Cap-independent translation element

{{Short description|RNA sequence found in some plant viruses}}

In molecular biology, a cap-independent translation element (CITE or 3'CITE) is an RNA sequence found in the 3'UTR of many RNA plant viruses.

Eukaryotic mRNAs contain a 5' cap structure which is required for efficient binding of translation initiation factors. Many viral mRNAs lack the 5' cap, animal virus mRNAs often contain an internal ribosome entry site which functions in translation initiation. Many plant viral mRNAs contain a cap-independent translation element.{{cite journal|last=Miller|first=WA|author2=Wang, Z |author3=Treder, K |title=The amazing diversity of cap-independent translation elements in the 3'-untranslated regions of plant viral RNAs.|journal=Biochemical Society Transactions|date=Dec 2007|volume=35|issue=Pt 6|pages=1629–1633|pmid=18031280|doi=10.1042/BST0351629|pmc=3081161}} These elements mediate initiation of translation of the proteins encoded in the mRNA by either recruiting translation initiation factors or the 60S ribosomal subunit to the viral RNA.{{cite journal|last=Nicholson|first=BL|author2=White, KA|title=3' Cap-independent translation enhancers of positive-strand RNA plant viruses.|journal=Current Opinion in Virology|date=Nov 2011|volume=1|issue=5|pages=373–380|pmid=22440838|doi=10.1016/j.coviro.2011.10.002}} In RNA2 of Red clover necrotic mosaic virus (RCNMV) the cap-independent translation element is required for negative strand RNA synthesis.{{cite journal|last=An|first=M|author2=Iwakawa, HO |author3=Mine, A |author4=Kaido, M |author5=Mise, K |author6= Okuno, T |title=A Y-shaped RNA structure in the 3' untranslated region together with the trans-activator and core promoter of Red clover necrotic mosaic virus RNA2 is required for its negative-strand RNA synthesis.|journal=Virology|date=Sep 15, 2010|volume=405|issue=1|pages=100–109|pmid=20561661|doi=10.1016/j.virol.2010.05.022|url=https://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/128764/1/j.virol.2010.05.022.pdf|doi-access=free}}

There are many different structural classes of cap-independent translation element, with no apparent structural or sequence similarity:

class="wikitable"
Structure	Example species
TED (translation enhancer domain)	Satellite tobacco necrosis virus (STNV)
BTE (BYDV-like translation element)	Barley yellow dwarf virus (BYDV)
PTE (PMV-like translation element)	Panicum mosaic virus (PMV)
TSS (T-shaped structure)	Turnip crinkle virus (TCV)
Y-shaped	Tomato bushy stunt virus (TBSV)
I-shaped	Maize necrotic streak virus (MNeSV)