Evidence for a novel mitochondrial promoter preceding the cox2 gene of perennial teosintes.

Newton, Kathleen J.; Winberg, B.; Yamato, Katsuyuki T.; Lupold, S.; Stern, David B.

doi:10.1002/j.1460-2075.1995.tb07034.x

Cited by 58 publications

(24 citation statements)

References 40 publications

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“…Environmental effects on DNA topology have been noted in Chlamydomonas and barley chloroplasts, where light has been shown to affect chromosome structure, as determined by their ability to intercalate crosslinking agents into the genome (50,51). Mutants affecting cox2 expression may help elucidate its role during plant development (52), including the role of specific promoters (53).…”

Section: Discussionmentioning

confidence: 99%

Genomic context influences the activity of maize mitochondrial cox2 promoters

Lupold

Caoile²,

Stern³

1999

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

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Plant mitochondrial genomes are highly recombinogenic, with a variety of species-specific direct and inverted repeats leading to in vivo accumulation of multiple DNA forms. In maize, the cox2 gene, which encodes subunit II of cytochrome c oxidase, lies immediately downstream of a 0.7-kilobase direct repeat, which is present in two copies in the 570-kilobase master chromosome. Promoters for cox2 exist upstream of both of these copies, in regions we have termed A and B. Three region B promoters are active for cox2 transcription in the master chromosome, whereas two region A promoters are active for cox2 transcription after recombination across the direct repeats. We have measured the proportion of genomes carrying region A or B upstream of cox2 in maize seedlings and found a ratio of approximately 1:6. Promoter strength, based on run-on transcription assays, shows a ratio of 1:4 for region A to region B promoters. These data allowed us to predict the relative contributions of region A and B to mitochondrial transcript accumulation, based on a simple product of genome-form abundance and promoter strength. When promoter use was determined by using quantitative reverse transcriptase-PCR, however, we found that region A promoters were used at an unexpectedly high rate when upstream of cox2 and used less than expected when not upstream of cox2. Thus, the use of this set of promoters seems to respond to genomic context. These results suggest a role for intragenomic and intergenomic recombination in regulating plant mitochondrial gene expression.

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Section: Discussionmentioning

confidence: 99%

Genomic context influences the activity of maize mitochondrial cox2 promoters

Lupold

Caoile²,

Stern³

1999

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

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“…The known promoters, rather than functioning as elements controlling transcription through recruitment of a specific RNA polymerase, may simply function as sites at which the double helix is easily opened to initiate transcription. Although mitochondrial promoter selection has been reported to be controlled by nucleus-encoded factors in alloplasmic lines of Nicotiana tabacum and maize (Zea mays; Newton et al, 1995;Edqvist and Bergman, 2002), these factors and their possible roles in regulating mitochondrial function remain to be identified. Due to frequent rearrangements of mitochondrial sequences, the mtDNAs of dicotyledonous plant species show occasional substitutions of promoters between different mitochondrial genes (Unseld et al, 1997;Kubo et al, 2000;Handa, 2003;Forner et al, 2008).…”

Section: Rpotmp Activity Is Gene Specific Rather Than Promoter Specificmentioning

confidence: 99%

Phage-Type RNA Polymerase RPOTmp Performs Gene-Specific Transcription in Mitochondria of Arabidopsis thaliana

et al. 2009

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Transcription of mitochondrial genes in animals, fungi, and plants relies on the activity of T3/T7 phage-type RNA polymerases. Two such enzymes, RPOTm and RPOTmp, are present in the mitochondria of eudicotyledonous plants; RPOTmp is additionally found in plastids. We have characterized the transcriptional role of the dual-targeted RNA polymerase in mitochondria of Arabidopsis thaliana. Examination of mitochondrial transcripts in rpoTmp mutants revealed major differences in transcript abundances between wild-type and rpoTmp plants. Decreased levels of specific transcripts were correlated with reduced abundances of the respiratory chain complexes I and IV. Altered transcript levels in rpoTmp were found to result from gene-specific transcriptional changes, establishing that RPOTmp functions in distinct transcriptional processes within mitochondria. Decreased transcription of specific genes in rpoTmp was not associated with changes in promoter utilization; therefore, RPOTmp function is not promoter specific but gene specific. This implies that additional gene-specific elements direct the transcription of a subset of mitochondrial genes by RPOTmp.

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“…Even this degenerate sequence, however, is not found near all 5Ј termini identified as transcription start sites based on their ability to be capped in vitro by guanylyl transferase (11). While some of these promoters may be recognized by specific transcription factors (12), the frequency of active promoters has not been surveyed over large regions of any plant mitochondrial genome. Such an approach might aid in identifying contextual features other than YRTAT that constitute functional promoters, at least in maize mitochondria.…”

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confidence: 99%

The Maize Mitochondrial cox2 Gene Has Five Promoters in Two Genomic Regions, Including a Complex Promoter Consisting of Seven Overlapping Units

Lupold¹,

Caoile²,

Stern³

1999

Journal of Biological Chemistry

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Plant mitochondrial genes are often transcribed into complex sets of RNAs, resulting from multiple initiation sites and processing steps. To elucidate the role of initiation in generating the more than 10 cox2 transcripts found in maize mitochondria, we surveyed sequences upstream of cox2 for active promoters. Because the cox2 coding region is immediately downstream of a 0.7-kb recombination repeat, cox2 is under the control of two different sets of potential expression signals. Using an in vitro transcription assay, we localized four promoters upstream of the coding region in the so-called master chromosome, and two promoters upstream of the coding region in the recombinant subgenome. Ribonuclease protection analysis of labeled primary transcripts confirmed that all but one of these promoters is active in vivo. Primer extension was used to identify the promoter sequences and initiation sites, which agree with the consensus established earlier for maize mitochondria. This study identified two unusual promoters, the core sequences of which were composed entirely of adenines and thymines, and one of which was a complex promoter consisting of seven overlapping units. Deletion mutagenesis of the complex promoter suggested that each of its units was recognized independently by RNA polymerase. While each active promoter fit the maize core consensus sequence YRTAT, not all such sequences surveyed supported initiation. We conclude that in vitro transcription is a powerful tool for locating mitochondrial promoters and that, in the case of cox2, promoter multiplicity contributes strongly to transcript complexity.The transcriptional strategies of vascular plant mitochondrial genomes differ from those of their fungal and metazoan counterparts, with a major region being genome structure. Plant mitochondrial genomes are relatively large and the genes are mostly dispersed (1, 2). In contrast, metazoan genomes are compact and have a single promoter for each DNA strand, and the Saccharomyces cerevisiae mitochondrial genome is 75 kb, 1 and contains about 20 promoters (reviewed in Ref.3). The maize mitochondrial genome, the expression of which we have studied, can be mapped as a 570-kb circle with numerous repeated elements mediating recombination, leading to a complex set of overlapping molecules (4). Based on recent microscopic studies (5), these molecules are likely to be linearly permuted.Promoter analysis in plant mitochondria has been accelerated in the last several years by the development of in vitro transcription systems from wheat (6), maize (7), and pea (8). Extensive mutational analysis of the maize atpA and cox3 promoters showed that the only universally-present sequence required for transcription initiation in vitro was YRTAT (Y ϭ T or C and R ϭ G or A), located at or immediately upstream of the start site (9, 10). Even this degenerate sequence, however, is not found near all 5Ј termini identified as transcription start sites based on their ability to be capped in vitro by guanylyl transferase (11). While some of the...

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Evidence for a novel mitochondrial promoter preceding the cox2 gene of perennial teosintes.

Cited by 58 publications

References 40 publications

Genomic context influences the activity of maize mitochondrial cox2 promoters

Genomic context influences the activity of maize mitochondrial cox2 promoters

Phage-Type RNA Polymerase RPOTmp Performs Gene-Specific Transcription in Mitochondria of Arabidopsis thaliana

The Maize Mitochondrial cox2 Gene Has Five Promoters in Two Genomic Regions, Including a Complex Promoter Consisting of Seven Overlapping Units

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