Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Theses & dissertations (Interdisciplinary)


Molecular, Cellular, and Developmental Biology

First Advisor

W. Allen Miller


While the presence of a 5' cap and a 3' poly(A) tail are key elements for efficient translation of eukaryotic mRNAs, many viral mRNAs lack one or both of such structures and yet translate efficiently. Owing to the absence of a 5' cap, Barley yellow dwarf virus (BYDV, Luteoviridae family) genomic and subgenomic RNA1 rely on a cap-independent translation element (BTE), which is an RNA domain capable of promoting translation. In contrast to an internal ribosome entry site (IRES), the BTE is located at the 3' end of the viral mRNA, while translation initiation occurs at the 5' end proximal AUG. For its activity, the BTE requires a cis-acting element within the 5' untranslated region (UTR) of the RNA, with which it shares a five base sequence complementarity. We propose that the BTE recruits part of the translation machinery and the long distance base pairing of the BTE to this BTE-complementary loop (BCL)---across 4000 bases---facilitates delivery of the factors from the 3' UTR to the 5' end, where translation initiates.;In this study, we have revealed the importance and the constraints of the long distance 5'-3' interaction, and we have explored the mechanism of ribosome entry into the mRNA. The kissing interaction achieves several important functions: (i) it enables the BYDV viral mRNAs to comply with the eukaryotic requirement of RNA circularization as a prerequisite for recruitment of the translation machinery, (ii) it regulates the loading of the translation machinery onto the mRNA, and (iii) it controls in a unique fashion the efficiency with which the genomic and subgenomic viral mRNAs compete for the host translation machinery, and therefore the ratio of different viral gene products.;Just as with cellular mRNAs, BTE-mediated translation requires 5' end-dependent ribosome scanning to reach the initiation codon. In such a scheme, the long distance interaction must be continuously disrupted by the scanning ribosome, and reformed to allow the delivery of the factors to the next 43S ribosomal complex. We have provided the first evidence suggesting that the initial entry of the ribosomal complex occurs at the 5' end of the uncapped viral mRNA. Due to the structure nature of the BYDV 5' UTRs, the efficiency of ribosome scanning remains highly dependent on the BTE for the delivery of the initiation factors, which are necessary for unwinding of the local 5' end structure. In such a view, the 5' UTR become a rate limiting-factor under low factor availability.;BTE-mediated translation is a novel mechanism for the recruitment of the ribosomes to the mRNA. It differs from cap-dependent translation and known IRESs through its combination of (i) cap-independence, (ii) location in the 3' UTR, and (iii) requirement for scanning from the 5' end of the mRNA.



Digital Repository @ Iowa State University,

Copyright Owner

Aurélie Mamisoa Rakotondrafara



Proquest ID


OCLC Number




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File Size

223 pages