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Article ; Online: Retroviral hijacking of host transport pathways for genome nuclear export.

Behrens, Ryan T / Sherer, Nathan M

2023 , Page(s) e0007023

Abstract: Recent advances in the study of virus-cell interactions have improved our understanding of how viruses that replicate their genomes in the nucleus (e.g., retroviruses, hepadnaviruses, herpesviruses, and a subset of RNA viruses) hijack cellular pathways ... ...

Abstract	Recent advances in the study of virus-cell interactions have improved our understanding of how viruses that replicate their genomes in the nucleus (e.g., retroviruses, hepadnaviruses, herpesviruses, and a subset of RNA viruses) hijack cellular pathways to export these genomes to the cytoplasm where they access virion egress pathways. These findings shed light on novel aspects of viral life cycles relevant to the development of new antiviral strategies and can yield new tractable, virus-based tools for exposing additional secrets of the cell. The goal of this review is to summarize defined and emerging modes of virus-host interactions that drive the transit of viral genomes out of the nucleus across the nuclear envelope barrier, with an emphasis on retroviruses that are most extensively studied. In this context, we prioritize discussion of recent progress in understanding the trafficking and function of the human immunodeficiency virus type 1 Rev protein, exemplifying a relatively refined example of stepwise, cooperativity-driven viral subversion of multi-subunit host transport receptor complexes.
Language	English
Publishing date	2023-11-01
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.00070-23
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Live Cell Imaging Reveals HBV Capsid Translocation from the Nucleus To the Cytoplasm Enabled by Cell Division.

Romero, Sofia / Unchwaniwala, Nuruddin / Evans, Edward L / Eliceiri, Kevin W / Loeb, Daniel D / Sherer, Nathan M

mBio

2023 Volume 14, Issue 2, Page(s) e0330322

Abstract: Hepatitis B virus (HBV) capsid assembly is traditionally thought to occur predominantly in the cytoplasm, where the virus gains access to the virion egress pathway. To better define sites of HBV capsid assembly, we carried out single cell imaging of HBV ... ...

Abstract	Hepatitis B virus (HBV) capsid assembly is traditionally thought to occur predominantly in the cytoplasm, where the virus gains access to the virion egress pathway. To better define sites of HBV capsid assembly, we carried out single cell imaging of HBV Core protein (Cp) subcellular trafficking over time under conditions supporting genome packaging and reverse transcription in Huh7 hepatocellular carcinoma cells. Time-course analyses including live cell imaging of fluorescently tagged Cp derivatives showed Cp to accumulate in the nucleus at early time points (~24 h), followed by a marked re-distribution to the cytoplasm at 48 to 72 h. Nucleus-associated Cp was confirmed to be capsid and/or high-order assemblages using a novel dual label immunofluorescence strategy. Nuclear-to-cytoplasmic re-localization of Cp occurred predominantly during nuclear envelope breakdown in conjunction with cell division, followed by strong cytoplasmic retention of Cp. Blocking cell division resulted in strong nuclear entrapment of high-order assemblages. A Cp mutant, Cp-V124W, predicted to exhibit enhanced assembly kinetics, also first trafficked to the nucleus to accumulate at nucleoli, consistent with the hypothesis that Cp's transit to the nucleus is a strong and constitutive process. Taken together, these results provide support for the nucleus as an early-stage site of HBV capsid assembly, and provide the first dynamic evidence of cytoplasmic retention after cell division as a mechanism underpinning capsid nucleus-to-cytoplasm relocalization.
MeSH term(s)	Humans ; Capsid/metabolism ; Hepatitis B virus/genetics ; Carcinoma, Hepatocellular/metabolism ; Capsid Proteins/metabolism ; Virus Assembly ; Hepatitis B ; Cell Nucleus/metabolism ; Cytoplasm/metabolism ; Liver Neoplasms ; Cell Division ; Virus Replication
Chemical Substances	Capsid Proteins
Language	English
Publishing date	2023-02-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.03303-22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Long-distance relationships: do membrane nanotubes regulate cell-cell communication and disease progression?

Sherer, Nathan M

Molecular biology of the cell

2013 Volume 24, Issue 8, Page(s) 1095–1098

Abstract: Metazoan cells rapidly exchange signals at tight cell-cell interfaces, including synapses and gap junctions. Advances in imaging recently exposed a third mode of intercellular cross-talk mediated by thin, actin-containing membrane extensions broadly ... ...

Abstract	Metazoan cells rapidly exchange signals at tight cell-cell interfaces, including synapses and gap junctions. Advances in imaging recently exposed a third mode of intercellular cross-talk mediated by thin, actin-containing membrane extensions broadly known as "membrane" or "tunneling" nanotubes. An explosion of research suggests diverse functions for nanotubular superhighways, including cell-cell electrical coupling, calcium signaling, small-molecule exchange, and, remarkably, the transfer of bulky cargoes, including organelles or pathogenic agents. Despite great enthusiasm for all things nanotubular and their potential roles in cell signaling and pathogenesis, key questions remain regarding the mechanisms by which these structures regulate directional cell-cell exchange; how these linkages are formed and between which cells and, critically, whether nanotubes are as prevalent in vivo as they appear to be in the incubator.
MeSH term(s)	Actins/physiology ; Actins/ultrastructure ; Animals ; Biological Transport ; Cell Communication ; Cell Surface Extensions/physiology ; Cell Surface Extensions/ultrastructure ; Cells, Cultured ; Humans
Chemical Substances	Actins
Language	English
Publishing date	2013-04-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1098979-1
ISSN	1939-4586 ; 1059-1524
ISSN (online)	1939-4586
ISSN	1059-1524
DOI	10.1091/mbc.E12-08-0622
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Zs.A 2853: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Subcellular Localization of HIV-1

Becker, Jordan T / Sherer, Nathan M

Journal of virology

2017 Volume 91, Issue 6

Abstract: Full-length unspliced human immunodeficiency virus type 1 (HIV-1) RNAs serve dual roles in the cytoplasm as mRNAs encoding the Gag and Gag-Pol capsid proteins as well as genomic RNAs (gRNAs) packaged by Gag into virions undergoing assembly at the plasma ... ...

Abstract	Full-length unspliced human immunodeficiency virus type 1 (HIV-1) RNAs serve dual roles in the cytoplasm as mRNAs encoding the Gag and Gag-Pol capsid proteins as well as genomic RNAs (gRNAs) packaged by Gag into virions undergoing assembly at the plasma membrane (PM). Because Gag is sufficient to drive the assembly of virus-like particles even in the absence of gRNA binding, whether viral RNA trafficking plays an active role in the native assembly pathway is unknown. In this study, we tested the effects of modulating the cytoplasmic abundance or distribution of full-length viral RNAs on Gag trafficking and assembly in the context of single cells. Increasing full-length viral RNA abundance or distribution had little-to-no net effect on Gag assembly competency when provided in
MeSH term(s)	Cell Line ; Cell Membrane/chemistry ; Cytoplasm/chemistry ; HIV-1/physiology ; Humans ; RNA, Messenger/analysis ; RNA, Viral/analysis ; Virion/metabolism ; Virus Assembly ; gag Gene Products, Human Immunodeficiency Virus/metabolism
Chemical Substances	RNA, Messenger ; RNA, Viral ; gag Gene Products, Human Immunodeficiency Virus
Language	English
Publishing date	2017-03-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.02315-16
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Article: HIV-1 Protease Inhibitors Slow HPV16-Driven Cell Proliferation through Targeted Depletion of Viral E6 and E7 Oncoproteins.

Park, Soyeong / Auyeung, Andrew / Lee, Denis L / Lambert, Paul F / Carchman, Evie H / Sherer, Nathan M

Cancers

2021 Volume 13, Issue 5

Abstract: High-risk human papillomavirus strain 16 (HPV16) causes oral and anogenital cancers through the activities of two viral oncoproteins, E6 and E7, that dysregulate the host p53 and pRb tumor suppressor pathways, respectively. The maintenance of HPV16- ... ...

Abstract	High-risk human papillomavirus strain 16 (HPV16) causes oral and anogenital cancers through the activities of two viral oncoproteins, E6 and E7, that dysregulate the host p53 and pRb tumor suppressor pathways, respectively. The maintenance of HPV16-positive cancers requires constitutive expression of E6 and E7. Therefore, inactivating these proteins could provide the basis for an anticancer therapy. Herein we demonstrate that a subset of aspartyl protease inhibitor drugs currently used to treat HIV/AIDS cause marked reductions in HPV16 E6 and E7 protein levels using two independent cell culture models: HPV16-transformed CaSki cervical cancer cells and NIKS16 organotypic raft cultures (a 3-D HPV16-positive model of epithelial pre-cancer). Treatment of CaSki cells with some (lopinavir, ritonavir, nelfinavir, and saquinavir) but not other (indinavir and atazanavir) protease inhibitors reduced E6 and E7 protein levels, correlating with increased p53 protein levels and decreased cell viability. Long-term (>7 day) treatment of HPV16-positive NIKS16 raft cultures with saquinavir caused epithelial atrophy with no discernible effects on HPV-negative rafts, demonstrating selectivity. Saquinavir also reduced HPV16's effects on markers of the cellular autophagy pathway in NIKS16 rafts, a hallmark of HPV-driven pre-cancers. Taken together, these data suggest HIV-1 protease inhibitors be studied further in the context of treating or preventing HPV16-positive cancers.
Language	English
Publishing date	2021-02-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers13050949
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Article ; Online: Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1.

Miller, Rachel M / Knoener, Rachel A / Benner, Bayleigh E / Frey, Brian L / Scalf, Mark / Shortreed, Michael R / Sherer, Nathan M / Smith, Lloyd M

Journal of proteome research

2022 Volume 21, Issue 4, Page(s) 993–1001

Abstract: Human immunodeficiency virus type 1 (HIV-1) remains a deadly infectious disease despite existing antiretroviral therapies. A comprehensive understanding of the specific mechanisms of viral infectivity remains elusive and currently limits the development ... ...

Abstract	Human immunodeficiency virus type 1 (HIV-1) remains a deadly infectious disease despite existing antiretroviral therapies. A comprehensive understanding of the specific mechanisms of viral infectivity remains elusive and currently limits the development of new and effective therapies. Through in-depth proteomic analysis of HIV-1 virions, we discovered the novel post-translational modification of highly conserved residues within the viral matrix and capsid proteins to the dehydroamino acids, dehydroalanine and dehydrobutyrine. We further confirmed their presence by labeling the reactive alkene, characteristic of dehydroamino acids, with glutathione via Michael addition. Dehydroamino acids are rare, understudied, and have been observed mainly in select bacterial and fungal species. Until now, they have not been observed in HIV proteins. We hypothesize that these residues are important in viral particle maturation and could provide valuable insight into HIV infectivity mechanisms.
MeSH term(s)	Capsid/chemistry ; Capsid/metabolism ; Capsid Proteins/analysis ; Capsid Proteins/chemistry ; Capsid Proteins/genetics ; HIV-1/genetics ; Humans ; Proteomics ; Virion
Chemical Substances	Capsid Proteins
Language	English
Publishing date	2022-02-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00867
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Article: Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1

Miller, Rachel M. / Knoener, Rachel A. / Benner, Bayleigh E. / Frey, Brian L. / Scalf, Mark / Shortreed, Michael R. / Sherer, Nathan M. / Smith, Lloyd M.

Journal of proteome research. 2022 Feb. 22, v. 21, no. 4

2022

Abstract	Human immunodeficiency virus type 1 (HIV-1) remains a deadly infectious disease despite existing antiretroviral therapies. A comprehensive understanding of the specific mechanisms of viral infectivity remains elusive and currently limits the development of new and effective therapies. Through in-depth proteomic analysis of HIV-1 virions, we discovered the novel post-translational modification of highly conserved residues within the viral matrix and capsid proteins to the dehydroamino acids, dehydroalanine and dehydrobutyrine. We further confirmed their presence by labeling the reactive alkene, characteristic of dehydroamino acids, with glutathione via Michael addition. Dehydroamino acids are rare, understudied, and have been observed mainly in select bacterial and fungal species. Until now, they have not been observed in HIV proteins. We hypothesize that these residues are important in viral particle maturation and could provide valuable insight into HIV infectivity mechanisms.
Keywords	Human immunodeficiency virus 1 ; amino acids ; antiretroviral agents ; capsid ; chemical reactions ; fungi ; glutathione ; infectious diseases ; pathogenicity ; post-translational modification ; proteome ; proteomics ; research ; virion
Language	English
Dates of publication	2022-0222
Size	p. 993-1001.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00867
Database	NAL-Catalogue (AGRICOLA)

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Article: Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs.

Whitworth, Isabella T / Knoener, Rachel A / Puray-Chavez, Maritza / Halfmann, Peter / Romero, Sofia / Baddouh, M'bark / Scalf, Mark / Kawaoka, Yoshihiro / Kutluay, Sebla B / Smith, Lloyd M / Sherer, Nathan M

bioRxiv : the preprint server for biology

2023

Abstract: Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral defense mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different ... ...

Abstract	Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral defense mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different aspects of viral replication. Here, for the first time, we demonstrate the successful isolation of SARS-CoV-2 genomic RNA and three distinct sgRNAs (N, S, and ORF8) from a single population of infected cells and characterize their protein interactomes. Over 500 protein interactors (including 260 previously unknown) were identified as associated with one or more target RNA at either of two time points. These included protein interactors unique to a single RNA pool and others present in multiple pools, highlighting our ability to discriminate between distinct viral RNA interactomes despite high sequence similarity. The interactomes indicated viral associations with cell response pathways including regulation of cytoplasmic ribonucleoprotein granules and posttranscriptional gene silencing. We validated the significance of five protein interactors predicted to exhibit antiviral activity (APOBEC3F, TRIM71, PPP1CC, LIN28B, and MSI2) using siRNA knockdowns, with each knockdown yielding increases in viral production. This study describes new technology for studying SARS-CoV-2 and reveals a wealth of new viral RNA-associated host factors of potential functional significance to infection.
Language	English
Publishing date	2023-05-16
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.15.540806
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Article ; Online: Exploiting a rodent cell block for intrinsic resistance to HIV-1 gene expression in human T cells.

Behrens, Ryan T / Rajashekar, Jyothi Krishnaswamy / Bruce, James W / Evans, Edward L / Hansen, Amelia M / Salazar-Quiroz, Natalia / Simons, Lacy M / Ahlquist, Paul / Hultquist, Judd F / Kumar, Priti / Sherer, Nathan M

mBio

2023 Volume 14, Issue 5, Page(s) e0042023

Abstract: Importance: Unlike humans, mice are unable to support HIV-1 infection. This is due, in part, to a constellation of defined minor, species-specific differences in conserved host proteins needed for viral gene expression. Here, we used precision CRISPR/ ... ...

Abstract	Importance: Unlike humans, mice are unable to support HIV-1 infection. This is due, in part, to a constellation of defined minor, species-specific differences in conserved host proteins needed for viral gene expression. Here, we used precision CRISPR/Cas9 gene editing to engineer a "mousified" version of one such host protein, cyclin T1 (CCNT1), in human T cells. CCNT1 is essential for efficient HIV-1 transcription, making it an intriguing target for gene-based inactivation of virus replication. We show that isogenic cell lines engineered to encode CCNT1 bearing a single mouse-informed amino acid change (tyrosine in place of cysteine at position 261) exhibit potent, durable, and broad-spectrum resistance to HIV-1 and other pathogenic lentiviruses, and with no discernible impact on host cell biology. These results provide proof of concept for targeting
MeSH term(s)	Humans ; Mice ; Animals ; HIV-1/physiology ; Rodentia ; Cell Line ; Cyclin T/genetics ; Cyclin T/metabolism ; HIV Seropositivity ; HIV Infections ; Gene Expression ; T-Lymphocytes
Chemical Substances	Cyclin T
Language	English
Publishing date	2023-09-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.00420-23
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Article ; Online: Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs.

Journal of proteome research

2023 Volume 23, Issue 1, Page(s) 149–160

Abstract: Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different aspects of ... ...

Abstract	Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different aspects of viral replication. Here, for the first time, we demonstrate the successful isolation of SARS-CoV-2 genomic RNA and three distinct sgRNAs (N, S, and ORF8) from a single population of infected cells and characterize their protein interactomes. Over 500 protein interactors (including 260 previously unknown) were identified as associated with one or more target RNA. These included protein interactors unique to a single RNA pool and others present in multiple pools, highlighting our ability to discriminate between distinct viral RNA interactomes despite high sequence similarity. Individual interactomes indicated viral associations with cell response pathways, including regulation of cytoplasmic ribonucleoprotein granules and posttranscriptional gene silencing. We tested the significance of three protein interactors in these pathways (APOBEC3F, PPP1CC, and MSI2) using siRNA knockdowns, with several knockdowns affecting viral gene expression, most consistently PPP1CC. This study describes a new technology for high-resolution studies of SARS-CoV-2 RNA regulation and reveals a wealth of new viral RNA-associated host factors of potential functional significance to infection.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Subgenomic RNA ; RNA, Viral/genetics ; RNA, Viral/metabolism ; COVID-19/genetics ; Virus Replication/genetics ; Genomics ; RNA-Binding Proteins/genetics
Chemical Substances	Subgenomic RNA ; RNA, Viral ; MSI2 protein, human ; RNA-Binding Proteins
Language	English
Publishing date	2023-12-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00506
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