Mechanisms of Dual-Targeting Arabidopsis HEMERA to the Chloroplasts and Nucleus

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Nevarez, Patrick Andrew


Benfey, Philip N

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When a plant emerges from the soil, it faces a critical developmental transition from utilizing stored energy to grow rapidly toward the light, to developing chloroplasts and beginning photosynthesis. While it is known that this process involves massive transcriptional reprogramming of the nuclear and plastidial genomes, the connections between chloroplast development and nuclear light signaling events are not well understood. One very promising target for investigating these connections is HEMERA (HMR), a dual-localized regulatory protein that is found in both nuclei and chloroplasts. HMR was previously identified as pTAC12, an essential component of the plastid-encoded RNA polymerase complex responsible for transcription of chloroplast photosynthetic genes. In the nucleus, HMR acts within the phytochrome signaling pathway as a transcriptional co-activator of a subset of growth-relevant genes in response to light, to regulate the elongation of the embryonic stem, or hypocotyl. HMR’s combination of roles in the nucleus and chloroplasts are dramatically demonstrated by the phenotypes of the hmr mutant, with a long hypocotyl and albino leaves when grown in the light.

While the functions of HMR in each compartment have been studied separately, the mechanisms by which the HMR protein is targeted to each compartment have not yet been determined. To address this, I characterized the localization signals of HMR with a combination of in vitro approaches and characterization of transgenic Arabidopsis lines. These experiments revealed that HMR has a cleavable N-terminal chloroplast transit peptide within its first 50 amino acids, while two predicted nuclear localization signals proved not to be highly functional. Surprisingly, HMR in the chloroplasts and nucleus appeared to both be the same cleaved form of the protein. We thus identified the mature form of HMR by mass spectrometry, finding that it begins from lysine as the result of transit peptide cleavage and possibly additional N-terminal processing. Through GST pull-down assays, we determined that this mature form of HMR was fully capable of interacting light signaling components. However, analysis of transgenic lines showed that expression of mature HMR alone could not complement the long-hypocotyl phenotype of the hmr mutant. Analysis of the transcription of HMR nuclear target genes confirmed that mature HMR lacked nuclear functionality.

Further investigation revealed that mature HMR does not accumulate within the nucleus, most likely as a result of its nonfunctional nuclear localization signals. However, addition of the transit peptide from the small subunit of Rubisco fully restored nuclear accumulation and function of mature HMR in Arabidopsis. Additional experiments testing the localization of a simple model of dual-targeted proteins with two types of localization signal showed that transit peptides might take priority over nuclear localization signals. These results together suggest an unexpected model of localization where HMR is first targeted to the chloroplasts, and then it is subsequently re-localized to the nucleus, thus connecting its nuclear and plastidial functions. Further investigation of this proposed retrograde plastid-to-nucleus translocation pathway promises to shed additional light on the link between nuclear light signaling events and chloroplast development.





Nevarez, Patrick Andrew (2016). Mechanisms of Dual-Targeting Arabidopsis HEMERA to the Chloroplasts and Nucleus. Dissertation, Duke University. Retrieved from


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