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The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants.

Colasanti J, Tremblay R, Wong AY, Coneva V, Kozaki A, Mable BK - BMC Genomics (2006)

Bottom Line: The maize INDETERMINATE1 gene, ID1, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs.The zinc fingers and surrounding sequence make up the signature ID domain (IDD), which appears to be found in all higher plant genomes.These similarities between ID1 and closely related genes in other grasses point to possible similarities in function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada. jcolasan@uoguelph.ca

ABSTRACT

Background: The maize INDETERMINATE1 gene, ID1, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs. The zinc fingers and surrounding sequence make up the signature ID domain (IDD), which appears to be found in all higher plant genomes. The presence of zinc finger domains and previous biochemical studies showing that ID1 binds to DNA suggests that members of this gene family are involved in transcriptional regulation.

Results: Comparison of IDD genes identified in Arabidopsis and rice genomes, and all IDD genes discovered in maize EST and genomic databases, suggest that ID1 is a unique member of this gene family. High levels of sequence similarity amongst all IDD genes from maize, rice and Arabidopsis suggest that they are derived from a common ancestor. Several unique features of ID1 suggest that it is a divergent member of the maize IDD family. Although no clear ID1 ortholog was identified in the Arabidopsis genome, highly similar genes that encode proteins with identity extending beyond the ID domain were isolated from rice and sorghum. Phylogenetic comparisons show that these putative orthologs, along with maize ID1, form a group separate from other IDD genes. In contrast to ID1 mRNA, which is detected exclusively in immature leaves, several maize IDD genes showed a broad range of expression in various tissues. Further, Western analysis with an antibody that cross-reacts with ID1 protein and potential orthologs from rice and sorghum shows that all three proteins are detected in immature leaves only.

Conclusion: Comparative genomic analysis shows that the IDD zinc finger family is highly conserved among both monocots and dicots. The leaf-specific ID1 expression pattern distinguishes it from other maize IDD genes examined. A similar leaf-specific localization pattern was observed for the putative ID1 protein orthologs from rice and sorghum. These similarities between ID1 and closely related genes in other grasses point to possible similarities in function.

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Western blot analysis of ID1, OsID and SbID protein accumulation in maize, rice and sorghum tissues with anti-ID antibody. Ap, apical region containing shoot meristem and leaf primordia; ImL, Immature leaves, approximately 2 to 8 cm above the apical region; ML, mature green leaf blades; FP, floral primordial tissues, which included ear tissue for maize, and yet to emerge spikelet primordia for rice and sorghum. Mature spikelet inflorescence, F, was also examined for rice and sorghum. Arrows at left indicate molecular weight standards of 84 kD and 61 kD.
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Figure 6: Western blot analysis of ID1, OsID and SbID protein accumulation in maize, rice and sorghum tissues with anti-ID antibody. Ap, apical region containing shoot meristem and leaf primordia; ImL, Immature leaves, approximately 2 to 8 cm above the apical region; ML, mature green leaf blades; FP, floral primordial tissues, which included ear tissue for maize, and yet to emerge spikelet primordia for rice and sorghum. Mature spikelet inflorescence, F, was also examined for rice and sorghum. Arrows at left indicate molecular weight standards of 84 kD and 61 kD.

Mentions: To investigate whether these related grass genes have similar expression patterns, an anti-ID1 antibody specific for the C-terminal 20 amino acids of ID1 was used to analyse where OsID and SbID proteins are localized in developing rice and sorghum. The deduced C-terminal peptide sequences of SbID and OsID proteins are nearly identical to the C-terminal 20 amino acids of ID1; i.e., SbID and OsID share 19/20 and 18/20 amino acids, respectively (Figure 5). Figure 6 shows that this antibody cross-reacts with a single protein of the expected size in each species. Interestingly, similar to maize ID1, OsID and SbID proteins are detected exclusively in immature leaves and are absent in mature leaves and the region of the shoot apex (Figure 6). Furthermore, all three IDD proteins are absent in floral tissues in all species. Therefore the identical localization patterns of ID1 and its putative orthologs SbID and OsID show that all three genes have similar expression patterns.


The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants.

Colasanti J, Tremblay R, Wong AY, Coneva V, Kozaki A, Mable BK - BMC Genomics (2006)

Western blot analysis of ID1, OsID and SbID protein accumulation in maize, rice and sorghum tissues with anti-ID antibody. Ap, apical region containing shoot meristem and leaf primordia; ImL, Immature leaves, approximately 2 to 8 cm above the apical region; ML, mature green leaf blades; FP, floral primordial tissues, which included ear tissue for maize, and yet to emerge spikelet primordia for rice and sorghum. Mature spikelet inflorescence, F, was also examined for rice and sorghum. Arrows at left indicate molecular weight standards of 84 kD and 61 kD.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1586020&req=5

Figure 6: Western blot analysis of ID1, OsID and SbID protein accumulation in maize, rice and sorghum tissues with anti-ID antibody. Ap, apical region containing shoot meristem and leaf primordia; ImL, Immature leaves, approximately 2 to 8 cm above the apical region; ML, mature green leaf blades; FP, floral primordial tissues, which included ear tissue for maize, and yet to emerge spikelet primordia for rice and sorghum. Mature spikelet inflorescence, F, was also examined for rice and sorghum. Arrows at left indicate molecular weight standards of 84 kD and 61 kD.
Mentions: To investigate whether these related grass genes have similar expression patterns, an anti-ID1 antibody specific for the C-terminal 20 amino acids of ID1 was used to analyse where OsID and SbID proteins are localized in developing rice and sorghum. The deduced C-terminal peptide sequences of SbID and OsID proteins are nearly identical to the C-terminal 20 amino acids of ID1; i.e., SbID and OsID share 19/20 and 18/20 amino acids, respectively (Figure 5). Figure 6 shows that this antibody cross-reacts with a single protein of the expected size in each species. Interestingly, similar to maize ID1, OsID and SbID proteins are detected exclusively in immature leaves and are absent in mature leaves and the region of the shoot apex (Figure 6). Furthermore, all three IDD proteins are absent in floral tissues in all species. Therefore the identical localization patterns of ID1 and its putative orthologs SbID and OsID show that all three genes have similar expression patterns.

Bottom Line: The maize INDETERMINATE1 gene, ID1, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs.The zinc fingers and surrounding sequence make up the signature ID domain (IDD), which appears to be found in all higher plant genomes.These similarities between ID1 and closely related genes in other grasses point to possible similarities in function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada. jcolasan@uoguelph.ca

ABSTRACT

Background: The maize INDETERMINATE1 gene, ID1, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs. The zinc fingers and surrounding sequence make up the signature ID domain (IDD), which appears to be found in all higher plant genomes. The presence of zinc finger domains and previous biochemical studies showing that ID1 binds to DNA suggests that members of this gene family are involved in transcriptional regulation.

Results: Comparison of IDD genes identified in Arabidopsis and rice genomes, and all IDD genes discovered in maize EST and genomic databases, suggest that ID1 is a unique member of this gene family. High levels of sequence similarity amongst all IDD genes from maize, rice and Arabidopsis suggest that they are derived from a common ancestor. Several unique features of ID1 suggest that it is a divergent member of the maize IDD family. Although no clear ID1 ortholog was identified in the Arabidopsis genome, highly similar genes that encode proteins with identity extending beyond the ID domain were isolated from rice and sorghum. Phylogenetic comparisons show that these putative orthologs, along with maize ID1, form a group separate from other IDD genes. In contrast to ID1 mRNA, which is detected exclusively in immature leaves, several maize IDD genes showed a broad range of expression in various tissues. Further, Western analysis with an antibody that cross-reacts with ID1 protein and potential orthologs from rice and sorghum shows that all three proteins are detected in immature leaves only.

Conclusion: Comparative genomic analysis shows that the IDD zinc finger family is highly conserved among both monocots and dicots. The leaf-specific ID1 expression pattern distinguishes it from other maize IDD genes examined. A similar leaf-specific localization pattern was observed for the putative ID1 protein orthologs from rice and sorghum. These similarities between ID1 and closely related genes in other grasses point to possible similarities in function.

Show MeSH