The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b

Abstract

ymf39 is a conserved hypothetical protein-coding gene found in mitochondrial genomes of land plants and certain protists. We speculated earlier, based on a weak sequence similarity between Ymf39 from a green alga and the atpF gene product from Bradyrhizobium, that ymf39 might code for subunit b of mitochondrial F(0)F(1)-ATP synthase. To test this hypothesis, we have sequenced ymf39 from five protists with minimally derived mitochondrial genomes, the jakobids. In addition, we isolated the mitochondrial ATP synthase complex of the jakobid Seculamonas ecuadoriensis and determined the partial protein sequence of the 19-kDa subunit, the size expected for Ymf39. The obtained peptide sequence matches perfectly with a 3'-proximal region of the ymf39 gene of this organism, confirming that Ymf39 is indeed an ATP synthase subunit. Finally, we employed statistical tests to assess the significance of sequence similarity of Ymf39 proteins with each other, their nucleus-encoded functional counterparts, ATP4/ATP5F, from fungi and animals and alpha-proteobacterial ATP synthase b-subunits. This analysis provides clear evidence that ymf39 is an atpF homolog, while ATP4/ATP5F appears to be a highly diverged form of ymf39 that has migrated to the nucleus. We propose to designate ymf39 from now on atp4.

Extreme Features of the Galdieria sulphuraria Organellar Genomes: A Consequence of Polyextremophily?

“…The G. sulphuraria rrnL and rrnS genes, which were difficult to identify due to their divergence (only a few short fragments match homologs in other red algae), nevertheless have a syntenic gene order of rrnS-nad4L-ccmC-rrnL-sdhC , confirming their genomic position. In addition, the size and genomic position of a 468-bp ORF suggests that it probably encodes a divergent ATP4 protein, which is further supported by results from a Pfam domain search ( e -value = 0.057) and by the presence of a predicted transmembrane domain at position 21–43 in the protein, similar to other mitochondrion-encoded ATP4 proteins ( Burger et al 2003 ).…”

Extreme Features of the Galdieria sulphuraria Organellar Genomes: A Consequence of Polyextremophily?

“…The G. sulphuraria rrnL and rrnS genes, which were difficult to identify due to their divergence (only a few short fragments match homologs in other red algae), nevertheless have a syntenic gene order of rrnS-nad4L-ccmC-rrnL-sdhC , confirming their genomic position. In addition, the size and genomic position of a 468-bp ORF suggests that it probably encodes a divergent ATP4 protein, which is further supported by results from a Pfam domain search ( e -value = 0.057) and by the presence of a predicted transmembrane domain at position 21–43 in the protein, similar to other mitochondrion-encoded ATP4 proteins ( Burger et al 2003 ).…”

Overexpression of a mitochondrial ATP synthase small subunit gene (AtMtATP6) confers tolerance to several abiotic stresses in Saccharomyces cerevisiae and Arabidopsis thaliana

“…Analysis of the complex from Arabidopsis identified two mitochondrial-encoded ORFs as components of the F 0 subcomplex, which probably represent the plant equivalents of the subunit 8 and the subunit 4, and encoded by orfB and orf25 in plant mitochondrial genomes (Heazlewood et al 2003a). These ATP synthase associations were also made for orfb in sunflower (Sabar et al 2003) and ORF ymf39 (an orf25 ortholog) in protests (Burger et al 2003). In rice, the RMtATP6 gene was Fig.…”

Mitochondrial Biogenesis and Function in Arabidopsis†

“…Thus five subunits of the ATP synthase are mitochondrial-encoded in plants, four being the core components of the F O complex. These identifications were confirmed by the report that orfb in sunflower was ATP8 (Sabar et al, 2003) and identification of ORF ymf39 (an orf25 otholog) as a probable ATP4 subunit in protists (Burger et al, 2003). Subsequently, Eubel et al (2003) has noted 13 protein bands in ATP synthase separated from Arabidopsis by BN-PAGE, and tentatively identified a putative g subunit (At4g29480).…”

Extreme Features of the Galdieria sulphuraria Organellar Genomes: A Consequence of Polyextremophily?

“…The G. sulphuraria rrnL and rrnS genes, which were difficult to identify due to their divergence (only a few short fragments match homologs in other red algae), nevertheless have a syntenic gene order of rrnS-nad4L-ccmC-rrnL-sdhC , confirming their genomic position. In addition, the size and genomic position of a 468-bp ORF suggests that it probably encodes a divergent ATP4 protein, which is further supported by results from a Pfam domain search ( e -value = 0.057) and by the presence of a predicted transmembrane domain at position 21–43 in the protein, similar to other mitochondrion-encoded ATP4 proteins ( Burger et al 2003 ).…”

Overexpression of a mitochondrial ATP synthase small subunit gene (AtMtATP6) confers tolerance to several abiotic stresses in Saccharomyces cerevisiae and Arabidopsis thaliana

“…Analysis of the complex from Arabidopsis identified two mitochondrial-encoded ORFs as components of the F 0 subcomplex, which probably represent the plant equivalents of the subunit 8 and the subunit 4, and encoded by orfB and orf25 in plant mitochondrial genomes (Heazlewood et al 2003a). These ATP synthase associations were also made for orfb in sunflower (Sabar et al 2003) and ORF ymf39 (an orf25 ortholog) in protests (Burger et al 2003). In rice, the RMtATP6 gene was Fig.…”

Mitochondrial Biogenesis and Function in Arabidopsis†

“…Thus five subunits of the ATP synthase are mitochondrial-encoded in plants, four being the core components of the F O complex. These identifications were confirmed by the report that orfb in sunflower was ATP8 (Sabar et al, 2003) and identification of ORF ymf39 (an orf25 otholog) as a probable ATP4 subunit in protists (Burger et al, 2003). Subsequently, Eubel et al (2003) has noted 13 protein bands in ATP synthase separated from Arabidopsis by BN-PAGE, and tentatively identified a putative g subunit (At4g29480).…”

Extreme Features of the Galdieria sulphuraria Organellar Genomes: A Consequence of Polyextremophily?

“…The G. sulphuraria rrnL and rrnS genes, which were difficult to identify due to their divergence (only a few short fragments match homologs in other red algae), nevertheless have a syntenic gene order of rrnS-nad4L-ccmC-rrnL-sdhC , confirming their genomic position. In addition, the size and genomic position of a 468-bp ORF suggests that it probably encodes a divergent ATP4 protein, which is further supported by results from a Pfam domain search ( e -value = 0.057) and by the presence of a predicted transmembrane domain at position 21–43 in the protein, similar to other mitochondrion-encoded ATP4 proteins ( Burger et al 2003 ).…”

Overexpression of a mitochondrial ATP synthase small subunit gene (AtMtATP6) confers tolerance to several abiotic stresses in Saccharomyces cerevisiae and Arabidopsis thaliana

“…Analysis of the complex from Arabidopsis identified two mitochondrial-encoded ORFs as components of the F 0 subcomplex, which probably represent the plant equivalents of the subunit 8 and the subunit 4, and encoded by orfB and orf25 in plant mitochondrial genomes (Heazlewood et al 2003a). These ATP synthase associations were also made for orfb in sunflower (Sabar et al 2003) and ORF ymf39 (an orf25 ortholog) in protests (Burger et al 2003). In rice, the RMtATP6 gene was Fig.…”

Mitochondrial Biogenesis and Function in Arabidopsis†

“…Thus five subunits of the ATP synthase are mitochondrial-encoded in plants, four being the core components of the F O complex. These identifications were confirmed by the report that orfb in sunflower was ATP8 (Sabar et al, 2003) and identification of ORF ymf39 (an orf25 otholog) as a probable ATP4 subunit in protists (Burger et al, 2003). Subsequently, Eubel et al (2003) has noted 13 protein bands in ATP synthase separated from Arabidopsis by BN-PAGE, and tentatively identified a putative g subunit (At4g29480).…”