Chloroplast Gene Expression—RNA Synthesis and Processing

Börner, Thomas; Zhelyazkova, Petya; Legen, Julia; Schmitz‐Linneweber, Christian

doi:10.1007/978-1-4939-1136-3_1

Cited by 15 publications

(14 citation statements)

References 341 publications

(301 reference statements)

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“…Loss of housekeeping genes was also observed in other holoparasitic plants, for example, the plastid genome of Balanophora laxiflora is only 15,505 bp in size, with most genes being lost [24], and Rafflesia lagascae has even lost its whole plastid genome [25]. Some housekeeping genes have been transferred to the nuclear genome and their proteins can move back to the plastid to perform their functions [26]. In this study, 27 lost plastid genes in A.…”

Section: The Loss Of Photosynthesis Related Genes Is a Common Phenomesupporting

confidence: 52%

The loss of photosynthesis pathway and genomic locations of the lost plastid genes in a holoparasitic plant Aeginetia indica

Chen

Dai

et al. 2020

Preprint

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Background: With three origins of holoparasitism, Orobanchaceae provides an ideal system to study the evolution of holoparasitic lifestyle in plants. The evolution of holoparasitism can be revealed by plastid genome degradation and coordinated changes in the nuclear genome, since holoparasitic plants lost the capability of photosynthesis. Among the three clades with holoparasitic plants in Orobanchaceae, only Clade VI has no available plastid genome sequences for holoparasitic plants. In this study, we sequenced the plastome and transcriptome of Aeginetia indica, a holoparasitic plant in Clade VI of Orobanchaceae, to study its plastome evolution and the corresponding changes in the nuclear genome as a response of the loss of photosynthetic function. Results: The plastome of A. indica is reduced to 86,212 bp in size, and almost all photosynthesis-related genes were lost. Massive fragments of the lost plastid genes were transferred into the mitochondrial or nuclear genomes. These fragments could not be detected in its transcriptomes, suggesting that they were non-functional. Most protein coding genes in the plastome showed the signal of relaxation of purifying selection. Plastome and transcriptome analyses indicated that the photosynthesis pathway is completely lost, and that the porphyrin and chlorophyll metabolism pathways are partially retained, although chlorophyll synthesis is not possible.Conclusions: Our study suggests the loss of photosynthesis-related functions in A. indica in both the nuclear and plastid genomes. The lost plastid genes are transferred into its nuclear and mitochondrial genomes, and exist in very small fragments with no expression and are thus non-functional. The Aeginetia indica plastome also provides a resource for comparative studies on the repeated evolution of holoparasitism in Orobanchaceae.

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Section: The Loss Of Photosynthesis Related Genes Is a Common Phenomesupporting

confidence: 52%

The loss of photosynthesis pathway and genomic locations of the lost plastid genes in a holoparasitic plant Aeginetia indica

Chen

Dai

et al. 2020

Preprint

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“…Most mycoheterotrophic lineages have lost PEP, although it appears to be retained in Aneura , a mycoheterotrophic liverwort (Table ). This retention, if functional, could be related to a requirement for high transcription of retained Rubisco large subunit ( rbc L) or ATP synthase genes in this taxon, as PEP is involved in high transcriptional activity in chloroplasts of green plants (Börner et al ., ). Alternatively, its rpo (PEP) genes may be nonfunctional but retained as a consequence of a recent loss of photosynthesis (Wickett et al ., ).…”

Section: Modelling Plastid Genome Degradation In Mycoheterotrophsmentioning

confidence: 97%

Plastomes on the edge: the evolutionary breakdown of mycoheterotroph plastid genomes

2017

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Contents 48I.48II.50III.5354References54 Summary We examine recent evidence for ratchet‐like genome degradation in mycoheterotrophs, plants that obtain nutrition from fungi. Initial loss of the NADH dehydrogenase‐like (NDH) complex may often set off an irreversible evolutionary cascade of photosynthetic gene losses. Genes for plastid‐encoded subunits of RNA polymerase and photosynthetic enzymes with secondary functions (Rubisco and ATP synthase) can persist initially, with nonsynchronous and quite broad windows in the relative timing of their loss. Delayed losses of five core nonbioenergetic genes (especially trnE and accD, which respectively code for glutamyl tRNA and a subunit of acetyl‐CoA carboxylase) probably explain long‐term persistence of heterotrophic plastomes. The observed range of changes of mycoheterotroph plastomes is similar to that of holoparasites, although greater diversity of both probably remains to be discovered. These patterns of gene loss/retention can inform research programs on plastome function.

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“…For example, DNA polymerase processivity could vary with distance relative to the origins of replication. Furthermore, collision of the replication with the transcription complexes or other DNA binding proteins might differ depending on gene position or the usage of the nuclear-or plastid-encoded RNA polymerase (Börner et al, 2014). Whereas the interference of the DNA replication complex with other DNA binding proteins is a matter of speculation, the relative position of a gene to an origin of replication does not seem to have an influence on a mutational hot spot.…”

Section: Reasons For Biased Mutation Recoverymentioning

confidence: 99%

Spontaneous Chloroplast Mutants Mostly Occur by Replication Slippage and Show a Biased Pattern in the Plastome of Oenothera

et al. 2016

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Spontaneous plastome mutants have been used as a research tool since the beginning of genetics. However, technical restrictions have severely limited their contributions to research in physiology and molecular biology. Here, we used full plastome sequencing to systematically characterize a collection of 51 spontaneous chloroplast mutants in Oenothera (evening primrose). Most mutants carry only a single mutation. Unexpectedly, the vast majority of mutations do not represent single nucleotide polymorphisms but are insertions/deletions originating from DNA replication slippage events. Only very few mutations appear to be caused by imprecise double-strand break repair, nucleotide misincorporation during replication, or incorrect nucleotide excision repair following oxidative damage. U-turn inversions were not detected. Replication slippage is induced at repetitive sequences that can be very small and tend to have high A/T content. Interestingly, the mutations are not distributed randomly in the genome. The underrepresentation of mutations caused by faulty double-strand break repair might explain the high structural conservation of seed plant plastomes throughout evolution. In addition to providing a fully characterized mutant collection for future research on plastid genetics, gene expression, and photosynthesis, our work identified the spectrum of spontaneous mutations in plastids and reveals that this spectrum is very different from that in the nucleus.

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Chloroplast Gene Expression—RNA Synthesis and Processing

Cited by 15 publications

References 341 publications

The loss of photosynthesis pathway and genomic locations of the lost plastid genes in a holoparasitic plant Aeginetia indica

The loss of photosynthesis pathway and genomic locations of the lost plastid genes in a holoparasitic plant Aeginetia indica

Plastomes on the edge: the evolutionary breakdown of mycoheterotroph plastid genomes

Spontaneous Chloroplast Mutants Mostly Occur by Replication Slippage and Show a Biased Pattern in the Plastome of Oenothera

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