Sun
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu, China; Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, Jiangsu, China
| |
Collapse
|
45
|
Williams SC, Angerer ND, Johnson PF. C/EBP proteins contain nuclear localization signals imbedded in their basic regions. Gene Expr 2018; 6:371-85. [PMID: 9495318 PMCID: PMC6148256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The C/EBP-related proteins (C/EBPalpha, CRP1, C/EBPbeta, and C/EBPdelta) form a subfamily of bZIP (basic region/leucine zipper) transcription factors that display sequence homology within the bZIP domain. The conserved basic region contains two motifs that exhibit significant homology to the bipartite nuclear localization signal (NLS) first described in nucleoplasmin. CRP1 and C/EBPbeta proteins bearing deletions of the basic region accumulate in the cytoplasm, in contrast to their normal nuclear location. Analysis of chimeric proteins consisting of CRP1 basic region sequences fused to beta-galactosidase revealed that the CRP1 basic region contains a single NLS that differs from conventional bipartite signals in two ways. First, mutation of a pair of arginine residues at the N-terminus of the proposed NLS does not disrupt its function. Second, the CRP1 NLS requires additional nonbasic residues at its C-terminus. A basic residue within the CRP1 NLS that is not conserved within the C/EBP family is occupied instead by an uncharged residue in C/EBPalpha and C/EBPbeta. When this nonconserved arginine residue was changed to alanine the CRP1 NLS behaved as a classical bipartite signal, suggesting that bipartite NLSs are present in all family members but that NLSs of the individual members differ slightly. Additionally, mutation of critical NLS residues in the intact CRP1 and C/EBPbeta proteins showed that these elements exhibit more bipartite-like characteristics when present in their normal sequence context. Finally, we observed that a C/EBPbeta protein lacking its NLS can be localized to the nucleus when coexpressed with C/EBPalpha, indicating that a single NLS is sufficient to promote nuclear transport of a bZIP dimer.
Collapse
Affiliation(s)
- Simon C. Williams
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430
| | - Nicholas D. Angerer
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430
| | - Peter F. Johnson
- ABL-Basic Research Program, NCI-Frederick Cancer Research and Development Center, Frederick, MD 21702-1201
- Address correspondence to Peter F. Johnson. Tel: (301) 846-1627; Fax: (301) 846-5991; E-mail:
| |
Collapse
|
46
|
Feng M, Zuo D, Jiang X, Li S, Chen J, Jiang L, Zhou X, Jiang T. Identification of Strawberry vein banding virus encoded P6 as an RNA silencing suppressor. Virology 2018; 520:103-110. [PMID: 29843054 DOI: 10.1016/j.virol.2018.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 11/25/2022]
Abstract
RNA silencing is a common mechanism that plays a key role in antiviral defense. To overcome host defense responses, plant viruses encode silencing-suppressor proteins to target one or several key steps in the silencing machinery. Here, we report that the P6 protein encoded by Strawberry vein banding virus (SVBV) is an RNA silencing suppressor through Agrobacterium-mediated co-infiltration assays. SVBV P6 protein can suppress green fluorescent protein (GFP) gene silencing induced by single-stranded RNA but not by double-stranded RNA. The P6 protein can also inhibit systemic silencing of GFP through interfering the systemic spread of GFP silencing signal. Subcellular localization study indicated that P6 protein formed irregular bodies and distributed in both cytoplasm and nucleus of Nicotiana benthamiana cells. Furthermore, deletion analysis indicated that a nuclear localization signal (NLS, aa 402-426) in the P6 protein is responsible for the silencing suppression efficiency. In addition, expression of the P6 protein via a Potato virus X (PVX)-based vectors induced more severe mosaic symptoms in N. benthamiana leaves, and transgenic N. benthamiana plants expressing P6 showed obvious vein yellowing as well as severe mosaic symptoms in leaves. Taken together, our results demonstrates that SVBV P6 is a suppressor of RNA silencing, possibly acting at a upstream step for dsRNA generation.
Collapse
Affiliation(s)
- Mingfeng Feng
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Dengpan Zuo
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Xizi Jiang
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Shuai Li
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Jing Chen
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Lei Jiang
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Tong Jiang
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, People's Republic of China.
| |
Collapse
|
47
|
Luo KR, Huang NC, Yu TS. Selective Targeting of Mobile mRNAs to Plasmodesmata for Cell-to-Cell Movement. Plant Physiol 2018; 177:604-614. [PMID: 29581179 PMCID: PMC6001314 DOI: 10.1104/pp.18.00107] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/13/2018] [Indexed: 05/20/2023]
Abstract
Many plant mRNAs move from cell to cell or long distance to execute non-cell-autonomous functions. These mobile mRNAs traffic through the phloem to regulate many developmental processes, but despite the burgeoning discovery of mobile mRNAs, little is known about the mechanism underlying the intracellular sorting of these mRNAs. Here, we exploited a fluorescence-based mRNA labeling system, using the bacteriophage coat protein MS2, fused to GFP (MS2-GFP) and an MS2 recognition site in the RNA of interest, to visualize the intracellular trafficking of mobile mRNAs in living plant cells of Nicotiana benthamiana We first improved this system by using the nuclear localization sequence from FD, which substantially reduced the fluorescent background of MS2-GFP in the cytoplasm. The modified system allowed us to observe the cytoplasmic fluorescent foci dependent on MS2-binding sites. Coexpressing the MS2-GFP system with a virus movement protein, which is a plasmodesmata (PD)-localized nonspecific RNA-binding protein, targeted cytoplasmic fluorescent foci to the PD, suggesting that the cytoplasmic fluorescent foci contain mRNA and MS2-GFP. Our ex vivo RNA imaging revealed that mobile but not nonmobile mRNAs were selectively targeted to PD. Real-time images of intracellular translocation revealed that the translocation of mRNA and organelles in the transvacuolar strands may be governed by the same mechanism. Our study suggests that PD targeting of mRNA is a selective step in determining mRNA cell-to-cell movement of mRNAs.
Collapse
Affiliation(s)
- Kai-Ren Luo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Nien-Chen Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Tien-Shin Yu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| |
Collapse
|
48
|
Abstract
The ability of the matrix (M) protein of potato yellow dwarf virus (PYDV) to remodel nuclear membranes is controlled by a di-leucine motif located at residues 223 and 224 of its primary structure. This function can be uncoupled from that of its nuclear localization signal (NLS), which is controlled primarily by lysine and arginine residues immediately downstream of the LL motif. In planta localization of green fluorescent protein fusions, bimolecular fluorescence complementation assays with nuclear import receptor importin-α1 and yeast-based nuclear import assays provided three independent experimental approaches to validate the authenticity of the M-NLS. The carboxy terminus of M is predicted to contain a nuclear export signal, which is belived to be functional, given the ability of M to bind the Arabidopsis nuclear export receptor 1 (XPO1). The nuclear shuttle activity of M has implications for the cell-to-cell movement of PYDV nucleocapsids, based upon its interaction with the N and Y proteins.
Collapse
Affiliation(s)
- Gavin Anderson
- Anderson Craft Ales, 1030 Elias St, London, ON N5W 3P6, Canada
| | - Chanyong Jang
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| | - Renyuan Wang
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| | - Michael Goodin
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| |
Collapse
|
49
|
Xiao Y, Zhao P, Du J, Li X, Lu W, Hao X, Dong B, Yu Y, Wang L. High-level expression and immunogenicity of porcine circovirus type 2b capsid protein without nuclear localization signal expressed in Hansenula polymorpha. Biologicals 2017; 51:18-24. [PMID: 29225046 DOI: 10.1016/j.biologicals.2017.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 12/11/2022] Open
Abstract
Currently, porcine circovirus type 2b (PCV2b) is the dominant PCV2 genotype causing postweaning multisystemic wasting disease (PMWS) in pigs worldwide. Efforts have been made to develop various recombinant capsid proteins of PCV2b used in vaccines against PCV2b. However, the nuclear localization signal (NLS) of PCV2b capsid protein (CP) was found to inhibit the expression of the whole length capsid protein in E.coli. Here, we expressed a NLS-deleted capsid protein (ΔCP) of PCV2b in Hansenula polymorpha based on the capsid protein of PCV2b strain Y-7 isolated in China. Comparatively, the ΔCP was expressed at a higher level than the CP. The purified ΔCP could self-assemble into virus like particles (VLPs) with similar morphology of the VLPs formed by CP. The purified ΔCP could be recognized by the anti-sera derived from the mice immunized by inactivated PCV2b particles. Furthermore, it induced higher levels of PCV2b specific antibodies than the purified CP in mice. These results showed that the ΔCP, a recombinant PCV2b capsid protein without nuclear localization signal sequence, could be efficiently expressed in Hansenula polymorpha, and used as a candidate antigen for the development of PCV2b vaccines.
Collapse
Affiliation(s)
- Yue Xiao
- Department of Molecular Biology in College of Basic Medical Sciences and Institute of Pediatrics in First Hospital, Jilin University, Changchun 130021, China
| | - Peiyan Zhao
- Department of Molecular Biology in College of Basic Medical Sciences and Institute of Pediatrics in First Hospital, Jilin University, Changchun 130021, China
| | - Junyang Du
- Department of Immunology in College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Xin Li
- Department of Molecular Biology in College of Basic Medical Sciences and Institute of Pediatrics in First Hospital, Jilin University, Changchun 130021, China
| | - Wenting Lu
- Department of Molecular Biology in College of Basic Medical Sciences and Institute of Pediatrics in First Hospital, Jilin University, Changchun 130021, China
| | - Xu Hao
- Department of Immunology in College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Boqi Dong
- Department of Immunology in College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Yongli Yu
- Department of Immunology in College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Liying Wang
- Department of Molecular Biology in College of Basic Medical Sciences and Institute of Pediatrics in First Hospital, Jilin University, Changchun 130021, China.
| |
Collapse
|
50
|
Gerth K, Lin F, Daamen F, Menzel W, Heinrich F, Heilmann M. Arabidopsis phosphatidylinositol 4-phosphate 5-kinase 2 contains a functional nuclear localization sequence and interacts with alpha-importins. Plant J 2017; 92:862-878. [PMID: 28949047 DOI: 10.1111/tpj.13724] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 08/22/2017] [Accepted: 09/11/2017] [Indexed: 05/22/2023]
Abstract
The Arabidopsis phosphoinositide kinase PIP5K2 has been implicated in the control of membrane trafficking and is important for development and growth. In addition to cytosolic functions of phosphoinositides, a nuclear phosphoinositide system has been proposed, but evidence for nuclear phosphoinositides in plants is limited. Fluorescence-tagged variants of PIP5K2 reside in the nucleus of Arabidopsis root meristem cells, in addition to reported plasma membrane localization. Here we report on the interaction of PIP5K2 with alpha-importins and characterize its nuclear localization sequences (NLSs). The PIP5K2 sequence contains four putative NLSs (NLSa-NLSd) and only a PIP5K2 fragment containing NLSs is imported into nuclei of onion epidermis cells upon transient expression. PIP5K2 interacts physically with alpha-importin isoforms in cytosolic split-ubiquitin-based yeast two-hybrid tests, in dot-blot experiments and in immuno-pull-downs. A 27-amino-acid fragment of PIP5K2 containing NLSc is necessary and sufficient to mediate the nuclear import of a large cargo fusion consisting of two mCherry markers fused to RubisCO large subunit. Substitution of basic residues in NLSc results in reduced import of PIP5K2 or other cargoes into plant nuclei. The data suggest that PIP5K2 is subject to active, alpha-importin-mediated nuclear import, consistent with a nuclear role for PIP5K2 in addition to its reported cytosolic functions. The detection of both substrate and product of PIP5K2 in plant nuclei according to reporter fluorescence and immunofluorescence further supports the notion of a nuclear phosphoinositide system in plants. Variants of PIP5K2 with reduced nuclear residence might serve as tools for the future functional study of plant nuclear phosphoinositides.
Collapse
Affiliation(s)
- Katharina Gerth
- Department of Cellular Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Feng Lin
- Department of Cellular Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Franziska Daamen
- Department of Cellular Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Wilhelm Menzel
- Department of Cellular Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Franziska Heinrich
- Department of Cellular Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Mareike Heilmann
- Department of Cellular Biochemistry, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| |
Collapse
|