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
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) ha...
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MDPI AG
2020-08-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/16/5633 |
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| author | Benjamin Lenzen Thilo Rühle Marie-Kristin Lehniger Ayako Okuzaki Mathias Labs Jose M. Muino Uwe Ohler Dario Leister Christian Schmitz-Linneweber |
| author_facet | Benjamin Lenzen Thilo Rühle Marie-Kristin Lehniger Ayako Okuzaki Mathias Labs Jose M. Muino Uwe Ohler Dario Leister Christian Schmitz-Linneweber |
| author_sort | Benjamin Lenzen |
| collection | DOAJ |
| description | 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 <i>ndh</i> mRNAs are all down-regulated in <i>cp31a</i> 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. |
| first_indexed | 2024-03-10T17:52:41Z |
| format | Article |
| id | doaj.art-4b25e0800fa14cc8b96086a682417a05 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T17:52:41Z |
| publishDate | 2020-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-4b25e0800fa14cc8b96086a682417a052023-11-20T09:17:00ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-08-012116563310.3390/ijms21165633The 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 AccumulationBenjamin Lenzen0Thilo Rühle1Marie-Kristin Lehniger2Ayako Okuzaki3Mathias Labs4Jose M. Muino5Uwe Ohler6Dario Leister7Christian Schmitz-Linneweber8Molecular Genetics, Humboldt-University Berlin, 10115 Berlin, GermanyPlant Molecular Biology, Department of Biology, Ludwig Maximilian University of Munich, 82152 Munich, GermanyMolecular Genetics, Humboldt-University Berlin, 10115 Berlin, GermanyMolecular Genetics, Humboldt-University Berlin, 10115 Berlin, GermanyPlant Molecular Biology, Department of Biology, Ludwig Maximilian University of Munich, 82152 Munich, GermanyComputational Regulatory Genomics, Humboldt-University Berlin/Max Delbrück Centre for Molecular Medicine, 10115 Berlin, GermanyComputational Regulatory Genomics, Humboldt-University Berlin/Max Delbrück Centre for Molecular Medicine, 10115 Berlin, GermanyPlant Molecular Biology, Department of Biology, Ludwig Maximilian University of Munich, 82152 Munich, GermanyMolecular Genetics, Humboldt-University Berlin, 10115 Berlin, GermanyChloroplast 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 <i>ndh</i> mRNAs are all down-regulated in <i>cp31a</i> 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.https://www.mdpi.com/1422-0067/21/16/5633chloroplastRNA processingRNA bindingNDH complexRRMorganelle |
| spellingShingle | Benjamin Lenzen Thilo Rühle Marie-Kristin Lehniger Ayako Okuzaki Mathias Labs Jose M. Muino Uwe Ohler Dario Leister Christian Schmitz-Linneweber 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 chloroplast RNA processing RNA binding NDH complex RRM organelle |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | chloroplast RNA processing RNA binding NDH complex RRM organelle |
| url | https://www.mdpi.com/1422-0067/21/16/5633 |
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