TMEM41B and VMP1 modulate cellular lipid and energy metabolism for facilitating dengue virus infection

Abstract

Transmembrane Protein 41B (TMEM41B) and Vacuole Membrane Protein 1 (VMP1) are two ER-associated lipid scramblases that play a role in autophagosome formation and cellular lipid metabolism. TMEM41B is also a recently validated host factor required by flaviviruses and coronaviruses. However, the exact underlying mechanism of TMEM41B in promoting viral infections remains an open question. Here, we validated that both TMEM41B and VMP1 are essential host dependency factors for all four serotypes of dengue virus (DENV) and human coronavirus OC43 (HCoV-OC43), but not chikungunya virus (CHIKV). While HCoV-OC43 failed to replicate entirely in both TMEM41B- and VMP1-deficient cells, we detected diminished levels of DENV infections in these cell lines, which were accompanied by upregulation of the innate immune dsRNA sensors, RIG-I and MDA5. Nonetheless, this upregulation did not correspondingly induce the downstream effector TBK1 activation and Interferon-beta expression. Despite low levels of DENV replication, classical DENV replication organelles were undetectable in the infected TMEM41B-deficient cells, suggesting that the upregulation of the dsRNA sensors is likely a consequence of aberrant viral replication rather than a causal factor for reduced DENV infection. Intriguingly, we uncovered that the inhibitory effect of TMEM41B deficiency on DENV replication, but not HCoV-OC43, can be partially reversed using exogenous fatty acid supplements. In contrast, VMP1 deficiency cannot be rescued using the metabolite treatment. In line with the observed phenotypes, we found that both TMEM41B- and VMP1-deficient cells harbor higher levels of compromised mitochondria, especially in VMP1 deficiency which results in severe dysregulations of mitochondrial beta-oxidation. Using a metabolomic profiling approach, we revealed distinctive global dysregulations of the cellular metabolome, particularly lipidome, in TMEM41B- and VMP1-deficient cells. Our findings highlight a central role for TMEM41B and VMP1 in modulating multiple cellular pathways, including lipid mobilization, mitochondrial beta-oxidation, and global metabolic regulations, to facilitate the replication of flaviviruses and coronaviruses.

A fast-growing dengue virus mutant reveals a dual role of STING in response to infection

“…However, at 24 hpi, a decrease in D2C, but not D2A replication was observed (figure 5d). Autophagy is critical for DENV infection, as verified by infecting HEK293FT cells that were deficient in autophagosomemodulating genes, TMEM41B and VMP1 [28][29][30]. Similarly, we found no D2A or D2C progeny produced at 24 hpi when TMEM41B or VMP1 genes were removed (figure 5e).…”

Betacoronaviruses SARS-CoV-2 and HCoV-OC43 infections in IGROV-1 cell line require aryl hydrocarbon receptor

“…Lentiviruses were packaged by the 3rd generation lentivirus packaging system plasmids pRSV-Rev, pMD2 VSV-G, and pMDLg/pRRE as previously described [ 18 ] with modifications. In brief, 293FT cells were seeded and cultured at 37°C for 16–24 h. At 2 h prior to transfection, the cells were replenished with IMDM medium (Gibco Life Technologies) containing 1× penicillin-streptomycin, 1× L-glutamine, and 10% heat-inactivated fetal bovine serum.…”

TMEM41B is an endoplasmic reticulum Ca2+release channel maintaining T cell metabolic quiescence and responsiveness

“…On day 7.5 post-infection, mice were sacrificed and splenocytes were isolated to measure antigen-specific CD8 T cell response by flow cytometry. Briefly, splenocytes were stained with CD8a-PB, TCRb-APC, CD44-Percp-Cy5.5 together with PE conjugated H-2D b -gp [33][34][35][36][37][38][39][40][41] -tetramer for 30 min at room temperature. Cells were washed twice with FACS buffer and analyzed by a LSR Fortessa cytometer (BD).…”

“…Amidst the COVID-19 pandemic, while searching for viral host factors through CRISPR screening, multiple groups independently identified TMEM41B as a pan-flavivirus and pan-coronavirus (including SARS-CoV2) host factor [29][30][31] . Biochemically, TMEM41B exhibits phospholipid scramblases activity 32,33 , and may regulate lipid metabolism and viral infection via such activity [34][35][36] . Despite these insights, the biological function of TMEM41B in the ER remains enigmatic.…”