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Visualization by cryo-electron microscopy of genomic RNA that binds to the protein capsid inside bacteriophage MS2
Roman Koning1, Sjoerd van den Worm, Jasper R Plaisier
1Department of Molecular Cell Biology, Leiden University Medical Hospital, Wassenaarseweg 72, 2300 RA Leiden, The Netherlands. r.i.koning@lumc.nl
Abstract:
The icosahedrally symmetrized structure of bacteriophage MS2 as determined by cryo-electron microscopy (EM) reveals the presence of genomic RNA that attaches to coat-protein dimers. Earlier X-ray diffraction studies revealed similar interactions between the unique operator hairpin of the MS2 genomic RNA and the coat-protein dimer. This observation leads us to conclude that not only the operator, but also many other RNA sequences in the genome of MS2, are able to bind to the coat-protein dimer. A substantial number of potential coat-protein-dimer binding sites are present in the genome of MS2 that can account for the observed RNA densities in the EM map. Moreover, it appears that these stem-loop structures are able to bind in a similar fashion to the coat protein dimer as the wild-type operator hairpin. The EM map also shows additional density between the potential operator-binding sites, linking the RNA stem-loops together to form an icosahedral network around the 3 and 5-fold axes. This RNA network is bound to the inside of the MS2 capsid and probably influences both capsid stability and formation, supporting the idea that capsid formation and RNA packaging are intimately linked to each other.
Insights
Bacteriophage MS2 genomic RNA binds to coat-protein dimers at multiple sites, forming an icosahedral network. This RNA network influences capsid stability and formation, linking RNA packaging and capsid assembly.
Area of Science:
- Structural biology
- Virology
- Biochemistry
Background:
- Bacteriophage MS2 genomic RNA interacts with coat-protein dimers.
- Previous X-ray diffraction studies identified specific RNA-protein interactions.
Purpose of the Study:
- To investigate the binding sites of MS2 genomic RNA within the bacteriophage capsid.
- To elucidate the structural basis of RNA-protein interactions and their role in capsid formation.
Main Methods:
- Cryo-electron microscopy (EM) was used to determine the icosahedrally symmetrized structure of bacteriophage MS2.
- Analysis of RNA densities within the EM map to identify potential binding sites.
Main Results:
- Cryo-EM revealed genomic RNA attached to coat-protein dimers throughout the MS2 capsid.
- Multiple RNA stem-loop structures, beyond the operator, bind to coat-protein dimers.
- An icosahedral RNA network is formed by these bound RNA segments, linking them together.
- This network is situated inside the capsid, interacting with its inner surface.
Conclusions:
- Bacteriophage MS2 utilizes numerous RNA sequences for binding to coat-protein dimers, not just the operator.
- The genomic RNA forms a structured network within the capsid, influencing its stability and assembly.
- Capsid formation and RNA packaging are intrinsically linked processes in bacteriophage MS2.