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Identification of potential transcriptional regulators of actinorhizal symbioses in Casuarina glauca and Alnus glutinosa.

Diédhiou I, Tromas A, Cissoko M, Gray K, Parizot B, Crabos A, Alloisio N, Fournier P, Carro L, Svistoonoff S, Gherbi H, Hocher V, Diouf D, Laplaze L, Champion A - BMC Plant Biol. (2014)

Bottom Line: Based on published transcriptome datasets and quantitative PCR analysis, we found that 39% and 26% of these transcription factors were regulated during C. glauca and A. glutinosa-Frankia interactions, respectively.We also identified an actinorhizal-specific transcription factor belonging to the zinc finger C1-2i subfamily we named CgZF1 in C. glauca and AgZF1 in A. glutinosa.Interestingly, comparison of the non-legume and legume TF with signaling elements from actinorhizal species revealed a new subgroup of nodule-specific C2H2 TF that could be specifically involved in actinorhizal symbioses.

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ABSTRACT

Background: Trees belonging to the Casuarinaceae and Betulaceae families play an important ecological role and are useful tools in forestry for degraded land rehabilitation and reforestation. These functions are linked to their capacity to establish symbiotic relationships with a nitrogen-fixing soil bacterium of the genus Frankia. However, the molecular mechanisms controlling the establishment of these symbioses are poorly understood. The aim of this work was to identify potential transcription factors involved in the establishment and functioning of actinorhizal symbioses.

Results: We identified 202 putative transcription factors by in silico analysis in 40 families in Casuarina glauca (Casuarinaceae) and 195 in 35 families in Alnus glutinosa (Betulaceae) EST databases. Based on published transcriptome datasets and quantitative PCR analysis, we found that 39% and 26% of these transcription factors were regulated during C. glauca and A. glutinosa-Frankia interactions, respectively. Phylogenetic studies confirmed the presence of common key transcription factors such as NSP, NF-YA and ERN-related proteins involved in nodule formation in legumes, which confirm the existence of a common symbiosis signaling pathway in nitrogen-fixing root nodule symbioses. We also identified an actinorhizal-specific transcription factor belonging to the zinc finger C1-2i subfamily we named CgZF1 in C. glauca and AgZF1 in A. glutinosa.

Conclusions: We identified putative nodulation-associated transcription factors with particular emphasis on members of the GRAS, NF-YA, ERF and C2H2 families. Interestingly, comparison of the non-legume and legume TF with signaling elements from actinorhizal species revealed a new subgroup of nodule-specific C2H2 TF that could be specifically involved in actinorhizal symbioses. In silico identification, transcript analysis, and phylogeny reconstruction of transcription factor families paves the way for the study of specific molecular regulation of symbiosis in response to Frankia infection.

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Expression profiles of potential transcription factors inCasuarina glaucaandAlnus glutinosanodules compared to non-inoculated roots. Purple and orange bars represent putative transcriptional regulators from C. glauca and A. glutinosa respectively. Bars represent fold change in nodules compared to non-inoculated roots (Fold change or FC ≥ 2 or ≤ −2 and p-value < 0.01). Transcription factors induced and repressed in C. glauca and A. glutinosa nodules are highlighted in tanned brown and light pink respectively. Astericks identify the genes confirmed by Q-PCR. Red triangles identify the transcription factors (CgZF1 and AgZF1) most strongly induced in the nodules.
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Fig1: Expression profiles of potential transcription factors inCasuarina glaucaandAlnus glutinosanodules compared to non-inoculated roots. Purple and orange bars represent putative transcriptional regulators from C. glauca and A. glutinosa respectively. Bars represent fold change in nodules compared to non-inoculated roots (Fold change or FC ≥ 2 or ≤ −2 and p-value < 0.01). Transcription factors induced and repressed in C. glauca and A. glutinosa nodules are highlighted in tanned brown and light pink respectively. Astericks identify the genes confirmed by Q-PCR. Red triangles identify the transcription factors (CgZF1 and AgZF1) most strongly induced in the nodules.

Mentions: Microarray data was retrieved from previous published studies [5,7]. First, we used a simple comparative transcriptomics tool called Casuarina Transcriptome Compendium (CTC) to compare the microarray data and generate expression profiles in different conditions. Using CTC, we identified 54 repressed transcription factors and 25 induced in C. glauca nodules compared to non-inoculated roots with a nodule/root fold change ≥ 2 or ≤ −2 and a p-value ≤ 0.01 (Figure 1 and Additional file 3). The C2H2 family was the most frequently represented in the up-regulated class followed by the ERF and bHLH families (Additional file 4). Induction of 11 transcription factors in C. glauca nodules was confirmed by quantitative PCR, which also revealed similar induction values than microarray data (Additional file 5). Induction of CgZF1 was validated by semi-quantitative PCR because its expression was not detectable in the non-inoculated roots needed to calibrate Q-PCR analysis (Additional file 6).Figure 1


Identification of potential transcriptional regulators of actinorhizal symbioses in Casuarina glauca and Alnus glutinosa.

Diédhiou I, Tromas A, Cissoko M, Gray K, Parizot B, Crabos A, Alloisio N, Fournier P, Carro L, Svistoonoff S, Gherbi H, Hocher V, Diouf D, Laplaze L, Champion A - BMC Plant Biol. (2014)

Expression profiles of potential transcription factors inCasuarina glaucaandAlnus glutinosanodules compared to non-inoculated roots. Purple and orange bars represent putative transcriptional regulators from C. glauca and A. glutinosa respectively. Bars represent fold change in nodules compared to non-inoculated roots (Fold change or FC ≥ 2 or ≤ −2 and p-value < 0.01). Transcription factors induced and repressed in C. glauca and A. glutinosa nodules are highlighted in tanned brown and light pink respectively. Astericks identify the genes confirmed by Q-PCR. Red triangles identify the transcription factors (CgZF1 and AgZF1) most strongly induced in the nodules.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4264327&req=5

Fig1: Expression profiles of potential transcription factors inCasuarina glaucaandAlnus glutinosanodules compared to non-inoculated roots. Purple and orange bars represent putative transcriptional regulators from C. glauca and A. glutinosa respectively. Bars represent fold change in nodules compared to non-inoculated roots (Fold change or FC ≥ 2 or ≤ −2 and p-value < 0.01). Transcription factors induced and repressed in C. glauca and A. glutinosa nodules are highlighted in tanned brown and light pink respectively. Astericks identify the genes confirmed by Q-PCR. Red triangles identify the transcription factors (CgZF1 and AgZF1) most strongly induced in the nodules.
Mentions: Microarray data was retrieved from previous published studies [5,7]. First, we used a simple comparative transcriptomics tool called Casuarina Transcriptome Compendium (CTC) to compare the microarray data and generate expression profiles in different conditions. Using CTC, we identified 54 repressed transcription factors and 25 induced in C. glauca nodules compared to non-inoculated roots with a nodule/root fold change ≥ 2 or ≤ −2 and a p-value ≤ 0.01 (Figure 1 and Additional file 3). The C2H2 family was the most frequently represented in the up-regulated class followed by the ERF and bHLH families (Additional file 4). Induction of 11 transcription factors in C. glauca nodules was confirmed by quantitative PCR, which also revealed similar induction values than microarray data (Additional file 5). Induction of CgZF1 was validated by semi-quantitative PCR because its expression was not detectable in the non-inoculated roots needed to calibrate Q-PCR analysis (Additional file 6).Figure 1

Bottom Line: Based on published transcriptome datasets and quantitative PCR analysis, we found that 39% and 26% of these transcription factors were regulated during C. glauca and A. glutinosa-Frankia interactions, respectively.We also identified an actinorhizal-specific transcription factor belonging to the zinc finger C1-2i subfamily we named CgZF1 in C. glauca and AgZF1 in A. glutinosa.Interestingly, comparison of the non-legume and legume TF with signaling elements from actinorhizal species revealed a new subgroup of nodule-specific C2H2 TF that could be specifically involved in actinorhizal symbioses.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Trees belonging to the Casuarinaceae and Betulaceae families play an important ecological role and are useful tools in forestry for degraded land rehabilitation and reforestation. These functions are linked to their capacity to establish symbiotic relationships with a nitrogen-fixing soil bacterium of the genus Frankia. However, the molecular mechanisms controlling the establishment of these symbioses are poorly understood. The aim of this work was to identify potential transcription factors involved in the establishment and functioning of actinorhizal symbioses.

Results: We identified 202 putative transcription factors by in silico analysis in 40 families in Casuarina glauca (Casuarinaceae) and 195 in 35 families in Alnus glutinosa (Betulaceae) EST databases. Based on published transcriptome datasets and quantitative PCR analysis, we found that 39% and 26% of these transcription factors were regulated during C. glauca and A. glutinosa-Frankia interactions, respectively. Phylogenetic studies confirmed the presence of common key transcription factors such as NSP, NF-YA and ERN-related proteins involved in nodule formation in legumes, which confirm the existence of a common symbiosis signaling pathway in nitrogen-fixing root nodule symbioses. We also identified an actinorhizal-specific transcription factor belonging to the zinc finger C1-2i subfamily we named CgZF1 in C. glauca and AgZF1 in A. glutinosa.

Conclusions: We identified putative nodulation-associated transcription factors with particular emphasis on members of the GRAS, NF-YA, ERF and C2H2 families. Interestingly, comparison of the non-legume and legume TF with signaling elements from actinorhizal species revealed a new subgroup of nodule-specific C2H2 TF that could be specifically involved in actinorhizal symbioses. In silico identification, transcript analysis, and phylogeny reconstruction of transcription factor families paves the way for the study of specific molecular regulation of symbiosis in response to Frankia infection.

Show MeSH
Related in: MedlinePlus