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==Annotated Information== | ==Annotated Information== | ||
===Function=== | ===Function=== | ||
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===Expression=== | ===Expression=== | ||
| − | + | When performing the partial protein sequencing of the mitochondrial subunit 9 of ATP synthase (ATP 9), some residues differ from those encoded for by the mitochondrial ''atp9'' gene. The differences are explained by assuming C-to-U transitions at the mRNA level. Thus, mRNA modifications by RNA editing are reflected at the translational level <ref name="ref4" />. | |
| − | = | + | Extended observations to the cDNA sequence of ''atp9'' demonstrate the presence of partially modified mRNA molecules. One C-to-U conversion transforms an argininecodon into a stop codon, shortening the protein to the “standard” size when compared with other mitochondrial ATP 9. The analysis of subunit 9 by peptide sequencing and amino acid composition confirms these results. The ''atp9'' transcripts are modified by C-to-U changes in a process called RNA editing. Eight codons are involved in RNA editing: five lead to an amino acid change, two give no modification, and one transforms an Arg codon into astop codon. The editing process for wheat ATP 9 represents an important modification in genetic information, considering that the gene is only 243 nucleotides long <ref name="ref5" />. |
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| − | + | Transcription of the single-copy rice mitochondrial ''atp9'' gene has been analyzed. A hypothesis shows that transcription initiates from this promoter to yield a 0.65 kb precursor mRNA and that this primary transcript is processed to a smaller 0.45 kb mature mRNA. This smaller mRNA ends at a putative double stem-loop structure <ref name="ref6" />. | |
| − | == | + | ===Evolution=== |
| − | + | The three ''atp9'' transcripts and positions of RNA editing were not identical. However, the deduced peptide sequences were identical, indicating conservation of the amino acid sequence. And in their study, peptide sequences encoded by fully, partially and excessively edited clones were deduced to be the same <ref name="ref7" />. Thus, the rice mitochondrial ATP9 polypeptide seems to be highly homogeneous and RNA editing might be necessary for production of the functional ATP9 peptide. | |
| − | = | + | The molecular weight of the rice atp9 protein is predicted to be 8.945kd. This is larger than in other species because of an additional 13 codons (compared to maize) at the 3' end of the gene. The nucleotide and amino acid sequence homologies to other sequenced plant atp9 genes (assuming no mRNA editing) are shown as follows: |
| − | + | Nucleotide sequence homology and Amino Acid sequence homology in rice show 96.4% and 94.6% identity in wheat, 95.6% and 98.7% in maize, 91.6% and 96.1% in petunia, 92.0% and 96.1% in tobacco, and 86.2% and 94.7% in pea, respectively <ref name="ref8" />. | |
| − | == | + | ===Knowledge extension=== |
| + | RNA editing is a biological phenomenon consisting of the modificationof the genetic message leadingto the creation of new codons or to the alteration of reading frames. Severa1 mechanisms have been described such as the addition/deletion of uridine residues in trypanosome mitochondria <ref name="ref9" /> and the addition of guanosine residues on paramyxovirus RNA <ref name="ref10" />. In the case of higher plant mitochondria, RNA editing is found in several species and has been described for several protein coding genes <ref name="ref11" />. The post-transcriptionalmodifications, observed by RNA or cDNA sequence analysis, occur mainly by C-to-U transitions, similar to the situation described for apolipoprotein B in mammalians <ref name="ref12" />. The mechanism by which the C-to-U changes occur is unknown. | ||
| − | + | Cytoplasmic male sterility (CMS) is a maternally inherited inability of a plant to produce functional pollen. Sterility-inducing cytoplasms have been identified in over 150 plant species <ref name="ref13" />. The action of specific nuclear genes can suppress the cytoplasmic dysfunction and restore fertility. For several plant species CMS-associated DNA sequences have been identified <ref name="ref14" />. They are located in the mitochondrial genome and often contain chimeric open reading frames (ORFs). | |
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| − | + | ==Labs working on this gene== | |
| − | + | *Laboratoire de Biologie Mol6culaire Vdgetale, Institut de Biochimie Cellulaire et Neurochimie-Centre National de la Recherche Scientifique, 1 rue Camille Saint Sacns, 33077 Bordeaux, France | |
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| − | + | *Department of Genetics, Plant Breeding and Seed Science, Cracow Agricultural University, Al. 29-go Listopada 54, 31-425 Cracow, Poland | |
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| − | + | *Department of Plant Molecular Biology, Miedzychodzka 5,60-371 Poznan, Poland | |
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| − | + | *Institute of Biology (Genetics), Humboldt University, Chausseestr. 117, D-10115 Berlin, Germany | |
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| − | + | *Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA | |
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| − | + | *Department of Biochemistry, and Centre for Molecular Biology and Medicine, Monash University, Clayton | |
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| − | + | ==References== | |
| − | + | <references> | |
| − | + | <ref name="ref1"> | |
| − | + | Hernould M, Suharsono S, Litvak S, Araya A, Mouras A (1993) Male sterility induction in transgenic tobacco plants with an unedited ATP9 mitochondrial gene from wheat. Proc Natl Acad Sci USA 90:2370-2374.</ref> | |
| − | + | <ref name="ref2"> | |
| − | + | Zabaleta E, Mouras A, Hernould M, Suharsono S, Araya A (1996) Transgenic male-sterile plant induced by an unedited atp9 gene is restored to fertility by inhibiting its expression with antisense RNA. Proc Natl Acad Sci USA 93:11259–11263.</ref> | |
| − | + | <ref name="ref3"> | |
| − | + | Wei L, Yan ZX, Ding Y (2008) Mitochondrial RNA editing of F0-ATPase subunit 9 gene (atp9) transcripts of Yunnan purple rice cytoplasmic male sterile line and its maintainer line. Acta Physiol Plant 30:657–662.</ref> | |
| − | + | <ref name="ref4"> | |
| − | + | 4.Graves PV, Bégu D, Velours J, Neau E, Belloc F, Litvak S, Araya A (1990). Direct protein sequencing of wheat mitochondrial ATP-synthasesubunit 9 confirms RNA editing in plants. J. MOI.Biol. 214: 1-6.</ref> | |
| − | + | <ref name="ref5"> | |
| − | + | 5.Dominique B, Pierre VG, Christine D, Geneviève A, Simon L, Alejandro A (1990) RNA Editing of Wheat Mitochondrial ATP Synthase Subunit 9: Direct Protein and cDNA Sequencing. The Plant Cell 2: 1283-1290.</ref> | |
| − | + | <ref name="ref6"> | |
| − | + | 6.Edward K, Kaleikau, Charles P, André, Virginia W (1993) Transcription of the gene coding for subunit 9 of ATP synthase in rice. Plant Molecular Biology 22: 899-905.</ref> | |
| − | + | <ref name="ref7"> | |
| − | + | 7.Ishikawa M, Kadowaki KI (1993) Excess RNA editing in Rice mitochondrial atp9 transcripts. Plant Cell Physiol 34(6):959–963.</ref> | |
| − | + | <ref name="ref8"> | |
| − | + | 8.Edward K, Kaleikau, Charles P, Andre, Virginia W (1990) Sequence of the Fo-atpase proteolipid (atp9) gene from rice mitochondria. Nucleic Acids Research 18: 370.</ref> | |
| − | + | <ref name="ref9"> | |
| − | + | 9.Simpson L, Shaw J (1989) RNA editing and the mitochondrial cryptogenes of kinetoplastid protozoa. Cell 57: 355-366.</ref> | |
| − | + | <ref name="ref10"> | |
| − | + | 10.Cattaneo R, Kaelin K, Baczko K, Billeter MA (1989) Measles virus editing provides an additional cysteine-rich protein. Cell 56： 759-764.</ref> | |
| − | + | <ref name="ref11"> | |
| − | + | 11.Covello PS, Gray MW (1989) RNA editing in wheat mitochondria.Nature 341: 662-666.</ref> | |
| − | + | <ref name="ref12"> | |
| − | + | 12.Higuchi K, Hospattankar AV, Law SW, Meglin N, Cortright J, Brewer B, Jr (1988) Human apolipoprotein B (apoB) mRNA: ldentificationof two distinct apoB mRNAs, an mRNA with the apoB-1O0 sequence and an apoB mRNA containing a premature in frame translational stop codon in both liver and intestine. Proc. Natl. Acad. Sci. USA 85: 1772-1776.</ref> | |
| − | + | <ref name="ref13"> | |
| − | + | 13.Mackenzie S, He S, Lyznik A (1994) The elusive plant mitochondrion as a genetic system. Plant Physiol 105: 775-780.</ref> | |
| − | + | <ref name="ref14"> | |
| − | + | 14 Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic male sterility and fertility restoration. Trends Plant Sci 3: 175-180.</ref> | |
| − | + | </references> | |
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Revision as of 11:50, 5 June 2014
Please input one-sentence summary here.
Contents
Annotated Information
Function
Expression
When performing the partial protein sequencing of the mitochondrial subunit 9 of ATP synthase (ATP 9), some residues differ from those encoded for by the mitochondrial atp9 gene. The differences are explained by assuming C-to-U transitions at the mRNA level. Thus, mRNA modifications by RNA editing are reflected at the translational level [1].
Extended observations to the cDNA sequence of atp9 demonstrate the presence of partially modified mRNA molecules. One C-to-U conversion transforms an argininecodon into a stop codon, shortening the protein to the “standard” size when compared with other mitochondrial ATP 9. The analysis of subunit 9 by peptide sequencing and amino acid composition confirms these results. The atp9 transcripts are modified by C-to-U changes in a process called RNA editing. Eight codons are involved in RNA editing: five lead to an amino acid change, two give no modification, and one transforms an Arg codon into astop codon. The editing process for wheat ATP 9 represents an important modification in genetic information, considering that the gene is only 243 nucleotides long [2].
Transcription of the single-copy rice mitochondrial atp9 gene has been analyzed. A hypothesis shows that transcription initiates from this promoter to yield a 0.65 kb precursor mRNA and that this primary transcript is processed to a smaller 0.45 kb mature mRNA. This smaller mRNA ends at a putative double stem-loop structure [3].
Evolution
The three atp9 transcripts and positions of RNA editing were not identical. However, the deduced peptide sequences were identical, indicating conservation of the amino acid sequence. And in their study, peptide sequences encoded by fully, partially and excessively edited clones were deduced to be the same [4]. Thus, the rice mitochondrial ATP9 polypeptide seems to be highly homogeneous and RNA editing might be necessary for production of the functional ATP9 peptide.
The molecular weight of the rice atp9 protein is predicted to be 8.945kd. This is larger than in other species because of an additional 13 codons (compared to maize) at the 3' end of the gene. The nucleotide and amino acid sequence homologies to other sequenced plant atp9 genes (assuming no mRNA editing) are shown as follows: Nucleotide sequence homology and Amino Acid sequence homology in rice show 96.4% and 94.6% identity in wheat, 95.6% and 98.7% in maize, 91.6% and 96.1% in petunia, 92.0% and 96.1% in tobacco, and 86.2% and 94.7% in pea, respectively [5].
Knowledge extension
RNA editing is a biological phenomenon consisting of the modificationof the genetic message leadingto the creation of new codons or to the alteration of reading frames. Severa1 mechanisms have been described such as the addition/deletion of uridine residues in trypanosome mitochondria [6] and the addition of guanosine residues on paramyxovirus RNA [7]. In the case of higher plant mitochondria, RNA editing is found in several species and has been described for several protein coding genes [8]. The post-transcriptionalmodifications, observed by RNA or cDNA sequence analysis, occur mainly by C-to-U transitions, similar to the situation described for apolipoprotein B in mammalians [9]. The mechanism by which the C-to-U changes occur is unknown.
Cytoplasmic male sterility (CMS) is a maternally inherited inability of a plant to produce functional pollen. Sterility-inducing cytoplasms have been identified in over 150 plant species [10]. The action of specific nuclear genes can suppress the cytoplasmic dysfunction and restore fertility. For several plant species CMS-associated DNA sequences have been identified [11]. They are located in the mitochondrial genome and often contain chimeric open reading frames (ORFs).
Labs working on this gene
- Laboratoire de Biologie Mol6culaire Vdgetale, Institut de Biochimie Cellulaire et Neurochimie-Centre National de la Recherche Scientifique, 1 rue Camille Saint Sacns, 33077 Bordeaux, France
- Department of Genetics, Plant Breeding and Seed Science, Cracow Agricultural University, Al. 29-go Listopada 54, 31-425 Cracow, Poland
- Department of Plant Molecular Biology, Miedzychodzka 5,60-371 Poznan, Poland
- Institute of Biology (Genetics), Humboldt University, Chausseestr. 117, D-10115 Berlin, Germany
- Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA
- Department of Biochemistry, and Centre for Molecular Biology and Medicine, Monash University, Clayton
References
- ↑ 4.Graves PV, Bégu D, Velours J, Neau E, Belloc F, Litvak S, Araya A (1990). Direct protein sequencing of wheat mitochondrial ATP-synthasesubunit 9 confirms RNA editing in plants. J. MOI.Biol. 214: 1-6.
- ↑ 5.Dominique B, Pierre VG, Christine D, Geneviève A, Simon L, Alejandro A (1990) RNA Editing of Wheat Mitochondrial ATP Synthase Subunit 9: Direct Protein and cDNA Sequencing. The Plant Cell 2: 1283-1290.
- ↑ 6.Edward K, Kaleikau, Charles P, André, Virginia W (1993) Transcription of the gene coding for subunit 9 of ATP synthase in rice. Plant Molecular Biology 22: 899-905.
- ↑ 7.Ishikawa M, Kadowaki KI (1993) Excess RNA editing in Rice mitochondrial atp9 transcripts. Plant Cell Physiol 34(6):959–963.
- ↑ 8.Edward K, Kaleikau, Charles P, Andre, Virginia W (1990) Sequence of the Fo-atpase proteolipid (atp9) gene from rice mitochondria. Nucleic Acids Research 18: 370.
- ↑ 9.Simpson L, Shaw J (1989) RNA editing and the mitochondrial cryptogenes of kinetoplastid protozoa. Cell 57: 355-366.
- ↑ 10.Cattaneo R, Kaelin K, Baczko K, Billeter MA (1989) Measles virus editing provides an additional cysteine-rich protein. Cell 56： 759-764.
- ↑ 11.Covello PS, Gray MW (1989) RNA editing in wheat mitochondria.Nature 341: 662-666.
- ↑ 12.Higuchi K, Hospattankar AV, Law SW, Meglin N, Cortright J, Brewer B, Jr (1988) Human apolipoprotein B (apoB) mRNA: ldentificationof two distinct apoB mRNAs, an mRNA with the apoB-1O0 sequence and an apoB mRNA containing a premature in frame translational stop codon in both liver and intestine. Proc. Natl. Acad. Sci. USA 85: 1772-1776.
- ↑ 13.Mackenzie S, He S, Lyznik A (1994) The elusive plant mitochondrion as a genetic system. Plant Physiol 105: 775-780.
- ↑ 14 Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic male sterility and fertility restoration. Trends Plant Sci 3: 175-180.
Cite error: <ref> tag with name "ref1" defined in <references> is not used in prior text.
Cite error: <ref> tag with name "ref2" defined in <references> is not used in prior text.
Cite error: <ref> tag with name "ref3" defined in <references> is not used in prior text.
