Does mitochondrial DNA replication in <i>Chlamydomonas</i> require a reverse transcriptase?

Smith, David Roy; Craig, Rory J.

doi:10.1111/nph.16930

Cited by 10 publications

(6 citation statements)

References 29 publications

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“…The linear 15.8-kb mitogenome carries eight protein-coding genes, which are expressed from a single bidirectional promoter. Seven of these genes encode components of the respiratory complex, while the eighth, reverse transcriptase-like ( rtl ), is likely required for mitogenome replication ( Smith and Craig 2021 ). We incorporated the more accurate annotations of Salinas-Giegé et al (2017) , who demonstrated that the 5′-end of each mature mitochondrial transcript begins immediately at the start codon (i.e.…”

Section: Resultsmentioning

confidence: 99%

The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory

et al. 2022

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Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive manual curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of the helicase RECQ3, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference organism.

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Section: Resultsmentioning

confidence: 99%

The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory

et al. 2022

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“…If circular, the mitogenome would then have a length of ~104,812 bp. The suspected circularity of the mitogenome is also compatible with the absence of the rtl gene, which is present in all linear mitogenomes of Chlamydomonadales characterised to date and encodes a reverse transcriptase-like protein implicated in the replication of the mitogenome termini [ 32 ]. Apart from rtl , the gene content of the L. pallida mitogenome is essentially the same as in other previously sequenced chlamydomonadalean mitogenomes and includes seven protein-coding genes (with cox1 interrupted by an ORF-free group II intron), only three tRNA genes, and regions corresponding to the 16S and 23S rRNA genes.…”

Section: Resultsmentioning

confidence: 99%

A new lineage of non-photosynthetic green algae with extreme organellar genomes

et al. 2022

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Background The plastid genomes of the green algal order Chlamydomonadales tend to expand their non-coding regions, but this phenomenon is poorly understood. Here we shed new light on organellar genome evolution in Chlamydomonadales by studying a previously unknown non-photosynthetic lineage. We established cultures of two new Polytoma-like flagellates, defined their basic characteristics and phylogenetic position, and obtained complete organellar genome sequences and a transcriptome assembly for one of them. Results We discovered a novel deeply diverged chlamydomonadalean lineage that has no close photosynthetic relatives and represents an independent case of photosynthesis loss. To accommodate these organisms, we establish the new genus Leontynka, with two species (L. pallida and L. elongata) distinguishable through both their morphological and molecular characteristics. Notable features of the colourless plastid of L. pallida deduced from the plastid genome (plastome) sequence and transcriptome assembly include the retention of ATP synthase, thylakoid-associated proteins, the carotenoid biosynthesis pathway, and a plastoquinone-based electron transport chain, the latter two modules having an obvious functional link to the eyespot present in Leontynka. Most strikingly, the ~362 kbp plastome of L. pallida is by far the largest among the non-photosynthetic eukaryotes investigated to date due to an extreme proliferation of sequence repeats. These repeats are also present in coding sequences, with one repeat type found in the exons of 11 out of 34 protein-coding genes, with up to 36 copies per gene, thus affecting the encoded proteins. The mitochondrial genome of L. pallida is likewise exceptionally large, with its >104 kbp surpassed only by the mitogenome of Haematococcus lacustris among all members of Chlamydomonadales hitherto studied. It is also bloated with repeats, though entirely different from those in the L. pallida plastome, which contrasts with the situation in H. lacustris where both the organellar genomes have accumulated related repeats. Furthermore, the L. pallida mitogenome exhibits an extremely high GC content in both coding and non-coding regions and, strikingly, a high number of predicted G-quadruplexes. Conclusions With its unprecedented combination of plastid and mitochondrial genome characteristics, Leontynka pushes the frontiers of organellar genome diversity and is an interesting model for studying organellar genome evolution.

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“…Nevertheless, its transcript has reproducibly been found in the total mitochondrial fraction 19 , 28 . Its function is unclear, but it might be involved in mitochondrial genome maintenance, which involves telomere-like structures in Chlamydomonas , as the L2b sequence is highly similar to both ends of the linear Chlamydomonas mitochondrial genome 66 , 67 . Alternatively, the observation that the L2b RNA level is decreased in the mS105 -mutant strain may hint at a function related to mS105, and thus, possibly to mitoribosome or SSU biogenesis.…”

Section: Discussionmentioning

confidence: 99%

How to build a ribosome from RNA fragments in Chlamydomonas mitochondria

et al. 2021

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Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the few essential messenger RNAs still encoded by mitochondrial genomes. Here, we present a biochemical and structural characterization of the mitoribosome in the model green alga Chlamydomonas reinhardtii, as well as a functional study of some of its specific components. Single particle cryo-electron microscopy resolves how the Chlamydomonas mitoribosome is assembled from 13 rRNA fragments encoded by separate non-contiguous gene pieces. Additional proteins, mainly OPR, PPR and mTERF helical repeat proteins, are found in Chlamydomonas mitoribosome, revealing the structure of an OPR protein in complex with its RNA binding partner. Targeted amiRNA silencing indicates that these ribosomal proteins are required for mitoribosome integrity. Finally, we use cryo-electron tomography to show that Chlamydomonas mitoribosomes are attached to the inner mitochondrial membrane via two contact points mediated by Chlamydomonas-specific proteins. Our study expands our understanding of mitoribosome diversity and the various strategies these specialized molecular machines adopt for membrane tethering.

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Does mitochondrial DNA replication in Chlamydomonas require a reverse transcriptase?

Abstract: Forum mitogenomes sequenced are colonial algae (e.g. Tetrabaena socialis and Gonium pectorale).

Cited by 10 publications

References 29 publications

The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory

The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory

A new lineage of non-photosynthetic green algae with extreme organellar genomes

How to build a ribosome from RNA fragments in Chlamydomonas mitochondria

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