UC Riverside

Chloroplasts are essential semi-autonomous organelles that regulate energy production, metabolites synthesis, signal transduction, and stress response in plants and algae. They are responsible for photosynthesis, a process that converts carbon dioxide and water to sugars and oxygen, using light to support nearly all organisms on Earth. Despite their functional importance and their ability to perform transcription and translation within themselves, the chloroplast genome size is very small. Consequently, proper function of the chloroplasts largely relies on anterograde signaling from the nucleus. The mechanisms that regulate the import of nucleus-encoded proteins into chloroplasts have been extensively studied. However, much less is known about nucleus-encoded RNAs imported into chloroplasts, and it has been unclear whether chloroplast RNAs are modified for their proper function. In addition to their function in energy production, chloroplasts are also significant in plant defense. Retrograde signaling of the chloroplast can reprogram numerous nucleus-encoded genes which are involved in plant immunity. Chloroplasts are capable of modulating levels of defense-related molecules by controlling photosynthesis.

This project had its beginnings in a study in which our lab discovered the target of a bacterial-induced small RNA: Arabidopsis thaliana protein containing an RNA-binding domain abundant in Apicomplexans (AtRAP). Two separate approaches were taken to further study the function of AtRAP:

1) AtRAP was characterized as the target protein of a siRNA induced by bacteria Pseudomonas syringae pv. tomato (Pst) (avrRpt2). We show that AtRAP acts as a negative regulator of plant defense by using loss-of-function and gain-of-function analysis. AtRAP functions through direct interaction with Low Sulfur Upregulated 2 (LSU2), a positive regulator of plant defense. AtRAP also regulates transcription factor GOLDEN2-LIKE 1 (GLK1) that is involved in plant biotic and abiotic stress responses. Thus, this approach aims to study the functional mechanism of AtRAP in plant immunity.

2) AtRAP was characterized as a chloroplast-localized RNA-binding protein. By characterizing AtRAP-associated RNAs, we discovered a group of nucleus-encoded RNAs, which are translocated into chloroplasts. Further structural analysis suggests that many of these AtRAP-bound chloroplast-localized nuclear RNAs are small nucleolar RNAs (snoRNAs). These nucleus-encoded snoRNAs are imported into chloroplasts, where they methylate chloroplast-encoded rRNAs and mRNAs. Thus, this approach aims to study the translocation and function of nucleus-encoded RNAs, mainly snoRNAs, inside chloroplasts.