Autophagy and SARS-CoV-2-Old Players in New Games
Abstract
:1. Introduction
2. Autophagy as a Process—Biological Importance and Types of Autophagy
3. Autophagy in Infectious Diseases
3.1. Antiviral Functions of Autophagy
3.2. Blocking of Autophagy by Viruses
3.3. Pro-Viral Role of Autophagy
4. Autophagy and COVID-19
4.1. Early Autophagy Reprogramming
4.2. Late-Stage Incomplete Autophagy
4.3. Mitophagy and Innate Immune Responses Reprograming
4.4. Putative Pexophagy Involvement
4.5. Treatment and Pharmacological Modulation
4.6. Adverse Effects of Autophagy-Targeting Drugs
5. Models to Study Autophagy in Infections
6. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviation
a | |
A549 | human lung cells |
ACE2 | angiotensin-converting enzyme 2 |
AKT-mTOR signaling | protein kinase B-mammalian target of rapamycin complex |
APCs | antigen presenting cells |
Arl8b | Arf-like GTPases |
ARP2/3 | actin-related protein 2/3 complex |
ARH-77 | B lymphoblast cell line |
ASC | adaptor apoptosis-associated speck-like protein with a caspase-1 recruitment domain |
ATG | autophagy-related genes |
ATP6AP1 | S1 subunit of the enzyme V-type proton ATPase. |
b | |
BCL-xL | B-cell lymphoma-extra large |
BECN1(Beclin-1) | mammalian ortholog of the yeast autophagy-related gene 6 |
BORC-ARL8b | complex multisubunit complex- regulates lysosome positioning |
c | |
Calu-3 | human bronchial epithelial cells |
CARD | caspase recruitment domain |
CatB/L | cathepsin B and L |
CAV | Coxsackie viruses |
c-Myc | proto-oncogene |
CNS | central nervous system |
CXCR-4 | C-X-C chemokine receptor type 4 |
d | |
3D organoids | miniature 3-dimensional structures that can mimic the structure and function of different tissues |
DAMPs | damage-associated molecular patterns |
DENV | Dengue virus |
DMV | double-membrane vesicles |
Dolutegravir | antiretroviral medication |
e | |
EBV | Epstein Bar virus |
eIF2a | translation elongation factor |
Emtricitabine | nucleoside reverse-transcriptase inhibitor |
ER | endoplasmic reticulum |
f | |
FAM134 | reticulon protein- ER-phagy receptor |
g | |
GABARAP | GABA type receptor-associated protein |
GSDMD | gasdermin D |
GTPase | hydrolase enzyme binding nucleotide guanosine triphosphate |
h | |
HCV | hepatitis C virus |
HEK 293T | human embryonic kidney cells |
HIF-1 | hypoxia-induced transcription factor-1 |
Hsc70 | heat shock cognate 71 kDa protein |
HSV | herpes simplex virus type I |
HOPS | homotypic fusion and protein sorting |
i | |
ICP34.5 | infected cell protein 34.5 |
IFN | interferon |
iPSCs | human induced pluripotent stem cells |
j | |
JAK1/2 | Janus kinase- (tyrosine kinases) |
k | |
KSHV | Kaposi’s sarcoma-associated herpes virus |
l | |
LAMP1 | lysosomal associated membrane glycoprotein 1 |
LAMP2A | lysosomal associated membrane protein 2 |
LC3 | microtubule associated protein 1 light chain 3B |
LIR | LC3-interacting region |
Lopinavir | antiretroviral protease inhibitor |
m | |
MAVS | mitochondrial antiviral-signaling protein |
MCL-1 | induced myeloid leukemia cell differentiation protein |
MHC | major histocompatibility complex |
MHV | murine hepatitis virus |
mTORC1/S6K/4EBP1 | mammalian target of rapamycin complex 1/p70 ribosomal S6 kinases/4E-binding protein 1 |
n | |
NBR1 | neighbor of BRCA1 gene |
NCI-BL 2171 | small cell lung carcinoma |
NDP52 | calcium binding and coiled-coil domain 2 |
NF-kB | nuclear factor-κB (transcription factor) |
NIC | niclosamide |
NK | natural killer cells |
NLRP3 | NLR family pyrin domain containing 3 inflammasome |
NS4B | membrane-associated protein involved in viral replication or assembly |
NSPs | non-structural proteins |
o | |
OPTN | Organ Procurement and Transplantation Network |
ORFs | Open Reading Frames |
ORF3a | encodes a viral accessory protein |
ORF8 | encodes viral accessory protein, Betacoronavirus NS8 protein |
p | |
p62 | SQSTM1(sequestosome 1)- ubiquitin-binding scaffold protein |
PAMPs | pathogen-associated molecular patterns |
PCD | programmed cell death |
PEX3 | peroxisomal Biogenesis Factor |
PI3K | phosphoinositide 3-kinase, also known as VPS34. |
PI3P | phosphatidylinositol 3-phosphate |
PINK1 | PTEN induced kinase 1 |
PKR | protein kinase R |
PMP | peroxisome membrane protein |
PP1a | protein phosphatase 1 |
PRKN | Parkin RBR E3 ubiquitin protein ligase |
PTEN | fosfatidilinositol-3,4,5-trisfosfato 3-fosfatasa |
PV | Poliovirus |
PYCARD | apoptosis-associated speck-like protein containing a CARD (or ASC) |
PYD | pyrin domain |
r | |
Rab-7a | Ras-related protein late-endosomal / lysosomal GTPase |
RCD | regulated cell death |
RHIM | homotypic interaction motif |
Ribavirin | antiretroviral medication inhibits- RNA/DNA viruses |
RIP | proteins containing a receptor-interacting protein |
Ritonavir | antiretroviral medication, protease inhibitors |
RNP | ribonucleoprotein complexes |
ROS | reactive oxygen species |
RTC | replication and transcription complex |
Ruxolitinib | Janus kinase inhibitor |
s | |
SMVs | single-membrane vesicles |
SNAP | soluble N-ethylmaleimidesSensitive factor attachment proteins |
SNAP29 | synaptosome associated protein 29, SNARE protein, in autophagy |
SNARE | SNAP receptor |
SNX27 | sorting nexin family member 27 |
STX17 | Syntaxin 17, autophagosomal SNARE protein |
t | |
TAK1 | transforming growth factor beta-activated kinase 1 |
Tax1BP1 | Tax1-binding protein 1 |
TGN | trans-Golgi network |
TNFR1 | tumor necrosis factor receptor 1 |
TMEM41B | transmembrane protein 41B |
TMPRSS2 | transmembrane serine 2 protease |
Tenofovir DF | tenofovir disoproxil fumarate, HIV medication |
v | |
VAMP8 | vesicle-associated membrane protein 8 |
Vero E6 | epithelial cell from African green monkey |
Viroporin | small hydrophobic multifunctional viral proteins |
VMP1 | vacuolar membrane protein 1 |
VPS | vacuolar protein sorting proteins (as VPS26, VPS29 and VPS35) |
Vps34 | class III phosphoinositide 3-kinase (PI3K) |
VZV | Varicella zoster virus |
w | |
WHO | World Health Organization |
z | |
ZBP1 | Z-DNA binding protein |
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Ivanova, T.; Mariienko, Y.; Mehterov, N.; Kazakova, M.; Sbirkov, Y.; Todorova, K.; Hayrabedyan, S.; Sarafian, V. Autophagy and SARS-CoV-2-Old Players in New Games. Int. J. Mol. Sci. 2023, 24, 7734. https://doi.org/10.3390/ijms24097734
Ivanova T, Mariienko Y, Mehterov N, Kazakova M, Sbirkov Y, Todorova K, Hayrabedyan S, Sarafian V. Autophagy and SARS-CoV-2-Old Players in New Games. International Journal of Molecular Sciences. 2023; 24(9):7734. https://doi.org/10.3390/ijms24097734
Chicago/Turabian StyleIvanova, Tsvetomira, Yuliia Mariienko, Nikolay Mehterov, Maria Kazakova, Yordan Sbirkov, Krassimira Todorova, Soren Hayrabedyan, and Victoria Sarafian. 2023. "Autophagy and SARS-CoV-2-Old Players in New Games" International Journal of Molecular Sciences 24, no. 9: 7734. https://doi.org/10.3390/ijms24097734