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Vascular gene expression: a hypothesis.

Martínez-Navarro AC, Galván-Gordillo SV, Xoconostle-Cázares B, Ruiz-Medrano R - Front Plant Sci (2013)

Bottom Line: Both lycophyte and bryophyte display motifs similar to those found in Arabidopsis with a significantly low E-value, while the chlorophytes showed either a different conserved motif or no conserved motif at all.These results suggest that these same genes are expressed coordinately in non-vascular plants; this coordinate expression may have been one of the prerequisites for the development of conducting tissues in plants.The presence of CmPP16, APL, FT, and YDA in chlorophytes suggests the recruitment of ancient regulatory networks for the development of the vascular tissue during evolution while OPS is a novel protein specific to vascular plants.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology and Bioengineering, CINVESTAV-IPN Mexico DF, Mexico.

ABSTRACT
The phloem is the conduit through which photoassimilates are distributed from autotrophic to heterotrophic tissues and is involved in the distribution of signaling molecules that coordinate plant growth and responses to the environment. Phloem function depends on the coordinate expression of a large array of genes. We have previously identified conserved motifs in upstream regions of the Arabidopsis genes, encoding the homologs of pumpkin phloem sap mRNAs, displaying expression in vascular tissues. This tissue-specific expression in Arabidopsis is predicted by the overrepresentation of GA/CT-rich motifs in gene promoters. In this work we have searched for common motifs in upstream regions of the homologous genes from plants considered to possess a "primitive" vascular tissue (a lycophyte), as well as from others that lack a true vascular tissue (a bryophyte), and finally from chlorophytes. Both lycophyte and bryophyte display motifs similar to those found in Arabidopsis with a significantly low E-value, while the chlorophytes showed either a different conserved motif or no conserved motif at all. These results suggest that these same genes are expressed coordinately in non-vascular plants; this coordinate expression may have been one of the prerequisites for the development of conducting tissues in plants. We have also analyzed the phylogeny of conserved proteins that may be involved in phloem function and development. The presence of CmPP16, APL, FT, and YDA in chlorophytes suggests the recruitment of ancient regulatory networks for the development of the vascular tissue during evolution while OPS is a novel protein specific to vascular plants.

No MeSH data available.


Related in: MedlinePlus

(A,B) MEME analysis of SETPHs from monocots (upper panel) and dicots (lower panel). Shown are the three overrepresented motifs in each promoter set identified by MEME analysis with the lowest Expectation (E) values below each motif.
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Figure 1: (A,B) MEME analysis of SETPHs from monocots (upper panel) and dicots (lower panel). Shown are the three overrepresented motifs in each promoter set identified by MEME analysis with the lowest Expectation (E) values below each motif.

Mentions: A probabilistic method, Multiple EM for Motif Elicitation (Bailey and Elkan, 1994) has been used previously in our group in order to detect common motifs in upstream regions of Arabidopsis homologs of pumpkin genes for transcripts isolated from phloem sap exudates (Ruiz-Medrano et al., 2011). Indeed, this method predicted the most abundant motif in this promoter set, GA/CT repeats, which coincided with those found using enumerative methods. More importantly, promoters harboring such repeats were found to be active in vascular tissues, as well as in other tissues. Also recently, the CT rich motifs were reported in CRF (cytokinin response factors) family genes which have strongest expression in phloem tissue, supporting the notion that these motifs are conserved and overrepresented in promoters of genes expressed in this tissue (Zwack et al., 2012). Thus, this method was used for detection of common motifs, if any, in the same gene promoter set in other species. These are shown in Table S1, which includes most members of Viridiplantae, the genomes of which have been deciphered. These are mostly embryophytes, including the moss Physcomitrella patens as the sole representative of bryophytes; a tracheophyte with a less developed conducting tissue, Selaginella moellendorffii; and several dicot and monocot species. Also included are five species of chlorophytes showing colonial organization (Volvox carteri) as well as unicellular algae. The results of this analysis suggest that most dicots harbor a GA/CT rich motif similar to the Arabidopsis SETPs (Figures 1A,B). The three motifs with the lowest E-value are shown for each SETPH. In addition, common motifs were searched for in the same, shuffled sequences as a control. A cutoff value of E = 10−6 for Motif 1 was set; no common motifs were found in shuffled sequences whatsoever below this value. In the “native” sequences (i.e., not subjected to shuffling) those that did show such high values were present in few promoters and were quite degenerate. For example, in Coccomyxa subellipsoidea no motif with an E-value smaller than 1 was found, indeed, it was the only SETPH set in which no common motifs were found (Table S1).


Vascular gene expression: a hypothesis.

Martínez-Navarro AC, Galván-Gordillo SV, Xoconostle-Cázares B, Ruiz-Medrano R - Front Plant Sci (2013)

(A,B) MEME analysis of SETPHs from monocots (upper panel) and dicots (lower panel). Shown are the three overrepresented motifs in each promoter set identified by MEME analysis with the lowest Expectation (E) values below each motif.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3713349&req=5

Figure 1: (A,B) MEME analysis of SETPHs from monocots (upper panel) and dicots (lower panel). Shown are the three overrepresented motifs in each promoter set identified by MEME analysis with the lowest Expectation (E) values below each motif.
Mentions: A probabilistic method, Multiple EM for Motif Elicitation (Bailey and Elkan, 1994) has been used previously in our group in order to detect common motifs in upstream regions of Arabidopsis homologs of pumpkin genes for transcripts isolated from phloem sap exudates (Ruiz-Medrano et al., 2011). Indeed, this method predicted the most abundant motif in this promoter set, GA/CT repeats, which coincided with those found using enumerative methods. More importantly, promoters harboring such repeats were found to be active in vascular tissues, as well as in other tissues. Also recently, the CT rich motifs were reported in CRF (cytokinin response factors) family genes which have strongest expression in phloem tissue, supporting the notion that these motifs are conserved and overrepresented in promoters of genes expressed in this tissue (Zwack et al., 2012). Thus, this method was used for detection of common motifs, if any, in the same gene promoter set in other species. These are shown in Table S1, which includes most members of Viridiplantae, the genomes of which have been deciphered. These are mostly embryophytes, including the moss Physcomitrella patens as the sole representative of bryophytes; a tracheophyte with a less developed conducting tissue, Selaginella moellendorffii; and several dicot and monocot species. Also included are five species of chlorophytes showing colonial organization (Volvox carteri) as well as unicellular algae. The results of this analysis suggest that most dicots harbor a GA/CT rich motif similar to the Arabidopsis SETPs (Figures 1A,B). The three motifs with the lowest E-value are shown for each SETPH. In addition, common motifs were searched for in the same, shuffled sequences as a control. A cutoff value of E = 10−6 for Motif 1 was set; no common motifs were found in shuffled sequences whatsoever below this value. In the “native” sequences (i.e., not subjected to shuffling) those that did show such high values were present in few promoters and were quite degenerate. For example, in Coccomyxa subellipsoidea no motif with an E-value smaller than 1 was found, indeed, it was the only SETPH set in which no common motifs were found (Table S1).

Bottom Line: Both lycophyte and bryophyte display motifs similar to those found in Arabidopsis with a significantly low E-value, while the chlorophytes showed either a different conserved motif or no conserved motif at all.These results suggest that these same genes are expressed coordinately in non-vascular plants; this coordinate expression may have been one of the prerequisites for the development of conducting tissues in plants.The presence of CmPP16, APL, FT, and YDA in chlorophytes suggests the recruitment of ancient regulatory networks for the development of the vascular tissue during evolution while OPS is a novel protein specific to vascular plants.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology and Bioengineering, CINVESTAV-IPN Mexico DF, Mexico.

ABSTRACT
The phloem is the conduit through which photoassimilates are distributed from autotrophic to heterotrophic tissues and is involved in the distribution of signaling molecules that coordinate plant growth and responses to the environment. Phloem function depends on the coordinate expression of a large array of genes. We have previously identified conserved motifs in upstream regions of the Arabidopsis genes, encoding the homologs of pumpkin phloem sap mRNAs, displaying expression in vascular tissues. This tissue-specific expression in Arabidopsis is predicted by the overrepresentation of GA/CT-rich motifs in gene promoters. In this work we have searched for common motifs in upstream regions of the homologous genes from plants considered to possess a "primitive" vascular tissue (a lycophyte), as well as from others that lack a true vascular tissue (a bryophyte), and finally from chlorophytes. Both lycophyte and bryophyte display motifs similar to those found in Arabidopsis with a significantly low E-value, while the chlorophytes showed either a different conserved motif or no conserved motif at all. These results suggest that these same genes are expressed coordinately in non-vascular plants; this coordinate expression may have been one of the prerequisites for the development of conducting tissues in plants. We have also analyzed the phylogeny of conserved proteins that may be involved in phloem function and development. The presence of CmPP16, APL, FT, and YDA in chlorophytes suggests the recruitment of ancient regulatory networks for the development of the vascular tissue during evolution while OPS is a novel protein specific to vascular plants.

No MeSH data available.


Related in: MedlinePlus