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Function annotation of an SBP-box gene in Arabidopsis based on analysis of co-expression networks and promoters.

Wang Y, Hu Z, Yang Y, Chen X, Chen G - Int J Mol Sci (2009)

Bottom Line: The interactome analysis of the correlation genes suggests that SPL genes also take part in metabolism of glucose, inorganic salts, and ATP production.Furthermore, the promoters of the correlated genes contain a core binding cis-element (GTAC).All of these analyses suggest that SPL genes have varied functions in Arabidopsis.

View Article: PubMed Central - PubMed

Affiliation: College of Bioengineering, Chongqing University, Chongqing 400030, P.R. China. dna.wangyi@yahoo.com.cn

ABSTRACT
The SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family is an SBP-box transcription family in Arabidopsis. While several physiological responses to SPL genes have been reported, their biological role remains elusive. Here, we use a combined analysis of expression correlation, the interactome, and promoter content to infer the biological role of the SPL genes in Arabidopsis thaliana. Analysis of the SPL-correlated gene network reveals multiple functions for SPL genes. Network analysis shows that SPL genes function by controlling other transcription factor families and have relatives with membrane protein transport activity. The interactome analysis of the correlation genes suggests that SPL genes also take part in metabolism of glucose, inorganic salts, and ATP production. Furthermore, the promoters of the correlated genes contain a core binding cis-element (GTAC). All of these analyses suggest that SPL genes have varied functions in Arabidopsis.

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Promoter and network analysis of SPL genes. (A) The distribution of the occurrence of the GTAC motif in 1000 sets of SPL genes promoters randomly selected from the Arabidopsis genome. Distribution in 1,000 randomly generated promoter sets: Average 29.7. Distribution in 1,000 bootstraps of our promoter set: Average 42.9. Z-score, Significance: 2.2,0.05. (B) A putative network of SPL genes (a solid line indicates co-expression, and a dashed line indicates protein interactions).
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f5-ijms-10-00116: Promoter and network analysis of SPL genes. (A) The distribution of the occurrence of the GTAC motif in 1000 sets of SPL genes promoters randomly selected from the Arabidopsis genome. Distribution in 1,000 randomly generated promoter sets: Average 29.7. Distribution in 1,000 bootstraps of our promoter set: Average 42.9. Z-score, Significance: 2.2,0.05. (B) A putative network of SPL genes (a solid line indicates co-expression, and a dashed line indicates protein interactions).

Mentions: Our analysis indicates that the cis-element shared by SPL genes, the GTAC motif, is necessary for binding of SPL proteins to DNA. In the co-expression network, the expression of some SPL genes correlates with that of other SPL genes; these genes may form a complex within the network (Figure 1B). Therefore, we propose that SPL genes regulate themselves. Using promoter analysis, we found the GTAC motif to be present in the 1 kb upstream region in 13/16 of SPL genes a total of 56 times (Supplementary Table 3), which was significantly higher than the occurrence in tetramer sets of randomly selected promoters (Figure 5A). In the AtPID database [38], we found that SPL9 can interact with SPL15, and SPL4 can interact with SPL5. SPL genes may therefore regulate themselves using a feedback loop based on protein interactions and transcriptional regulation (Figure 5B).


Function annotation of an SBP-box gene in Arabidopsis based on analysis of co-expression networks and promoters.

Wang Y, Hu Z, Yang Y, Chen X, Chen G - Int J Mol Sci (2009)

Promoter and network analysis of SPL genes. (A) The distribution of the occurrence of the GTAC motif in 1000 sets of SPL genes promoters randomly selected from the Arabidopsis genome. Distribution in 1,000 randomly generated promoter sets: Average 29.7. Distribution in 1,000 bootstraps of our promoter set: Average 42.9. Z-score, Significance: 2.2,0.05. (B) A putative network of SPL genes (a solid line indicates co-expression, and a dashed line indicates protein interactions).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2662457&req=5

f5-ijms-10-00116: Promoter and network analysis of SPL genes. (A) The distribution of the occurrence of the GTAC motif in 1000 sets of SPL genes promoters randomly selected from the Arabidopsis genome. Distribution in 1,000 randomly generated promoter sets: Average 29.7. Distribution in 1,000 bootstraps of our promoter set: Average 42.9. Z-score, Significance: 2.2,0.05. (B) A putative network of SPL genes (a solid line indicates co-expression, and a dashed line indicates protein interactions).
Mentions: Our analysis indicates that the cis-element shared by SPL genes, the GTAC motif, is necessary for binding of SPL proteins to DNA. In the co-expression network, the expression of some SPL genes correlates with that of other SPL genes; these genes may form a complex within the network (Figure 1B). Therefore, we propose that SPL genes regulate themselves. Using promoter analysis, we found the GTAC motif to be present in the 1 kb upstream region in 13/16 of SPL genes a total of 56 times (Supplementary Table 3), which was significantly higher than the occurrence in tetramer sets of randomly selected promoters (Figure 5A). In the AtPID database [38], we found that SPL9 can interact with SPL15, and SPL4 can interact with SPL5. SPL genes may therefore regulate themselves using a feedback loop based on protein interactions and transcriptional regulation (Figure 5B).

Bottom Line: The interactome analysis of the correlation genes suggests that SPL genes also take part in metabolism of glucose, inorganic salts, and ATP production.Furthermore, the promoters of the correlated genes contain a core binding cis-element (GTAC).All of these analyses suggest that SPL genes have varied functions in Arabidopsis.

View Article: PubMed Central - PubMed

Affiliation: College of Bioengineering, Chongqing University, Chongqing 400030, P.R. China. dna.wangyi@yahoo.com.cn

ABSTRACT
The SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family is an SBP-box transcription family in Arabidopsis. While several physiological responses to SPL genes have been reported, their biological role remains elusive. Here, we use a combined analysis of expression correlation, the interactome, and promoter content to infer the biological role of the SPL genes in Arabidopsis thaliana. Analysis of the SPL-correlated gene network reveals multiple functions for SPL genes. Network analysis shows that SPL genes function by controlling other transcription factor families and have relatives with membrane protein transport activity. The interactome analysis of the correlation genes suggests that SPL genes also take part in metabolism of glucose, inorganic salts, and ATP production. Furthermore, the promoters of the correlated genes contain a core binding cis-element (GTAC). All of these analyses suggest that SPL genes have varied functions in Arabidopsis.

Show MeSH