Red clover necrotic

mosaic virus A mosaic virus is any virus that causes infected plant foliage to have a mottled appearance. Such viruses come from a variety of unrelated lineages and consequently there is no taxon that unites all mosaic viruses. Examples Virus species tha ...

(RCNMV) contains several structural elements present within the 3′ and 5′

untranslated region In molecular genetics, an untranslated region (or UTR) refers to either of two sections, one on each side of a coding sequence on a strand of mRNA. If it is found on the Directionality (molecular biology), 5' side, it is called the Five prime ...

s (UTR) of the genome that enhance

translation Translation is the communication of the semantics, meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The English la ...

. In eukaryotes

transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, often th ...

is a prerequisite for

. During transcription the pre-mRNA transcript is processes where a

5′ cap In molecular biology, the five-prime cap (5′ cap) is a specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA. This process, known as mRNA capping, is highly regulated and vital in the creation ...

is attached onto mRNA and this 5′ cap allows for

ribosome Ribosomes () are molecular machine, macromolecular machines, found within all cell (biology), cells, that perform Translation (biology), biological protein synthesis (messenger RNA translation). Ribosomes link amino acids together in the order s ...

assembly onto the mRNA as it acts as a binding site for the

eukaryotic initiation factor Eukaryotic initiation factors (eIFs) are proteins or protein complexes involved in the initiation phase of eukaryotic translation. These proteins help stabilize the formation of ribosomal preinitiation complexes around the start codon and are an ...

eIF4F. Once eIF4F is bound to the mRNA this protein complex interacts with the poly(A) binding protein which is present within the 3′ UTR and results in mRNA circularization. This multiprotein-mRNA complex then recruits the ribosome subunits and scans the mRNA until it reaches the start codon. Transcription of viral genomes differs from eukaryotes as viral genomes produce mRNA transcripts that lack a 5’ cap site. Despite lacking a cap site viral genes contain a structural element within the 5’ UTR known as an

internal ribosome entry site An internal ribosome entry site, abbreviated IRES, is an RNA element that allows for translation initiation in a cap-independent manner, as part of the greater process of protein synthesis. Initiation of eukaryotic translation nearly always occur ...

(IRES). IRES is a structural element that recruits the 40s ribosome subunit to the mRNA within close proximity of the start codon. RCNMV contains a genome that encodes for two positive sense RNA strands known as RNA1 and RNA2 and both these RNA strands lack a 5’ cap and a 3’ poly (A) tail. RNA1 is required in replication as it encodes for RNA replicase components. This RNA contains structural elements within the 3’ and 5’ UTR that bring about cap independent translation. Unlike RNA1, RNA2 encodes for a movement protein (MP) and the mRNA of RNA2 contains no structural elements within the UTRs that can bring about cap independent translation. The translation of the mRNA of RNA2 is linked with RNA2 replication. RNA1 contains several structural elements within its

s (UTRs) which allow for cap independent translation. The 3′ UTR contains a translation enhancer element, 3′TE-DR1 that brings about cap independent translation (a Cap-independent translation element) and is predicted to have 5

stem loop Stem-loops are nucleic acid secondary structural elements which form via intramolecular base pairing in single-stranded DNA or RNA. They are also referred to as hairpins or hairpin loops. A stem-loop occurs when two regions of the same nucleic ...

structures. For 3′TE-DR1 to have an effect on translation it was shown that both specific sequences and structures need to be present within the 5′UTR of RNA1. The 5′UTR was shown to contain four stem loop structures where all of these secondary structures contribute to affecting translation efficiently. Stem loop1 has been shown to be the most important secondary structure within the 5′UTR as mutating or removing this stem loop structure significantly decreases translation efficiency and this effect can be overcome by compensatory mutations. The secondary structures within the 5′UTR was shown to also play a role in RNA stability. Removal of the secondary structure correlated with a decrease in RNA stability. One possibly explanation for this is that the secondary structure may protect the RNA from 5′–3′

exonuclease Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3′ or the 5′ end occurs. Its close relative is th ...

activity. In RNA1 both structural elements within the 3′ and 5′ UTR are required to translation to occur as the 3′UTR contains the translation enhancer element and the 5′UTR contains structures that aid in recruiting translation factors but also act to increase RNA stability. The 3′UTR of RNA2 contains a Y-shaped Cap-independent translation element. This structure and several downstream stem-loops are required for synthesis of the negative strand RNA.

References

External links

Rfam entry for 3′TE-DR1 translation enhancer element

Rfam entry for 5′UTR enhancer element
{{DEFAULTSORT:Rcnmv Translation Enhancer Elements Viral plant pathogens and diseases Tombusviridae Non-coding RNA Viral genes