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Identification of transcription factor genes and their correlation with the high diversity of stramenopiles.

Buitrago-Flórez FJ, Restrepo S, Riaño-Pachón DM - PLoS ONE (2014)

Bottom Line: In some species we found gene families with high relative importance.Additionally, we found gains and losses in TF and TR families specific to some species and clades, as well as, two families with high abundance specific to the autotrophic species and three families with high abundance specific to the heterotropic species.Specific TF and TR families identified in this work appear to be correlated with particular traits in the Stramenopiles group and may be correlated with the high complexity and diversity in Stramenopiles.

View Article: PubMed Central - PubMed

Affiliation: Group of Computational and Evolutionary Biology, Universidad de los Andes, Bogotá, Colombia; Micology and Plant Pathology Laboratory, Universidad de los Andes, Bogotá, Colombia.

ABSTRACT
The biological diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they embrace many ecologically important autothrophic (e.g., diatoms, brown algae), and heterotrophic (e.g., oomycetes) groups. Transcription factors (TFs) and other transcription regulators (TRs) regulate spatial and temporal gene expression. A plethora of transcriptional regulatory proteins have been identified and classified into families on the basis of sequence similarity. The purpose of this work is to identify the TF and TR complement in diverse species belonging to Stramenopiles in order to understand how these regulators may contribute to their observed diversity. We identified and classified 63 TF and TR families in 11 species of Stramenopiles. In some species we found gene families with high relative importance. Taking into account the 63 TF and TR families identified, 28 TF and TR families were established to be positively correlated with specific traits like number of predicted proteins, number of flagella and number of cell types during the life cycle. Additionally, we found gains and losses in TF and TR families specific to some species and clades, as well as, two families with high abundance specific to the autotrophic species and three families with high abundance specific to the heterotropic species. For the first time, there is a systematic search of TF and TR families in Stramenopiles. The attempts to uncover relationships between these families and the complexity of this group may be of great impact, considering that there are several important pathogens of plants and animals, as well as, important species involved in carbon cycling. Specific TF and TR families identified in this work appear to be correlated with particular traits in the Stramenopiles group and may be correlated with the high complexity and diversity in Stramenopiles.

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Relative Importance of TF and TR families in Stramenopiles.The Y axis represents the relative importance of each family, the X axis represents the 9 species used in this study. For each species, families with a high relative importance and correlated with the number of predicted proteins, number of cell types and number of flagella are shown (C2H2 in orange, HSF in green in and MYB-related in blue). Moreover, some families with a low relative importance are shown in the figure as a control for comparison (CSD in yellow, SWI/SNF-BAF60b in purple and TFIIS in pink).
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pone-0111841-g001: Relative Importance of TF and TR families in Stramenopiles.The Y axis represents the relative importance of each family, the X axis represents the 9 species used in this study. For each species, families with a high relative importance and correlated with the number of predicted proteins, number of cell types and number of flagella are shown (C2H2 in orange, HSF in green in and MYB-related in blue). Moreover, some families with a low relative importance are shown in the figure as a control for comparison (CSD in yellow, SWI/SNF-BAF60b in purple and TFIIS in pink).

Mentions: We found 38 TF and 25 TR families in the 11 Stramenopiles evaluated, i.e., about 50% of the total of rules included (Table S3). The relative importance analysis (Figure 1), shows a comparison between the families with a high relative importance like GNAT (proteins with acetyltransferase domain), MYB-related (DNA binding domains from Myb proteins), and C2H2 (protein structural zinc finger that bind DNA, RNA or proteins) with contrasting families with low relative importance across the species, such as CSD, SWI/SNF-BAF60b and TFIIS.


Identification of transcription factor genes and their correlation with the high diversity of stramenopiles.

Buitrago-Flórez FJ, Restrepo S, Riaño-Pachón DM - PLoS ONE (2014)

Relative Importance of TF and TR families in Stramenopiles.The Y axis represents the relative importance of each family, the X axis represents the 9 species used in this study. For each species, families with a high relative importance and correlated with the number of predicted proteins, number of cell types and number of flagella are shown (C2H2 in orange, HSF in green in and MYB-related in blue). Moreover, some families with a low relative importance are shown in the figure as a control for comparison (CSD in yellow, SWI/SNF-BAF60b in purple and TFIIS in pink).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222949&req=5

pone-0111841-g001: Relative Importance of TF and TR families in Stramenopiles.The Y axis represents the relative importance of each family, the X axis represents the 9 species used in this study. For each species, families with a high relative importance and correlated with the number of predicted proteins, number of cell types and number of flagella are shown (C2H2 in orange, HSF in green in and MYB-related in blue). Moreover, some families with a low relative importance are shown in the figure as a control for comparison (CSD in yellow, SWI/SNF-BAF60b in purple and TFIIS in pink).
Mentions: We found 38 TF and 25 TR families in the 11 Stramenopiles evaluated, i.e., about 50% of the total of rules included (Table S3). The relative importance analysis (Figure 1), shows a comparison between the families with a high relative importance like GNAT (proteins with acetyltransferase domain), MYB-related (DNA binding domains from Myb proteins), and C2H2 (protein structural zinc finger that bind DNA, RNA or proteins) with contrasting families with low relative importance across the species, such as CSD, SWI/SNF-BAF60b and TFIIS.

Bottom Line: In some species we found gene families with high relative importance.Additionally, we found gains and losses in TF and TR families specific to some species and clades, as well as, two families with high abundance specific to the autotrophic species and three families with high abundance specific to the heterotropic species.Specific TF and TR families identified in this work appear to be correlated with particular traits in the Stramenopiles group and may be correlated with the high complexity and diversity in Stramenopiles.

View Article: PubMed Central - PubMed

Affiliation: Group of Computational and Evolutionary Biology, Universidad de los Andes, Bogotá, Colombia; Micology and Plant Pathology Laboratory, Universidad de los Andes, Bogotá, Colombia.

ABSTRACT
The biological diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they embrace many ecologically important autothrophic (e.g., diatoms, brown algae), and heterotrophic (e.g., oomycetes) groups. Transcription factors (TFs) and other transcription regulators (TRs) regulate spatial and temporal gene expression. A plethora of transcriptional regulatory proteins have been identified and classified into families on the basis of sequence similarity. The purpose of this work is to identify the TF and TR complement in diverse species belonging to Stramenopiles in order to understand how these regulators may contribute to their observed diversity. We identified and classified 63 TF and TR families in 11 species of Stramenopiles. In some species we found gene families with high relative importance. Taking into account the 63 TF and TR families identified, 28 TF and TR families were established to be positively correlated with specific traits like number of predicted proteins, number of flagella and number of cell types during the life cycle. Additionally, we found gains and losses in TF and TR families specific to some species and clades, as well as, two families with high abundance specific to the autotrophic species and three families with high abundance specific to the heterotropic species. For the first time, there is a systematic search of TF and TR families in Stramenopiles. The attempts to uncover relationships between these families and the complexity of this group may be of great impact, considering that there are several important pathogens of plants and animals, as well as, important species involved in carbon cycling. Specific TF and TR families identified in this work appear to be correlated with particular traits in the Stramenopiles group and may be correlated with the high complexity and diversity in Stramenopiles.

Show MeSH