Characterization of plastid psb T sense and antisense RNAs

Zghidi-Abouzid, Ouafa; Merendino, Livia; Buhr, F.; Ghulam, Mustafa Malik; Lerbs-Mache, Silva

doi:10.1093/nar/gkr143

Cited by 45 publications

(35 citation statements)

References 27 publications

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“…To confirm the structure and composition of the poly(U) tracts, we carried out RT-PCR on circularized transcripts of psbA and psbC ( Fig. S2 and Dataset S1) (35,36). We found that the poly(U) tracts observed were generally between 15 and 30 nt in length, homopolymeric, and on the 3′ end of each transcript (as opposed to an internal insertion).…”

Section: ′mentioning

confidence: 92%

Functional remodeling of RNA processing in replacement chloroplasts by pathways retained from their predecessors

Dorrell

Howe

2012

Proc. Natl. Acad. Sci. U.S.A.

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Chloroplasts originate through the endosymbiotic integration of a host and a photosynthetic symbiont, with processes established within the host for the biogenesis and maintenance of the nascent chloroplast. It is thought that several photosynthetic eukaryotes have replaced their original chloroplasts with others derived from different source organisms in a process termed "serial endosymbiosis of chloroplasts." However, it is not known whether replacement chloroplasts are affected by the biogenesis and maintenance pathways established to support their predecessors. Here, we investigate whether pathways established during a previous chloroplast symbiosis function in the replacement chloroplasts of the dinoflagellate alga Karenia mikimotoi. We show that chloroplast transcripts in K. mikimotoi are subject to 3′ polyuridylylation and extensive sequence editing. We confirm that these processes do not occur in free-living relatives of the replacement chloroplast lineage, but are otherwise found only in the ancestral, red algalderived chloroplasts of dinoflagellates and their closest relatives. This indicates that these unusual RNA-processing pathways have been retained from the original symbiont lineage and made use of by the replacement chloroplast. Our results constitute an addition to current theories of chloroplast evolution in which chloroplast biogenesis may be radically remodeled by pathways remaining from previous symbioses.organelle | fucoxanthin | haptophyte | poly(U) | alveolate

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Section: ′mentioning

confidence: 92%

Functional remodeling of RNA processing in replacement chloroplasts by pathways retained from their predecessors

Dorrell

Howe

2012

Proc. Natl. Acad. Sci. U.S.A.

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“…Mechanistically, one could expect that enhanced antisense transcript accumulation interferes with translation efficiency of the corresponding sense transcript due to duplex formation, as it was suggested for the plastid psbT gene (Zghidi-Abouzid et al, 2011). This would provide a gene-group-specific mechanism that could prevent the formation of functional photosystem II and Cytb 6 f complexes.…”

Section: Impact Of Pap7-1 Deficiency On Plastid Gene Expressionmentioning

confidence: 96%

Light and Plastid Signals Regulate Different Sets of Genes in the Albino Mutant Pap7-1

et al. 2017

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Plants possessing dysfunctional plastids due to defects in pigment biosynthesis or translation are known to repress photosynthesisassociated nuclear genes via retrograde signals from the disturbed organelles toward the nucleus. These signals are thought to be essential for proper biogenesis and function of the plastid. Mutants lacking plastid-encoded RNA polymerase-associated proteins (PAPs) display a genetic arrest in eoplast-chloroplast transition leading to an albino phenotype in the light. Retrograde signaling in these mutants, therefore, could be expected to be similar as under conditions inducing plastid dysfunction. To answer this question, we performed plastome-and genomewide array analyses in the pap7-1 mutant of Arabidopsis (Arabidopsis thaliana). In parallel, we determined the potential overlap with light-regulated expression networks. To this end, we performed a comparative expression profiling approach using light-and dark-grown wild-type plants as relative control for the expression profiles obtained from lightgrown pap7-1 mutants. Our data indicate a specific impact of retrograde signals on metabolism-related genes in pap7-1 mutants reflecting the starvation situation of the albino seedlings. In contrast, light regulation of PhANGs and other nuclear gene groups appears to be fully functional in this mutant, indicating that a block in chloroplast biogenesis per se does not repress expression of them as suggested by earlier studies. Only genes for light harvesting complex proteins displayed a significant repression indicating an exclusive retrograde impact on this gene family. Our results indicate that chloroplasts and arrested plastids each emit specific signals that control different target gene modules both in positive and negative manner.

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“…They focus on single RNAs and do not point to ncRNAs as a more general regulatory principle (Nishimura et al, 2004;Georg et al, 2010;Hotto et al, 2010;Zghidi-Abouzid et al, 2011). One study identified 12 ncRNAs in tobacco chloroplasts (Lung et al, 2006).…”

Section: Plastid Ncrnasmentioning

confidence: 99%

“…Cyanobacteria, the chloroplast progenitors, have a plethora of noncoding RNAs at their disposal to regulate gene expression . However, only a few potentially regulatory RNAs have been reported to be transcribed from plastid genes (Nishimura et al, 2004;Georg et al, 2010;Hotto et al, 2010;Zghidi-Abouzid et al, 2011). Therefore, chloroplasts may contain additional hitherto undetected genes for regulatory ncRNAs.…”

Section: Introductionmentioning

confidence: 99%

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase

et al. 2012

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Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here, we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identification of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons, indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions and opposite to annotated genes, demonstrating the existence of numerous noncoding RNA candidates.

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Characterization of plastid psb T sense and antisense RNAs

Cited by 45 publications

References 27 publications

Functional remodeling of RNA processing in replacement chloroplasts by pathways retained from their predecessors

Functional remodeling of RNA processing in replacement chloroplasts by pathways retained from their predecessors

Light and Plastid Signals Regulate Different Sets of Genes in the Albino Mutant Pap7-1

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase

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