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Article ; Online: Capsid-dependent lentiviral restrictions.

Twentyman, Joy / Emerman, Michael / Ohainle, Molly

2024 Volume 98, Issue 4, Page(s) e0030824

Abstract: Host antiviral proteins inhibit primate lentiviruses and other retroviruses by targeting many features of the viral life cycle. The lentiviral capsid protein and the assembled viral core are known to be inhibited through multiple, directly acting ... ...

Abstract	Host antiviral proteins inhibit primate lentiviruses and other retroviruses by targeting many features of the viral life cycle. The lentiviral capsid protein and the assembled viral core are known to be inhibited through multiple, directly acting antiviral proteins. Several phenotypes, including those known as
MeSH term(s)	Animals ; Capsid/metabolism ; Capsid Proteins/genetics ; Capsid Proteins/metabolism ; Lentivirus/metabolism ; Host-Pathogen Interactions ; Lentivirus Infections/metabolism
Chemical Substances	Capsid Proteins
Language	English
Publishing date	2024-03-18
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.00308-24
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Article ; Online: HIV-1 Vif Gained Breadth in APOBEC3G Specificity after Cross-Species Transmission of Its Precursors.

Chesarino, Nicholas M / Emerman, Michael

Journal of virology

2021 Volume 96, Issue 4, Page(s) e0207121

Abstract: APOBEC3G (A3G) is a host-encoded cytidine deaminase that potently restricts retroviruses such as HIV-1 and depends on its ability to package into virions. As a consequence of this, HIV-1 protein Vif has evolved to antagonize human A3G by targeting it for ...

Abstract	APOBEC3G (A3G) is a host-encoded cytidine deaminase that potently restricts retroviruses such as HIV-1 and depends on its ability to package into virions. As a consequence of this, HIV-1 protein Vif has evolved to antagonize human A3G by targeting it for ubiquitination and subsequent degradation. There is an ancient arms race between Vif and A3G highlighted by amino acids 128 and 130 in A3G that have evolved under positive selection due to Vif-mediated selective pressure in Old World primates. Nonetheless, not all possible amino acid combinations at these sites have been sampled by nature, and the evolutionary potential of species to resist Vif antagonism is not clear. To explore the evolutionary space of positively selected sites in the Vif-binding region of A3G, we designed a combinatorial mutagenesis screen to introduce all 20 amino acids at sites 128 and 130. Our screen uncovered mutants of A3G with several interesting phenotypes, including loss of antiviral activity and resistance of Vif antagonism. However, HIV-1 Vif exhibited remarkable flexibility in antagonizing A3G 128 and 130 mutants, which significantly reduces viable Vif resistance strategies for hominid primates. Importantly, we find that broadened Vif specificity was conferred through loop 5 adaptations that were required for cross-species adaptation from Old World monkey A3G to hominid A3G. Our evidence suggests that Vif adaptation to novel A3G interfaces during cross-species transmission may train Vif toward broadened specificity that can further facilitate cross-species transmissions and raise the barrier to host resistance.
MeSH term(s)	APOBEC-3G Deaminase/antagonists & inhibitors ; APOBEC-3G Deaminase/genetics ; Adaptation, Physiological/genetics ; Amino Acids ; Animals ; HIV Infections/transmission ; HIV Infections/virology ; HIV-1/genetics ; HIV-1/physiology ; Host Microbial Interactions ; Humans ; Mutation ; Primates ; Simian Immunodeficiency Virus/genetics ; Viral Zoonoses/transmission ; Viral Zoonoses/virology ; vif Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors ; vif Gene Products, Human Immunodeficiency Virus/genetics
Chemical Substances	Amino Acids ; vif Gene Products, Human Immunodeficiency Virus ; vif protein, Human immunodeficiency virus 1 ; APOBEC-3G Deaminase (EC 3.5.4.5) ; APOBEC3G protein, human (EC 3.5.4.5)
Language	English
Publishing date	2021-12-15
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.02071-21
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Article ; Online: A human-specific motif facilitates CARD8 inflammasome activation after HIV-1 infection.

Kulsuptrakul, Jessie / Turcotte, Elizabeth A / Emerman, Michael / Mitchell, Patrick S

eLife

2023 Volume 12

Abstract: Inflammasomes are cytosolic innate immune complexes that assemble upon detection of diverse pathogen-associated cues and play a critical role in host defense and inflammatory pathogenesis. Here, we find that the human inflammasome-forming sensor CARD8 ... ...

Abstract	Inflammasomes are cytosolic innate immune complexes that assemble upon detection of diverse pathogen-associated cues and play a critical role in host defense and inflammatory pathogenesis. Here, we find that the human inflammasome-forming sensor CARD8 senses HIV-1 infection via site-specific cleavage of the CARD8 N-terminus by the HIV protease (HIV-1
MeSH term(s)	Animals ; Humans ; Inflammasomes/metabolism ; HIV-1 ; Pan troglodytes/metabolism ; HIV Infections ; Simian Immunodeficiency Virus ; Apoptosis Regulatory Proteins/metabolism ; Neoplasm Proteins/metabolism ; CARD Signaling Adaptor Proteins/metabolism
Chemical Substances	Inflammasomes ; Apoptosis Regulatory Proteins ; CARD8 protein, human ; Neoplasm Proteins ; CARD Signaling Adaptor Proteins
Language	English
Publishing date	2023-07-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.84108
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Article ; Online: Evolutionary Landscapes of Host-Virus Arms Races.

Tenthorey, Jeannette L / Emerman, Michael / Malik, Harmit S

Annual review of immunology

2022 Volume 40, Page(s) 271–294

Abstract: Vertebrate immune systems suppress viral infection using both innate restriction factors and adaptive immunity. Viruses mutate to escape these defenses, driving hosts to counterevolve to regain fitness. This cycle recurs repeatedly, resulting in an ... ...

Abstract	Vertebrate immune systems suppress viral infection using both innate restriction factors and adaptive immunity. Viruses mutate to escape these defenses, driving hosts to counterevolve to regain fitness. This cycle recurs repeatedly, resulting in an evolutionary arms race whose outcome depends on the pace and likelihood of adaptation by host and viral genes. Although viruses evolve faster than their vertebrate hosts, their proteins are subject to numerous functional constraints that impact the probability of adaptation. These constraints are globally defined by evolutionary landscapes, which describe the fitness and adaptive potential of all possible mutations. We review deep mutational scanning experiments mapping the evolutionary landscapes of both host and viral proteins engaged in arms races. For restriction factors and some broadly neutralizing antibodies, landscapes favor the host, which may help to level the evolutionary playing field against rapidly evolving viruses. We discuss the biophysical underpinnings of these landscapes and their therapeutic implications.
MeSH term(s)	Animals ; Biological Evolution ; Humans ; Mutation ; Viral Proteins ; Virus Diseases/genetics ; Viruses/genetics
Chemical Substances	Viral Proteins
Language	English
Publishing date	2022-01-26
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	604953-9
ISSN	1545-3278 ; 0732-0582
ISSN (online)	1545-3278
ISSN	0732-0582
DOI	10.1146/annurev-immunol-072621-084422
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Article ; Online: Polymorphisms in Human APOBEC3H Differentially Regulate Ubiquitination and Antiviral Activity.

Chesarino, Nicholas M / Emerman, Michael

Viruses

2020 Volume 12, Issue 4

Abstract: The APOBEC3 family of cytidine deaminases are an important part of the host innate immune defense against endogenous retroelements and retroviruses like Human Immunodeficiency Virus (HIV). APOBEC3H (A3H) is the most polymorphic of the human APOBEC3 genes, ...

Abstract	The APOBEC3 family of cytidine deaminases are an important part of the host innate immune defense against endogenous retroelements and retroviruses like Human Immunodeficiency Virus (HIV). APOBEC3H (A3H) is the most polymorphic of the human APOBEC3 genes, with four major haplotypes circulating in the population. Haplotype II is the only antivirally-active variant of A3H, while the majority of the population possess independently destabilizing polymorphisms present in haplotype I (R105G) and haplotypes III and IV (N15del). In this paper, we show that instability introduced by either polymorphism is positively correlated with degradative ubiquitination, while haplotype II is protected from this modification. Inhibiting ubiquitination by mutating all of the A3H lysines increased the expression of haplotypes III and IV, but these stabilized forms of haplotype III and IV had a strict nuclear localization, and did not incorporate into virions, nor exhibit antiviral activity. Fusion chimeras with haplotype II allowed for stabilization, cytoplasmic retention, and packaging of the N15del-containing haplotype III, but the haplotype III component of these chimeras was unable to restrict HIV-1 on its own. Thus, the evolutionary loss of A3H activity in many humans involves functional deficiencies independent of protein stability.
MeSH term(s)	Aminohydrolases/genetics ; Cell Line ; HIV Infections/genetics ; HIV Infections/immunology ; HIV Infections/virology ; Haplotypes ; Humans ; Polymorphism, Genetic ; Protein Stability ; Ubiquitination ; Virus Assembly ; Virus Diseases/genetics ; Virus Diseases/immunology ; Virus Diseases/virology ; Virus Physiological Phenomena
Chemical Substances	APOBEC3H protein, human (EC 3.5.4.-) ; Aminohydrolases (EC 3.5.4.-)
Language	English
Publishing date	2020-03-30
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v12040378
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Article: A CRISPR screen of HIV dependency factors reveals

Hafer, Terry L / Felton, Abby / Delgado, Yennifer / Srinivasan, Harini / Emerman, Michael

bioRxiv : the preprint server for biology

2023

Abstract: We sought to explore the hypothesis that host factors required for HIV-1 replication also play a role in latency reversal. Using a CRISPR gene library of putative HIV dependency factors, we performed a screen to identify genes required for latency ... ...

Abstract	We sought to explore the hypothesis that host factors required for HIV-1 replication also play a role in latency reversal. Using a CRISPR gene library of putative HIV dependency factors, we performed a screen to identify genes required for latency reactivation. We identified several HIV-1 dependency factors that play a key role in HIV-1 latency reactivation including
Language	English
Publishing date	2023-07-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.07.28.551016
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Article: Primate TRIM34 is a broadly-acting, TRIM5-dependent lentiviral restriction factor.

Twentyman, Joy / Khalifeh, Anthony / Felton, Abby L / Emerman, Michael / OhAinle, Molly

bioRxiv : the preprint server for biology

2023

Abstract: Human immunodeficiency virus (HIV) and other lentiviruses adapt to new hosts by evolving to evade host-specific innate immune proteins that differ in sequence and often viral recognition between host species. Understanding how these host antiviral ... ...

Abstract	Human immunodeficiency virus (HIV) and other lentiviruses adapt to new hosts by evolving to evade host-specific innate immune proteins that differ in sequence and often viral recognition between host species. Understanding how these host antiviral proteins, called restriction factors, constrain lentivirus replication and transmission is key to understanding the emergence of pandemic viruses like HIV-1. Human TRIM34, a paralogue of the well-characterized lentiviral restriction factor TRIM5α, was previously identified by our lab via CRISPR-Cas9 screening as a restriction factor of certain HIV and SIV capsids. Here, we show that diverse primate TRIM34 orthologues from non-human primates can restrict a range of Simian Immunodeficiency Virus (SIV) capsids including SIV
Language	English
Publishing date	2023-03-25
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.24.534139
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Article ; Online: Primate TRIM34 is a broadly-acting, TRIM5-dependent lentiviral restriction factor.

Twentyman, Joy / Khalifeh, Anthony / Felton, Abby L / Emerman, Michael / Ohainle, Molly

Retrovirology

2023 Volume 20, Issue 1, Page(s) 15

Abstract	Human immunodeficiency virus (HIV) and other lentiviruses adapt to new hosts by evolving to evade host-specific innate immune proteins that differ in sequence and often viral recognition between host species. Understanding how these host antiviral proteins, called restriction factors, constrain lentivirus replication and transmission is key to understanding the emergence of pandemic viruses like HIV-1. Human TRIM34, a paralogue of the well-characterized lentiviral restriction factor TRIM5α, was previously identified by our lab via CRISPR-Cas9 screening as a restriction factor of certain HIV and SIV capsids. Here, we show that diverse primate TRIM34 orthologues from non-human primates can restrict a range of Simian Immunodeficiency Virus (SIV) capsids including SIV
MeSH term(s)	Animals ; Macaca mulatta ; Lentivirus ; Simian Immunodeficiency Virus/genetics ; Antiviral Agents ; HIV Infections
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2023-08-22
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2142602-8
ISSN	1742-4690 ; 1742-4690
ISSN (online)	1742-4690
ISSN	1742-4690
DOI	10.1186/s12977-023-00629-4
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Article ; Online: A CRISPR Screen of HIV Dependency Factors Reveals That

Hafer, Terry L / Felton, Abby / Delgado, Yennifer / Srinivasan, Harini / Emerman, Michael

Viruses

2023 Volume 15, Issue 9

Abstract	We sought to explore the hypothesis that host factors required for HIV-1 replication also play a role in latency reversal. Using a CRISPR gene library of putative HIV dependency factors, we performed a screen to identify genes required for latency reactivation. We identified several HIV-1 dependency factors that play a key role in HIV-1 latency reactivation including ELL, UBE2M, TBL1XR1, HDAC3, AMBRA1, and ALYREF. The knockout of Cyclin T1 (
MeSH term(s)	Humans ; Adaptor Proteins, Signal Transducing/genetics ; CD4-Positive T-Lymphocytes ; Clustered Regularly Interspaced Short Palindromic Repeats ; Cyclin T/genetics ; Cyclin T/metabolism ; HIV Infections ; HIV-1/physiology ; Ubiquitin-Conjugating Enzymes/genetics ; Virus Activation ; Virus Latency
Chemical Substances	Adaptor Proteins, Signal Transducing ; AMBRA1 protein, human ; Cyclin T ; UBE2M protein, human (EC 6.3.2.-) ; Ubiquitin-Conjugating Enzymes (EC 2.3.2.23) ; CCNT1 protein, human
Language	English
Publishing date	2023-08-31
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15091863
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Article: Indels allow antiviral proteins to evolve functional novelty inaccessible by missense mutations.

Tenthorey, Jeannette L / Del Banco, Serena / Ramzan, Ishrak / Klingenberg, Hayley / Liu, Chang / Emerman, Michael / Malik, Harmit S

bioRxiv : the preprint server for biology

2024

Abstract: Antiviral proteins often evolve rapidly at virus-binding interfaces to defend against new viruses. We investigated whether antiviral adaptation via missense mutations might face limits, which insertion or deletion mutations (indels) could overcome. We ... ...

Abstract	Antiviral proteins often evolve rapidly at virus-binding interfaces to defend against new viruses. We investigated whether antiviral adaptation via missense mutations might face limits, which insertion or deletion mutations (indels) could overcome. We report one such case of a nearly insurmountable evolutionary challenge: the human anti-retroviral protein TRIM5α requires more than five missense mutations in its specificity-determining v1 loop to restrict a divergent simian immunodeficiency virus (SIV). However, duplicating just one amino acid in v1 enables human TRIM5α to potently restrict SIV in a single evolutionary step. Moreover, natural primate TRIM5α v1 loops have evolved indels that confer novel antiviral specificities. Thus, indels enable antiviral proteins to overcome viral challenges inaccessible by missense mutations, revealing the potential of these often-overlooked mutations in driving protein innovation.
Language	English
Publishing date	2024-05-10
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.05.07.592993
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