Unification and extensive diversification of M/Orf3-related ion channel proteins in coronaviruses and other nidoviruses

Abstract

The coronavirus, SARS-CoV-2, responsible for the ongoing COVID-19 pandemic, has emphasized the need for a better understanding of the evolution of virus-host interactions. ORF3a in both SARS-CoV-1 and SARS-CoV-2 are ion channels (viroporins) implicated in virion assembly and membrane budding. Using sensitive profile-based homology detection methods, we unify the SARS-CoV ORF3a family with several families of viral proteins, including ORF5 from MERS-CoVs, proteins from beta-CoVs (ORF3c), alpha-CoVs (ORF3b), most importantly, the Matrix (M) proteins from CoVs, and more distant homologs from other nidoviruses. We present computational evidence that these viral families might utilize specific conserved polar residues to constitute an aqueous pore within the membrane-spanning region. We reconstruct an evolutionary history of these families and objectively establish the common origin of the M proteins of CoVs and Toroviruses. We also show that the divergent ORF3 clade (ORF3a/ORF3b/ORF3c/ORF5 families) represents a duplication stemming from the M protein in alpha- and beta-CoVs. By phyletic profiling of major structural components of primary nidoviruses, we present a hypothesis for their role in virion assembly of CoVs, ToroVs and Arteriviruses. The unification of diverse M/ORF3 ion channel families in a wide range of nidoviruses, especially the typical M protein in CoVs, reveal a conserved, previously under-appreciated role of ion channels in virion assembly and membrane budding. We show that M and ORF3 are under different evolutionary pressures; in contrast to the slow evolution of M as core structural component, the ORF3 clade is under selection for diversification, which suggests it might act at the interface with host molecules and/or immune attack.

Comparative Phylogenomic Analysis Reveals Evolutionary Genomic Changes and Novel Toxin Families in Endophytic Liberibacter Pathogens

“…4B and C ), distinct from other genomic regions and other types of prophages. This rapid evolutionary pattern of the SC prophage suggests that some of its components may have acted at the interface of host-pathogen interactions and gained the upper hand during the evolutionary arms race ( 67 , 68 ).…”

“…The major contribution of our research in this regard is to use dedicated protein domain-centric analysis strategies, comparative genomics, and evolutionary theory to identify such toxin/effector components and to formulate the principle of the systems behind these interactions ( 47 , 48 , 73 , 74 ). This approach has led to the discovery of several distinct classes of conflict systems, including bacterial polymorphic toxin systems involved in kin selection and bacteria-host interactions ( 47 , 48 , 50 ), Crinkler-RHS (CR) effector systems at the interface of eukaryotic pathogen/symbiont-host interactions ( 73 ), nucleotide-centric conflict systems ( 75 ), DNA modification systems deployed in phage-bacteria interactions ( 76 ), and viral pathogenicity factors involved in coronavirus-host interactions ( 67 , 68 ). Many of our computational predictions in protein function and the organizational principles of the systems have facilitated the creation of new concepts and directions in several research fields and have been later experimentally validated, including the recent discoveries of the enzymatic function of animal and plant Toll/interleukin-1 receptor (TIR) proteins ( 77 , 78 ), adenosine methylation enzymes ( 79 , 80 ), type III CRISPR-Cas systems ( 81 , 82 ), and novel immunoglobulin proteins and ion channel proteins in SARS-CoV-2 ( 67 , 68 ), in addition to much work on PTSs ( 47 , 48 , 50 ).…”

An Issue of Concern: Unique Truncated ORF8 Protein Variants of SARS-CoV-2

“…ORF8 is not a viroporin like ORF3a of both SARS-CoV-1 and SARS-CoV-2 which are ion channels (viroporins) implicated in virion assembly and membrane budding. So, the viruses lacking E and ORDF3a are not viable and full-length E and ORF3a proteins are required for maximal SARS-CoV replication and virulence [48,49,50]. It seems that the ORF8 has only a minor or non-impact on these activities and/or SARS-CoV-2 life cycle as it can survive without functional ORF8, due to many mutations and truncations raised in its gene and protein as above mentioned [23,51].…”

Comparative phylogenomic analysis reveals evolutionary genomic changes and novel toxin families in endophyticLiberibacterpathogens

“…To be noted, we observed an unusual divergence between the SC prophage loci from different Liberibacter pathogens and different strains of the same pathogen, distinct from other genomic regions and other types of prophages. This rapid evolutionary pattern of the SC prophage suggests that some of its components may have acted at the interface of host-pathogen interactions and gained the upper hand during the evolutionary arms race 57,58 .…”

“…Driven by the evolutionary arms race, the proteins mediating these interactions, such as toxins, effectors, or virulence factors, typically evolve rapidly and are difficult to identify using traditional experimental and computational methods 63 . The major contribution of our research in this regard is to use dedicated protein domain-centric analysis strategies, comparative genomics, and evolutionary theory to identify such toxin/effector components and to formulate the principle of the systems behinds these interactions 42,43,62,63 .Previously, this approach has led to the discovery of several distinct classes of conflict systems, including bacterial polymorphic toxin systems involved in kin selection and bacteriahost interactions 42,43,45 , Crinkler-RHS (CR) effector systems at the interface of eukaryotic pathogen/symbiont-host interactions , nucleotide-centric conflict systems 64 , DNA modification systems deployed in phage-bacteria interactions 65 , and viral pathogenicity factors involved in coronavirus-host interactions 57,58 . Many of our computational predictions in protein function and the organizational principles of the systems have facilitated the creation of new concepts and directions in several research fields and have been later experimentally validated, including the recent discoveries of the enzymatic function of animal and plant TIR proteins 66,67 , adenosine methylation enzymes 68,69 , type III CRISPR-Cas systems 70,71 , and novel immunoglobulin proteins and ion channel proteins in SARS-CoV-2 57,58 , in addition to many work on PTSs 42,43,45 .…”