The Chloroplast Ribonucleoprotein CP33B Quantitatively Binds the psbA mRNA

Marlene Teubner,Hannes Ruwe,Janina Fuss,Lucas Bernal Espenberger,Benjamin Lenzen,Jörg Nickelsen,Kirsten Krause,Christian Schmitz-Linneweber

doi:10.3390/plants9030367

Marlene Teubner, Hannes Ruwe + Show 6 more

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https://doi.org/10.3390/plants9030367

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Abstract

Chloroplast RNAs are stabilized and processed by a multitude of nuclear-encoded RNA-binding proteins, often in response to external stimuli like light and temperature. A particularly interesting RNA-based regulation occurs with the psbA mRNA, which shows light-dependent translation. Recently, the chloroplast ribonucleoprotein CP33B was identified as a ligand of the psbA mRNA. We here characterized the interaction of CP33B with chloroplast RNAs in greater detail using a combination of RIP-chip, quantitative dot-blot, and RNA-Bind-n-Seq experiments. We demonstrate that CP33B prefers psbA over all other chloroplast RNAs and associates with the vast majority of the psbA transcript pool. The RNA sequence target motif, determined in vitro, does not fully explain CP33B’s preference for psbA, suggesting that there are other determinants of specificity in vivo.

Highlights

The maturation and translation of chloroplast RNAs depends on numerous RNA-binding proteins (RBPs)
In addition to PPR proteins, several smaller RBP families exist in the chloroplast, including the family of chloroplast ribonucleoproteins, whose members are extremely abundant, bind multiple mRNAs, and which are regulated in response to various biotic and abiotic signals [2]
This is supported by the recent finding that a maize orthologue of CP33B was isolated from chloroplast stroma by precipitating the psbA mRNA [9]

Summary

Introduction

The maturation and translation of chloroplast RNAs depends on numerous RNA-binding proteins (RBPs). All RBPs involved in chloroplast RNA metabolism are encoded in the nucleus and are post-translationally imported into plastids. In addition to PPR proteins, several smaller RBP families exist in the chloroplast, including the family of chloroplast ribonucleoproteins (cpRNPs), whose members are extremely abundant, bind multiple mRNAs, and which are regulated in response to various biotic and abiotic signals [2]. CpRNPs are able to interact with different nucleic acids (ssDNA, dsDNA and RNA) [3,4], but the strongest association in vitro is with ribonucleic acids [5]. In vitro and in vivo interactions with specific plastid mRNAs were demonstrated [6], cumulating in transcriptome-wide binding studies that showed a broad range

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