Abstract
As cell-invading molecular machinery, coronavirus spike proteins pose an evolutionary conundrum due to their high divergence. In this study, we determined the cryo-EM structure of avian infectious bronchitis coronavirus (IBV) spike protein from the γ-genus. The trimeric IBV spike ectodomain contains three receptor-binding S1 heads and a trimeric membrane-fusion S2 stalk. While IBV S2 is structurally similar to those from the other genera, IBV S1 possesses structural features that are unique to different other genera, thereby bridging these diverse spikes into an evolutionary spectrum. Specifically, among different genera, the two domains of S1, the N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD), diverge from simpler tertiary structures and quaternary packing to more complex ones, leading to different functions of the spikes in receptor usage and membrane fusion. Based on the above structural and functional comparisons, we propose that the evolutionary spectrum of coronavirus spikes follows the order of α-, δ-, γ-, and β-genus. This study has provided insight into the evolutionary relationships among coronavirus spikes and deepened our understanding of their structural and functional diversity.
Highlights
As large enveloped RNA viruses, coronaviruses are capable of adapting to new hosts with relative ease through mutations and recombinations [1,2,3]
A critical missing piece in understanding the evolution of coronavirus spikes is the unavailability of the tertiary structure of γ-coronavirus spikes
infectious bronchitis coronavirus (IBV) spike gene was synthesized (Genscript) with codons optimized for insect cell expression
Summary
As large enveloped RNA viruses, coronaviruses are capable of adapting to new hosts with relative ease through mutations and recombinations [1,2,3]. Coronaviruses from the four genera all contain envelope-anchored spike proteins that mediate viral entry into host cells [5, 6]. The spikes bind to host receptors through their S1 subunits and fuse viral and host membranes through their S2 subunits. The spikes interact with host receptors and other host factors, needing to evolve for better adaptation to these host factors [7,8,9,10]. The spikes are the most divergent among all coronavirus proteins [6]. How coronavirus spikes have evolved to their current diverse structures imposes a major evolutionary conundrum
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