How the replication and transcription complex of SARS-CoV-2 functions in leader-to-body fusion

Abstract

Background Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although unprecedented efforts are underway to develop therapeutic strategies against this disease, scientists have acquired only a little knowledge regarding the structures and functions of the CoV replication and transcription complex (RTC) and 16 non-structural proteins, named NSP1-16. Results In the present study, we determined the theoretical arrangement of NSP12-16 in the global RTC structure. This arrangement answered how the CoV RTC functions in the “leader-to-body fusion” process. More importantly, our results revealed the associations between multiple functions of the RTC, including RNA synthesis, NSP15 cleavage, RNA methylation, and CoV replication and transcription at the molecular level. As the most important finding, transcription regulatory sequence (TRS) hairpins were reported for the first time to help understand the multiple functions of CoV RTCs and the strong recombination abilities of CoVs. Conclusions TRS hairpins can be used to identify recombination regions in CoV genomes. We provide a systematic understanding of the structures and functions of the RTC, leading to the eventual determination of the global CoV RTC structure. Our findings enrich fundamental knowledge in the field of gene expression and its regulation, providing a basis for future studies. Future drug design targeting SARS-CoV-2 needs to consider protein-protein and protein-RNA interactions in the RTC, particularly the complex structure of NSP15 and NSP16 with the TRS hairpin.