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Article ; Online: Synthetic regulatory reconstitution reveals principles of mammalian

Pinglay, Sudarshan / Bulajić, Milica / Rahe, Dylan P / Huang, Emily / Brosh, Ran / Mamrak, Nicholas E / King, Benjamin R / German, Sergei / Cadley, John A / Rieber, Lila / Easo, Nicole / Lionnet, Timothée / Mahony, Shaun / Maurano, Matthew T / Holt, Liam J / Mazzoni, Esteban O / Boeke, Jef D

Science (New York, N.Y.)

2022 Volume 377, Issue 6601, Page(s) eabk2820

Abstract: ... ...

Abstract	Precise
MeSH term(s)	Animals ; Body Patterning/genetics ; Enhancer Elements, Genetic ; Gene Expression Regulation, Developmental ; Genes, Homeobox ; Genome ; Homeodomain Proteins/genetics ; Mice ; Rats ; Transcription, Genetic
Chemical Substances	Homeodomain Proteins
Language	English
Publishing date	2022-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abk2820
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Zs.A 27: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 77: Show issues

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Article ; Online: The use of novel epitope-tagged arenaviruses reveals that Rab5c-positive endosomal membranes are targeted by the LCMV matrix protein.

Ziegler, Christopher M / Bruce, Emily A / Kelly, Jamie A / King, Benjamin R / Botten, Jason W

The Journal of general virology

2017 Volume 99, Issue 2, Page(s) 187–193

Abstract: We report the development of recombinant New World (Junín; JUNV) and Old World (lymphocytic choriomeningitis virus; LCMV) mammarenaviruses that encode an HA-tagged matrix protein (Z). These viruses permit the robust affinity purification of Z from ... ...

Abstract	We report the development of recombinant New World (Junín; JUNV) and Old World (lymphocytic choriomeningitis virus; LCMV) mammarenaviruses that encode an HA-tagged matrix protein (Z). These viruses permit the robust affinity purification of Z from infected cells or virions, as well as the detection of Z by immunofluorescent microscopy. Importantly, the HA-tagged viruses grow with wild-type kinetics in a multi-cycle growth assay. Using these viruses, we report a novel description of JUNV Z localization in infected cells, as well as the first description of colocalization between LCMV Z and the GTPase Rab5c. This latter result, when combined with our previous findings that LCMV genome and glycoprotein also colocalize with Rab5c, suggest that LCMV may target Rab5c-positive membranes for preassembly of virus particles prior to budding. The recombinant viruses reported here will provide the field with new tools to better study Z protein functionality and identify key Z protein interactions with host machinery.
MeSH term(s)	A549 Cells ; Arenavirus/immunology ; Arenavirus/physiology ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; Endosomes/metabolism ; Endosomes/virology ; Epitopes/immunology ; GTP Phosphohydrolases/genetics ; GTP Phosphohydrolases/metabolism ; Genes, Reporter ; Glycoproteins/genetics ; Glycoproteins/metabolism ; Host-Pathogen Interactions ; Humans ; Intracellular Membranes/metabolism ; Intracellular Membranes/virology ; Intracellular Signaling Peptides and Proteins ; Lymphocytic choriomeningitis virus/immunology ; Lymphocytic choriomeningitis virus/physiology ; Microscopy, Fluorescence ; Virus Assembly
Chemical Substances	Carrier Proteins ; Epitopes ; Glycoproteins ; Intracellular Signaling Peptides and Proteins ; p11 Z protein, Lymphocytic choriomeningitis virus ; GTP Phosphohydrolases (EC 3.6.1.-)
Language	English
Publishing date	2017-04-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	219316-4
ISSN	1465-2099 ; 0022-1317
ISSN (online)	1465-2099
ISSN	0022-1317
DOI	10.1099/jgv.0.001004
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Zs.A 610: Show issues

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Article ; Online: Visualization of Arenavirus RNA Species in Individual Cells by Single-Molecule Fluorescence

King, Benjamin R / Samacoits, Aubin / Eisenhauer, Philip L / Ziegler, Christopher M / Bruce, Emily A / Zenklusen, Daniel / Zimmer, Christophe / Mueller, Florian / Botten, Jason

Journal of virology

2018 Volume 92, Issue 12

Abstract: Lymphocytic choriomeningitis mammarenavirus (LCMV) is an enveloped, negative-strand RNA virus that causes serious disease in humans but establishes an asymptomatic, lifelong infection in reservoir rodents. Different models have been proposed to describe ... ...

Abstract	Lymphocytic choriomeningitis mammarenavirus (LCMV) is an enveloped, negative-strand RNA virus that causes serious disease in humans but establishes an asymptomatic, lifelong infection in reservoir rodents. Different models have been proposed to describe how arenaviruses regulate the replication and transcription of their bisegmented, single-stranded RNA genomes, particularly during persistent infection. However, these models were based largely on viral RNA profiling data derived from entire populations of cells. To better understand LCMV replication and transcription at the single-cell level, we established a high-throughput, single-molecule fluorescence
MeSH term(s)	A549 Cells ; Cell Line ; Genome, Viral/genetics ; Humans ; In Situ Hybridization, Fluorescence/methods ; Lymphocytic choriomeningitis virus/genetics ; RNA Probes/genetics ; RNA, Viral/genetics ; Staining and Labeling/methods ; Virus Replication/genetics
Chemical Substances	RNA Probes ; RNA, Viral
Language	English
Publishing date	2018-05-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.02241-17
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Zs.A 609: Show issues

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Article ; Online: Visualization of the lymphocytic choriomeningitis mammarenavirus (LCMV) genome reveals the early endosome as a possible site for genome replication and viral particle pre-assembly.

King, Benjamin R / Kellner, Samuel / Eisenhauer, Philip L / Bruce, Emily A / Ziegler, Christopher M / Zenklusen, Daniel / Botten, Jason William

The Journal of general virology

2017 Volume 98, Issue 10, Page(s) 2454–2460

Abstract: We report a ... ...

Abstract	We report a fluorescence
Language	English
Publishing date	2017-09-26
Publishing country	England
Document type	Journal Article
ZDB-ID	219316-4
ISSN	1465-2099 ; 0022-1317
ISSN (online)	1465-2099
ISSN	0022-1317
DOI	10.1099/jgv.0.000930
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Zs.A 610: Show issues

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Article ; Online: NEDD4 family ubiquitin ligases associate with LCMV Z's PPXY domain and are required for virus budding, but not via direct ubiquitination of Z.

Ziegler, Christopher M / Dang, Loan / Eisenhauer, Philip / Kelly, Jamie A / King, Benjamin R / Klaus, Joseph P / Manuelyan, Inessa / Mattice, Ethan B / Shirley, David J / Weir, Marion E / Bruce, Emily A / Ballif, Bryan A / Botten, Jason

PLoS pathogens

2019 Volume 15, Issue 11, Page(s) e1008100

Abstract: Viral late domains are used by many viruses to recruit the cellular endosomal sorting complex required for transport (ESCRT) to mediate membrane scission during viral budding. Unlike the P(S/T)AP and YPX(1-3)L late domains, which interact directly with ... ...

Abstract	Viral late domains are used by many viruses to recruit the cellular endosomal sorting complex required for transport (ESCRT) to mediate membrane scission during viral budding. Unlike the P(S/T)AP and YPX(1-3)L late domains, which interact directly with the ESCRT proteins Tsg101 and ALIX, the molecular linkage connecting the PPXY late domain to ESCRT proteins is unclear. The mammarenavirus lymphocytic choriomeningitis virus (LCMV) matrix protein, Z, contains only one late domain, PPXY. We previously found that this domain in LCMV Z, as well as the ESCRT pathway, are required for the release of defective interfering (DI) particles but not infectious virus. To better understand the molecular mechanism of ESCRT recruitment by the PPXY late domain, affinity purification-mass spectrometry was used to identify host proteins that interact with the Z proteins of the Old World mammarenaviruses LCMV and Lassa virus. Several Nedd4 family E3 ubiquitin ligases interact with these matrix proteins and in the case of LCMV Z, the interaction was PPXY-dependent. We demonstrated that these ligases directly ubiquitinate LCMV Z and mapped the specific lysine residues modified. A recombinant LCMV containing a Z that cannot be ubiquitinated maintained its ability to produce both infectious virus and DI particles, suggesting that direct ubiquitination of LCMV Z alone is insufficient for recruiting ESCRT proteins to mediate virus release. However, Nedd4 ligases appear to be important for DI particle release suggesting that ubiquitination of targets other than the Z protein itself is required for efficient viral ESCRT recruitment.
MeSH term(s)	Humans ; Intracellular Signaling Peptides and Proteins/metabolism ; Lymphocytic Choriomeningitis/metabolism ; Lymphocytic Choriomeningitis/virology ; Lymphocytic choriomeningitis virus/physiology ; Nedd4 Ubiquitin Protein Ligases/metabolism ; Protein Domains ; Protein Interaction Domains and Motifs ; Ubiquitination ; Virus Assembly ; Virus Replication
Chemical Substances	Intracellular Signaling Peptides and Proteins ; p11 Z protein, Lymphocytic choriomeningitis virus ; Nedd4 Ubiquitin Protein Ligases (EC 2.3.2.26)
Keywords	covid19
Language	English
Publishing date	2019-11-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7366
ISSN (online)	1553-7374
ISSN	1553-7366
DOI	10.1371/journal.ppat.1008100
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Article ; Online: A novel phosphoserine motif in the LCMV matrix protein Z regulates the release of infectious virus and defective interfering particles.

Ziegler, Christopher M / Eisenhauer, Philip / Bruce, Emily A / Beganovic, Vedran / King, Benjamin R / Weir, Marion E / Ballif, Bryan A / Botten, Jason

The Journal of general virology

2016 Volume 97, Issue 9, Page(s) 2084–2089

Abstract: We report that the lymphocytic choriomeningitis virus (LCMV) matrix protein, which drives viral budding, is phosphorylated at serine 41 (S41). A recombinant (r)LCMV bearing a phosphomimetic mutation (S41D) was impaired in infectious and defective ... ...

Abstract	We report that the lymphocytic choriomeningitis virus (LCMV) matrix protein, which drives viral budding, is phosphorylated at serine 41 (S41). A recombinant (r)LCMV bearing a phosphomimetic mutation (S41D) was impaired in infectious and defective interfering (DI) particle release, while a non-phosphorylatable mutant (S41A) was not. The S41D mutant was disproportionately impaired in its ability to release DI particles relative to infectious particles. Thus, DI particle production by LCMV may be dynamically regulated via phosphorylation of S41.
MeSH term(s)	Amino Acid Motifs ; Amino Acid Substitution ; Defective Viruses/metabolism ; Lymphocytic choriomeningitis virus/physiology ; Mutant Proteins/genetics ; Mutant Proteins/metabolism ; Phosphoserine/analysis ; Viral Matrix Proteins/chemistry ; Viral Matrix Proteins/genetics ; Viral Matrix Proteins/metabolism ; Virion/metabolism
Chemical Substances	Mutant Proteins ; Viral Matrix Proteins ; Phosphoserine (17885-08-4)
Language	English
Publishing date	2016-07-15
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	219316-4
ISSN	1465-2099 ; 0022-1317
ISSN (online)	1465-2099
ISSN	0022-1317
DOI	10.1099/jgv.0.000550
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Zs.A 610: Show issues

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Article ; Online: A Proteomics Survey of Junín Virus Interactions with Human Proteins Reveals Host Factors Required for Arenavirus Replication.

Ziegler, Christopher M / Eisenhauer, Philip / Kelly, Jamie A / Dang, Loan N / Beganovic, Vedran / Bruce, Emily A / King, Benjamin R / Shirley, David J / Weir, Marion E / Ballif, Bryan A / Botten, Jason

Journal of virology

2018 Volume 92, Issue 4

Abstract: Arenaviruses are negative-strand, enveloped RNA viruses that cause significant human disease. In particular, Junín mammarenavirus (JUNV) is the etiologic agent of Argentine hemorrhagic fever. At present, little is known about the cellular proteins that ... ...

Abstract	Arenaviruses are negative-strand, enveloped RNA viruses that cause significant human disease. In particular, Junín mammarenavirus (JUNV) is the etiologic agent of Argentine hemorrhagic fever. At present, little is known about the cellular proteins that the arenavirus matrix protein (Z) hijacks to accomplish its various functions, including driving the process of virus release. Furthermore, there is little knowledge regarding host proteins incorporated into arenavirus particles and their importance for virion function. To address these deficiencies, we used mass spectrometry to identify human proteins that (i) interact with the JUNV matrix protein inside cells or within virus-like particles (VLPs) and/or (ii) are incorporated into
MeSH term(s)	HEK293 Cells ; Hemorrhagic Fever, American/metabolism ; Hemorrhagic Fever, American/virology ; Host-Pathogen Interactions ; Humans ; Junin virus/isolation & purification ; Junin virus/pathogenicity ; Proteome/analysis ; Proteome/metabolism ; Proteomics/methods ; Viral Matrix Proteins/metabolism ; Virus Release ; Virus Replication
Chemical Substances	Proteome ; Viral Matrix Proteins
Keywords	covid19
Language	English
Publishing date	2018-01-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.01565-17
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Zs.A 609: Show issues

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Article ; Online: Proliferating γδ T cells manifest high and spatially confined caspase-3 activity.

Koenig, Andreas / Fortner, Karen A / King, Benjamin R / Madden, Jonathan / Buskiewicz, Iwona A / Budd, Ralph C

Immunology

2011 Volume 135, Issue 4, Page(s) 276–286

Abstract: Caspase-8 serves two paradoxical roles in T lymphocytes: it initiates apoptosis following death receptor engagement, and is also indispensible for proliferation following T-cell antigen receptor (TCR) signalling. These opposing processes appear to be ... ...

Abstract	Caspase-8 serves two paradoxical roles in T lymphocytes: it initiates apoptosis following death receptor engagement, and is also indispensible for proliferation following T-cell antigen receptor (TCR) signalling. These opposing processes appear to be controlled by both spatial and quantitative differences in caspase-8 activation. Given differences in the turnover of T-cell subsets, we compared caspase activity and susceptibility to cell death following TCR restimulation in murine CD4(+) and CD8(+) αβ T cells and γδ T cells. We observed a spectrum of caspase activity in non-dying effector T cells in which CD4(+) T cells manifested the lowest levels of active caspases whereas γδ T cells manifested the highest levels. Further analysis revealed that most of the difference in T-cell subsets was the result of high levels of active caspase-3 in non-dying effector γδ T cells. Despite this, γδ T cells manifested little spontaneous or CD3 restimulation-induced cell death as the result of confinement of active caspases to the cell membrane. By contrast, CD4(+) T cells were highly sensitive to CD3-induced cell death, associated with the appearance of active caspases in the cytoplasm and cleavage of the caspase substrates Bid and ICAD. Hence, the location and amount of active caspases distinguishes effector T-cell subsets and profoundly influences the fate of the T-cell response.
MeSH term(s)	Animals ; Apoptosis ; CD4-Positive T-Lymphocytes/cytology ; CD4-Positive T-Lymphocytes/immunology ; CD4-Positive T-Lymphocytes/metabolism ; CD8-Positive T-Lymphocytes/cytology ; CD8-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/metabolism ; Caspase 3/genetics ; Caspase 3/metabolism ; Caspase 8/metabolism ; Cells, Cultured ; Lymphocyte Activation/immunology ; Mice ; Mice, Inbred C57BL ; Receptors, Antigen, T-Cell, alpha-beta/metabolism ; Receptors, Antigen, T-Cell, gamma-delta/metabolism ; Signal Transduction
Chemical Substances	Receptors, Antigen, T-Cell, alpha-beta ; Receptors, Antigen, T-Cell, gamma-delta ; Caspase 3 (EC 3.4.22.-) ; Caspase 8 (EC 3.4.22.-)
Language	English
Publishing date	2011-11-25
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80124-0
ISSN	1365-2567 ; 0019-2805 ; 0953-4954
ISSN (online)	1365-2567
ISSN	0019-2805 ; 0953-4954
DOI	10.1111/j.1365-2567.2011.03540.x
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Ud II Zs.181: Show issues

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Article ; Online: A Map of the Arenavirus Nucleoprotein-Host Protein Interactome Reveals that Junín Virus Selectively Impairs the Antiviral Activity of Double-Stranded RNA-Activated Protein Kinase (PKR).

King, Benjamin R / Hershkowitz, Dylan / Eisenhauer, Philip L / Weir, Marion E / Ziegler, Christopher M / Russo, Joanne / Bruce, Emily A / Ballif, Bryan A / Botten, Jason

Journal of virology

2017 Volume 91, Issue 15

Abstract: Arenaviruses are enveloped negative-strand RNA viruses that cause significant human disease. These viruses encode only four proteins to accomplish the viral life cycle, so each arenavirus protein likely plays unappreciated accessory roles during ... ...

Abstract	Arenaviruses are enveloped negative-strand RNA viruses that cause significant human disease. These viruses encode only four proteins to accomplish the viral life cycle, so each arenavirus protein likely plays unappreciated accessory roles during infection. Here we used immunoprecipitation and mass spectrometry to identify human proteins that interact with the nucleoproteins (NPs) of the Old World arenavirus lymphocytic choriomeningitis virus (LCMV) and the New World arenavirus Junín virus (JUNV) strain Candid #1. Bioinformatic analysis of the identified protein partners of NP revealed that host translation appears to be a key biological process engaged during infection. In particular, NP associates with the double-stranded RNA (dsRNA)-activated protein kinase (PKR), a well-characterized antiviral protein that inhibits cap-dependent protein translation initiation via phosphorylation of eIF2α. JUNV infection leads to increased expression of PKR as well as its redistribution to viral replication and transcription factories. Further, phosphorylation of PKR, which is a prerequisite for its ability to phosphorylate eIF2α, is readily induced by JUNV. However, JUNV prevents this pool of activated PKR from phosphorylating eIF2α, even following exposure to the synthetic dsRNA poly(I·C), a potent PKR agonist. This blockade of PKR function is highly specific, as LCMV is unable to similarly inhibit eIF2α phosphorylation. JUNV's ability to antagonize the antiviral activity of PKR appears to be complete, as silencing of PKR expression has no impact on viral propagation. In summary, we provide a detailed map of the host machinery engaged by arenavirus NPs and identify an antiviral pathway that is subverted by JUNV.
MeSH term(s)	Cell Line ; Host-Pathogen Interactions ; Humans ; Immune Evasion ; Immunoprecipitation ; Junin virus/pathogenicity ; Lymphocytic choriomeningitis virus/pathogenicity ; Mass Spectrometry ; Nucleocapsid Proteins/metabolism ; Protein Interaction Mapping ; eIF-2 Kinase/antagonists & inhibitors
Chemical Substances	Nucleocapsid Proteins ; EIF2AK2 protein, human (EC 2.7.11.1) ; eIF-2 Kinase (EC 2.7.11.1)
Keywords	covid19
Language	English
Publishing date	2017-07-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.00763-17
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Article ; Online: The Lymphocytic Choriomeningitis Virus Matrix Protein PPXY Late Domain Drives the Production of Defective Interfering Particles.

Ziegler, Christopher M / Eisenhauer, Philip / Bruce, Emily A / Weir, Marion E / King, Benjamin R / Klaus, Joseph P / Krementsov, Dimitry N / Shirley, David J / Ballif, Bryan A / Botten, Jason

PLoS pathogens

2016 Volume 12, Issue 3, Page(s) e1005501

Abstract: Arenaviruses cause severe diseases in humans but establish asymptomatic, lifelong infections in rodent reservoirs. Persistently-infected rodents harbor high levels of defective interfering (DI) particles, which are thought to be important for ... ...

Abstract	Arenaviruses cause severe diseases in humans but establish asymptomatic, lifelong infections in rodent reservoirs. Persistently-infected rodents harbor high levels of defective interfering (DI) particles, which are thought to be important for establishing persistence and mitigating virus-induced cytopathic effect. Little is known about what drives the production of DI particles. We show that neither the PPXY late domain encoded within the lymphocytic choriomeningitis virus (LCMV) matrix protein nor a functional endosomal sorting complex transport (ESCRT) pathway is absolutely required for the generation of standard infectious virus particles. In contrast, DI particle release critically requires the PPXY late domain and is ESCRT-dependent. Additionally, the terminal tyrosine in the PPXY motif is reversibly phosphorylated and our findings indicate that this posttranslational modification may regulate DI particle formation. Thus we have uncovered a new role for the PPXY late domain and a possible mechanism for its regulation.
MeSH term(s)	Cell Line ; Defective Viruses/metabolism ; Endosomal Sorting Complexes Required for Transport/metabolism ; Endosomes/metabolism ; Humans ; Lymphocytic choriomeningitis virus/physiology ; Phosphorylation ; Protein Structure, Tertiary ; Virion/metabolism ; Virus Release
Chemical Substances	Endosomal Sorting Complexes Required for Transport
Keywords	covid19
Language	English
Publishing date	2016-03-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7366
ISSN (online)	1553-7374
ISSN	1553-7366
DOI	10.1371/journal.ppat.1005501
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