The OPR Protein MTHI1 Controls the Expression of Two Different Subunits of ATP Synthase CFo in <i>Chlamydomonas reinhardtii</i>

Ozawa, Shinichiro; Cavaiuolo, Marina; Jarrige, Domitille; Kuras, Richard; Rütgers, Mark; Eberhard, Stephan; Drapier, Dominique; Wollman, Françis Andrè; Choquet, Yves

doi:10.1105/tpc.19.00770

Cited by 24 publications

(18 citation statements)

References 114 publications

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“…For strain CC-1690 (‘21gr’), recently released Nanopore raw sequencing data ( 62 ) were base-called and de novo assembled into chromosomes as described in ( 63 )(GenBank accession: JABWPN000000000 ). For the present work, we used a version prior to the Illimuna polishing step and used linkage data ( 65 ) to further scaffold the last unplaced contig (unplaced_1) to the end of chromosome 15, forming its right arm. Compared to our released genome ( 63 ), we corrected a mistake in the assembly of subtelomere 9_R (a replacement contig is appended to the genome), which was distorted at the telomere-proximal side of the Sultan array by reads from 15_R.…”

Section: Methodsmentioning

confidence: 99%

Architecture and evolution of subtelomeres in the unicellular green algaChlamydomonas reinhardtii

Chaux-Jukic

O’Donnell

Craig

et al. 2021

Nucleic Acids Research

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In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements. However, their repetitive nature has complicated the efforts to sequence them, analyse their structure and infer how they evolved. Here, we use recent genome assemblies of Chlamydomonas reinhardtii based on long-read sequencing to comprehensively describe the subtelomere architecture of the 17 chromosomes of this model unicellular green alga. We identify three main repeated elements present at subtelomeres, which we call Sultan, Subtile and Suber, alongside three chromosome extremities with ribosomal DNA as the only identified component of their subtelomeres. The most common architecture, present in 27 out of 34 subtelomeres, is a heterochromatic array of Sultan elements adjacent to the telomere, followed by a transcribed Spacer sequence, a G-rich microsatellite and transposable elements. Sequence similarity analyses suggest that Sultan elements underwent segmental duplications within each subtelomere and rearranged between subtelomeres at a much lower frequency. Analysis of other green algae reveals species-specific repeated elements that are shared across subtelomeres, with an overall organization similar to C. reinhardtii. This work uncovers the complexity and evolution of subtelomere architecture in green algae.

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Section: Methodsmentioning

confidence: 99%

Architecture and evolution of subtelomeres in the unicellular green algaChlamydomonas reinhardtii

Chaux-Jukic

O’Donnell

Craig

et al. 2021

Nucleic Acids Research

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“…For strain CC-1690 (“21gr”), recently released Nanopore raw sequencing data (Liu et al 2019) were base-called and de novo assembled into chromosomes as described in (O'Donnell et al 2020)(GenBank accession: JABWPN000000000). For the present work, we used a version prior to the Illimuna polishing step and used linkage data (Ozawa et al 2020) to further scaffold the last unplaced contig (unplaced_1) to the end of chromosome 15, forming its right arm. Compared to our released genome (O'Donnell et al 2020), we corrected a mistake in the assembly of subtelomere 9_R (a replacement contig is appended to the genome), which was distorted at the telomere-proximal side of the Sultan array by reads from 15_R.…”

Section: Methodsmentioning

confidence: 99%

Architecture and evolution of subtelomeres in the unicellular green algaChlamydomonas reinhardtii

Chaux-Jukic

O’Donnell

Craig

et al. 2021

Preprint

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In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements. However, their repetitive nature has complicated the efforts to sequence them, analyze their structure and infer how they evolved. Here, we use recent and forthcoming genome assemblies of Chlamydomonas reinhardtii based on long-read sequencing to comprehensively describe the subtelomere architecture of the 17 chromosomes of this model unicellular green alga. We identify three main repeated elements present at subtelomeres, which we call Sultan, Subtile and Suber, alongside three chromosome extremities with ribosomal DNA as the only identified component of their subtelomeres. The most common architecture, present in 27 out of 34 subtelomeres, is an array of 1 to 46 tandem copies of Sultan elements adjacent to the telomere and followed by a transcribed centromere-proximal Spacer sequence, a G-rich microsatellite and a region rich in transposable elements. Sequence similarity analyses suggest that Sultan elements underwent segmental duplications within each subtelomere and rearranged between subtelomeres at a much lower frequency. Comparison of genomic sequences of three laboratory strains and a wild isolate of C. reinhardtii shows that the overall subtelomeric architecture was already present in their last common ancestor, although subtelomeric rearrangements are on-going at the species level. Analysis of other green algae reveals the presence of species-specific repeated elements, highly conserved across subtelomeres and unrelated to the Sultan element, but with a subtelomere structure similar to C. reinhardtii. Overall, our work uncovers the complexity and evolution of subtelomere architecture in green algae.

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“…Post-transcriptional steps of transcript processing, stabilisation, and translation initiation are mediated by nuclearencoded factors, most of which are pentatricopeptide repeat (PPR), tetratricopeptide repeat (TPR), or octatricopeptide repeat (OPR) proteins (Gorchs-Rovira and Smith, 2019). Many of the cis elements on chloroplast transcripts that are the binding targets for these factors have been mapped (Cavaiuolo et al, 2017), and an increasing number of the factors themselves have been characterised in Chlamydomonas, including identification of their target genes (Johnson et al, 2010;Jalal et al, 2015;Marx et al, 2015;Cline et al, 2017;Viola et al, 2019;Ozawa et al, 2020).…”

Section: Evolution and Tractability Of The Chloroplast Genetic Systemmentioning

confidence: 99%

The Algal Chloroplast as a Testbed for Synthetic Biology Designs Aimed at Radically Rewiring Plant Metabolism

et al. 2021

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Sustainable and economically viable support for an ever-increasing global population requires a paradigm shift in agricultural productivity, including the application of biotechnology to generate future crop plants. Current genetic engineering approaches aimed at enhancing the photosynthetic efficiency or composition of the harvested tissues involve relatively simple manipulations of endogenous metabolism. However, radical rewiring of central metabolism using new-to-nature pathways, so-called “synthetic metabolism”, may be needed to really bring about significant step changes. In many cases, this will require re-programming the metabolism of the chloroplast, or other plastids in non-green tissues, through a combination of chloroplast and nuclear engineering. However, current technologies for sophisticated chloroplast engineering (“transplastomics”) of plants are limited to just a handful of species. Moreover, the testing of metabolic rewiring in the chloroplast of plant models is often impractical given their obligate phototrophy, the extended time needed to create stable non-chimeric transplastomic lines, and the technical challenges associated with regeneration of whole plants. In contrast, the unicellular green alga, Chlamydomonas reinhardtii is a facultative heterotroph that allows for extensive modification of chloroplast function, including non-photosynthetic designs. Moreover, chloroplast engineering in C. reinhardtii is facile, with the ability to generate novel lines in a matter of weeks, and a well-defined molecular toolbox allows for rapid iterations of the “Design-Build-Test-Learn” (DBTL) cycle of modern synthetic biology approaches. The recent development of combinatorial DNA assembly pipelines for designing and building transgene clusters, simple methods for marker-free delivery of these clusters into the chloroplast genome, and the pre-existing wealth of knowledge regarding chloroplast gene expression and regulation in C. reinhardtii further adds to the versatility of transplastomics using this organism. Herein, we review the inherent advantages of the algal chloroplast as a simple and tractable testbed for metabolic engineering designs, which could then be implemented in higher plants.

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The OPR Protein MTHI1 Controls the Expression of Two Different Subunits of ATP Synthase CFo in Chlamydomonas reinhardtii

Abstract: The OPR protein MTHI1 is a major actor in the biogenesis of chloroplast ATP synthase that co-regulates the expression of AtpH and AtpI, the two subunits of the proton channel in green algae.

Cited by 24 publications

References 114 publications

Architecture and evolution of subtelomeres in the unicellular green algaChlamydomonas reinhardtii

Architecture and evolution of subtelomeres in the unicellular green algaChlamydomonas reinhardtii

Architecture and evolution of subtelomeres in the unicellular green algaChlamydomonas reinhardtii

The Algal Chloroplast as a Testbed for Synthetic Biology Designs Aimed at Radically Rewiring Plant Metabolism

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