Genetics Assignment #3

Article Summary

In the primary article “New Structure Model for the Packaging Signal in the Genome of Group IIa Coronaviruses”, authors and scientists Shih-Cheng Chen, Erwin van den Born, Sjoerd H. E. van den Worm, Cornelis W. A. Pleij, Eric J. Snijder, and René C. L. Olsthoorn proposed that “repeating AA bulges are characteristic features of group IIa PSs”. The Scientists used structure probing and phylogenetic data to find a “95-nt hairpin within the 190-nt PS domain which is conserved in all group IIa coronaviruses”. The scientists did not identify a 95-nt hairpin within the 190-nt PS domain in group I coronaviruses, severe acute respiratory syndrome coronavirus (group IIb), or group III coronaviruses. 

The article discusses the methods the scientists used to support their new model for the packaging signal in the genome of group IIa Coronavirus. To support their data the scientists used the basic local alignment search tool (BLAST) to search for “MHV PS homologs in the available group IIa CoV sequences”. To further support their model the scientist’s “PCR amplified a DNA fragment containing the MHV A59 PS with the primers”. During the experiments the scientists attempted to reconcile unexpected results found in previous research that used mutagenesis of the 69-nt PS to identify structural elements that are important for packaging. 

The scientists concluded that their new structure model for the packaging signal in the genome of group IIa Coronaviruses gives a better explanation and helps fill in some of the unexpected results acquired by other scientists during their own experiments. The scientists also concluded that another scientist’s proposal that a stem-loop structure can be found in the 3’ part of SARS CoV ORF1b was incorrect as they themselves were not able to identify a hairpin in this region that conforms to the model proposed by this other scientist.

Reference

1.  Chen SC, van den Born E, van den Worm SH, Pleij CW, Snijder EJ, Olsthoorn RC. 2007. New structure model for the packaging signal in the genome of group IIa coronaviruses. J. Virol 81:6771–6774.