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Principal Investigator: Eugene V Koonin
Organization: NATIONAL LIBRARY OF MEDICINE
Fiscal Year: 2020
Award: $413,126
Funding agency: National Library of Medicine
The rapid accumulation of genome sequences and protein structures during the last decade has been paralleled by major advances in sequence database search methods. The powerful Position-Specific Iterating BLAST (PSI-BLAST) method developed at the NCBI forms the basis of our work on protein motif analysis. In addition, Hidden Markov Models (HMM), protein profile-against-profile comparison implemented in the HHSearch method, protein structure comparison methods, homology modeling of protein structure and genome context analysis were extensively and increasingly applied. Furthermore, custom libraries of protein domain profiles as well as computational pipelines for novel domain identification have been developed and applied. Lately, these methods for protein motif search are being complemented by deep learning computational methods.
During the year under review, we have continued and expanded our investigation of the proteins domains that are involved in virus-host interactions, and in particular, antivirus defense in prokaryotes. Bacteria and archaea are frequently attacked by viruses and other mobile genetic elements and rely on dedicated antiviral defense systems, such as restriction endonucleases and CRISPR, to survive. The enormous diversity of viruses suggests that more types of defense systems exist than are currently known. We developed computational methodology for systematic prediction of genes involved in antivirus defense and comprehensively characterized the domain architectures of the proteins encoded by these genes. As a result of these predictions followed by prediction and heterologous reconstitution, in collaboration with the laboratory of Dr. Feng Zhang (Broad Institute of MIT and Harvard), 29 widespread antiviral gene cassettes, collectively present in 32% of all sequenced bacterial and archaeal genomes, that mediate protection against specific bacteriophages. These systems incorporate enzymatic activities not previously implicated in antiviral defense, including RNA editing and retron satellite DNA synthesis. In addition, we computationally predict a diverse set of other putative defense genes that remain to be characterized. These results highlight an immense array of molecular functions that microbes use against viruses.
We further expanded our study of proteins domains involved in antivirus defense by performing a comprehensive computational census of the oligonucleotide-binding domains that are the key components of signal transduction pathways associated with CRISPR-Cas systems of adaptive immunity. CRISPR-associated Rossmann Fold (CARF) and SMODS-associated and fused to various effector domains (SAVED) are key components of cyclic oligonucleotide-based antiphage signaling systems (CBASS) that sense cyclic oligonucleotides and transmit the signal to an effector inducing cell dormancy or death. Most of the CARFs are components of a CBASS built into type III CRISPR-Cas systems, where the CARF domain binds cyclic oligoA (cOA) synthesized by Cas10 polymerase-cyclase and allosterically activates the effector, typically a promiscuous ribonuclease. Additionally, this signaling pathway includes a ring nuclease, often also a CARF domain (either the sensor itself or a specialized enzyme) that cleaves cOA and mitigates dormancy or death induction. We present a comprehensive census of CARF and SAVED domains in bacteria and archaea, and their sequence- and structure-based classification. There are 10 major families of CARF domains and multiple smaller groups that differ in structural features, association with distinct effectors, and presence or absence of the ring nuclease activity. By comparative genome analysis, we predicted specific functions of CARF and SAVED domains and partition the CARF domains into those with both sensor and ring nuclease functions, and sensor-only ones. Several families of ring nucleases functionally associated with sensor-only CARF domains were also predicted.
In the incessant host-parasite arms race, viruses evolved multiple anti-defense mechanisms including diverse anti-CRISPR proteins (Acrs) that specifically inhibit CRISPR-Cas and therefore have enormous potential for application as modulators of genome editing tools. Most Acrs are small and highly variable proteins which makes their bioinformatic prediction a formidable task. We developed a machine-learning approach for comprehensive Acr prediction. The model shows high predictive power when tested against an unseen test set and was employed to predict 2,500 candidate Acr families. Experimental validation of top candidates revealed two unknown Acrs (AcrIC9, IC10) and three other top candidates were coincidentally identified and found to possess anti-CRISPR activity. These results substantially expand the repertoire of predicted Acrs and provide a resource for experimental Acr discovery.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses an immediate, major threat to public health across the globe. Given this new major public health problem, we launched a new research direction aimed at the identification of motifs in coronavirus proteins that are likely to be associated with increased virulence in humans and zoonotic transmission into the human population. We performed an in-depth molecular analysis to reconstruct the evolutionary origins of the enhanced pathogenicity of SARS-CoV-2 and other coronaviruses that are severe human pathogens. Using integrated comparative genomics and machine learning techniques, we identified key genomic features that differentiate SARS-CoV-2 and the viruses behind the two previous deadly coronavirus outbreaks, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), from less pathogenic coronaviruses. These features include enhancement of the nuclear localization signals in the nucleocapsid protein and distinct inserts in the spike glycoprotein that appear to be associated with high case fatality rate of these coronaviruses as well as the host switch from animals to humans. The identified features could be crucial contributors to coronavirus pathogenicity and possible targets for diagnostics, prognostication, and interventions.
The research on protein domains and motifs performed during the last year has led to further progress in the study of the classification, evolution, and functions of several classes of proteins and domains, particularly, those involved in host-parasite interactions and other forms of biological conflicts. These findings have potential implications for human health and for developments in biotechnology. Additionally, protein motifs that are likely to contribute to coronavirus pathogenicity have been identified.
Terms: <2019 novel coronavirus><2019-nCoV><Amino Acid Motifs><Amino Acid Sequence><Animals><Antiviral Agents><Antiviral Drugs><Antivirals><Archaea><Archaeal Genome><Archaebacteria><Archaeobacteria><Archaeon><Architecture><Bacteria><Bacterial Genome><Bacteriophages><Binding><Bio-Informatics><Bioinformatics><Biological><Biotech><Biotechnology><COVID-19 epidemic><COVID-19 pandemic><COVID19 epidemic><COVID19 pandemic><CRISPR><CRISPR/Cas system><Case Fatality Rates><Cell Body><Cell Communication and Signaling><Cell Signaling><Cells><Censuses><Cessation of life><Classification><Cleaved cell><Clustered Regularly Interspaced Short Palindromic Repeats><Collaborations><Collection><Complement><Complement Proteins><Computing Methodologies><Conflict><Conflict (Psychology)><Coronaviridae><Coronavirus><Custom><Cyclicity><DNA Replication><DNA Restriction Enzymes><DNA Synthesis><DNA biosynthesis><DNA cassette><Death><Defense Mechanisms><Development><Diagnostic><Disease Outbreaks><Dissection><Engineering / Architecture><Enzyme Gene><Enzymes><Evolution><Family><Genes><Genome><Genomics><Glycoproteins><Goals><Health><Homology Modeling><Human><Institutes><Intervention><Intervention Strategies><Intracellular Communication and Signaling><Investigation><Laboratories><Libraries><MERS corona virus><MERS coronavirus><MERS virus><MERS-CoV><Machine Learning><Mediating><Methods><Microbe><Middle East Respiratory Syndrome Corona Virus><Middle East Respiratory Syndrome Coronavirus><Middle East Respiratory Syndrome Virus><Middle East Respiratory Syndrome-CoV><Middle Eastern Respiratory Syndrome Corona virus><Middle Eastern Respiratory Syndrome Coronavirus><Middle Eastern Respiratory Syndrome Virus><Middle Eastern Respiratory Syndrome-CoV><Mobile Genetic Elements><Modeling><Modern Man><Molecular Analysis><Molecular Interaction><NLS Peptide><Nuclear Localization Signal><Nuclear Localization Signal Peptide><Nucleocapsid Proteins><Oligo><Oligonucleotides><Outbreaks><PSI><Parasites><Pathogenicity><Pattern><Peptide Domain><Periodicity><Phages><Polymerase><Population><Position><Positioning Attribute><Primary Protein Structure><Prokaryotae><Prokaryotic Cells><Protein Analysis><Protein Domains><Protein Family><Protein Motifs><Protein Structure Initiative><Proteins><Public Health><RNA Editing><RNA Nucleases><RNA, Messenger, Editing><RNase><Race><Racial Group><Racial Stocks><Research><Research Resources><Resources><Restriction Endonucleases><Rhythmicity><Ribonuclease Family Protein><Ribonucleases><SARS Virus><SARS corona virus><SARS coronavirus><SARS-Associated Coronavirus><SARS-CoV><SARS-CoV-2><SARS-CoV2><SARS-Related Coronavirus><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related coronavirus 2><Satellite DNA><Severe Acute Respiratory Syndrome Virus><Severe Acute Respiratory Syndrome corona virus><Severe Acute Respiratory Syndrome coronavirus><Severe acute respiratory syndrome coronavirus 2><Signal Pathway><Signal Transduction><Signal Transduction Pathway><Signal Transduction Systems><Signaling><Structure><System><Systematics><Techniques><Tertiary Protein Structure><Testing><Transmission><Validation><Viral Gene Products><Viral Gene Proteins><Viral Proteins><Virulence><Virus><Work><Wuhan coronavirus><Zoonoses><Zoonotic><Zoonotic Infection><adaptive immunity><anti-viral agents><anti-viral drugs><anti-virals><arm><bacterial virus><base><biological signal transduction><cleaved><comparative><comparative genomics><computational methodology><computational methods><computational pipelines><computer based method><computer methods><computing method><corona virus><corona virus disease 2019 epidemic><corona virus disease 2019 pandemic><coronavirus disease 2019 epidemic><coronavirus disease 2019 pandemic><cross-species spillover><cross-species transmission><data base structure><database structure><deep learning><developmental><enhancer cassette><expression cassette><gene cassette><genetic cassette><genome analysis><genome editing><genomic editing><host jump><host switching><human pathogen><integration cassette><interspecies transmission><interventional strategy><machine learned><markov model><molecular array><molecular sequence database><novel><nuclease><oligos><prognostic><prokaryote><promoter cassette><protein profiling><protein sequence><protein structure><protein structures><proteins structure><psychological defense mechanism><reconstitute><reconstitution><reporter cassette><resistance cassette><response><selectable cassette><selection cassette><sensor><sequence database><sequencing database><severe acute respiratory syndrome-CoV><stop cassette><tool><transcription cassette><transcriptional cassette><transgene cassette><transmission across species><transmission between species><transmission process><transmitted across species><transmitted between species><transmitted cross-species><virus host interaction><virus protein>