RNA (New York, N.Y.)Jan 6, 2001

Structure and function of a translation element active in either the beginning or end non-coding regions of RNA

mRNA Technology Weekly Brief ↗PubMed ↗DOI ↗

Updated Apr 2, 2026

Abstract

The 105-nucleotide translation element (TE105) forms a cruciform secondary structure that is essential for efficient translation of uncapped barley yellow dwarf virus RNA.

TE105 is located in the 3' UTR and aids in translation initiation at the closest AUG codon.
Nuclease probing and mutagenesis studies indicate that the TE105 structure consists of four helices and single-stranded regions.
The presence of a longer viral sequence, up to 869 nucleotides, is necessary for complete cap-independent translation in plant cells.
Combining TE105 with a poly(A) tail enables significant translation of uncapped mRNAs in plant cells.
Mutations in all secondary structural elements and most primary sequences are required for cap-independent translation in both UTR contexts.

Simplified

Barley yellow dwarf virus RNA lacks both a 5' cap and a poly(A) tail, yet it is translated efficiently. It contains a cap-independent translation element (TE), located in the 3' UTR, that confers efficient translation initiation at the AUG closest to the 5' end of the mRNA. We propose that the TE must both recruit ribosomes and facilitate 3'-5' communication. To dissect its function, we determined the secondary structure of the TE and roles of domains within it. Nuclease probing and structure-directed mutagenesis revealed that the 105-nt TE (TE105) forms a cruciform secondary structure containing four helices connected by single-stranded regions. TE105 can function in either UTR in wheat germ translation extracts. A longer viral sequence (at most 869 nt) is required for full cap-independent translation in plant cells. However, substantial translation of uncapped mRNAs can be obtained in plant cells with TE105 combined with a poly(A) tail. All secondary structural elements and most primary sequences that were mutated are required for cap-independent translation in the 3' and 5' UTR contexts. A seven-base loop sequence was needed only in the 3' UTR context. Thus, this loop sequence may be involved only in communication between the UTRs and not directly in recruiting translational machinery. This structural and functional analysis provides a framework for understanding an emerging class of cap-independent translation elements distinguished by their location in the 3' UTR.

Structure and function of a translation element active in either the beginning or end non-coding regions of RNA

Abstract

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