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A subtracted cDNA library identifies genes up-regulated during PHOT1-mediated early step of de-etiolation in tomato (Solanum lycopersicum L.).

Hloušková P, Bergougnoux V - BMC Genomics (2016)

Bottom Line: Our conclusions based on bioinformatics data were supported by qRT-PCR analyses the specific investigation of V-H(+)-ATPase during de-etiolation in tomato.The profound induction of transcription/translation, as well as modification of chromatin structure, is relevant in regard to the fact that the entry into photomorphogenesis is based on a deep reprograming of the cell.Also, we postulated that BL restrains the cell expansion by the rapid modification of the cell wall.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research and Faculty of Science, Palacký University in Olomouc, Šlechtitelů 11, CZ-783 71, Olomouc, Czech Republic.

ABSTRACT

Background: De-etiolation is the switch from skoto- to photomorphogenesis, enabling the heterotrophic etiolated seedling to develop into an autotrophic plant. Upon exposure to blue light (BL), reduction of hypocotyl growth rate occurs in two phases: a rapid inhibition mediated by phototropin 1 (PHOT1) within the first 30-40 min of illumination, followed by the cryptochrome 1 (CRY1)-controlled establishment of the steady-state growth rate. Although some information is available for CRY1-mediated de-etiolation, less attention has been given to the PHOT1 phase of de-etiolation.

Results: We generated a subtracted cDNA library using the suppression subtractive hybridization method to investigate the molecular mechanisms of BL-induced de-etiolation in tomato (Solanum lycopersicum L.), an economically important crop. We focused our interest on the first 30 min following the exposure to BL when PHOT1 is required to induce the process. Our library generated 152 expressed sequence tags that were found to be rapidly accumulated upon exposure to BL and consequently potentially regulated by PHOT1. Annotation revealed that biological functions such as modification of chromatin structure, cell wall modification, and transcription/translation comprise an important part of events contributing to the establishment of photomorphogenesis in young tomato seedlings. Our conclusions based on bioinformatics data were supported by qRT-PCR analyses the specific investigation of V-H(+)-ATPase during de-etiolation in tomato.

Conclusions: Our study provides the first report dealing with understanding the PHOT1-mediated phase of de-etiolation. Using subtractive cDNA library, we were able to identify important regulatory mechanisms. The profound induction of transcription/translation, as well as modification of chromatin structure, is relevant in regard to the fact that the entry into photomorphogenesis is based on a deep reprograming of the cell. Also, we postulated that BL restrains the cell expansion by the rapid modification of the cell wall.

No MeSH data available.


Related in: MedlinePlus

Analysis by qPCR of the expression of two genes encoding proteins involved in translation and transcription: Histone 2B (a) and 26S proteasome regulatory complex, subunit RPN10/PSMD4 (b). The data represent the average fold change of 3 independent biological replicates ± SEM. Normalization was done using the pp2ase gene as housekeeping gene. Fold change was calculated compared to the value obtained for the dark control sample. The non-parametric Mann-Whitney U test (Statistica 12) was used to determine the significance of the results
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Fig4: Analysis by qPCR of the expression of two genes encoding proteins involved in translation and transcription: Histone 2B (a) and 26S proteasome regulatory complex, subunit RPN10/PSMD4 (b). The data represent the average fold change of 3 independent biological replicates ± SEM. Normalization was done using the pp2ase gene as housekeeping gene. Fold change was calculated compared to the value obtained for the dark control sample. The non-parametric Mann-Whitney U test (Statistica 12) was used to determine the significance of the results

Mentions: In our study, we found by SSH screening and confirmed by qPCR analysis that H2B is up-regulated during PHOT1-mediated de-etiolation in tomato, indicating that it could play a role during the establishment of photomorphogenesis in tomato (Fig. 4a). Histones form the protein core of the nucleosome around which the DNA helix is wrapped. In this compact state, histones block the association of transcription factors to their binding sites, thus repressing transcription. Several post-translational modifications (acetylation, methylation or phosphorylation) of histone “tails” can influence nucleosome compaction and access to DNA. Moreover, their spatio-temporal regulation as well as their ability for cross-talk renders the regulation of gene expression even more complex [26]. In plants, chromatin remodeling plays an important role during plant growth and development, especially in response to light. Indeed, a large-scale reorganization of chromatin can be observed during the floral transition in Arabidopsis [27]. During de-etiolation, the perception of light induces a remarkable reprogramming of gene expression that leads the heterotrophic seedling to become an autotrophic organism which will be able to complete its life cycle. In darkness, the photomorphogenic repressor DET1 binds to the H2B tails of the nucleosomes surrounding the genes which are repressed in this condition. When light is perceived, the H2B acetylation concomitant with the release of DET1 enables the activation of genes involved in photomorphogenesis [28]. It would be interesting in the near future to validate the potential involvement of H2B in the control of de-etiolation in tomato and thereby to follow the relationship between gene expression and H2B enrichment during this process. Finally, we could identify and confirm that the subunit RPN10/PSMD4 of the 26S proteasome regulatory complex is up-regulated during de-etiolation (Fig. 4b). For this reason, it is tempting to hypothesize that light-regulated histone expression/modification and ubiquitin-proteasome-mediated protein degradation might interact during tomato de-etiolation.Fig. 4


A subtracted cDNA library identifies genes up-regulated during PHOT1-mediated early step of de-etiolation in tomato (Solanum lycopersicum L.).

Hloušková P, Bergougnoux V - BMC Genomics (2016)

Analysis by qPCR of the expression of two genes encoding proteins involved in translation and transcription: Histone 2B (a) and 26S proteasome regulatory complex, subunit RPN10/PSMD4 (b). The data represent the average fold change of 3 independent biological replicates ± SEM. Normalization was done using the pp2ase gene as housekeeping gene. Fold change was calculated compared to the value obtained for the dark control sample. The non-parametric Mann-Whitney U test (Statistica 12) was used to determine the significance of the results
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4835860&req=5

Fig4: Analysis by qPCR of the expression of two genes encoding proteins involved in translation and transcription: Histone 2B (a) and 26S proteasome regulatory complex, subunit RPN10/PSMD4 (b). The data represent the average fold change of 3 independent biological replicates ± SEM. Normalization was done using the pp2ase gene as housekeeping gene. Fold change was calculated compared to the value obtained for the dark control sample. The non-parametric Mann-Whitney U test (Statistica 12) was used to determine the significance of the results
Mentions: In our study, we found by SSH screening and confirmed by qPCR analysis that H2B is up-regulated during PHOT1-mediated de-etiolation in tomato, indicating that it could play a role during the establishment of photomorphogenesis in tomato (Fig. 4a). Histones form the protein core of the nucleosome around which the DNA helix is wrapped. In this compact state, histones block the association of transcription factors to their binding sites, thus repressing transcription. Several post-translational modifications (acetylation, methylation or phosphorylation) of histone “tails” can influence nucleosome compaction and access to DNA. Moreover, their spatio-temporal regulation as well as their ability for cross-talk renders the regulation of gene expression even more complex [26]. In plants, chromatin remodeling plays an important role during plant growth and development, especially in response to light. Indeed, a large-scale reorganization of chromatin can be observed during the floral transition in Arabidopsis [27]. During de-etiolation, the perception of light induces a remarkable reprogramming of gene expression that leads the heterotrophic seedling to become an autotrophic organism which will be able to complete its life cycle. In darkness, the photomorphogenic repressor DET1 binds to the H2B tails of the nucleosomes surrounding the genes which are repressed in this condition. When light is perceived, the H2B acetylation concomitant with the release of DET1 enables the activation of genes involved in photomorphogenesis [28]. It would be interesting in the near future to validate the potential involvement of H2B in the control of de-etiolation in tomato and thereby to follow the relationship between gene expression and H2B enrichment during this process. Finally, we could identify and confirm that the subunit RPN10/PSMD4 of the 26S proteasome regulatory complex is up-regulated during de-etiolation (Fig. 4b). For this reason, it is tempting to hypothesize that light-regulated histone expression/modification and ubiquitin-proteasome-mediated protein degradation might interact during tomato de-etiolation.Fig. 4

Bottom Line: Our conclusions based on bioinformatics data were supported by qRT-PCR analyses the specific investigation of V-H(+)-ATPase during de-etiolation in tomato.The profound induction of transcription/translation, as well as modification of chromatin structure, is relevant in regard to the fact that the entry into photomorphogenesis is based on a deep reprograming of the cell.Also, we postulated that BL restrains the cell expansion by the rapid modification of the cell wall.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research and Faculty of Science, Palacký University in Olomouc, Šlechtitelů 11, CZ-783 71, Olomouc, Czech Republic.

ABSTRACT

Background: De-etiolation is the switch from skoto- to photomorphogenesis, enabling the heterotrophic etiolated seedling to develop into an autotrophic plant. Upon exposure to blue light (BL), reduction of hypocotyl growth rate occurs in two phases: a rapid inhibition mediated by phototropin 1 (PHOT1) within the first 30-40 min of illumination, followed by the cryptochrome 1 (CRY1)-controlled establishment of the steady-state growth rate. Although some information is available for CRY1-mediated de-etiolation, less attention has been given to the PHOT1 phase of de-etiolation.

Results: We generated a subtracted cDNA library using the suppression subtractive hybridization method to investigate the molecular mechanisms of BL-induced de-etiolation in tomato (Solanum lycopersicum L.), an economically important crop. We focused our interest on the first 30 min following the exposure to BL when PHOT1 is required to induce the process. Our library generated 152 expressed sequence tags that were found to be rapidly accumulated upon exposure to BL and consequently potentially regulated by PHOT1. Annotation revealed that biological functions such as modification of chromatin structure, cell wall modification, and transcription/translation comprise an important part of events contributing to the establishment of photomorphogenesis in young tomato seedlings. Our conclusions based on bioinformatics data were supported by qRT-PCR analyses the specific investigation of V-H(+)-ATPase during de-etiolation in tomato.

Conclusions: Our study provides the first report dealing with understanding the PHOT1-mediated phase of de-etiolation. Using subtractive cDNA library, we were able to identify important regulatory mechanisms. The profound induction of transcription/translation, as well as modification of chromatin structure, is relevant in regard to the fact that the entry into photomorphogenesis is based on a deep reprograming of the cell. Also, we postulated that BL restrains the cell expansion by the rapid modification of the cell wall.

No MeSH data available.


Related in: MedlinePlus