Degradation-Independent Inhibition of APOBEC3G by the HIV-1 Vif Protein

The ubiquitin–proteasome system plays an important role in the cell under normal physiological conditions but also during viral infections. Indeed, many auxiliary proteins from the (HIV-1) divert this system to its own advantage, notably to induce the degradation of cellular restriction factors. For instance, the HIV-1 viral infectivity factor (Vif) has been shown to specifically counteract several cellular deaminases belonging to the apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC3 or A3) family (A3A to A3H) by recruiting an E3-ubiquitin ligase complex and inducing their polyubiquitination and degradation through the proteasome. Although this pathway has been extensively characterized so far, Vif has also been shown to impede A3s through degradation-independent processes, but research on this matter remains limited. In this review, we describe our current knowledge regarding the degradation-independent inhibition of A3s, and A3G in particular, by the HIV-1 Vif protein, the molecular mechanisms involved, and highlight important properties of this small viral protein.

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Insight into the HIV-1 Vif SOCS-box–ElonginBC interaction

Open Biology ◽

10.1098/rsob.130100 ◽

2013 ◽

Vol 3 (11) ◽

pp. 130100 ◽

Cited By ~ 7

Author(s):

Zhisheng Lu ◽

Julien R. C. Bergeron ◽

R. Andrew Atkinson ◽

Torsten Schaller ◽

Dennis A. Veselkov ◽

...

Keyword(s):

Solution Structure ◽

Hydrophobic Interactions ◽

Dynamic Information ◽

Ubiquitin Ligase Complex ◽

Biophysical Studies ◽

Viral Infectivity Factor ◽

Β Sheet ◽

Socs Box ◽

Insight Into ◽

Hiv 1

The HIV-1 viral infectivity factor (Vif) neutralizes cell-encoded antiviral APOBEC3 proteins by recruiting a cellular ElonginB (EloB)/ElonginC (EloC)/Cullin5-containing ubiquitin ligase complex, resulting in APOBEC3 ubiquitination and proteolysis. The suppressors-of-cytokine-signalling-like domain (SOCS-box) of HIV-1 Vif is essential for E3 ligase engagement, and contains a BC box as well as an unusual proline-rich motif. Here, we report the NMR solution structure of the Vif SOCS–ElonginBC (EloBC) complex. In contrast to SOCS-boxes described in other proteins, the HIV-1 Vif SOCS-box contains only one α-helical domain followed by a β-sheet fold. The SOCS-box of Vif binds primarily to EloC by hydrophobic interactions. The functionally essential proline-rich motif mediates a direct but weak interaction with residues 101–104 of EloB, inducing a conformational change from an unstructured state to a structured state. The structure of the complex and biophysical studies provide detailed insight into the function of Vif's proline-rich motif and reveal novel dynamic information on the Vif–EloBC interaction.

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Foamy Viruses, Bet, and APOBEC3 Restriction

Viruses ◽

10.3390/v13030504 ◽

2021 ◽

Vol 13 (3) ◽

pp. 504

Author(s):

Ananda Ayyappan Jaguva Vasudevan ◽

Daniel Becker ◽

Tom Luedde ◽

Holger Gohlke ◽

Carsten Münk

Keyword(s):

Current Knowledge ◽

Regulatory Protein ◽

Host Population ◽

Life Cycles ◽

Restriction Factors ◽

Host Restriction ◽

Open Questions ◽

Foamy Viruses ◽

Natural Hosts ◽

Hiv 1

Non-human primates (NHP) are an important source of viruses that can spillover to humans and, after adaptation, spread through the host population. Whereas HIV-1 and HTLV-1 emerged as retroviral pathogens in humans, a unique class of retroviruses called foamy viruses (FV) with zoonotic potential are occasionally detected in bushmeat hunters or zookeepers. Various FVs are endemic in numerous mammalian natural hosts, such as primates, felines, bovines, and equines, and other animals, but not in humans. They are apathogenic, and significant differences exist between the viral life cycles of FV and other retroviruses. Importantly, FVs replicate in the presence of many well-defined retroviral restriction factors such as TRIM5α, BST2 (Tetherin), MX2, and APOBEC3 (A3). While the interaction of A3s with HIV-1 is well studied, the escape mechanisms of FVs from restriction by A3 is much less explored. Here we review the current knowledge of FV biology, host restriction factors, and FV–host interactions with an emphasis on the consequences of FV regulatory protein Bet binding to A3s and outline crucial open questions for future studies.

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The antiviral factor APOBEC3G improves CTL recognition of cultured HIV-infected T cells

Journal of Experimental Medicine ◽

10.1084/jem.20091933 ◽

2009 ◽

Vol 207 (1) ◽

pp. 39-49 ◽

Cited By ~ 63

Author(s):

Nicoletta Casartelli ◽

Florence Guivel-Benhassine ◽

Romain Bouziat ◽

Samantha Brandler ◽

Olivier Schwartz ◽

...

Keyword(s):

Cytidine Deaminase ◽

Adaptive Immune System ◽

Antiviral Effect ◽

Inhibitory Effect ◽

Hiv Replication ◽

Viral Infectivity Factor ◽

Cellular Immune ◽

Vif Protein ◽

The Impact ◽

Hiv 1

The cytidine deaminase APOBEC3G (A3G) enzyme exerts an intrinsic anti–human immunodeficiency virus (HIV) defense by introducing lethal G-to-A hypermutations in the viral genome. The HIV-1 viral infectivity factor (Vif) protein triggers degradation of A3G and counteracts this antiviral effect. The impact of A3G on the adaptive cellular immune response has not been characterized. We examined whether A3G-edited defective viruses, which are known to express truncated or misfolded viral proteins, activate HIV-1–specific (HS) CD8+ cytotoxic T lymphocytes (CTLs). To this end, we compared the immunogenicity of cells infected with wild-type or Vif-deleted viruses in the presence or absence of the cytidine deaminase. The inhibitory effect of A3G on HIV replication was associated with a strong activation of cocultivated HS-CTLs. CTL activation was particularly marked with Vif-deleted HIV and with viruses harboring A3G. Enzymatically inactive A3G mutants failed to enhance CTL activation. We also engineered proviruses bearing premature stop codons in their genome as scars of A3G editing. These viruses were not infectious but potently activated HS-CTLs. Therefore, the pool of defective viruses generated by A3G represents an underestimated source of viral antigens. Our results reveal a novel function for A3G, acting not only as an intrinsic antiviral factor but also as an inducer of the adaptive immune system.

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An UBR-box from a non-N-recognin: Crystal Structure of the UBR domain of UBR6

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314096934 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C306-C306

Author(s):

Juliana Muñoz-Escobar ◽

Guennadi Kozlov ◽

Jean-François Trempe ◽

Kalle Gehring

Keyword(s):

Crystal Structure ◽

Ubiquitin Proteasome System ◽

Zinc Binding ◽

Binding Motifs ◽

Clear Explanation ◽

Ubiquitin Ligase Complex ◽

Ubiquitin Proteasome ◽

Binding Pockets ◽

F Box Protein

The degradation of many short-lived proteins in eukaryotic cells is carried out by the Ubiquitin Proteasome System. The N-end rule pathway links the half-life of proteins to the identity of its N-terminal residue, also called N-degron. Destabilizing N-degrons, are recognized by E3 ubiquitin ligases termed N-recognins. N-degrons are grouped into type 1, composed of basic residues, and type 2, composed of bulky hydrophobic residues. In mammals, four N-recognins mediate the N-end rule pathway: UBR1, UBR2, UBR4 and UBR5. These proteins share a ~70-residue zinc finger-like motif termed the Ubiquitin Recognin (UBR) box, responsible for their specificity. The mammalian genome encodes at least three more UBR-box proteins: UBR3, UBR6/FBXO11 and UBR7. However, these UBRs cannot recognize any type of N-degrons. Our lab reported the crystal structures of the UBR boxes from the human UBR1 and UBR2, rationalizing the empirical rules for the classification of type 1 N-degrons. Despite the valuable information obtained from those structures there is not a clear explanation for the no recognition of N-degrons by other UBR-box proteins. Here we report the crystal structure of the UBR-box domain from UBR6 also known as FBXO11. UBR6 is a F-box protein of the SKP1-Cullin1-F-box (SCF) ubiquitin ligase complex and does not recognize any type of N-degrons. We crystallized a 77-residue fragment of the UBR-box of UBR6 and determined its structure at 1.7 Å resolution. Unexpectedly, this domain adopts an open conformation compared to UBR1-box, without any N-degron binding pockets. Its zinc-binding residues are conserved as in the N-recognins, but they are arranged in different zinc-binding motifs. Molecules form dimmers stabilized by zinc ions. The crystal had 4 molecules per asymmetric unit and space group P212121. For phasing we used Zn-SAD. With this structure we hope to obtain clues that explain the absence of N-degron recognition in some members of the UBR family.

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Towards Inhibition of Vif-APOBEC3G Interaction: Which Protein to Target?

Advances in Virology ◽

10.1155/2010/649315 ◽

2010 ◽

Vol 2010 ◽

pp. 1-10 ◽

Cited By ~ 4

Author(s):

Iris Cadima-Couto ◽

Joao Goncalves

Keyword(s):

Antiviral Activity ◽

Protein Binding ◽

Mechanism Of Action ◽

Cellular Immunity ◽

Viral Infectivity ◽

Binding Partners ◽

Viral Infectivity Factor ◽

Vif Protein ◽

Hiv 1 ◽

Antiretroviral Activity

APOBEC proteins appeared in the cellular battle against HIV-1 as part of intrinsic cellular immunity. The antiretroviral activity of some of these proteins is overtaken by the action of HIV-1 Viral Infectivity Factor (Vif) protein. Since the discovery of APOBEC3G (A3G) as an antiviral factor, many advances have been made to understand its mechanism of action in the cell and how Vif acts in order to counteract its activity. The mainstream concept is that Vif overcomes the innate antiviral activity of A3G by direct protein binding and promoting its degradation via the cellular ubiquitin/proteasomal pathway. Vif may also inhibit A3G through mechanisms independent of proteasomal degradation. Binding of Vif to A3G is essential for its degradation since disruption of this interaction is predicted to stimulate intracellular antiviral immunity. In this paper we will discuss the different binding partners between both proteins as one of the major challenges for the development of new antiviral drugs.

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Interaction between Parkin and α-Synuclein in PARK2-Mediated Parkinson’s Disease

Cells ◽

10.3390/cells10020283 ◽

2021 ◽

Vol 10 (2) ◽

pp. 283

Author(s):

Daniel Aghaie Madsen ◽

Sissel Ida Schmidt ◽

Morten Blaabjerg ◽

Morten Meyer

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Ubiquitin Ligase ◽

Current Knowledge ◽

Lewy Bodies ◽

Ubiquitin Proteasome System ◽

Loss Of Function ◽

Functional Interaction ◽

Future Studies ◽

Ubiquitin Proteasome

Parkin and α-synuclein are two key proteins involved in the pathophysiology of Parkinson’s disease (PD). Neurotoxic alterations of α-synuclein that lead to the formation of toxic oligomers and fibrils contribute to PD through synaptic dysfunction, mitochondrial impairment, defective endoplasmic reticulum and Golgi function, and nuclear dysfunction. In half of the cases, the recessively inherited early-onset PD is caused by loss of function mutations in the PARK2 gene that encodes the E3-ubiquitin ligase, parkin. Parkin is involved in the clearance of misfolded and aggregated proteins by the ubiquitin-proteasome system and regulates mitophagy and mitochondrial biogenesis. PARK2-related PD is generally thought not to be associated with Lewy body formation although it is a neuropathological hallmark of PD. In this review article, we provide an overview of post-mortem neuropathological examinations of PARK2 patients and present the current knowledge of a functional interaction between parkin and α-synuclein in the regulation of protein aggregates including Lewy bodies. Furthermore, we describe prevailing hypotheses about the formation of intracellular micro-aggregates (synuclein inclusions) that might be more likely than Lewy bodies to occur in PARK2-related PD. This information may inform future studies aiming to unveil primary signaling processes involved in PD and related neurodegenerative disorders.

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Molecular mechanisms of mammalian autophagy

Biochemical Journal ◽

10.1042/bcj20210314 ◽

2021 ◽

Vol 478 (18) ◽

pp. 3395-3421

Author(s):

Charles B. Trelford ◽

Gianni M. Di Guglielmo

Keyword(s):

Molecular Mechanisms ◽

Current Knowledge ◽

Molecular Pathways ◽

Zymogen Granules ◽

Ubiquitin Proteasome Pathway ◽

Lysine Residues ◽

Ubiquitin Proteasome ◽

Proteasome Pathway ◽

Functional Modulation ◽

Chaperone Mediated Autophagy

The ubiquitin-proteasome pathway (UPP) and autophagy play integral roles in cellular homeostasis. As part of their normal life cycle, most proteins undergo ubiquitination for some form of redistribution, localization and/or functional modulation. However, ubiquitination is also important to the UPP and several autophagic processes. The UPP is initiated after specific lysine residues of short-lived, damaged or misfolded proteins are conjugated to ubiquitin, which targets these proteins to proteasomes. Autophagy is the endosomal/lysosomal-dependent degradation of organelles, invading microbes, zymogen granules and macromolecules such as protein, carbohydrates and lipids. Autophagy can be broadly separated into three distinct subtypes termed microautophagy, chaperone-mediated autophagy and macroautophagy. Although autophagy was once thought of as non-selective bulk degradation, advancements in the field have led to the discovery of several selective forms of autophagy. Here, we focus on the mechanisms of primary and selective mammalian autophagy pathways and highlight the current knowledge gaps in these molecular pathways.

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The Roles of Ubiquitin-Binding Protein Shuttles in the Degradative Fate of Ubiquitinated Proteins in the Ubiquitin-Proteasome System and Autophagy

Cells ◽

10.3390/cells8010040 ◽

2019 ◽

Vol 8 (1) ◽

pp. 40 ◽

Cited By ~ 27

Author(s):

Katarzyna Zientara-Rytter ◽

Suresh Subramani

Keyword(s):

Protein Quality ◽

Current Knowledge ◽

Binding Protein ◽

Ubiquitin Proteasome System ◽

Oligomeric State ◽

Receptor Associated Protein ◽

Ubiquitin Proteasome ◽

Specific Proteins ◽

And Control ◽

Recognition Code

The ubiquitin-proteasome system (UPS) and autophagy are the two major intracellular protein quality control (PQC) pathways that are responsible for cellular proteostasis (homeostasis of the proteome) by ensuring the timely degradation of misfolded, damaged, and unwanted proteins. Ubiquitination serves as the degradation signal in both these systems, but substrates are precisely targeted to one or the other pathway. Determining how and when cells target specific proteins to these two alternative PQC pathways and control the crosstalk between them are topics of considerable interest. The ubiquitin (Ub) recognition code based on the type of Ub-linked chains on substrate proteins was believed to play a pivotal role in this process, but an increasing body of evidence indicates that the PQC pathway choice is also made based on other criteria. These include the oligomeric state of the Ub-binding protein shuttles, their conformation, protein modifications, and the presence of motifs that interact with ATG8/LC3/GABARAP (autophagy-related protein 8/microtubule-associated protein 1A/1B-light chain 3/GABA type A receptor-associated protein) protein family members. In this review, we summarize the current knowledge regarding the Ub recognition code that is bound by Ub-binding proteasomal and autophagic receptors. We also discuss how cells can modify substrate fate by modulating the structure, conformation, and physical properties of these receptors to affect their shuttling between both degradation pathways.

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Canonical and Noncanonical Autophagy as Potential Targets for COVID-19

Cells ◽

10.3390/cells9071619 ◽

2020 ◽

Vol 9 (7) ◽

pp. 1619 ◽

Cited By ~ 11

Author(s):

Melissa Bello-Perez ◽

Isabel Sola ◽

Beatriz Novoa ◽

Daniel J. Klionsky ◽

Alberto Falco

Keyword(s):

Molecular Mechanisms ◽

Viral Infections ◽

Current Knowledge ◽

Therapeutic Targets ◽

Innate Immune ◽

Interacting Proteins ◽

Innate Immune Responses ◽

Molecular Machinery ◽

Autophagy Pathway

The SARS-CoV-2 pandemic necessitates a review of the molecular mechanisms underlying cellular infection by coronaviruses, in order to identify potential therapeutic targets against the associated new disease (COVID-19). Previous studies on its counterparts prove a complex and concomitant interaction between coronaviruses and autophagy. The precise manipulation of this pathway allows these viruses to exploit the autophagy molecular machinery while avoiding its protective apoptotic drift and cellular innate immune responses. In turn, the maneuverability margins of such hijacking appear to be so narrow that the modulation of the autophagy, regardless of whether using inducers or inhibitors (many of which are FDA-approved for the treatment of other diseases), is usually detrimental to viral replication, including SARS-CoV-2. Recent discoveries indicate that these interactions stretch into the still poorly explored noncanonical autophagy pathway, which might play a substantial role in coronavirus replication. Still, some potential therapeutic targets within this pathway, such as RAB9 and its interacting proteins, look promising considering current knowledge. Thus, the combinatory treatment of COVID-19 with drugs affecting both canonical and noncanonical autophagy pathways may be a turning point in the fight against this and other viral infections, which may also imply beneficial prospects of long-term protection.

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p97 Negatively Regulates NRF2 by Extracting Ubiquitylated NRF2 from the KEAP1-CUL3 E3 Complex

Molecular and Cellular Biology ◽

10.1128/mcb.00660-16 ◽

2017 ◽

Vol 37 (8) ◽

Cited By ~ 36

Author(s):

Shasha Tao ◽

Pengfei Liu ◽

Gang Luo ◽

Montserrat Rojo de la Vega ◽

Heping Chen ◽

...

Keyword(s):

Ubiquitin Ligase ◽

Protein Complexes ◽

E3 Ubiquitin Ligase ◽

Ubiquitin Proteasome System ◽

Proteasomal Degradation ◽

Ubiquitin Ligase Complex ◽

Ubiquitin Proteasome ◽

Client Proteins

ABSTRACT Activation of the stress-responsive transcription factor NRF2 is the major line of defense to combat oxidative or electrophilic insults. Under basal conditions, NRF2 is continuously ubiquitylated by the KEAP1-CUL3-RBX1 E3 ubiquitin ligase complex and is targeted to the proteasome for degradation (the canonical mechanism). However, the path from the CUL3 complex to ultimate proteasomal degradation was previously unknown. p97 is a ubiquitin-targeted ATP-dependent segregase that extracts ubiquitylated client proteins from membranes, protein complexes, or chromatin and has an essential role in autophagy and the ubiquitin proteasome system (UPS). In this study, we show that p97 negatively regulates NRF2 through the canonical pathway by extracting ubiquitylated NRF2 from the KEAP1-CUL3 E3 complex, with the aid of the heterodimeric cofactor UFD1/NPL4 and the UBA-UBX-containing protein UBXN7, for efficient proteasomal degradation. Given the role of NRF2 in chemoresistance and the surging interest in p97 inhibitors to treat cancers, our results indicate that dual p97/NRF2 inhibitors may offer a more potent and long-term avenue of p97-targeted treatment.

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