Maize chlorotic mottle virus (MCMV) is the key player of Maize Lethal Necrosis Disease (MLND). MLND is caused by the co-infection and synergistic interaction of MCMV and any potyvirus that infects grasses. Recent outbreaks of MLND have ravaged maize fields in Kenya and neighboring regions of East Africa. The catastrophic economic losses brought back the interest of stakeholders to learn more about the synergistic interaction between MCMV and potyviruses and find ways to use this knowledge to create MLND resistant lines.

MCMV is a positive-sense single-stranded RNA virus from the Tombusviridae family. Similarly to other members of the Tombusviridae family, MCMV does not have a 5'-cap or a poly (A) tail and must use alternative mechanisms to translate viral proteins. The lack of a 5'-cap in the viral RNA does not prevent it from interacting with host translation factors. Instead of a 5'-cap, most tombusvirids are known to employ unconventional mechanisms to sequester translation factors to the viral RNA. One mechanism of recruiting host's translation factors is 3'-cap-independent translation elements (3'-CITEs). 3'-CITEs are secondary structures located at the 3'-end of the virus genome used to recruit the translation initiation machinery. The work presented in this dissertation revolves around finding out the translation initiation control elements of MCMV RNA.

The unearthing of MCMV's translation initiation process began with a series of deletions at the 3'-end of the virus genome. The genome sequence mapping indicated that there was an essential sequence for virus translation between nucleotides 4164 to 4333. Structural RNA probing of this region showed the presence of a panicum mosaic virus 3-CITE (PTE) -like structure located in the 3'-untranslated region (UTR) of the viral RNA. Similar to other PTEs, the MCMV 3'-CITE secondary structure was composed of a hammer-like helix structure that branched out into two side loops connected by a pyrimidine bridge. On the main stem of the hammer-like structure is a single-stranded bulge that is hyper-modified by SHAPE probing reagents in the presence of magnesium. PTEs are characterized by a pyrimidine rich bridge composed of cytosines and a purine-rich bulge that interacts with each other forming a pseudoknot. In contrary to most PTEs, the MTE was predicted to have a weak pseudoknot.

The PTE C-G pseudoknot formation enables the virus to interact with the cap-binding pocket of eIF4E. Although the establishment of a suitable pseudoknot between the C-G domains of MTE is questionable, MTE interacts with initiation factor 4E. Similar to other 3'CITEs, the MTE used long-distance base-pairing to bring the translation machinery to the 5' end. The eIF4E-MTE RNA-protein interaction model was investigated by mutating both the RNA and the protein. Comparison of electrophoretic mobility shift assays (EMSA) results using mutated eIF4E with other PTE-like structure indicated that even though MCMV interact with eIF4E, it might use a mechanism that has yet to be characterized.