Dengue virus pathogenesis and host molecular machineries

Abstract

Dengue viruses (DENV) are positive-stranded RNA viruses belonging to the Flaviviridae family. DENV is the causative agent of dengue, the most rapidly spreading viral disease transmitted by mosquitoes. Each year, millions of people contract the virus through bites from infected female mosquitoes of the Aedes species. In the majority of individuals, the infection is asymptomatic, and the immune system successfully manages to control virus replication within a few days. Symptomatic individuals may present with a mild fever (Dengue fever or DF) that may or may not progress to a more critical disease termed Dengue hemorrhagic fever (DHF) or the fatal Dengue shock syndrome (DSS). In the absence of a universally accepted prophylactic vaccine or therapeutic drug, treatment is mostly restricted to supportive measures. Similar to many other viruses that induce acute illness, DENV has developed several ways to modulate host metabolism to create an environment conducive to genome replication and the dissemination of viral progeny. To search for new therapeutic options, understanding the underlying host-virus regulatory system involved in various biological processes of the viral life cycle is essential. This review aims to summarize the complex interaction between DENV and the host cellular machinery, comprising regulatory mechanisms at various molecular levels such as epigenetic modulation of the host genome, transcription of host genes, translation of viral and host mRNAs, post-transcriptional regulation of the host transcriptome, post-translational regulation of viral proteins, and pathways involved in protein degradation.

Keywords: Dengue virus; Epigenomic regulation; Post-transcriptional modifications; Post-translational modifications; Stress granule formation; Transcription regulation; Translation regulation.

Fig. 1

Structural organization and life cycle of DENV: A The Dengue virus genome comprises 5’UTR, ORF, and 3’UTR. The ORF translates into a polyprotein, which is further processed into three structural proteins: C (Capsid), E (Envelope), and M (Membrane), and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, NS5). B The initiation of the DENV replication cycle occurs with the entry into the cell via various host cell receptors or through the Fc region of the virus-antibody immune complex, which attaches to Fc receptors present on the target host cell. 1. DENV attaches to host cell receptors and enters the cell. 2. Internalization occurs through receptor-mediated endocytosis, forming an early endosome. 3, 4. Genome uncoating occurs as the pH decreases inside the early endosome; conformational changes take place, releasing the nucleocapsid into the cytoplasm. 5, 6. Disassembly of the nucleocapsid allows viral RNA assembly in the cytoplasm. 7. Viral RNA translocates into the Endoplasmic Reticulum, where translation results in a single polyprotein that is cleaved down by both host and viral proteases. Additionally, a translation switch results in the transcription of viral RNA employing antisense viral RNA. 8. The capsid protein encases the freshly created viral RNA to form the nucleocapsid. 9. Virus assembly occurs on the surface of the Endoplasmic Reticulum. 10. Immature viral particles are transported to the trans-Golgi network, where acidification results in conformational changes, followed by exposure to the furin protease to form mature viral particles. 11. Mature viral particles are exocytosed into the extracellular matrix, completing their replication cycle

Fig. 2

Physiological roles of DENV proteins: A The NS1 protein interacts with TLR4 and activates macrophages, resulting in cytokine release. Cytokines disrupt tight junctions and endothelial barriers, leading to plasma leakage in severe cases of dengue [8]. B NS3, together with the co-factor NS2B, participates in the processing of the dengue polyprotein, assisting in efficient virus replication [9]. C The Capsid protein helps in packaging folded RNA released from the DENV replication complex [4]. D Envelope glycoproteins attach to host receptors and form the dengue-host membrane complex, resulting in virus internalization to process its replication and propagation inside the host cell [13]

Fig. 3

DENV and host epigenetic regulation: A DENV infection results in cytokine storm and leads to oxidative stress conditions in host cell, activating histone deacetylase (HDAC). HDAC activity condenses the chromatin and slows down the host transcription processes [28]. B DENV protein interacts with various host cellular genes/lnCRNAs and results in m6A RNA methylation. Their localization helps to enhance DENV replication [29, 30]. C DENV NS1 interacts with DIDO1, a master epigenetic regulator and somehow elevates DENV replication [35]. D Capsid protein interacts with core histones (H2A, H2B, H3, and H4) and localizes them in cytoplasm to participate in DENV replication and propagation [36]

Fig. 4

DENV and host transcriptional regulation: A DENV Envelope sequesters the transcription factor TAL-1 in the cytoplasm, affecting its transcriptional function in the nucleus [37]. B Various factors involved in transcription such as GATA-1, GATA-2, and NF-E2, which participate in the process of megakaryopoiesis, are dysregulated during dengue infection [38]. C During DENV infection, glucose and metabolic processes increase, enhancing RNA Polymerase II activity. This leads to higher expression of genes like Hexokinase and Microtubule-associated protein 1 light chain 3, promoting increased transcription of metabolic genes and enhancing DENV replication [39]. D P-TEFb interacts with DENV and activates NF-kB elements within the promoter region of IL-8 gene, enhancing IL-8 transcription which may play a significant role in DENV pathogenesis [66]

Fig. 5

DENV and host post-transcriptional regulations: A Dengue Virus NS5 associates with active spliceosomes, interacting with key components of the U5 snRNP and sequestering them in the cytoplasm. This reduces their levels in the nucleus and alters the events of alternative splicing [41]. B In the early stages of DENV infection, viral genomic RNA (vgRNA) binds to DDX6 via the 3’UTR and recruits mRNA decay enzymes to the viral replication complex. The exoribonuclease XRN-I initiates the degradation of vgRNA, resulting in the formation of sfRNA. These pseudoknot structures play a role in stalling the XRN1 enzyme near the 5’ border of the 3’ UTR, causing the inhibition of XRN-1 and leading to modulations in mRNA degradation pathways, consequently affecting the RNAi response [43]

Fig. 6

DENV and host post-translational regulation: A DENV NS3 interacts with TRIM69, induced as an Interferon Stimulated Gene (ISG), activating the ubiquitination pathway to restrict DENV replication [48]. B Conversely, ubiquitination of NS3 prevents the formation of the protease complex (NS2B3), inhibiting the cleavage of Interferon response-related genes, namely cGAS and STING. This results in an elevated host interferon response, targeting DENV replication [104, 105]. C Glycosylation of DENV proteins aids attachment to host surface receptors and various complementary proteins, contributing to immune evasion and viral propagation [–52]. D DENV NS5 interacts with STAT2, preventing its phosphorylation and targeting it for proteasomal degradation [53, 106]

Fig. 7

DENV and host stress responses: A Alterations in translation processes result in the assembly of stress granules. However, DENV prevents stress granule assembly by interacting with various stress granule markers. TIA1 and TIAR interact with DENV NS3, while various proteins such as G3BP1, G3BP2, DDX6, Caprin1, and USP10 bind to DENV 3’UTR. Additionally, VCP1, together with NPL4, forms a complex with DENV NS4B. These interactomes colocalize and participate in DENV replication [–57]. B During DENV infection, Angiogenin levels have been found to be enhanced compared to uninfected controls. The upregulated Angiogenin may play a crucial role in various processes, including immune modulation, angiogenesis, tRNA fragmentation, and ER stress, among others [116]

Fig. 8

DENV and antiviral therapeutics: A Interaction between DENV NS3-NS4B in the formation of the virus replication complex. Several novel small molecule inhibitors, including JNJ-1802, JNJ-A07, SDM25N, and NITD-688, have been identified to inhibit NS4B, disrupting its interaction with NS3 and thereby suppressing DENV replication [122, 125, 128]. B DENV fusion inhibitors such as Geraniin, DN59, NITD-488, and 1662G07 bind with envelope protein thereby prohibiting virus attachment and entry into the host membrane [–133]. C NS2B-NS3 protease complex participate in the processing of dengue polyprotein and supports virus replication. Inhibitors such as Nelfinavir, Protegrin-1, Carnosine, Palmatine, Compund 1, 32, C, D targets NS2B-NS3 protease complex and hinder virus replication [–137]. D Dengue capsid protein undergoes capsid disassembly, releasing viral RNA for translation and replication. Inhibitors such as VGTI-A3, VGTI-A3-03, and ST-148 interact with the capsid protein, inducing antiviral effects and hindering dengue virus translation and replication [138, 139]