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Principal Investigator: Michael S Cohen
Organization: UNIVERSITY OF KANSAS LAWRENCE
Fiscal Year: 2024
Award: $186,159
Funding agency: National Institute of Allergy and Infectious Diseases
PROJECT SUMMARY
Coronaviruses (CoVs) are a large class of positive-strand RNA viruses that are capable of causing severe
human disease and death, as is exemplified by the pandemic outbreak of SARS-CoV-2. The innate immune
response to coronavirus infection includes a battle between poly-ADP-ribose polymerases (PARPs) and the
coronavirus macrodomain (Mac1), which add and remove ADP-ribose from proteins, respectively. In the
absence of Mac1 enzyme activity, CoVs replicate poorly in the face of the innate immune response and cause
little to no disease in several animal models of infection, including SARS-CoV-2. These results demonstrate
the power of PARP-mediated ADP-ribosylation to limit CoV-induced disease and support our central
hypothesis that PARPs target host and viral proteins, and that the post-translational modification of these
targets (MARylation) induces an antiviral state that limits virus replication. Despite the clear importance of
PARP enzymes in driving the outcome of a CoV infection, a large gap in knowledge remains as to exactly how
this battle plays out during CoV infections, most notably i) what PARPs are heavily involved in this battle; and
ii) what cellular or viral proteins are ADP-ribosylated during infection. Functional redundancy, similar NAD+
binding sites, low protein abundance, and viral enzymes that reverse their effects have made it challenging to
identify direct targets of individual PARPs during coronavirus infection.
The objective of this proposal is to identify specific ADP-ribosylated targets of PARPs during a SARS-CoV-2
infection that will uncover novel mechanisms of virus restriction. This objective will be resolved with the
following specific aims: 1) Identify PARPs proteins that are expressed during and impact SARS-CoV-2
infection, and 2) Identify viral and cellular PARP targets using chemical genetics and proximity labeling. This
work is innovative because we will apply, for the first time, NAD+-based chemical proteomics, chemical
genetics, and BioID proximity labeling to uncover the specific targets of of MARylating PARPs that impact
SARS-CoV-2 infection. Furthermore, we have a unique tool, a virus that lacks the ability to counter PARP
activity, to aid in our identification of physiologically relevant PARP target proteins. Our rationale is that
identifying the targets of individual PARPs during SARS-CoV-2 infection will define novel mechanisms of virus
restriction that will dramatically expand the landscape of ADP-ribosylation and how it can impact virus
replication. Together, with our combined expertise in chemistry, PARP/ADP-ribose, and CoV biology, we are
poised to address these challenges and make seminal discoveries describing novel targets of PARP-mediated
ADP-ribosylation and how they can drive antiviral innate immune responses during SARS-CoV-2 infection. We
anticipate identifying dozens of ADP-ribosylated proteins during infection, which will alter the landscape of how
PTMs, outside of phosphorylation or ubiquitination, can impact the outcomes of virus infections, and will
provide new avenues for antiviral therapy.
Terms: <2019 novel corona virus><2019 novel coronavirus><2019-nCoV><ADP Ribose><ADP ribosylation><Address><Adenosine 5'-(trihydrogen diphosphate), P'-5-ester with D-ribose><Adenosine 5'-Diphosphoribose><Adenosine Diphosphate Ribose><Adenosine Diphosphoribose><Animal Model><Animal Models and Related Studies><Anti-viral Response><Anti-viral Therapy><Antibodies><Attenuated><Automobile Driving><Binding><Binding Sites><Biology><COVID-19 infection><COVID-19 outbreak><COVID-19 virus><COVID-19 virus infection><COVID19 infection><COVID19 outbreak><COVID19 virus><Cell Communication and Signaling><Cell Signaling><Cessation of life><Chemicals><Chemistry><CoV-2><CoV2><Combining Site><Complement><Complement Proteins><Coronaviridae><Coronaviridae Infections><Coronavirus><Coronavirus Infections><Death><Development><Dihydronicotinamide Adenine Dinucleotide><Diphosphopyridine Nucleotide><Disease><Disorder><Enzyme Gene><Enzymes><Future><Genes><Genetics-Mutagenesis><Goals><Host Defense><Human><IFN><Individual><Infection><Innate Immune Response><Innate Immunity><Interferon Type I><Interferons><Intracellular Communication and Signaling><Knowledge><Label><Mediating><Methods><Modern Man><Molecular Interaction><Mouse Hepatitis Coronavirus><Mouse Hepatitis Virus><Murine Gastroenteritis Virus><Murine hepatitis virus><Mutagenesis><Mutagenesis Molecular Biology><Nadide><Native Immunity><Natural Immunity><Nicotinamide adenine dinucleotide><Nicotinamide-Adenine Dinucleotide><Non-Specific Immunity><Nonspecific Immunity><Outcome><PARP Polymerase><PARP protein><PARS><Pathogenesis><Phosphorylation><Photoaffinity Labels><Physiologic><Physiological><Play><Poly(ADP-ribose) Polymerases><Poly(ADPribose) Polymerase><Position><Positioning Attribute><Post-Translational Modification Protein/Amino Acid Biochemistry><Post-Translational Modifications><Post-Translational Protein Modification><Post-Translational Protein Processing><Posttranslational Modifications><Posttranslational Protein Processing><Protein Modification><Protein Phosphorylation><Proteins><Proteomics><RNA Viruses><Reactive Site><Reporting><Role><SARS corona virus 2><SARS-CO-V2><SARS-COVID-2><SARS-CoV-2><SARS-CoV-2 infection><SARS-CoV-2 inhibitor><SARS-CoV-2 outbreak><SARS-CoV2><SARS-CoV2 infection><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><Seminal><Severe Acute Respiratory Coronavirus 2><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome coronavirus 2 infection><Severe acute respiratory syndrome coronavirus 2 inhibitor><Severe acute respiratory syndrome coronavirus 2 outbreak><Severe acute respiratory syndrome related corona virus 2><Signal Pathway><Signal Transduction><Signal Transduction Systems><Signaling><Site><Site-Directed Mutagenesis><Site-Specific Mutagenesis><System><Targeted DNA Modification><Targeted Modification><Time><Ubiquitilation><Ubiquitination><Ubiquitinoylation><Viral><Viral Diseases><Viral Gene Products><Viral Gene Proteins><Viral Proteins><Viral hepatitis><Virus><Virus Diseases><Virus Replication><Work><Wuhan coronavirus><analog><attenuate><attenuates><biological signal transduction><block SARS-CoV-2><block severe acute respiratory syndrome coronavirus 2><chemical genetics><complementation><corona virus><coronavirus disease 2019 infection><coronavirus disease 2019 outbreak><coronavirus disease 2019 virus><coronavirus disease-19 outbreak><coronavirus disease-19 virus><defense response><developmental><driving><enzyme activity><experiment><experimental research><experimental study><experiments><genetic approach><genetic strategy><hCoV19><hepatitis virus infection><human disease><in vivo><infected with COVID-19><infected with COVID19><infected with SARS-CoV-2><infected with SARS-CoV2><infected with coronavirus disease 2019><infected with severe acute respiratory syndrome coronavirus 2><inhibit SARS-CoV-2><inhibit severe acute respiratory syndrome coronavirus 2><innovate><innovation><innovative><interest><knock-down><knockdown><model of animal><murine hepatitis coronavirus><mutant><nCoV2><novel><outbreak of SARS-CoV-2><overexpress><overexpression><pandemic><pandemic disease><physiological defense response><poly ADP polymerase><poly ADP ribose synthetase><protein expression><social role><tool><ubiquination><ubiquitin conjugation><viral infection><viral infectious disease treatment><viral multiplication><viral replication><virus infection><virus multiplication><virus protein><virus-induced disease>