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Open AccessArticle

The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation

1
Molecular Genetics, Humboldt-University Berlin, 10115 Berlin, Germany
2
Plant Molecular Biology, Department of Biology, Ludwig Maximilian University of Munich, 82152 Munich, Germany
3
Computational Regulatory Genomics, Humboldt-University Berlin/Max Delbrück Centre for Molecular Medicine, 10115 Berlin, Germany
*
Author to whom correspondence should be addressed.
Current address: College of Agriculture, 6-1-1 Tamagawagakuen, Machida, Tokyo 194-8610, Japan.
Current address: KWS Gateway Research Center, Saint Louis, MO 63132, USA.
Int. J. Mol. Sci. 2020, 21(16), 5633; https://doi.org/10.3390/ijms21165633
Received: 27 June 2020 / Revised: 16 July 2020 / Accepted: 4 August 2020 / Published: 6 August 2020
(This article belongs to the Special Issue Chloroplast Development and Function)
Chloroplast RNA processing requires a large number of nuclear-encoded RNA binding proteins (RBPs) that are imported post-translationally into the organelle. Most of these RBPs are highly specific for one or few target RNAs. By contrast, members of the chloroplast ribonucleoprotein family (cpRNPs) have a wider RNA target range. We here present a quantitative analysis of RNA targets of the cpRNP CP31A using digestion-optimized RNA co-immunoprecipitation with deep sequencing (DO-RIP-seq). This identifies the mRNAs coding for subunits of the chloroplast NAD(P)H dehydrogenase (NDH) complex as main targets for CP31A. We demonstrate using whole-genome gene expression analysis and targeted RNA gel blot hybridization that the ndh mRNAs are all down-regulated in cp31a mutants. This diminishes the activity of the NDH complex. Our findings demonstrate how a chloroplast RNA binding protein can combine functionally related RNAs into one post-transcriptional operon. View Full-Text
Keywords: chloroplast; RNA processing; RNA binding; NDH complex; RRM; organelle; Arabidopsis thaliana chloroplast; RNA processing; RNA binding; NDH complex; RRM; organelle; Arabidopsis thaliana
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MDPI and ACS Style

Lenzen, B.; Rühle, T.; Lehniger, M.-K.; Okuzaki, A.; Labs, M.; Muino, J.M.; Ohler, U.; Leister, D.; Schmitz-Linneweber, C. The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation. Int. J. Mol. Sci. 2020, 21, 5633. https://doi.org/10.3390/ijms21165633

AMA Style

Lenzen B, Rühle T, Lehniger M-K, Okuzaki A, Labs M, Muino JM, Ohler U, Leister D, Schmitz-Linneweber C. The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation. International Journal of Molecular Sciences. 2020; 21(16):5633. https://doi.org/10.3390/ijms21165633

Chicago/Turabian Style

Lenzen, Benjamin; Rühle, Thilo; Lehniger, Marie-Kristin; Okuzaki, Ayako; Labs, Mathias; Muino, Jose M.; Ohler, Uwe; Leister, Dario; Schmitz-Linneweber, Christian. 2020. "The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation" Int. J. Mol. Sci. 21, no. 16: 5633. https://doi.org/10.3390/ijms21165633

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