Regulation of gene expression in plant mitochondria

Binder, Stefan; Marchfelder, Anita; Brennicke, Axel

doi:10.1007/978-94-009-0353-1_13

Cited by 20 publications

(28 citation statements)

References 75 publications

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“…The regulation of photosynthesis and respiration requires myriad factors to coordinate the coexpression of nucleus-and organelle-encoded partners in response to environmental cues, developmental signals, and other processes (Gruissem and Tonkyn, 1993;Surpin and Chory, 1997;Leon et al, 1998;Yu et al, 2001). Although nuclear gene regulation often is transcriptional, organellar gene regulation has been documented at both the transcriptional (Mulligan et al, 1991;Rapp et al, 1992;Mullet, 1993;Kristal et al, 1994;Binder et al, 1996) and post-transcriptional (Finnegan and Brown, 1990;Rochaix, 1992;Gillham et al, 1994;Menassa et al, 1999;Giege et al, 2000) levels. However, these individual studies remain to be integrated into a global analysis of organellar responses to abiotic stimuli.…”

Section: Introductionmentioning

confidence: 99%

Retracted: The Chlamydomonas reinhardtii Organellar Genomes Respond Transcriptionally and Post-Transcriptionally to Abiotic Stimuli

2002

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The Chlamydomonas reinhardtii plastid and mitochondrial transcriptomes were surveyed for changes in RNA profiles resulting from growth in 12 culture conditions representing 8 abiotic stimuli. Organellar RNA abundance exhibited marked changes during nutrient stress and exposure to UV light, as revealed by both RNA gel blot and DNA microarray analyses. Of particular note were large increases in tufA and clpP transcript abundance during nutrient limitation. Phosphate and sulfur limitation resulted in the most global, yet opposite, effects on organellar RNA abundance, changes that were dissected further using run-on transcription assays. Removal of sulfate from the culture medium, which is known to reduce photosynthesis, resulted in 2-fold to 10-fold decreases in transcription rates, which were reflected in lower RNA abundance. The decrease in transcriptional activity was completely reversible and recovered to twice the control level after sulfate replenishment. Conversely, phosphate limitation resulted in a twofold to threefold increase in RNA abundance that was found to be a post-transcriptional effect, because it could be accounted for by increased RNA stability. This finding is consistent with the known metabolic slowdown under phosphate stress. Additionally, inhibitor studies suggested that unlike those in higher plants, Chlamydomonas chloroplasts lack a nucleusencoded plastid RNA polymerase. The apparently single type of polymerase could contribute to the rapid and genomewide transcriptional responses observed within the chloroplast.

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Section: Introductionmentioning

confidence: 99%

Retracted: The Chlamydomonas reinhardtii Organellar Genomes Respond Transcriptionally and Post-Transcriptionally to Abiotic Stimuli

2002

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“…The transcription complex assembles on a unique promoter sequence, which in the case of yeast is reiterated at least nine times, while in humans, mouse and Xenopus it is present only twice, once on each of the two (light and heavy) DNA strands (Tzagolo and Myers 1986;Clayton 1984, 1986;Antoshechkin and Bogenhagen 1995). Plant mitochondrial transcription appears to have diverged from that of other eukaryotes, with most genes possessing several transcription initiation sites (Tracy and Stern 1995;Binder et al 1996) which show little relatedness. The only consensus between plant mitochondrial promoters that has been noted is that of a 5¢-CRTA motif, which itself is not highly conserved.…”

Section: Introductionmentioning

confidence: 96%

Characterization of a gene encoding a single-subunit bacteriophage-type RNA polymerase from maize which is alternatively spliced

Young¹,

Allen²,

Harvey³

et al. 1998

Mol Gen Genet

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Single-subunit RNA polymerases belonging to the T3/T7 bacteriophage family are thought to be common throughout eukaryotes. We report the isolation and characterization of a nucleus-encoded single-subunit RNA polymerase gene from maize. This gene is highly homologous to other single-subunit RNA polymerase genes from Arabidopsis, Chenopodium. yeast and Neurospora crassa involved in organellar transcription. Genomic Southern analysis reveals 10 to 15 hybridising fragments, suggesting that maize contains a small gene family. The isolated gene contains 19 exons and its genomic structure is highly conserved when compared to the three Arabidopsis homologues. Unlike the case in Arabidopsis, intron-12 of the maize bacteriophage-type RNA polymerase gene is alternatively spliced. Quantitative RT-PCR revealed that the resultant alternatively spliced transcript represents approximately 21 to 26% of the total polymerase mRNA in maize coleoptiles. The orthologous wheat bacteriophage-type RNA polymerase is also alternatively spliced and the intron exhibits 78% identity to maize intron-12. The conservation in alternative splicing between wheat and maize and its absence from Arabidopsis suggest a functional requirement for the alternatively spliced product.

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“…These are further processed, mostly by tRNA removal (i.e., animal mtDNA, the green alga Prototheca wickerhamii, the fungi Aspergillus nidulans, and Neurospora crassa) (Ojala et al 1981;Burger et al 1985;Dyson et al 1989;Wolff and Kuck 1996), but also by cleavage inside tRNAs (the red alga Chondrus crispus) (Richard et al 1998(Richard et al , 1999 or at other specific primary or secondary structures (Burger et al 1985;Dyson et al 1989;Wolff and Kuck 1996). Large mt genomes with relaxed packaging of genetic information are transcribed into multiple small transcripts from individual promoters scattered over the genome (i.e., the yeast Saccharomyces cerevisiae and plants) (Costanzo and Fox 1990;Binder et al 1996). The details of transcription have been investigated widely only in mammals (human and rodents), whereas partial data on mapping and processing of mt transcripts are available for a few other animals, such as sea urchin Paracentrotus lividus (Elliott and Jacobs 1989;Cantatore et al 1990), and Drosophila (Berthier et al 1986).…”

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confidence: 99%

Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data

Gissi

Pesole²

2003

Genome Res.

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Mitochondrial transcripts of two ascidian species were reconstructed through sequence assembly of publicly available ESTs resembling mitochondrial DNA sequences (mt-ESTs). This strategy allowed us to analyze processing and mapping of the mitochondrial transcripts and to investigate the gene organization of a previously uncharacterized mitochondrial genome (mtDNA). This new strategy would greatly facilitate the sequencing and annotation of mtDNAs. In Ciona intestinalis, the assembled mt-ESTs covered 22 mitochondrial genes (∼12,000 bp) and provided the partial sequence of the mtDNA and the prediction of its gene organization. Such sequences were confirmed by amplification and sequencing of the entire Ciona mtDNA. For Halocynthia roretzi, for which the mtDNA sequence was already available, the inferred mt transcripts allowed better definition of gene boundaries (16S rRNA, ND1, ATP6, and tRNA-Ser genes) and the identification of a new gene (an additional Phe-tRNA). In both species, polycistronic and immature transcripts, creation of stop codons by polyadenylation, tRNA signal processing, and rRNA transcript termination signals were identified, thus suggesting that the main features of mitochondrial transcripts are conserved in Chordata.

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Regulation of gene expression in plant mitochondria

Cited by 20 publications

References 75 publications

Retracted: The Chlamydomonas reinhardtii Organellar Genomes Respond Transcriptionally and Post-Transcriptionally to Abiotic Stimuli

Retracted: The Chlamydomonas reinhardtii Organellar Genomes Respond Transcriptionally and Post-Transcriptionally to Abiotic Stimuli

Characterization of a gene encoding a single-subunit bacteriophage-type RNA polymerase from maize which is alternatively spliced

Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data

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