The Chloroplast Trans-Splicing RNA–Protein Supercomplex from the Green Alga Chlamydomonas reinhardtii

Kück, Ulrich; Schmitt, Olga

doi:10.3390/cells10020290

Cited by 12 publications

(14 citation statements)

References 175 publications

(291 reference statements)

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“…This shows that retrograde signaling between mitochondrial and nucleus gene expression ensures the integrity of the mitochondrial intron splicing machinery [199]. One has to assume that a similar situation exists for chloroplast integrity and function and nuclear genome components that regulate the expression of plastid genes including the orderly splicing of introns [114].…”

Section: Maturase and Splicing Factorsmentioning

confidence: 99%

“…Plant mitochondria, in particular among the angiosperms, and to a lesser degree in the gymnosperms, have trans-split genes in which rearrangements have occurred due to various recombination events within Group II introns [110,111] so that exons (and flanking half-introns) are dispersed within the genome, independently transcribed and the mRNA is generated through splicing in trans by assembling the intron components into the proper intron fold [112]. Trans-splicing of organellar introns can be associated with the requirement of RNA editing and multiple protein co-factors [113,114].…”

Section: Figure 4 Schematic Representation Of Splicing For Group II Introns (A)mentioning

confidence: 99%

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Organellar Introns in Fungi, Algae, and Plants

Mukhopadhyay

Hausner

2021

Cells

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Introns are ubiquitous in eukaryotic genomes and have long been considered as ‘junk RNA’ but the huge energy expenditure in their transcription, removal, and degradation indicate that they may have functional significance and can offer evolutionary advantages. In fungi, plants and algae introns make a significant contribution to the size of the organellar genomes. Organellar introns are classified as catalytic self-splicing introns that can be categorized as either Group I or Group II introns. There are some biases, with Group I introns being more frequently encountered in fungal mitochondrial genomes, whereas among plants Group II introns dominate within the mitochondrial and chloroplast genomes. Organellar introns can encode a variety of proteins, such as maturases, homing endonucleases, reverse transcriptases, and, in some cases, ribosomal proteins, along with other novel open reading frames. Although organellar introns are viewed to be ribozymes, they do interact with various intron- or nuclear genome-encoded protein factors that assist in the intron RNA to fold into competent splicing structures, or facilitate the turn-over of intron RNAs to prevent reverse splicing. Organellar introns are also known to be involved in non-canonical splicing, such as backsplicing and trans-splicing which can result in novel splicing products or, in some instances, compensate for the fragmentation of genes by recombination events. In organellar genomes, Group I and II introns may exist in nested intronic arrangements, such as introns within introns, referred to as twintrons, where splicing of the external intron may be dependent on splicing of the internal intron. These nested or complex introns, with two or three-component intron modules, are being explored as platforms for alternative splicing and their possible function as molecular switches for modulating gene expression which could be potentially applied towards heterologous gene expression. This review explores recent findings on organellar Group I and II introns, focusing on splicing and mobility mechanisms aided by associated intron/nuclear encoded proteins and their potential roles in organellar gene expression and cross talk between nuclear and organellar genomes. Potential application for these types of elements in biotechnology are also discussed.

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Section: Maturase and Splicing Factorsmentioning

confidence: 99%

Section: Figure 4 Schematic Representation Of Splicing For Group II Introns (A)mentioning

confidence: 99%

Organellar Introns in Fungi, Algae, and Plants

Mukhopadhyay

Hausner

2021

Cells

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“…However, alternative splicing is unlikely to fully explain these findings, as only roughly 10.1% of Chlamydomonas's protein-coding loci have annotated alternative transcripts considering the latest genome annotation [13,54] compared to ~30% for flowering plants [55]. Alternatively, the changes in pre-mRNA processing introduced by these differential proteins could be related to noncoding RNAs (ncRNAs), which have been found to act in the regulation of certain stress response behaviors and chloroplast metabolism in Chlamydomonas [56][57][58][59]. Along with the changes observed in ribosomal proteins, these nuclear proteome findings highlight the early regulatory shift into a sustained, long-term salt stress response phenotype, markedly characterized by alterations in ribosome-related mechanisms and protein translation rate, even though the results observed for treatment condition did not indicate significant changes in the cell growth performance.…”

Section: Proteomic Analysis Of C Reinhardtii Nuclear Proteins In Salt...mentioning

confidence: 99%

Characterization of the Nuclear Proteome of Chlamydomonas in Response to Salt Stress

2022

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Microalgae biomass is considered a promising alternative feedstock for biodiesel production due to its high productivity of neutral lipids, especially under abiotic stress conditions. Among the unicellular microalgae that show this characteristic, Chlamydomonas reinhardtii appears as one of the most important model species with increased lipid production under abiotic stress conditions. In this study, we show that C. reinhardtii cells cultivated under mixotrophic condition supplemented with 0.1 M of NaCl rapidly raise their intracellular amount of neutral lipids without a reduction in their cellular growth rate, representing a promising condition for biomass production toward bioenergy applications. The nuclear proteome of these cells was investigated, and we identified 323 proteins with an enrichment of almost 60% of nuclear proteins in the total dataset. We found 61 proteins differentially regulated upon salt treatment, including proteins annotated in functional categories related to translation and nucleosome assembly functions. Additionally, we identified transcription factor proteins (TFs) and analyzed their likely transcription factor-binding regulatory elements, identifying target genes related to lipid metabolism and kinase functions, indicating possible regulatory pathways of lipid biosynthesis. Together, these data can help understand regulatory nuclear mechanisms, leading to an increase in lipids in the first 24 h of salt stress.

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“…Although not all of them have been characterized, at least six of these factors contain OPR motifs: RAT2, RAA1, RAA3, RAA8 (also known as OPR120), OPR1 (Cre01.g001501), and OPR104 (Cre17.g698750; Merendino et al, 2006 ; Marx et al, 2015 ; Lefebvre-Legendre et al, 2016 ; Reifschneider et al, 2016 ; Figure 1B ). All these factors are part of a post-transcriptional complex, presumably functioning as RNA interaction module ( Lefebvre-Legendre et al, 2016 ; Reifschneider et al, 2016 ; Kück and Schmitt, 2021 ). On the one hand, RAT2 (RNA-maturation of psaA-tscA ) is necessary to process tscA from a polycistronic precursor ( Balczun et al, 2005 ).…”

Section: Octotricopeptide Repeat Proteinsmentioning

confidence: 99%

Pas de Trois: An Overview of Penta-, Tetra-, and Octo-Tricopeptide Repeat Proteins From Chlamydomonas reinhardtii and Their Role in Chloroplast Gene Expression

2021

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Penta-, Tetra-, and Octo-tricopeptide repeat (PPR, TPR, and OPR) proteins are nucleus-encoded proteins composed of tandem repeats of 35, 34, and 38–40 amino acids, respectively. They form helix-turn-helix structures that interact with mRNA or other proteins and participate in RNA stabilization, processing, maturation, and act as translation enhancers of chloroplast and mitochondrial mRNAs. These helical repeat proteins are unevenly present in plants and algae. While PPR proteins are more abundant in plants than in algae, OPR proteins are more abundant in algae. In Arabidopsis, maize, and rice there have been 450, 661, and 477 PPR proteins identified, respectively, which contrasts with only 14 PPR proteins identified in Chlamydomonas reinhardtii. Likewise, more than 120 OPR proteins members have been predicted from the nuclear genome of C. reinhardtii and only one has been identified in Arabidopsis thaliana. Due to their abundance in land plants, PPR proteins have been largely characterized making it possible to elucidate their RNA-binding code. This has even allowed researchers to generate engineered PPR proteins with defined affinity to a particular target, which has served as the basis to develop tools for gene expression in biotechnological applications. However, fine elucidation of the helical repeat proteins code in Chlamydomonas is a pending task. In this review, we summarize the current knowledge on the role PPR, TPR, and OPR proteins play in chloroplast gene expression in the green algae C. reinhardtii, pointing to relevant similarities and differences with their counterparts in plants. We also recapitulate on how these proteins have been engineered and shown to serve as mRNA regulatory factors for biotechnological applications in plants and how this could be used as a starting point for applications in algae.

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The Chloroplast Trans-Splicing RNA–Protein Supercomplex from the Green Alga Chlamydomonas reinhardtii

Cited by 12 publications

References 175 publications

Organellar Introns in Fungi, Algae, and Plants

Organellar Introns in Fungi, Algae, and Plants

Characterization of the Nuclear Proteome of Chlamydomonas in Response to Salt Stress

Pas de Trois: An Overview of Penta-, Tetra-, and Octo-Tricopeptide Repeat Proteins From Chlamydomonas reinhardtii and Their Role in Chloroplast Gene Expression

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