PPR proteins – orchestrators of organelle RNA metabolism

Rovira, Aleix Gorchs; Smith, Alison G.

doi:10.1111/ppl.12950

Cited by 57 publications

(49 citation statements)

References 56 publications

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“…[1][2][3][4][5][6][7][8][9][10] In both the Pfam 11 and the SCOP (Structural Classification of Proteins) classification 12 of protein domains, TPR and PPR are recognized as allalpha domains and appear superficially similar; however, they are distinct in sequence ( Figure 1) and in their interactions with specific ligands, suggesting that apparently small differences in length and sequence in the members of the tricopeptide family may have important consequences on biological roles. While the TPR domains have been recognized for their role in proteinprotein interactions, 3 the PPR proteins are mostly involved in various steps of RNA metabolism in mitochondria and plant chloroplasts, [13][14][15] and have received attention relatively recently, even though they appear to be more prevalent in nature. 4,5 The 3-dimensional (3D) structures of a substantial number of PPR domains have been solved, which provided a glimpse to their ability to bind to type-specific substrates and ligands.…”

Section: Introductionmentioning

confidence: 99%

The Nature and Arrangement of Pentatricopeptide Domains and the Linker Sequences Between Them

Barik

2020

Bioinform Biol Insights

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The tricopeptide (amino acid number in the 30s) repeats constitute some of the most common amino acid repeats in proteins of diverse organisms. The most important representatives of this class are the 34-residue and 35-residue repeats, eponymously known as tetratricopeptide repeat (TPR) and pentatricopeptide repeat (PPR), respectively. The unit motif of both consists of a pair of alpha helices. As members of the large, all-helical repeat classes, TPR and PPR share structural similarities, but also play specific roles in protein function. In this study, a comprehensive bioinformatic analysis of the PPR units and the linkers that connect them was conducted. The results suggested the existence of PPR repeats of various formats, as well as smaller, PPR-unrelated repeats. Besides their length, these repeats differed in amino acid arrangements and location of key amino acids. These findings provide a broader and unified perspective of the pentatricopeptide family while raising provocative questions about the assembly and evolution of these domains.

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Section: Introductionmentioning

confidence: 99%

The Nature and Arrangement of Pentatricopeptide Domains and the Linker Sequences Between Them

Barik

2020

Bioinform Biol Insights

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“…The CRM domain proteins play key roles in plant growth and development [3,32]. Many intron splicing factors have been identified in different plants, involving PPR family and CRM family proteins [33,34]. For example, WSL4, SOT5, and THA8 affect chloroplast genes' intron splicing in rice, A. thaliana, and maize, respectively [35][36][37].…”

Section: Discussionmentioning

confidence: 99%

Characterization of the CRM Gene Family and Elucidating the Function of OsCFM2 in Rice

et al. 2020

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The chloroplast RNA splicing and ribosome maturation (CRM) domain-containing proteins regulate the expression of chloroplast or mitochondrial genes that influence plant growth and development. Although 14 CRM domain proteins have previously been identified in rice, there are few studies of these gene expression patterns in various tissues and under abiotic stress. In our study, we found that 14 CRM domain-containing proteins have a conservative motif1. Under salt stress, the expression levels of 14 CRM genes were downregulated. However, under drought and cold stress, the expression level of some CRM genes was increased. The analysis of gene expression patterns showed that 14 CRM genes were expressed in all tissues but especially highly expressed in leaves. In addition, we analyzed the functions of OsCFM2 and found that this protein influences chloroplast development by regulating the splicing of a group I and five group II introns. Our study provides information for the function analysis of CRM domain-containing proteins in rice.

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“…cluster 52). While the former three are typical of retrotransposons, pentatricopeptide repeat-containing proteins are commonly found in plants at large numbers (100s in the Arabidopsis and rice genomes), putatively involved in RNA editing 48 . Besides these overall commonalities, some high copy sub-scaffolds appear to also be functionally enriched for certain genes and their functions not related to transposition.…”

Section: High-copy Sub-scaffolds Are Enriched In Mobile Elementsmentioning

confidence: 99%

Chromosome-scale assembly of the coral endosymbiontSymbiodinium microadriaticumgenome provides insight into the unique biology of dinoflagellate chromosomes

Nand

Salazar

et al. 2020

Preprint

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AbstractDinoflagellates are major primary producers in the world’s oceans, the cause of harmful algal blooms, and endosymbionts of marine invertebrates. Much remains to be understood about their biology including their peculiar crystalline chromosomes. Here we used Hi-C to order short read-based sub-scaffolds into 94 chromosome-scale scaffolds of the genome of the coral endosymbiont Symbiodinium microadriaticum. Hi-C data show that chromosomes are folded as linear rods within which loci separated by up to several Mb are highly packed. Each chromosome is composed of a series of structural domains separated by boundaries. Genes are enriched towards the ends of chromosomes and are arranged in unidirectional blocks that alternate between top and bottom strands. Strikingly, the boundaries of chromosomal domains are positioned at sites where transcription of two gene blocks converges, indicating a correlation between gene orientation, transcription and chromosome folding. Some chromosomes are enriched for genes involved in specific biological processes (e.g., photosynthesis, and nitrogen-cycling), and functionally related genes tend to co-occur at adjacent sites in the genome. All chromosomes contain several repeated segments that are enriched in mobile elements. The assembly of the S. microadriaticum genome and initial description of its genetic and spatial organization provide a foundation for deeper exploration of the extraordinary biology of dinoflagellates and their chromosomes.

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PPR proteins – orchestrators of organelle RNA metabolism

Cited by 57 publications

References 56 publications

The Nature and Arrangement of Pentatricopeptide Domains and the Linker Sequences Between Them

The Nature and Arrangement of Pentatricopeptide Domains and the Linker Sequences Between Them

Characterization of the CRM Gene Family and Elucidating the Function of OsCFM2 in Rice

Chromosome-scale assembly of the coral endosymbiontSymbiodinium microadriaticumgenome provides insight into the unique biology of dinoflagellate chromosomes

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