Structure and expression of the rice mitochondrial apocytochrome b gene (cob-1) and pseudogene (cob-2)

Kaleikau, Edward K.; André, Charles P.; Walbot, Virginia

doi:10.1007/bf00326411

Cited by 31 publications

(16 citation statements)

References 49 publications

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“…In addition to rice atp9, the 11 bp motif is also found at 5' termini for three other rice mitochondrial mRNAs (Fig. 4A): cob [7], dicistronic orf25/cox3 [8] and atp6 (M. Iwabuchi and K. Shimamoto, personal communication); based on these comparisons we propose the rice mitochondrial consensus promoter shown in Fig. 4A.…”

Section: '-End Mappingmentioning

confidence: 99%

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Transcription of the gene coding for subunit 9 of ATP synthase in rice mitochondria

1993

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Transcription of the single-copy rice mitochondrial atp9 gene has been analyzed. We propose that there is a 0.65 kb primary transcript that is processed to an abundant 0.45 kb mRNA; a sequence motif at the 5' terminus of the 0.65 kb transcript shares 9 out of 11 nucleotides homology to the consensus promoter proposed for maize. There are several 3' termini based on RNase protection, and these termini map within or just distal to inverted repeats that could fold into a double stem-loop structure.

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Section: '-End Mappingmentioning

confidence: 99%

“…A. 5' sequence comparison between mapped 5' ends of four rice mitochondrial genes: atp9 (this report), cob [7], orf25/cox3 [8], and atp6 (M. Iwabuchi and K. Shimamoto, personal communication); and proposed mitochondrial consensus promoters for maize [ 13], wheat [4], and soybean [3]. Also shown in the proposed rice consensus promoter.…”

Section: '-End Mappingmentioning

confidence: 99%

Transcription of the gene coding for subunit 9 of ATP synthase in rice mitochondria

1993

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“…We report here nonencoded nucleotides at the 3Ј ends of pea and Oenothera mitochondrial transcripts containing double inverted repeats in their 3Ј untranslated regions (UTRs). These structures have been suggested to increase the stability of the RNA, and the stem-loop structures of pea atp9 transcripts as well as of orf138 mRNAs in Brassica were found to act as processing signals and/or stability elements at least in vitro (1,5,6,16,23). In this report special emphasis was dedicated to the interaction of the stabilizing effect of such double stem-loop structures and degradation-enhancing polyadenylation.…”

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confidence: 96%

Transcript Lifetime Is Balanced between Stabilizing Stem-Loop Structures and Degradation-Promoting Polyadenylation in Plant Mitochondria

2001

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To determine the influence of posttranscriptional modifications on 3 end processing and RNA stability in plant mitochondria, pea atp9 and Oenothera atp1 transcripts were investigated for the presence and function of 3 nonencoded nucleotides. A 3 rapid amplification of cDNA ends approach initiated at oligo(dT)-adapter primers finds the expected poly(A) tails predominantly attached within the second stem or downstream of the double stem-loop structures at sites of previously mapped 3 ends. Functional studies in a pea mitochondrial in vitro processing system reveal a rapid removal of the poly(A) tails up to termini at the stem-loop structure but little if any influence on further degradation of the RNA. In contrast 3 poly(A) tracts at RNAs without such stem-loop structures significantly promote total degradation in vitro. To determine the in vivo identity of 3 nonencoded nucleotides more accurately, pea atp9 transcripts were analyzed by a direct anchor primer ligation-reverse transcriptase PCR approach. This analysis identified maximally 3-nucleotide-long nonencoded extensions most frequently of adenosines combined with cytidines. Processing assays with substrates containing homopolymer stretches of different lengths showed that 10 or more adenosines accelerate RNA processivity, while 3 adenosines have no impact on RNA life span. Thus polyadenylation can generally stimulate the decay of RNAs, but processivity of degradation is almost annihilated by the stabilizing effect of the stem-loop structures. These antagonistic actions thus result in the efficient formation of 3 processed and stable transcripts.Control of the amount of translatable mRNA is a common parameter to regulate gene expression in many organisms. The available quantity of an RNA depends largely on the rate of synthesis and/or posttranscriptional processes which control the stability of a transcript by preventing it from degradation. Such posttranscriptional processes have been studied in prokaryotes and different subcellular compartments of eukaryotic cells. In spite of the many variations, some common features behind these processes emerge in all organisms and systems. These include the involvement of mRNA secondary structures and 3Ј polyadenylation of RNA. While organized RNA secondary structures generally support transcript stabilization, polyadenylation has opposing functions in eukaryotes and prokaryotes.In the nucleus of eukaryotic cells, pre-mRNAs are polyadenylated at 3Ј ends that have been generated by endonucleolytic cleavages. These poly(A) tails play important roles in translation initiation and mRNA export from the nucleus and also have a major function in stabilizing mRNAs (27). A completely different function has been attributed to polyadenylation in prokaryotes, where the degradation of mRNA is stimulated by the presence of 3Ј poly(A) tracts (4). The degradation-promoting effect of polyadenylation was even found in transcripts, which were otherwise protected and stabilized by stem-loop structures (3). A similar effect has also been ob...

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“…Second, it has been shown using an in vitro transcription system that inverted repeats that terminate some mitochondrial mRNAs are not recognized as transcription termination signals (5). These inverted repeats seem to be essential as processing signals in vitro (5) and in vivo (6,7). However, the ribonucleases involved in 3Ј mRNA maturation processes remain to be identified in plant mitochondria.…”

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Two Exoribonucleases Act Sequentially to Process Mature 3′-Ends of atp9 mRNAs in Arabidopsis Mitochondria

Perrin

Meyer

Zaepfel

et al. 2004

Journal of Biological Chemistry

100

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In plant mitochondria, transcription proceeds well beyond the region that will become mature 3 extremities of mRNAs, and the mechanisms of 3 maturation are largely unknown. Here, we show the involvement of two exoribonucleases, AtmtPNPase and AtmtRNaseII, in the 3 processing of atp9 mRNAs in Arabidopsis thaliana mitochondria. Down-regulation of AtmtPNPase results in the accumulation of pretranscripts of several times the size of mature atp9 mRNAs, indicating that 3 processing of these transcripts is performed mainly exonucleolytically by AtmtPNPase. This enzyme is however not sufficient to completely process atp9 mRNAs, because with down-regulation of another mitochondrial exoribonuclease, AtmtRNaseII, about half of atp9 transcripts exhibit short 3 nucleotide extensions compared with mature mRNAs. These short extensions can be efficiently removed by AtmtRNaseII in vitro. Taken together, these results show that 3 processing of atp9 mRNAs in Arabidopsis mitochondria is, at least, a twostep phenomenon. First, AtmtPNPase is involved in removing 3 extensions that may reach several kilobases. Second, AtmtRNaseII degrades short nucleotidic extensions to generate the mature 3 -ends.Functional RNAs are generated through a series of complex post-transcriptional processes. The nature of these processes can vary depending on the organism or cellular compartment considered and may include maturation of 5Ј and 3Ј termini, splicing of introns, capping, editing, base modifications, or addition of nongenomically-encoded nucleotides such as polyadenylation. Processing of mRNAs is well documented for bacterial and eukaryotic nuclear mRNAs (1, 2). Our knowledge of maturation of plastid transcripts is also extensive for both Chlamydomonas and higher plants (3). However, mRNA maturation processes in plant mitochondria are far less well characterized. Two lines of evidence suggest that processing of 3Ј extremities occurs for any RNA in plant mitochondria. First, run-on experiments have demonstrated that transcription proceeds beyond the region that corresponds to mature 3Ј-ends of mRNAs and rRNAs (4). Second, it has been shown using an in vitro transcription system that inverted repeats that terminate some mitochondrial mRNAs are not recognized as transcription termination signals (5). These inverted repeats seem to be essential as processing signals in vitro (5) and in vivo (6, 7). However, the ribonucleases involved in 3Ј mRNA maturation processes remain to be identified in plant mitochondria.Escherichia coli represents one of the model organisms for which the function, mechanism, and regulation of ribonucleases (RNases) are intensively studied (for example, see Refs. 1, 8, and 9). Among the eight characterized exoribonucleases in E. coli, polynucleotide phosphorylase (PNPase) 1 and RNaseII are the main exoribonucleases involved in degrading mRNAs in a 3Ј to 5Ј direction but participate also in processing events. PNPase-like proteins are also present in human mitochondria (10) and in chloroplasts. In the latter, it is involved both ...

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Structure and expression of the rice mitochondrial apocytochrome b gene (cob-1) and pseudogene (cob-2)

Cited by 31 publications

References 49 publications

Transcription of the gene coding for subunit 9 of ATP synthase in rice mitochondria

Transcription of the gene coding for subunit 9 of ATP synthase in rice mitochondria

Transcript Lifetime Is Balanced between Stabilizing Stem-Loop Structures and Degradation-Promoting Polyadenylation in Plant Mitochondria

Two Exoribonucleases Act Sequentially to Process Mature 3′-Ends of atp9 mRNAs in Arabidopsis Mitochondria

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