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Functional diversity of Arabidopsis organelle‐localized RNA ‐recognition motif‐containing proteins

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RNA‐Binding Proteins (RBPs) play key roles in plant gene expression and regulation. RBPs contain a variety of RNA‐binding motifs, the most abundant and most widespread one in eukaryotes is the RNA recognition motif (RRM). Many nucleus‐encoded RRM‐containing proteins are transported into chloroplasts and/or mitochondria, and participate in various RNA‐related processes in plant organelles. Loss of these proteins can have a detrimental effect on some critical processes such as photosynthesis and respiration, sometimes leading to lethality. Progress has been made in the last few years in understanding the function of particular organelle‐localized RRM‐containing proteins. Members of the Organelle RRM protein (ORRM, some also characterized as Glycine‐Rich RNA‐Binding Proteins) family and the Chloroplast RiboNucleoProtein (cpRNP) family, are involved in various types of RNA metabolism, including RNA editing, RNA stability and RNA processing. Organelle‐localized RRM proteins also function in plant development and stress responses, in some conditions acting as protein or RNA chaperones. There has been recent progress in characterizing the function of organelle‐localized RRM proteins in RNA‐related processes and how RRM proteins contribute to the normal growth and development of plants. WIREs RNA 2017, 8:e1420. doi: 10.1002/wrna.1420

Phylogenetic tree based on the amino acid sequences of the RRM in RRM‐containing proteins (80 amino acids considered). The subcellular localization of each protein is shown in brackets: C, chloroplast; M, mitochondrion; N, nucleus. Protein alignments were achieved by using Clustal X version 2.1 (http://www.clustal.org/clustal2/) and adjusted manually. The construction of phylogenetic trees was performed with MEGA7 (www.megasoftware.net). For proteins with two RRM, the difference caused by using either RRM for alignment was negligible. Thus, the second RRM was used for alignment. The tree was inferred using the Neighbor‐Joining method, and evolutionary distances were computed using the P‐distance method. All positions containing alignment gaps or missing data were eliminated using pairwise deletion. One‐thousand bootstrap replications were performed to determine the confidence level of the phylogenetic tree topology. The scale bar corresponds to 0.1 substitutions per site. A nuclear protein, flowering time control protein (FCA), was included as an outgroup for phylogenetic tree construction. Colored labels indicate the family name or the function of the protein discussed in the review.
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Functional diversity of organelle‐localized RRM proteins. Organelle‐localized RRM proteins participate in a variety of RNA‐related processes, including RNA editing (I), RNA processing (II) and RNA stability (III). Organelle‐localized RRM protein forms an editosome with other RNA editing factors, illustrated by the circles. Many organelle‐localized RRM proteins are also involved in plant stress response and/or plant development. However, the association between these processes still awaits investigation.
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Complementation of the morphological defects in the orrm4 mutants. Wild‐type, wild‐type Columbia plants; 35S‐ORRM4, orrm4 mutant plants transformed with the coding sequence of ORRM4 under a 35S promoter; 35S‐cORRM4 (amino acids 113–289), orrm4 mutant plants transformed with the C‐terminal GR motif of ORRM4 under a 35S promoter. Left panel: Measurement of flowering‐related traits in the orrm4 mutants, wild‐type plants and the transgenic lines expressing ORRM4 or cORRM4. Days taken for plants to reach these developmental stages: 1st bud, days until visible flower buds in the center of the rosette; stem 1 cm, days until inflorescence stem reached 1 cm in height; first flower, days until first open flower (n = 12). Right panel: Fresh weight of plants grown at 14 h of light per day for 26 and 40 days (n = 10). Student's t‐test; *p < 0.05, **p < 0.01, ***p < 0.001, in comparison to orrm4−/−, n = 12. Error bars represent SE.
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Motif arrangements of RRM proteins in plant organelles. Data are from several studies and also predicted by SMART (http://smart.embl‐heidelberg.de/) . The coding sequences of the RRM protein‐encoding genes were used for analysis.
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Known interactions of ORRM proteins with self and other editing factors. (a) Interaction between chloroplast ORRM proteins and other chloroplast editing factors. (b) Interaction between mitochondrial ORRM proteins and RIP1. Data are from yeast two‐hybrid and bimolecular fluorescence complementation assays. Positive signals are represented by a +, while negative signals are shown by a −. n.d., not determined.
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RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition

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