Secondary Structure of Chloroplast mRNAs In Vivo and In Vitro.

Piotr Gawroński,Aleksandra Pałac,Lars B Scharff

doi:10.3390/plants9030323

Piotr Gawroński, Aleksandra Pałac + Show 1 more

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https://doi.org/10.3390/plants9030323

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Abstract

mRNA secondary structure can influence gene expression, e.g., by influencing translation initiation. The probing of in vivo mRNA secondary structures is therefore necessary to understand what determines the efficiency and regulation of gene expression. Here, in vivo mRNA secondary structure was analyzed using dimethyl sulfate (DMS)-MaPseq and compared to in vitro-folded RNA. We used an approach to analyze specific, full-length transcripts. To test this approach, we chose low, medium, and high abundant mRNAs. We included both monocistronic and multicistronic transcripts. Because of the slightly alkaline pH of the chloroplast stroma, we could probe all four nucleotides with DMS. The structural information gained was evaluated using the known structure of the plastid 16S rRNA. This demonstrated that the results obtained for adenosines and cytidines were more reliable than for guanosines and uridines. The majority of mRNAs analyzed were less structured in vivo than in vitro. The in vivo secondary structure of the translation initiation region of most tested genes appears to be optimized for high translation efficiency.

Highlights

RNA secondary structure in plastids has diverse important functions
The mRNA secondary structure of the translation initiation region likely influences the efficiency of translation initiation [8,9], as it is described for E. coli [10,11]
Chloroplast in vivo mRNA secondary structure was analyzed in young Arabidopsis thaliana plants

Summary

Introduction

RNA secondary structure in plastids has diverse important functions. It is crucial for ribosome structure and function [1,2,3] as well as for tRNA function [4]. Besides rRNAs and tRNAs, so far, no other functional non-coding RNAs have been described in plastids. Plastid RNase P and signal recognition particle (SRP) lack the RNA component [5,6]. The RNA secondary structure is important for the function of plastid mRNAs. Start codons can be distinguished from other AUGs by local minima of the mRNA secondary structure [7,8,9]. The mRNA secondary structure of the translation initiation region likely influences the efficiency of translation initiation [8,9], as it is described for E. coli [10,11]

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