KHNYN is essential for the zinc finger antiviral protein (ZAP) to restrict HIV-1 containing clustered CpG dinucleotides

Ficarelli, Mattia; Wilson, Harry; Galão, Rui Pedro; Mazzon, Michela; Antzin-Anduetza, Irati; Marsh, Mark; Neil, Stuart J. D.; Swanson, Chad M.

doi:10.7554/elife.46767

Cited by 114 publications

(198 citation statements)

References 71 publications

(126 reference statements)

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“…For wild-type HIV-1, the magnitudes of inhibition were similar in the control and ZAP knockout cells ( Fig. 6A), which is consistent with the observation that endogenous ZAP does not target wild-type HIV-1 (16,31). The magnitude of IFN-I inhibition of HIV-1 env86 -561 CpG was reduced when ZAP was depleted, indicating that ZAP contributes to the antiviral effect of IFN-I on the virus.…”

supporting

confidence: 85%

“…It has previously been shown that introducing 36 CpGs into env nucleotides (nt) 86 to 561 (HIV-1 env86 -561 CpG) inhibits HIV-1 genomic-RNA abundance, Gag expression, Env expression, and infectious-virus production ( Fig. 3A, C, and E and Table 1) (16,31). Importantly, this restriction is eliminated in ZAP knockout cells ( Fig.…”

mentioning

confidence: 85%

“…However, ZAP does not restrict all viruses, and yellow fever virus, Zika virus, dengue virus, herpes simplex virus 1, vesicular stomatitis virus, and poliovirus are resistant to its antiviral activity (21,24). ZAP does not have enzymatic activity and interacts with other cellular proteins, such as TRIM25 and KHNYN, to restrict viral replication (29)(30)(31). Why some viruses are sensitive to ZAP and others are resistant, and whether the CpG abundance and context in viruses determines this, remains unknown.…”

mentioning

confidence: 99%

“…We have recently identified KHNYN as an essential ZAP cofactor for CpGs to inhibit HIV-1 env86 -561 CpG gene expression and infectious-virus production (31). Our previous work showed that KHNYN overexpression inhibited HIV-1 env86 -561 CpG much more potently than wild-type HIV-1, indicating that the introduced CpGs were required for KHNYN to inhibit HIV-1 (31). To determine if inhibition by KHNYN correlated with CpG abundance or ZAP sensitivity, we overexpressed KHNYN on wild-type HIV-1, HIV-1 env86 -561 CpG, or HIV-1 pol795-1386 CpG ( Fig.…”

mentioning

confidence: 99%

“…KHNYN antiviral activity was correlated with the sensitivity of the virus to endogenous ZAP, with HIV-1 env86 -561 CpG inhibited much more potently than HIV-1 pol795-1386 CpG or wild-type HIV-1. We also tested whether endogenous KHNYN was required to restrict HIV-1 env611-1014 CpG, HIV-1 env86 -1014 CpG, and HIV-1 pol795-1386 CpG using the KHNYN CRISPR cells that we previously characterized (31). Wild-type HIV-1 infectious-virus production was not affected by depleting KHNYN, while HIV-1 env86 -561 CpG infectious-virus production and gene expression were substantially increased (31) (Fig.…”

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confidence: 99%

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CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent Mechanisms

Ficarelli

Antzin-Anduetza

Hugh-White

et al. 2020

J Virol

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CpG dinucleotides are suppressed in the genomes of many vertebrate RNA viruses, including HIV-1. The cellular antiviral protein ZAP (zinc finger antiviral protein) binds CpGs and inhibits HIV-1 replication when CpGs are introduced into the viral genome. However, it is not known if ZAP-mediated restriction is the only mechanism driving CpG suppression. To determine how CpG dinucleotides affect HIV-1 replication, we increased their abundance in multiple regions of the viral genome and analyzed the effect on RNA expression, protein abundance, and infectious-virus production. We found that the antiviral effect of CpGs was not correlated with their abundance. Interestingly, CpGs inserted into some regions of the genome sensitize the virus to ZAP antiviral activity more efficiently than insertions into other regions, and this sensitivity can be modulated by interferon treatment or ZAP overexpression. Furthermore, the sensitivity of the virus to endogenous ZAP was correlated with its sensitivity to the ZAP cofactor KHNYN. Finally, we show that CpGs in some contexts can also inhibit HIV-1 replication by ZAP-independent mechanisms, and one of these is the activation of a cryptic splice site at the expense of a canonical splice site. Overall, we show that the location and sequence context of the CpG in the viral genome determines its antiviral activity. IMPORTANCE Some RNA virus genomes are suppressed in the nucleotide combination of a cytosine followed by a guanosine (CpG), indicating that they are detrimental to the virus. The antiviral protein ZAP binds viral RNA containing CpGs and prevents the virus from multiplying. However, it remains unknown how the number and position of CpGs in viral genomes affect restriction by ZAP and whether CpGs have other antiviral mechanisms. Importantly, manipulating the CpG content in viral genomes could help create new vaccines. HIV-1 shows marked CpG suppression, and by introducing CpGs into its genome, we show that ZAP efficiently targets a specific region of the viral genome, that the number of CpGs does not predict the magnitude of antiviral activity, and that CpGs can inhibit HIV-1 gene expression through a ZAP-independent mechanism. Overall, the position of CpGs in the HIV-1 genome determines the magnitude and mechanism through which they inhibit the virus.

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confidence: 85%

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confidence: 85%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent Mechanisms

Ficarelli

Antzin-Anduetza

Hugh-White

et al. 2020

J Virol

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TRIM25 and its emerging RNA‐binding roles in antiviral defense

2020

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The innate immune system is the body's first line of defense against viruses, with pattern recognition receptors (PRRs) recognizing molecules unique to viruses and triggering the expression of interferons and other anti-viral cytokines, leading to the formation of an anti-viral state. The tripartite motif containing 25 (TRIM25) is an E3 ubiquitin ligase thought to be a key component in the activation of signaling by the PRR retinoic acid-inducible gene I protein (RIG-I). TRIM25 has recently been identified as an RNA-binding protein, raising the question of whether its RNA-binding activity is important for its role in innate immunity. Here, we review TRIM25's mechanisms and pathways in noninfected and infected cells. We also introduce models that explain how

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Compositional biases in RNA viruses: Causes, consequences and applications

Gaunt

Digard

2021

WIREs RNA

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If each of the four nucleotides were represented equally in the genomes of viruses and the hosts they infect, each base would occur at a frequency of 25%. However, this is not observed in nature. Similarly, the order of nucleotides is not random (e.g., in the human genome, guanine follows cytosine at a frequency of ~0.0125, or a quarter the number of times predicted by random representation). Codon usage and codon order are also nonrandom. Furthermore, nucleotide and codon biases vary between species. Such biases have various drivers, including cellular proteins that recognize specific patterns in nucleic acids, that once triggered, induce mutations or invoke intrinsic or innate immune responses. In this review we examine the types of compositional biases identified in viral genomes and current understanding of the evolutionary mechanisms underpinning these trends. Finally, we consider the potential for large scale synonymous recoding strategies to engineer RNA virus vaccines, including those with pandemic potential, such as influenza A virus and Severe Acute Respiratory Syndrome Coronavirus Virus 2. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein‐RNA Recognition

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KHNYN is essential for the zinc finger antiviral protein (ZAP) to restrict HIV-1 containing clustered CpG dinucleotides

Cited by 114 publications

References 71 publications

CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent Mechanisms

CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent Mechanisms

TRIM25 and its emerging RNA‐binding roles in antiviral defense

Compositional biases in RNA viruses: Causes, consequences and applications

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