User:Jingyunz/leviviridae levivirus 5UTR

Background
The main constituent genera of the family Leviviridae are Levivirus and Allolevivirus. Though members in both genera encode four genes, they differ in the identity of the genes and the associated ORF orientation. Based on serological cross-reactivity and virion characteristics, Levivirus is further categorized into two groups known as group I and II. MS2 and GA are the typical species of group I, II coliphages of Levivirus, respectively.

As an example here, the RNA genome of MS2 is of positive-sense, encoding 4 proteins essential for the survivor and reproduction of the virion: maturation, coat, lysis, and replicase (starting from the 5' end to 3’ end). The structural components of the icosahedral virion consist of the maturation proteins and the coat proteins with a per-virion ratio of 1:180. The lysis protein is required to lyses the host cell; the replicase and a host factor comprise a holoenzyme responsible for the replication of strands in both polarities. As levivirus has a single-stranded RNA genome that can serve as the template for both translation and replication, there is competition between ribosome and replicase in binding the template. To alleviate this competition, the translations of the distal 3 genes (coat, lysis, replicase) are coupled so the bindings of replicase and ribosome are mutually exclusive. However, ribosome could still bind to the ORF of the maturation gene, which becomes the road block for the replicase travelling to 5' end. This problem is solved by an inhibitory final structure (RNA secondary structure folded by the 5'UTR of the maturation protein ORF) that imposes translational repression on the maturation protein, which yields the way to the replicase. However, maturation protein is required for the viral infection process because it proteolytically triggers the releasing of viral genome through contacting the F-pili of male Escherichia coli. For this, a transient structure produced along the folding pathway temporarily allows the ribosome to access the ORF of maturation protein, yielding adequate amount of maturation protein for the virion to survive.

Final structure inhibits the translation of maturation protein
This final and cloverleaf-like structure, assumed by the 5' UTR of equilibrated RNA from MS2, is composed of a 5' hairpin, and the downstream West, South and East arms. An inhibitory upstream complementary sequence (UCS), immediately downstream to the 5' hairpin, pairs with the 7-nt Shine-Dalgarno (AGGAGGU) sequence, forming a Long-Distance-Interaction (LDI). This LDI shields the SD sequence against the binding of ribosome. This inactive structure forms as soon as the first 123 nt of the plus-strand is synthesized before the ribosome can stably bind. Consequently, the translation of maturation protein is usually suppressed. This final structure is supported by phylogenetic analysis, Biochemical probing and Functional analysis.

Transient structure permits the translation of maturation protein
This transient hairpin emerges during the folding pathway and is eventually replaced by the mutually-exclusive final structure. This hairpin encompasses 4 nts from the 3' portion of the 5' hairpin, the UCS, and 7 nts from the 5' portion of the West arm from the final structure. Therefore, it disrupts the inhibitory LDI by freeing the SD sequence, temporarily permitting the nonequilibrated RNA to be captured by the translation machinery. That is, the maturation protein can be translated briefly when a positive strand is being replicated from an antisense template (between the synthesis of RBS and the formation of the inhibitory LDI). This kinetic model has been studied indirectly (rule out the contribution of maturation protein production from equilibrium model) and directly (altering the time allowed for RNA-folding does change the maturation protein produced accordingly). Mutational analysis involving compensatory double mutation also supports the functional importance of this metastable.