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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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Phylogenetic comparison of IDD amino acid sequences from several plant species. Mid-point rooted phylogram based on amino acid sequences for the same region used in Figure 7. IDD genes found in maize (red), rice (blue) and Arabidopsis (black), as well as PCP1 from potato (Solanum tuberosum; green) and a potential ortholog of ID1 from Sorghum bicolor, SbID (purple), with Bayesian posterior probability values above 80% indicated above the branches. Circles of the same colour and labeled with the same letter on both trees highlight differences between the two sets of analyses; in particular, circled groups indicate amino acid groupings between Arabidopsis and grasses that were not apparent in genomic DNA analyses. Sequences enclosed by rectangles labeled 'D' form a less-well supported Arabidopsis-grass amino acid assemblage.
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Figure 8: Phylogenetic comparison of IDD amino acid sequences from several plant species. Mid-point rooted phylogram based on amino acid sequences for the same region used in Figure 7. IDD genes found in maize (red), rice (blue) and Arabidopsis (black), as well as PCP1 from potato (Solanum tuberosum; green) and a potential ortholog of ID1 from Sorghum bicolor, SbID (purple), with Bayesian posterior probability values above 80% indicated above the branches. Circles of the same colour and labeled with the same letter on both trees highlight differences between the two sets of analyses; in particular, circled groups indicate amino acid groupings between Arabidopsis and grasses that were not apparent in genomic DNA analyses. Sequences enclosed by rectangles labeled 'D' form a less-well supported Arabidopsis-grass amino acid assemblage.

Mentions: Phylogenetic analyses based on amino acid sequences gave different trees than those based on nucleotide sequences, but may reflect functional similarities among highly divergent proteins between species (compare Figures 7 and 8). In particular, the amino acid analyses indicated mixed clustering of genes between Arabidopsis and grasses whereas this was not seen in the genomic DNA analysis. Circled sets of sequences with the same letters are those that form highly supported "mixed" groups in the amino acid but not the nucleotide-based analyses. Note in particular that the two most divergent groups of sequences within each group clustered together in the amino acid analysis (circles labeled 'A'), based on sharing of unique domains not found in the other sequence types (although the branch lengths separating them are very long). Similarly, AtIDD1 and AtIDD2 appeared to be functionally related to ZmIDD1 and OsIDD1 (circles labeled 'B') and ZmIDD7/OsIDD7 appeared to be most functionally related to Arabidopsis sequences AtIDD9, AtIDD10, AtIDD12 and AtIDD13 (circles labeled 'C'). Sequences in rectangles labeled 'D' are quite divergent from one another but formed a weakly supported (pp = 87) grouping between grasses and Arabidopsis (and potato) sequences. Importantly, no functional equivalent was found for the ID1/OsID/SbID group (circle labeled 'E') in Arabidopsis and their relationship to the ZmIDD6/OsIDD9 and ZmIDD8/ZmIDD10/OsIDD5 groups was not well resolved in the amino acid analysis.


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)

Phylogenetic comparison of IDD amino acid sequences from several plant species. Mid-point rooted phylogram based on amino acid sequences for the same region used in Figure 7. IDD genes found in maize (red), rice (blue) and Arabidopsis (black), as well as PCP1 from potato (Solanum tuberosum; green) and a potential ortholog of ID1 from Sorghum bicolor, SbID (purple), with Bayesian posterior probability values above 80% indicated above the branches. Circles of the same colour and labeled with the same letter on both trees highlight differences between the two sets of analyses; in particular, circled groups indicate amino acid groupings between Arabidopsis and grasses that were not apparent in genomic DNA analyses. Sequences enclosed by rectangles labeled 'D' form a less-well supported Arabidopsis-grass amino acid assemblage.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Phylogenetic comparison of IDD amino acid sequences from several plant species. Mid-point rooted phylogram based on amino acid sequences for the same region used in Figure 7. IDD genes found in maize (red), rice (blue) and Arabidopsis (black), as well as PCP1 from potato (Solanum tuberosum; green) and a potential ortholog of ID1 from Sorghum bicolor, SbID (purple), with Bayesian posterior probability values above 80% indicated above the branches. Circles of the same colour and labeled with the same letter on both trees highlight differences between the two sets of analyses; in particular, circled groups indicate amino acid groupings between Arabidopsis and grasses that were not apparent in genomic DNA analyses. Sequences enclosed by rectangles labeled 'D' form a less-well supported Arabidopsis-grass amino acid assemblage.
Mentions: Phylogenetic analyses based on amino acid sequences gave different trees than those based on nucleotide sequences, but may reflect functional similarities among highly divergent proteins between species (compare Figures 7 and 8). In particular, the amino acid analyses indicated mixed clustering of genes between Arabidopsis and grasses whereas this was not seen in the genomic DNA analysis. Circled sets of sequences with the same letters are those that form highly supported "mixed" groups in the amino acid but not the nucleotide-based analyses. Note in particular that the two most divergent groups of sequences within each group clustered together in the amino acid analysis (circles labeled 'A'), based on sharing of unique domains not found in the other sequence types (although the branch lengths separating them are very long). Similarly, AtIDD1 and AtIDD2 appeared to be functionally related to ZmIDD1 and OsIDD1 (circles labeled 'B') and ZmIDD7/OsIDD7 appeared to be most functionally related to Arabidopsis sequences AtIDD9, AtIDD10, AtIDD12 and AtIDD13 (circles labeled 'C'). Sequences in rectangles labeled 'D' are quite divergent from one another but formed a weakly supported (pp = 87) grouping between grasses and Arabidopsis (and potato) sequences. Importantly, no functional equivalent was found for the ID1/OsID/SbID group (circle labeled 'E') in Arabidopsis and their relationship to the ZmIDD6/OsIDD9 and ZmIDD8/ZmIDD10/OsIDD5 groups was not well resolved in the amino acid analysis.

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