Atp9

The rice atp9 sequence was first reported by Grabau et al. (1990) in soybean mitochondria.This gene encodes an extremely hydrophobic protein that, when relocated, is particularly challenging to import into mitochondria. .

Annotated Information

Function

atp9 gene, which encodes ATPase subunit 9, is an important functional gene in mitochondria, and is closely related with energy supply.RNA editing of atp9 gene was associated with male sterility in plants. The protein it encodes has only two transmembrane segments, yet is extremely hydrophobic and classified as a proteolipid because it can easily be extracted from mitochondria with organic solvents . Subunit 9 is present in several copies , forming a ring structure that is an essential component of the ATP synthase proton-translocating domain . During proton transport, the subunit 9-ring rotates, resulting in conformational changes that favour the production of ATP by the catalytic head of the ATP synthase and its release into the mitochondrial matrix.

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 . 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 . 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 .

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 . 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 .

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 and the addition of guanosine residues on paramyxovirus RNA . In the case of higher plant mitochondria, RNA editing is found in several species and has been described for several protein coding genes . 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 . 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 . 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 . 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

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Structured Information

Gene Name	atp9
Description	ATP synthase F0 subunit 9
Version	GeneID:6450130
Length	255 bp
Definition	Oryza sativa Japonica Group atp9, Mitochondrion gene.
Source	Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza.
Chromosome	Mitochondrion
Location	Mitochondrion:263141..263365
Sequence Coding Region	263141..263365
Genome Context	{{{GCID}}}
Gene Structure (RNA Editing)	{{{GSID}}}
Protein Sequence	<aaseq>MLEGAKLIGAGAATIALAGAAVGIGNVFSSLIHSVARNPSLAKQLFGYAILGFALTEAIALFALMMAFLILFVF</aaseq>
Gene Sequence	<dnaseqindica>1..225#atgttagaaggagctaaatcaataggtgccggagctgctacaattgctttagcgggagctgctgtcggtattggaaacgtcctcagttcttcgattcattccgtggcgcgaaatccttcattggctaaacaattatttggttatgccattttgggctttgctctcaccgaagctattgcattgtttgccccaatgatggcctttctgatttcattcgttttccga</dnaseqindica>
External Link(s)	NCBI Gene:atp6