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Hansen MMK, Desai RV, Simpson ML, Weinberger LS. Cytoplasmic Amplification of Transcriptional Noise Generates Substantial Cell-to-Cell Variability. Cell Syst 2018; 7:384-397.e6. [PMID: 30243562 PMCID: PMC6202163 DOI: 10.1016/j.cels.2018.08.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/14/2018] [Accepted: 08/02/2018] [Indexed: 12/15/2022]
Abstract
Transcription is an episodic process characterized by probabilistic bursts, but how the transcriptional noise from these bursts is modulated by cellular physiology remains unclear. Using simulations and single-molecule RNA counting, we examined how cellular processes influence cell-to-cell variability (noise). The results show that RNA noise is higher in the cytoplasm than the nucleus in ∼85% of genes across diverse promoters, genomic loci, and cell types (human and mouse). Measurements show further amplification of RNA noise in the cytoplasm, fitting a model of biphasic mRNA conversion between translation- and degradation-competent states. This multi-state translation-degradation of mRNA also causes substantial noise amplification in protein levels, ultimately accounting for ∼74% of intrinsic protein variability in cell populations. Overall, the results demonstrate how noise from transcriptional bursts is intrinsically amplified by mRNA processing, leading to a large super-Poissonian variability in protein levels.
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Affiliation(s)
- Maike M K Hansen
- Gladstone|UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ravi V Desai
- Gladstone|UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Michael L Simpson
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Leor S Weinberger
- Gladstone|UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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2
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Mathew C, Ghildyal R. CRM1 Inhibitors for Antiviral Therapy. Front Microbiol 2017; 8:1171. [PMID: 28702009 PMCID: PMC5487384 DOI: 10.3389/fmicb.2017.01171] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/08/2017] [Indexed: 12/22/2022] Open
Abstract
Infectious diseases are a major global concern and despite major advancements in medical research, still cause significant morbidity and mortality. Progress in antiviral therapy is particularly hindered by appearance of mutants capable of overcoming the effects of drugs targeting viral components. Alternatively, development of drugs targeting host proteins essential for completion of viral lifecycle holds potential as a viable strategy for antiviral therapy. Nucleocytoplasmic trafficking pathways in particular are involved in several pathological conditions including cancer and viral infections, where hijacking or alteration of function of key transporter proteins, such as Chromosome Region Maintenance1 (CRM1) is observed. Overexpression of CRM1-mediated nuclear export is evident in several solid and hematological malignancies. Interestingly, CRM1-mediated nuclear export of viral components is crucial in various stages of the viral lifecycle and assembly. This review summarizes the role of CRM1 in cancer and selected viruses. Leptomycin B (LMB) is the prototypical inhibitor of CRM1 potent against various cancer cell lines overexpressing CRM1 and in limiting viral infections at nanomolar concentrations in vitro. However, the irreversible shutdown of nuclear export results in high cytotoxicity and limited efficacy in vivo. This has prompted search for synthetic and natural CRM1 inhibitors that can potentially be developed as broadly active antivirals, some of which are summarized in this review.
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Affiliation(s)
| | - Reena Ghildyal
- Respiratory Virology Group, Centre for Research in Therapeutic Solutions, Health Research Institute, University of CanberraCanberra, ACT, Australia
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3
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Murphy J, Hall WW, Ratner L, Sheehy N. Novel interactions between the HTLV antisense proteins HBZ and APH-2 and the NFAR protein family: Implications for the HTLV lifecycles. Virology 2016; 494:129-42. [PMID: 27110706 DOI: 10.1016/j.virol.2016.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 01/17/2023]
Abstract
The human T-cell leukaemia virus type 1 and type 2 (HTLV-1/HTLV-2) antisense proteins HBZ and APH-2 play key roles in the HTLV lifecycles and persistence in the host. Nuclear Factors Associated with double-stranded RNA (NFAR) proteins NF90/110 function in the lifecycles of several viruses and participate in host innate immunity against infection and oncogenesis. Using GST pulldown and co-immunoprecipitation assays we demonstrate specific novel interactions between HBZ/APH-2 and NF90/110 and characterised the protein domains involved. Moreover we show that NF90/110 significantly enhance Tax mediated LTR activation, an effect that was abolished by HBZ but enhanced by APH-2. Additionally we found that HBZ and APH-2 modulate the promoter activity of survivin and are capable of antagonising NF110-mediated survivin activation. Thus interactions between HTLV antisense proteins and the NFAR protein family have an overall positive impact on HTLV infection. Hence NFARs may represent potential therapeutic targets in HTLV infected cells.
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Affiliation(s)
- Jane Murphy
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - William W Hall
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Lee Ratner
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Noreen Sheehy
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
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Li Y, Belshan M. NF45 and NF90 Bind HIV-1 RNA and Modulate HIV Gene Expression. Viruses 2016; 8:v8020047. [PMID: 26891316 PMCID: PMC4776202 DOI: 10.3390/v8020047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 01/27/2016] [Accepted: 02/04/2016] [Indexed: 01/03/2023] Open
Abstract
A previous proteomic screen in our laboratory identified nuclear factor 45 (NF45) and nuclear factor 90 (NF90) as potential cellular factors involved in human immunodeficiency virus type 1 (HIV-1) replication. Both are RNA binding proteins that regulate gene expression; and NF90 has been shown to regulate the expression of cyclin T1 which is required for Tat-dependent trans-activation of viral gene expression. In this study the roles of NF45 and NF90 in HIV replication were investigated through overexpression studies. Ectopic expression of either factor potentiated HIV infection, gene expression, and virus production. Deletion of the RNA binding domains of NF45 and NF90 diminished the enhancement of HIV infection and gene expression. Both proteins were found to interact with the HIV RNA. RNA decay assays demonstrated that NF90, but not NF45, increased the half-life of the HIV RNA. Overall, these studies indicate that both NF45 and NF90 potentiate HIV infection through their RNA binding domains.
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Affiliation(s)
- Yan Li
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68178, USA.
| | - Michael Belshan
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68178, USA.
- The Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583, USA.
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5
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NF90 isoforms, a new family of cellular proteins involved in viral replication? Biochimie 2015; 108:20-4. [DOI: 10.1016/j.biochi.2014.10.022] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/26/2014] [Indexed: 01/09/2023]
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6
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Castella S, Bernard R, Corno M, Fradin A, Larcher JC. Ilf3 and NF90 functions in RNA biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:243-56. [PMID: 25327818 DOI: 10.1002/wrna.1270] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/09/2014] [Accepted: 09/17/2014] [Indexed: 12/24/2022]
Abstract
Double-stranded RNA-binding proteins (DRBPs) are known to regulate many processes of RNA metabolism due, among others, to the presence of double-stranded RNA (dsRNA)-binding motifs (dsRBMs). Among these DRBPs, Interleukin enhancer-binding factor 3 (Ilf3) and Nuclear Factor 90 (NF90) are two ubiquitous proteins generated by mutually exclusive and alternative splicings of the Ilf3 gene. They share common N-terminal and central sequences but display specific C-terminal regions. They present a large heterogeneity generated by several post-transcriptional and post-translational modifications involved in their subcellular localization and biological functions. While Ilf3 and NF90 were first identified as activators of gene expression, they are also implicated in cellular processes unrelated to RNA metabolism such as regulation of the cell cycle or of enzymatic activites. The implication of Ilf3 and NF90 in RNA biology will be discussed with a focus on eukaryote transcription and translation regulation, on viral replication and translation as well as on noncoding RNA field.
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Affiliation(s)
- Sandrine Castella
- Laboratoire de Biologie du développement, Institut de Biologie Paris-Seine, Sorbonne Universités, UPMC Univ Paris 06, Paris, France; Laboratoire de Biologie du développement, Institut de Biologie Paris-Seine, CNRS, UMR 7622, Paris, France
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7
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Schweitzer CJ, Jagadish T, Haverland N, Ciborowski P, Belshan M. Proteomic analysis of early HIV-1 nucleoprotein complexes. J Proteome Res 2013; 12:559-72. [PMID: 23282062 PMCID: PMC3564510 DOI: 10.1021/pr300869h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
After entry into the cell, the early steps of the human immunodeficiency virus type 1 (HIV-1) replication cycle are mediated by two functionally distinct nucleoprotein complexes, the reverse transcription complex (RTC) and preintegration complex (PIC). These two unique viral complexes are responsible for the conversion of the single-stranded RNA genome into double-stranded DNA, transport of the DNA into the nucleus, and integration of the viral DNA into the host cell chromosome. Prior biochemical analyses suggest that these complexes are large and contain multiple undiscovered host cell factors. In this study, functional HIV-1 RTCs and PICs were partially purified by velocity gradient centrifugation and fractionation, concentrated, trypsin digested, and analyzed by LC-MS/MS. A total of seven parallel infected and control biological replicates were completed. Database searches were performed with Proteome Discoverer and a comparison of the HIV-1 samples to parallel uninfected control samples was used to identify unique cellular factors. The analysis produced a total data set of 11055 proteins. Several previously characterized HIV-1 factors were identified, including XRCC6, TFRC, and HSP70. The presence of XRCC6 was confirmed in infected fractions and shown to be associated with HIV-1 DNA by immunoprecipitation-PCR experiments. Overall, the analysis identified 94 proteins unique in the infected fractions and 121 proteins unique to the control fractions with ≥ 2 protein assignments. An additional 54 and 52 were classified as enriched in the infected and control samples, respectively, based on a 3-fold difference in total Proteome Discoverer probability score. The differential expression of several candidate proteins was validated by Western blot analysis. This study contributes additional novel candidate proteins to the growing published bioinformatic data sets of proteins that contribute to HIV-1 replication.
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MESH Headings
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Antigens, Nuclear/genetics
- Antigens, Nuclear/metabolism
- Cell Line
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Cell Nucleus/virology
- Centrifugation, Density Gradient
- Chromatography, Liquid
- DNA, Viral/genetics
- DNA, Viral/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Gene Expression Profiling
- HIV-1/genetics
- HIV-1/metabolism
- HSP70 Heat-Shock Proteins/genetics
- HSP70 Heat-Shock Proteins/metabolism
- Host-Pathogen Interactions
- Humans
- Ku Autoantigen
- Lymphocytes/metabolism
- Lymphocytes/virology
- Nucleoproteins/genetics
- Nucleoproteins/metabolism
- Protein Binding
- Proteome/genetics
- Proteome/metabolism
- Receptors, Transferrin/genetics
- Receptors, Transferrin/metabolism
- Reverse Transcription
- Tandem Mass Spectrometry
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Virus Integration
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Affiliation(s)
| | - Teena Jagadish
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE
| | - Nicole Haverland
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE
- The Nebraska Center for Virology, University of Nebraska, Lincoln, NE
| | - Michael Belshan
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE
- The Nebraska Center for Virology, University of Nebraska, Lincoln, NE
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Noguchi K, Ishibashi K, Miyokawa K, Hokari M, Kanno T, Hirano T, Yamamoto N, Takaku H. HIV-1 suppressive sequences are modulated by Rev transport of unspliced RNA and are required for efficient HIV-1 production. PLoS One 2012; 7:e51393. [PMID: 23251516 PMCID: PMC3519575 DOI: 10.1371/journal.pone.0051393] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 10/31/2012] [Indexed: 11/18/2022] Open
Abstract
The unspliced human immunodeficiency virus type 1 (HIV-1) RNAs are translated as Gag and Gag-Pol polyproteins or packaged as genomes into viral particles. Efficient translation is necessary before the transition to produce infective virions. The viral protein Rev exports all intron-containing viral RNAs; however, it also appears to enhance translation. Cellular microRNAs target cellular and viral mRNAs to silence their translation and enrich them at discrete cytoplasmic loci that overlap with the putative interim site of Gag and the genome. Here, we analyzed how Rev-mediated transport and the splicing status of the mRNA influenced the silencing status imposed by microRNA. Through identification and mutational analysis of the silencing sites in the HIV-1 genome, we elucidated the effect of silencing on virus production. Renilla luciferase mRNA, which contains a let-7 targeting site in its 3' untranslated region, was mediated when it was transported by Rev and not spliced, but it was either not mediated when it was spliced even in a partial way or it was Rev-independent. The silencing sites in the pol and env-nef regions of the HIV-1 genome, which were repressed in T cells and other cell lines, were Drosha-dependent and could also be modulated by Rev in an unspliced state. Mutant viruses that contained genomic mutations that reflect alterations to show more derepressive effects in the 3' untranslated region of the Renilla luciferase gene replicated more slowly than wild-type virus. These findings yield insights into the HIV-1 silencing sites that might allow the genome to avoid translational machinery and that might be utilized in coordinating virus production during initial virus replication. However, the function of Rev to modulate the silencing sites of unspliced RNAs would be advantageous for the efficient translation that is required to support protein production prior to viral packaging and particle production.
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Affiliation(s)
- Kousei Noguchi
- High Technology Research Center, Chiba Institute of Technology, Tsudanuma, Narashino-shi, Chiba, Japan
| | - Keisuke Ishibashi
- Department of Life and Environmental Science, Chiba Institute of Technology, Tsudanuma, Narashino-shi, Chiba, Japan
| | - Kaori Miyokawa
- Department of Life and Environmental Science, Chiba Institute of Technology, Tsudanuma, Narashino-shi, Chiba, Japan
| | - Manami Hokari
- Department of Life and Environmental Science, Chiba Institute of Technology, Tsudanuma, Narashino-shi, Chiba, Japan
| | - Tomoyuki Kanno
- Department of Life and Environmental Science, Chiba Institute of Technology, Tsudanuma, Narashino-shi, Chiba, Japan
| | - Tomoya Hirano
- Department of Life and Environmental Science, Chiba Institute of Technology, Tsudanuma, Narashino-shi, Chiba, Japan
| | - Norio Yamamoto
- Influenza Virus Research Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo, Japan
| | - Hiroshi Takaku
- Department of Life and Environmental Science, Chiba Institute of Technology, Tsudanuma, Narashino-shi, Chiba, Japan
- High Technology Research Center, Chiba Institute of Technology, Tsudanuma, Narashino-shi, Chiba, Japan
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Vandermeulen G, Athanasopoulos T, Trundley A, Foster K, Préat V, Yáñez-Muñoz RJ, Dickson G. Highly potent delivery method of gp160 envelope vaccine combining lentivirus-like particles and DNA electrotransfer. J Control Release 2012; 159:376-83. [DOI: 10.1016/j.jconrel.2012.01.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 01/19/2012] [Accepted: 01/23/2012] [Indexed: 12/01/2022]
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10
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Miyamoto F, Kodama EN. Novel HIV-1 fusion inhibition peptides: designing the next generation of drugs. Antivir Chem Chemother 2012; 22:151-8. [PMID: 22182762 DOI: 10.3851/imp1930] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2011] [Indexed: 10/16/2022] Open
Abstract
The development of over 20 antiretroviral drugs has led to efficient and successful suppression of HIV-1 replication. In addition to common viral targets, such as reverse transcriptase and protease, new targets have been recently exploited, including integrase, fusion and cellular CCR5. Hence, combination antiretroviral therapy is continually improved by the development of these new agents, especially for patients infected with drug-resistant HIV-1. In this review, we focused on fusion inhibitory peptides that have been developed since the first HIV-1 fusion inhibitor, enfuvirtide (T-20). T-20, approved for clinical use in 2003, is a polypeptide comprising 36 amino acids derived from the HIV-1 gp41 C-terminal heptad repeat and provides a novel treatment strategy for HIV-1 therapy. T-20 is able to suppress HIV-1 replication, including viruses resistant to reverse transcriptase or protease inhibitors. However, after prolonged T-20-containing treatment regimens, HIV-1 acquires resistance to T-20. Therefore, our laboratory and others have developed novel fusion inhibitors, termed next-generation fusion inhibitors, including electrostatically constrained, mutation introduced, and trimer-form peptides.
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Affiliation(s)
- Fusako Miyamoto
- Division of Emerging Infectious Diseases, Department of Internal Medicine, Tohoku University School of Medicine, Sendai, Japan
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