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Chloroplast RNA Metabolism and Biology
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Chloroplast RNA Metabolism and Biology

A special issue of Plants (ISSN 2223-7747).

Deadline for manuscript submissions: closed (31 January 2020) | Viewed by 37841

Special Issue Editors

Dr. Olivier Vallon

E-Mail Website
Guest Editor
UMR 7141, Institut de Biologie Physico-Chimique, CNRS/Sorbonne Université, F-75005 Paris, France
Interests: photosynthesis; chloroplast; gene expression; genomics; RNA-binding proteins; algae
Dr. Yves Choquet

E-Mail Website
Guest Editor
UMR 7141, Institut de Biologie Physico-Chimique, CNRS/Sorbonne Université, F-75005 Paris, France
Interests: photosynthesis; chloroplast; gene expression; genomics; RNA-binding proteins; algae

Special Issue Information

Dear Colleagues,

The bioenergetic organelles (chloroplast and mitochondria) both harbour their own genome, which is a relic of that of the original endosymbiont (resp. a cyanobacterium and an a-proteobacterium) after billions of years of gene loss and gene transfer to the nucleus. Accompanying this reductive evolution, most of the regulatory functions have been transferred to the nucleus, which encodes hundreds of Organelle Trans-Acting Factors (OTAFs) that, after being imported into the organelles, control the level of expression of the remaining genes. In the chloroplast, all steps of gene expression, from transcription to translation and including splicing, editing, nucleolytic maturation, and recruitment to the translation initiation complex, involve OTAFs, most of which act post-transcriptionally to govern RNA metabolism. Some OTAFs have general functions and bind to many transcripts, while other recognize specific sequences. The specificity of binding is often achieved through the modularity of the protein, which is composed of a short motif repeated up to dozens of times: as each motif shows specificity towards a certain nucleotide base, the specificity of the protein is dictated by that of its repeats.

The result is a huge network of OTAFs and RNA targets whose dynamics in time allow for the regulation of chloroplast gene expression, for example, as a function of development or environmental signals received by the cell. Understanding the physiology of the chloroplast (and in particular of photosynthesis) requires a comprehensive understanding of the function and specificity of these OTAFs and a precise description of the organellar RNAs, large and small, long- and short-lived. This Special Issue will highlight the latest results in this fast-developping area of organelle biology.

Dr. Olivier Vallon
Dr. Yves Choquet
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • RNA metabolism
  • organelle
  • promoter
  • splicing
  • RNA processing
  • transcriptome
  • translation
  • sRNA
  • RNA-binding proteins
  • PentatricoPeptide Repeat
  • TetatricoPeptide Repeat
  • OctotricoPeptide Repeat
  • RNases
  • photosynthesis
  • regulation

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Published Papers (8 papers)

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Research

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15 pages, 3043 KiB  
Article
The Chloroplast Ribonucleoprotein CP33B Quantitatively Binds the psbA mRNA
by Marlene Teubner, Benjamin Lenzen, Lucas Bernal Espenberger, Janina Fuss, Jörg Nickelsen, Kirsten Krause, Hannes Ruwe and Christian Schmitz-Linneweber
Plants 2020, 9(3), 367; https://doi.org/10.3390/plants9030367 - 17 Mar 2020
Cited by 3 | Viewed by 3156
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Chloroplast RNA Metabolism and Biology)
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13 pages, 1336 KiB  
Article
Secondary Structure of Chloroplast mRNAs In Vivo and In Vitro
by Piotr Gawroński, Aleksandra Pałac and Lars B. Scharff
Plants 2020, 9(3), 323; https://doi.org/10.3390/plants9030323 - 4 Mar 2020
Cited by 8 | Viewed by 4533
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Chloroplast RNA Metabolism and Biology)
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16 pages, 6613 KiB  
Article
The Analysis of the Editing Defects in the dyw2 Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins
by Bastien Malbert, Matthias Burger, Mauricio Lopez-Obando, Kevin Baudry, Alexandra Launay-Avon, Barbara Härtel, Daniil Verbitskiy, Anja Jörg, Richard Berthomé, Claire Lurin, Mizuki Takenaka and Etienne Delannoy
Plants 2020, 9(2), 280; https://doi.org/10.3390/plants9020280 - 21 Feb 2020
Cited by 18 | Viewed by 4550
Abstract
C to U editing is one of the post-transcriptional steps which are required for the proper expression of chloroplast and mitochondrial genes in plants. It depends on several proteins acting together which include the PLS-class pentatricopeptide repeat proteins (PPR). DYW2 was recently shown [...] Read more.
C to U editing is one of the post-transcriptional steps which are required for the proper expression of chloroplast and mitochondrial genes in plants. It depends on several proteins acting together which include the PLS-class pentatricopeptide repeat proteins (PPR). DYW2 was recently shown to be required for the editing of many sites in both organelles. In particular almost all the sites associated with the E+ subfamily of PPR proteins are depending on DYW2, suggesting that DYW2 is required for the function of E+-type PPR proteins. Here we strengthened this link by identifying 16 major editing sites controlled by 3 PPR proteins: OTP90, a DYW-type PPR and PGN and MEF37, 2 E+-type PPR proteins. A re-analysis of the DYW2 editotype showed that the 49 sites known to be associated with the 18 characterized E+-type PPR proteins all depend on DYW2. Considering only the 288 DYW2-dependent editing sites as potential E+-type PPR sites, instead of the 795 known editing sites, improves the performances of binding predictions systems based on the PPR code for E+-type PPR proteins. However, it does not compensate for poor binding predictions. Full article
(This article belongs to the Special Issue Chloroplast RNA Metabolism and Biology)
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9 pages, 1706 KiB  
Article
Functional Analysis of PSRP1, the Chloroplast Homolog of a Cyanobacterial Ribosome Hibernation Factor
by Kevin Swift, Prakitchai Chotewutmontri, Susan Belcher, Rosalind Williams-Carrier and Alice Barkan
Plants 2020, 9(2), 209; https://doi.org/10.3390/plants9020209 - 6 Feb 2020
Cited by 4 | Viewed by 3101
Abstract
Bacterial ribosome hibernation factors sequester ribosomes in an inactive state during the stationary phase and in response to stress. The cyanobacterial ribosome hibernation factor LrtA has been suggested to inactivate ribosomes in the dark and to be important for post-stress survival. In this [...] Read more.
Bacterial ribosome hibernation factors sequester ribosomes in an inactive state during the stationary phase and in response to stress. The cyanobacterial ribosome hibernation factor LrtA has been suggested to inactivate ribosomes in the dark and to be important for post-stress survival. In this study, we addressed the hypothesis that Plastid Specific Ribosomal Protein 1 (PSRP1), the chloroplast-localized LrtA homolog in plants, contributes to the global repression of chloroplast translation that occurs when plants are shifted from light to dark. We found that the abundance of PSRP1 and its association with ribosomes were similar in the light and the dark. Maize mutants lacking PSRP1 were phenotypically normal under standard laboratory growth conditions. Furthermore, the absence of PSRP1 did not alter the distribution of chloroplast ribosomes among monosomes and polysomes in the light or in the dark, and did not affect the light-regulated synthesis of the chloroplast psbA gene product. These results suggest that PSRP1 does not play a significant role in the regulation of chloroplast translation by light. As such, the physiological driving force for the retention of PSRP1 during chloroplast evolution remains unclear. Full article
(This article belongs to the Special Issue Chloroplast RNA Metabolism and Biology)
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13 pages, 1803 KiB  
Article
Exploring the Link between Photosystem II Assembly and Translation of the Chloroplast psbA mRNA
by Prakitchai Chotewutmontri, Rosalind Williams-Carrier and Alice Barkan
Plants 2020, 9(2), 152; https://doi.org/10.3390/plants9020152 - 25 Jan 2020
Cited by 27 | Viewed by 5097
Abstract
Photosystem II (PSII) in chloroplasts and cyanobacteria contains approximately fifteen core proteins, which organize numerous pigments and prosthetic groups that mediate the light-driven water-splitting activity that drives oxygenic photosynthesis. The PSII reaction center protein D1 is subject to photodamage, whose repair requires degradation [...] Read more.
Photosystem II (PSII) in chloroplasts and cyanobacteria contains approximately fifteen core proteins, which organize numerous pigments and prosthetic groups that mediate the light-driven water-splitting activity that drives oxygenic photosynthesis. The PSII reaction center protein D1 is subject to photodamage, whose repair requires degradation of damaged D1 and its replacement with nascent D1. Mechanisms that couple D1 synthesis with PSII assembly and repair are poorly understood. We address this question by using ribosome profiling to analyze the translation of chloroplast mRNAs in maize and Arabidopsis mutants with defects in PSII assembly. We found that OHP1, OHP2, and HCF244, which comprise a recently elucidated complex involved in PSII assembly and repair, are each required for the recruitment of ribosomes to psbA mRNA, which encodes D1. By contrast, HCF136, which acts upstream of the OHP1/OHP2/HCF244 complex during PSII assembly, does not have this effect. The fact that the OHP1/OHP2/HCF244 complex brings D1 into proximity with three proteins with dual roles in PSII assembly and psbA ribosome recruitment suggests that this complex is the hub of a translational autoregulatory mechanism that coordinates D1 synthesis with need for nascent D1 during PSII biogenesis and repair. Full article
(This article belongs to the Special Issue Chloroplast RNA Metabolism and Biology)
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Review

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11 pages, 2146 KiB  
Review
Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression
by Amber M. Hotto, David B. Stern and Gadi Schuster
Plants 2020, 9(3), 334; https://doi.org/10.3390/plants9030334 - 5 Mar 2020
Cited by 7 | Viewed by 4949
Abstract
RNA quality control is an indispensable but poorly understood process that enables organisms to distinguish functional RNAs from nonfunctional or inhibitory ones. In chloroplasts, whose gene expression activities are required for photosynthesis, retrograde signaling, and plant development, RNA quality control is of paramount [...] Read more.
RNA quality control is an indispensable but poorly understood process that enables organisms to distinguish functional RNAs from nonfunctional or inhibitory ones. In chloroplasts, whose gene expression activities are required for photosynthesis, retrograde signaling, and plant development, RNA quality control is of paramount importance, as transcription is relatively unregulated. The functional RNA population is distilled from this initial transcriptome by a combination of RNA-binding proteins and ribonucleases. One of the key enzymes is RNase J, a 5′→3′ exoribonuclease and an endoribonuclease that has been shown to trim 5′ RNA termini and eliminate deleterious antisense RNA. In the absence of RNase J, embryo development cannot be completed. Land plant RNase J contains a highly conserved C-terminal domain that is found in GT-1 DNA-binding transcription factors and is not present in its bacterial, archaeal, and algal counterparts. The GT-1 domain may confer specificity through DNA and/or RNA binding and/or protein–protein interactions and thus be an element in the mechanisms that identify target transcripts among diverse RNA populations. Further understanding of chloroplast RNA quality control relies on discovering how RNase J is regulated and how its specificity is imparted. Full article
(This article belongs to the Special Issue Chloroplast RNA Metabolism and Biology)
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17 pages, 4422 KiB  
Review
Arabidopsis RanBP2-Type Zinc Finger Proteins Related to Chloroplast RNA Editing Factor OZ1
by Andrew B. Gipson, Ludovic Giloteaux, Maureen R. Hanson and Stephane Bentolila
Plants 2020, 9(3), 307; https://doi.org/10.3390/plants9030307 - 1 Mar 2020
Cited by 6 | Viewed by 5302
Abstract
OZ1, an RNA editing factor that controls the editing of 14 cytidine targets in Arabidopsis chloroplasts, contains two RanBP2-type zinc finger (Znf) domains. The RanBP2 Znf is a C4-type member of the broader zinc finger family with unique functions and an unusually diverse [...] Read more.
OZ1, an RNA editing factor that controls the editing of 14 cytidine targets in Arabidopsis chloroplasts, contains two RanBP2-type zinc finger (Znf) domains. The RanBP2 Znf is a C4-type member of the broader zinc finger family with unique functions and an unusually diverse distribution in plants. The domain can mediate interactions with proteins or RNA and appears in protein types such as proteases, RNA editing factors, and chromatin modifiers; however, few characterized Arabidopsis proteins containing RanBP2 Znfs have been studied specifically with the domain in mind. In humans, RanBP2 Znf-containing proteins are involved in RNA splicing, transport, or transcription initiation. We present a phylogenetic overview of Arabidopsis RanBP2 Znf proteins and the functional niches that these proteins occupy in plants. OZ1 and its four-member family represent a branch of this family with major impact on the RNA biology of chloroplasts and mitochondria in Arabidopsis. We discuss what is known about other plant proteins carrying the RanBP2 Znf domain and point out how phylogenetic information can provide clues to functions of uncharacterized Znf proteins. Full article
(This article belongs to the Special Issue Chloroplast RNA Metabolism and Biology)
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15 pages, 1550 KiB  
Review
Co-Translational Protein Folding and Sorting in Chloroplasts
by Fabian Ries, Claudia Herkt and Felix Willmund
Plants 2020, 9(2), 214; https://doi.org/10.3390/plants9020214 - 7 Feb 2020
Cited by 24 | Viewed by 6065
Abstract
Cells depend on the continuous renewal of their proteome composition during the cell cycle and in order to replace aberrant proteins or to react to changing environmental conditions. In higher eukaryotes, protein synthesis is achieved by up to five million ribosomes per cell. [...] Read more.
Cells depend on the continuous renewal of their proteome composition during the cell cycle and in order to replace aberrant proteins or to react to changing environmental conditions. In higher eukaryotes, protein synthesis is achieved by up to five million ribosomes per cell. With the fast kinetics of translation, the large number of newly made proteins generates a substantial burden for protein homeostasis and requires a highly orchestrated cascade of factors promoting folding, sorting and final maturation. Several of the involved factors directly bind to translating ribosomes for the early processing of emerging nascent polypeptides and the translocation of ribosome nascent chain complexes to target membranes. In plant cells, protein synthesis also occurs in chloroplasts serving the expression of a relatively small set of 60–100 protein-coding genes. However, most of these proteins, together with nucleus-derived subunits, form central complexes majorly involved in the essential processes of photosynthetic light reaction, carbon fixation, metabolism and gene expression. Biogenesis of these heterogenic complexes adds an additional level of complexity for protein biogenesis. In this review, we summarize the current knowledge about co-translationally binding factors in chloroplasts and discuss their role in protein folding and ribosome translocation to thylakoid membranes. Full article
(This article belongs to the Special Issue Chloroplast RNA Metabolism and Biology)
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