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Identical substitutions in magnesium chelatase paralogs result in chlorophyll-deficient soybean mutants.

Campbell BW, Mani D, Curtin SJ, Slattery RA, Michno JM, Ort DR, Schaus PJ, Palmer RG, Orf JH, Stupar RM - G3 (Bethesda) (2014)

Bottom Line: This mutation was identified in the ChlI1b gene, a paralog of ChlI1a.Protein sequence alignments of the two Mg-chelatase subunits indicated that the sites of amino acid modification in MinnGold, T219H, and CD-5 are highly conserved among photosynthetic species.These results suggest that amino acid alterations in this critical domain may create competitive inhibitory interactions between the mutant and wild-type ChlI1a and ChlI1b proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.

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Polypeptide sequence alignment of the Mg-chelatase ChlI subunit for the interval surrounding the y11, y11-2, and CD-5 mutations. The 266N and 279R positions (bold and labeled in the Consensus sequence) indicate the amino acids predicted to be involved in an ATP binding domain and an arginine binding domain, respectively (Marchler-Bauer et al. 2013). The bold and underlined 273Q and 275R positions denote the y11-2 and y11 nonsynonymous amino acid changes in Glyma13g30560, respectively. The lower 275R position (in the ‘Glyma15g08680 CD-5′ sequence) denotes the CD-5 nonsynonymous amino acid change in Glyma15g08680. The bold and underlined 313C denotes the nonsynonymous amino acid change in Oryza sativa chl9. The letters indicate residues that are not completely conserved across species. The wild-type soybean sequence and the sequences of the other species, listed in order, are available in the National Center for Biotechnology Information database under accession numbers: XP_003543008, XP_003546019, XP_007148073, AFK38677, XP_003593716, AET86637, NP_193583, XP_002316838, NP_001050493, ACN32024, AAA99720, U38804, AF017642, and Z11165.
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fig5: Polypeptide sequence alignment of the Mg-chelatase ChlI subunit for the interval surrounding the y11, y11-2, and CD-5 mutations. The 266N and 279R positions (bold and labeled in the Consensus sequence) indicate the amino acids predicted to be involved in an ATP binding domain and an arginine binding domain, respectively (Marchler-Bauer et al. 2013). The bold and underlined 273Q and 275R positions denote the y11-2 and y11 nonsynonymous amino acid changes in Glyma13g30560, respectively. The lower 275R position (in the ‘Glyma15g08680 CD-5′ sequence) denotes the CD-5 nonsynonymous amino acid change in Glyma15g08680. The bold and underlined 313C denotes the nonsynonymous amino acid change in Oryza sativa chl9. The letters indicate residues that are not completely conserved across species. The wild-type soybean sequence and the sequences of the other species, listed in order, are available in the National Center for Biotechnology Information database under accession numbers: XP_003543008, XP_003546019, XP_007148073, AFK38677, XP_003593716, AET86637, NP_193583, XP_002316838, NP_001050493, ACN32024, AAA99720, U38804, AF017642, and Z11165.

Mentions: Palmer et al. (1989) found that the y11 and CD-5 chlorophyll deficient mutants display nearly identical chlorophyll deficient phenotypes (Figure S1). Allelism test results and similarity in phenotype led the authors (Palmer et al. 1989) to initially consider that the two mutants were allelic and thus were surprised to find that CD-5 cosegregated with the blunt pubescence tip locus (pb) on chromosome 15. After identifying the likely y11 causative mutation in a Mg-chelatase subunit, we identified a Mg-chelatase paralog on chromosome 15, Glyma15g08680, as a candidate gene for the CD-5. Sequencing of Glyma15g08680 from two homozygous CD-5 individuals and from two wild-type individuals all derived from a segregating family identified a single non-synonymous SNP in the third exon. A CAPS assay of seventeen individuals segregating for the presence of CD-5 showed prefect cosegregation of the candidate SNP with the mutant phenotype (Figure S3). These results suggest that the identified SNP is causative of the CD-5 chlorophyll-deficient phenotype. A comparative sequence analysis across 29 diverse soybean lines (McHale et al. 2012) found that the single base substitution in Glyma15g08680 was unique to CD-5. All 29 of the diverse lines exhibited the wild-type sequence (Figure S4A). Remarkably, the Glyma15g08680 amino acid change in CD-5 (Q275R) was identical in position and sequence to the Glyma13g30560 change in y11 (Q275R) (Figure 5 and Figure S4B).


Identical substitutions in magnesium chelatase paralogs result in chlorophyll-deficient soybean mutants.

Campbell BW, Mani D, Curtin SJ, Slattery RA, Michno JM, Ort DR, Schaus PJ, Palmer RG, Orf JH, Stupar RM - G3 (Bethesda) (2014)

Polypeptide sequence alignment of the Mg-chelatase ChlI subunit for the interval surrounding the y11, y11-2, and CD-5 mutations. The 266N and 279R positions (bold and labeled in the Consensus sequence) indicate the amino acids predicted to be involved in an ATP binding domain and an arginine binding domain, respectively (Marchler-Bauer et al. 2013). The bold and underlined 273Q and 275R positions denote the y11-2 and y11 nonsynonymous amino acid changes in Glyma13g30560, respectively. The lower 275R position (in the ‘Glyma15g08680 CD-5′ sequence) denotes the CD-5 nonsynonymous amino acid change in Glyma15g08680. The bold and underlined 313C denotes the nonsynonymous amino acid change in Oryza sativa chl9. The letters indicate residues that are not completely conserved across species. The wild-type soybean sequence and the sequences of the other species, listed in order, are available in the National Center for Biotechnology Information database under accession numbers: XP_003543008, XP_003546019, XP_007148073, AFK38677, XP_003593716, AET86637, NP_193583, XP_002316838, NP_001050493, ACN32024, AAA99720, U38804, AF017642, and Z11165.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4291463&req=5

fig5: Polypeptide sequence alignment of the Mg-chelatase ChlI subunit for the interval surrounding the y11, y11-2, and CD-5 mutations. The 266N and 279R positions (bold and labeled in the Consensus sequence) indicate the amino acids predicted to be involved in an ATP binding domain and an arginine binding domain, respectively (Marchler-Bauer et al. 2013). The bold and underlined 273Q and 275R positions denote the y11-2 and y11 nonsynonymous amino acid changes in Glyma13g30560, respectively. The lower 275R position (in the ‘Glyma15g08680 CD-5′ sequence) denotes the CD-5 nonsynonymous amino acid change in Glyma15g08680. The bold and underlined 313C denotes the nonsynonymous amino acid change in Oryza sativa chl9. The letters indicate residues that are not completely conserved across species. The wild-type soybean sequence and the sequences of the other species, listed in order, are available in the National Center for Biotechnology Information database under accession numbers: XP_003543008, XP_003546019, XP_007148073, AFK38677, XP_003593716, AET86637, NP_193583, XP_002316838, NP_001050493, ACN32024, AAA99720, U38804, AF017642, and Z11165.
Mentions: Palmer et al. (1989) found that the y11 and CD-5 chlorophyll deficient mutants display nearly identical chlorophyll deficient phenotypes (Figure S1). Allelism test results and similarity in phenotype led the authors (Palmer et al. 1989) to initially consider that the two mutants were allelic and thus were surprised to find that CD-5 cosegregated with the blunt pubescence tip locus (pb) on chromosome 15. After identifying the likely y11 causative mutation in a Mg-chelatase subunit, we identified a Mg-chelatase paralog on chromosome 15, Glyma15g08680, as a candidate gene for the CD-5. Sequencing of Glyma15g08680 from two homozygous CD-5 individuals and from two wild-type individuals all derived from a segregating family identified a single non-synonymous SNP in the third exon. A CAPS assay of seventeen individuals segregating for the presence of CD-5 showed prefect cosegregation of the candidate SNP with the mutant phenotype (Figure S3). These results suggest that the identified SNP is causative of the CD-5 chlorophyll-deficient phenotype. A comparative sequence analysis across 29 diverse soybean lines (McHale et al. 2012) found that the single base substitution in Glyma15g08680 was unique to CD-5. All 29 of the diverse lines exhibited the wild-type sequence (Figure S4A). Remarkably, the Glyma15g08680 amino acid change in CD-5 (Q275R) was identical in position and sequence to the Glyma13g30560 change in y11 (Q275R) (Figure 5 and Figure S4B).

Bottom Line: This mutation was identified in the ChlI1b gene, a paralog of ChlI1a.Protein sequence alignments of the two Mg-chelatase subunits indicated that the sites of amino acid modification in MinnGold, T219H, and CD-5 are highly conserved among photosynthetic species.These results suggest that amino acid alterations in this critical domain may create competitive inhibitory interactions between the mutant and wild-type ChlI1a and ChlI1b proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.

Show MeSH