SARS-CoV-2 inhibits cell apoptosis to promote virus replication through its N protein

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The coronavirus (CoV) is known to infect various systems in humans and other mammal animals, including the respiratory, alimentary, and central nervous systems. Previous outbreaks such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) were caused by different types of coronaviruses and were associated with animal-to-human transmission.

The current pandemic, Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2, is highly pathogenic and contagious, resulting in a wide range of symptoms from asymptomatic infections to severe respiratory distress and multi-organ failure.

Understanding the mechanisms of SARS-CoV-2 infection is crucial for developing effective therapeutic strategies and reducing its transmission. One significant aspect to consider is the presence of asymptomatic individuals who can transmit the virus to others. Studies have shown that asymptomatic individuals can have high viral loads and remain infectious.

The viral load, determined by the cycle threshold (Ct) values in real-time PCR tests, reflects the amount of virus present in an individual. Surprisingly, asymptomatic individuals can have high viral loads without exhibiting clinical symptoms, highlighting the need to investigate the underlying mechanisms.

Apoptosis, a regulated process of cell death, plays a critical role in maintaining organism homeostasis. It is involved in various physiological processes, including the host’s defense against viral infections.

The B-cell lymphoma 2 (BCL-2) family of proteins regulates the initiation of apoptosis through the mitochondrial pathway, while death receptors activate the extrinsic apoptotic pathways. Key proteins such as Caspase-3 (Casp-3) are responsible for the cleavage and activation of apoptotic pathways.

During viral infections, host cells activate apoptosis to eliminate infected cells. However, viruses can evolve mechanisms to inhibit apoptosis, allowing for their replication and survival.

Previous studies have shown that SARS-CoV and SARS-CoV-2 can both induce apoptosis through different pathways. For example, SARS-CoV initiates apoptosis through interactions with cell membrane death receptors and activation of specific signaling pathways. The N protein of SARS-CoV-2, responsible for encapsulating viral genomic RNA, has been found to regulate apoptosis and viral replication.

Additionally, it has been implicated in causing lung and kidney injuries, interfering with the cell cycle, suppressing interferon production, impairing stress granule formation, and suppressing antiviral immune responses. However, the precise molecular mechanisms by which the N protein regulates apoptosis and viral replication remain unclear.

In the context of the COVID-19 pandemic, co-infections of SARS-CoV-2 with other respiratory viruses pose a significant risk. Clinical analyses have shown that co-infection with SARS-CoV-2 and influenza virus leads to more severe symptoms and higher mortality rates compared to separate infections.

It has also been observed that influenza virus enhances SARS-CoV-2 infection by promoting the expression of the ACE2 receptor. However, the impact of SARS-CoV-2 on other respiratory virus infections and the underlying mechanisms involved in co-infections are not well understood.

In this study, the researchers discovered that the N protein of SARS-CoV-2 interacts with the anti-apoptotic protein MCL-1, extending its half-life and suppressing cell apoptosis. The N protein achieves this by promoting the deubiquitination of MCL-1, a process that stabilizes the protein.

The deubiquitinating enzyme USP15 was found to be involved in the N-mediated deubiquitination of MCL-1. Importantly, the researchers observed that the N protein promotes the replication of influenza A virus (IAV), Dengue virus (DENV-2), and Zika virus (ZIKV) by enhancing MCL-1 protein levels.

Furthermore, the researchers investigated the effects of N protein-mediated regulation of apoptosis and viral replication in vivo. They conducted experiments using mice infected with IAV and observed that the presence of the N protein exacerbated the death of IAV-infected mice. This suggests that the N protein’s modulation of apoptosis and viral replication has implications for the pathogenesis of co-infections.

To validate the specific role of MCL-1 in N protein-mediated effects, the researchers used S63845, a specific inhibitor of MCL-1. They found that treatment with S63845 blocked the N protein-induced enhancement of viral replication, indicating that MCL-1 is crucial for the N protein’s promotion of virus replication.

Overall, this study provides valuable insights into the molecular mechanisms underlying SARS-CoV-2 infection. The N protein of SARS-CoV-2 was found to interact with MCL-1, leading to the suppression of apoptosis through MCL-1 stabilization. Additionally, the N protein was shown to promote the replication of other respiratory viruses such as IAV, DENV-2, and ZIKV by enhancing MCL-1 levels. These findings contribute to our understanding of viral replication regulation, co-infections, and the pathogenesis of SARS-CoV-2.

Understanding the intricate interactions between SARS-CoV-2 and the host’s cellular processes, such as apoptosis and viral replication, is essential for the development of targeted therapeutic strategies. By identifying key molecular players, such as the N protein and MCL-1, researchers can potentially devise approaches to disrupt the virus’s replication cycle and enhance the host’s immune response.

Moreover, considering the increased risk of co-infections during the ongoing pandemic, investigating the impact of SARS-CoV-2 on other respiratory viruses and elucidating the underlying mechanisms can guide public health measures and clinical management.

In conclusion, this research sheds light on the molecular mechanisms by which SARS-CoV-2 modulates apoptosis and viral replication. The N protein of SARS-CoV-2 interacts with MCL-1, stabilizing the protein and suppressing apoptosis.

Additionally, the N protein promotes the replication of other respiratory viruses. These findings contribute to our understanding of SARS-CoV-2 pathogenesis, co-infections, and potential therapeutic targets. Further studies in this field will be crucial for developing effective treatments and strategies to mitigate the impact of the ongoing COVID-19 pandemic.


Some considerations….

In addition to the mechanisms involving specific viral proteins, SARS-CoV-2 may employ other strategies to inhibit cell apoptosis. Here are some additional factors that contribute to the inhibition of apoptosis by the virus:

  • Viral replication and hijacking of host cellular machinery: SARS-CoV-2 utilizes host cellular machinery to replicate and produce new viral particles. The virus may manipulate various cellular processes, including those involved in apoptosis, to create a favorable environment for its replication. By diverting cellular resources towards viral replication, the virus can inhibit apoptosis and prolong its survival within infected cells.
  • Modulation of host immune responses: SARS-CoV-2 has been shown to trigger dysregulated immune responses, including an excessive release of pro-inflammatory cytokines known as a cytokine storm. This cytokine storm can lead to tissue damage and contribute to the severity of COVID-19. Paradoxically, the dysregulated immune response may also suppress apoptosis in infected cells, allowing the virus to persist. The exact mechanisms by which SARS-CoV-2 manipulates the host immune system to inhibit apoptosis are still under investigation.
  • Evasion of innate immune sensing: SARS-CoV-2 has evolved mechanisms to evade detection by the host’s innate immune system, which includes pathways that induce apoptosis as a defense mechanism. The virus employs various strategies to interfere with innate immune sensing pathways, such as the interferon response, to avoid triggering apoptosis and other antiviral defenses. By evading innate immune sensing, SARS-CoV-2 can undermine apoptosis and establish a successful infection.
  • Modulation of host cell signaling pathways: SARS-CoV-2 may interfere with signaling pathways involved in apoptosis regulation. For example, the virus can manipulate pathways such as the PI3K/AKT pathway, which plays a crucial role in cell survival and apoptosis. By modulating these pathways, the virus can disrupt the balance between pro-apoptotic and anti-apoptotic signals, favoring cell survival and viral replication.

and ….

By evading apoptosis, the virus can ensure its own replication and survival within host cells. Several viral proteins and processes have been implicated in the inhibition of apoptosis by SARS-CoV-2.

One of the key viral proteins involved in the inhibition of apoptosis is the N protein (nucleocapsid protein). The N protein of SARS-CoV-2 has been shown to interact with various host factors and interfere with apoptotic pathways. It has been reported that the N protein can promote the deubiquitination of the anti-apoptotic protein MCL-1, leading to its stabilization and inhibition of apoptosis. By extending the half-life of MCL-1, the N protein prevents the activation of the apoptotic cascade and facilitates viral replication.

Furthermore, studies have suggested that the N protein of SARS-CoV-2 can activate the NLRP3 (NOD-like receptor pyrin domain-containing 3) inflammasome, which is involved in the regulation of inflammation and cell death. Activation of the NLRP3 inflammasome can lead to the production of pro-inflammatory cytokines, such as IL-1β, and induce pyroptosis, a form of inflammatory cell death. However, the exact mechanisms by which the N protein activates the NLRP3 inflammasome and its role in apoptosis inhibition require further investigation.

Apart from the N protein, other viral proteins of SARS-CoV-2 may also contribute to the inhibition of apoptosis. For example, the S protein (spike protein) of the virus has been reported to interact with cell membrane death receptors, such as ACE2 (angiotensin-converting enzyme 2), and activate signaling pathways that promote apoptosis. However, SARS-CoV-2 may have developed mechanisms to counteract these apoptotic signals and prevent premature cell death.

Additionally, viral proteins involved in stress response and immune evasion, such as the E protein (envelope protein), may play a role in inhibiting apoptosis. The E protein has been found to regulate stress responses in infected cells, and its inhibition of apoptosis may help the virus evade host immune surveillance. However, the specific mechanisms by which the E protein and other viral factors modulate apoptosis inhibition in SARS-CoV-2 infection require further investigation.

It is important to note that the inhibition of apoptosis by SARS-CoV-2 is a complex process involving the interplay between viral proteins and host factors. By evading apoptosis, the virus can persist within host cells and continue to replicate, leading to the progression of the infection. Understanding the precise molecular mechanisms by which SARS-CoV-2 inhibits apoptosis is crucial for the development of targeted therapeutic approaches that can disrupt these viral strategies and restore the host’s immune defense mechanisms.


reference link : https://www.nature.com/articles/s41392-023-01459-8#Sec9

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