Hayes Lab

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Our research revolves around understanding mechanisms that regulate chloroplast and mitochondrial transcripts. Every eukaryotic cell must coordinate the expression of a nuclear genome with the genomes present in functionally specialized organelles. One large class of nuclear encoded proteins involved in controlling organelle expression present in most eukaryotes is the pentatricopeptide repeat (PPR) family of proteins. PPR proteins bind ssRNA through a sequence specific mechanism. PPR proteins have been linked to C-to-U RNA editing, RNA maturation, splicing, RNA turnover, and translation. Since PPR proteins have such diverse functions, we are investigating how they alter transcripts in order to create new tools useful for the manipulation of RNAs.

We are currently working on investigating the biochemical mechanism responsible for C-to-U RNA editing in organelles. Proteins from at least 5 different protein families have been linked to RNA editing. The biochemical roles for OZ, RIP, and RRM proteins are under investigation. A model of the C-to-U RNA editing complex is shown below.  


Another focus of the laboratory is the catalytic function of the C-to-U RNA editing complex. Recently the DYW-deaminase has been implicated as an enzyme due its evolutionary coincidinece with RNA editing, structural features, zinc binding, and a requirement for an active site glutamate for function in vivo. Unlike other nucleotide deaminases the DYW deaminase has a second bound zinc ion of unknown function. We are investigating the role of metals in function of this domain. The traditional catalytic mechanism for cytidine deaminase likely shared by the DYW deaminase is shown below. 

Catalytic model

As part of this work we are investigating the role of proteins necessary for RNA editing. Plants with reduced chloroplastic RNA editing capabilities often exhibit albino/virescent phenotyoes due to photosynthetic dysfunctions. A loss of editing function mutant is shown below. This illustrates the importance of RNA editing for plant growth. The albino plants shown below have a diruption in a RNA editing factor.

Albino plant