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Research article
YuDong Liu
Shihezi University College of Agriculture
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: APETALA2/ethylene responsive factors (AP2/ERFs) are unique regulators found in the plant kingdom that are involved in all life activity processes, including flowering, fruit ripening, floral meristem growth, and defense responses. In tomato (Solanum lycopersicum), there are 60 DREB and 80 ERF subfamily members, however, their functionality remains poorly understood.
Results: In this work, the AP2 domain conserved amino acid sequences of 68 ERF proteins from 20 plant species were compared and a Multiple Em for Motif Elicitation (MEME) analysis was conducted. Results revealed that the 9th amino acid of the AP2 domain exhibited marked characteristics during the selection of DRE/CRT and/or GCC boxes as protein binding sites. Moreover, motifs near the AP2 domain may be involved in protein binding to DNA, whereas motifs far away from the AP2 domain may function as a part of the transactivation domain. Furthermore, we compared the expression levels of all ERF genes in 30 tomato organs and under biotic and abiotic stresses. Results indicated that most of 17 ERF and DREB repressor genes were highly expressed in almost all tomato organs and under some biotic and abiotic stress. The transcripts per million (TPM) value ratios of all repressor genes exceeded that of all activator genes in 16 tomato organs. Thus, it can be inferred that these repressor genes play vital roles in balancing the regulatory functions of activator genes and activator genes may also conversely compete with repressor genes to ensure normal growth, development, and defense responses in tomato.
Conclusions: This work uncovered the potential functions of all ERF and DREB genes that regulate tomato growth, development, and defense responses, and considers the binding ability of the AP2 domain unique sequences with DRE/CRT and GCC boxes, as well as the relationship of unique motifs with the transactivation domain. These findings will expand upon our understanding of the functions of ERF and DREB genes in tomato.
Keywords
AP2/ERF, tomato (Solanum lycopersicum), ERF, DREB, DRE/CRT, GCC, repressor, activator
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This is a list of supplementary files associated with this preprint. Click to download.
- TableS1.docx
Table S1. Accuracy and error analysis of all genes with single AP2 domain in tomato by comparing sequences of DNA, CDS, cDNA, and protein among genome sequencing version 2.0, 3.0, and 4.0.
- TableS1.docx
Table S1. Accuracy and error analysis of all genes with single AP2 domain in tomato by comparing sequences of DNA, CDS, cDNA, and protein among genome sequencing version 2.0, 3.0, and 4.0.
- TableS2.docx
Table S2. Protein sequences of all ERF and DREB subfamily members in tomato.
- TableS2.docx
Table S2. Protein sequences of all ERF and DREB subfamily members in tomato.
- TableS3.docx
Table S3. CDS sequences of all ERF and DREB subfamily members in tomato.
- TableS3.docx
Table S3. CDS sequences of all ERF and DREB subfamily members in tomato.
- TableS4.docx
Table S4. The 14th and 19th amino acids and EAR motif statistic of 60 DREB genes in tomato.
- TableS4.docx
Table S4. The 14th and 19th amino acids and EAR motif statistic of 60 DREB genes in tomato.
- TableS5.docx
Table S5. The 14th and 19th amino acids and EAR motif statistic of 80 ERF genes in tomato.
- TableS5.docx
Table S5. The 14th and 19th amino acids and EAR motif statistic of 80 ERF genes in tomato.
- DataS1.xlsx
Data S1. The TPM mean value of 60 DREB and 80 ERF genes in tomato 30 organs.
- DataS1.xlsx
Data S1. The TPM mean value of 60 DREB and 80 ERF genes in tomato 30 organs.
- DataS2.xlsx
Data S2. The TPM mean value of 60 DREB and 80 ERF genes in tomato leaves under different abiotic stresses.
- DataS2.xlsx
Data S2. The TPM mean value of 60 DREB and 80 ERF genes in tomato leaves under different abiotic stresses.
- DataS3.xlsx
Data S3. The TPM mean value of 60 DREB and 80 ERF genes in tomato leaves and roots under different biotic stresses.
- DataS3.xlsx
Data S3. The TPM mean value of 60 DREB and 80 ERF genes in tomato leaves and roots under different biotic stresses.
- FigureS1.jpg
Figure S1. Number and TPM ratio analysis of repressor and activator ERF genes in tomato.
- FigureS1.jpg
Figure S1. Number and TPM ratio analysis of repressor and activator ERF genes in tomato.
- FigureS2.jpg
Figure S2. AP2 domain and expression analysis of activators with EDLL motif in tomato.
- FigureS2.jpg
Figure S2. AP2 domain and expression analysis of activators with EDLL motif in tomato.
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research article
YuDong Liu
Shihezi University College of Agriculture
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
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CURRENT STATUS: Posted
Version 1
Posted 15 Dec, 2020
No community comments so far
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Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: APETALA2/ethylene responsive factors (AP2/ERFs) are unique regulators found in the plant kingdom that are involved in all life activity processes, including flowering, fruit ripening, floral meristem growth, and defense responses. In tomato (Solanum lycopersicum), there are 60 DREB and 80 ERF subfamily members, however, their functionality remains poorly understood.
Results: In this work, the AP2 domain conserved amino acid sequences of 68 ERF proteins from 20 plant species were compared and a Multiple Em for Motif Elicitation (MEME) analysis was conducted. Results revealed that the 9th amino acid of the AP2 domain exhibited marked characteristics during the selection of DRE/CRT and/or GCC boxes as protein binding sites. Moreover, motifs near the AP2 domain may be involved in protein binding to DNA, whereas motifs far away from the AP2 domain may function as a part of the transactivation domain. Furthermore, we compared the expression levels of all ERF genes in 30 tomato organs and under biotic and abiotic stresses. Results indicated that most of 17 ERF and DREB repressor genes were highly expressed in almost all tomato organs and under some biotic and abiotic stress. The transcripts per million (TPM) value ratios of all repressor genes exceeded that of all activator genes in 16 tomato organs. Thus, it can be inferred that these repressor genes play vital roles in balancing the regulatory functions of activator genes and activator genes may also conversely compete with repressor genes to ensure normal growth, development, and defense responses in tomato.
Conclusions: This work uncovered the potential functions of all ERF and DREB genes that regulate tomato growth, development, and defense responses, and considers the binding ability of the AP2 domain unique sequences with DRE/CRT and GCC boxes, as well as the relationship of unique motifs with the transactivation domain. These findings will expand upon our understanding of the functions of ERF and DREB genes in tomato.
Figure 1
Figure 1
Figure 2
Figure 2
Figure 3
Figure 3
Figure 4
Figure 4
Figure 5
Figure 5
Figure 6
Figure 6
Figure 7
Figure 7
This is a list of supplementary files associated with this preprint. Click to download.
- TableS1.docx
Table S1. Accuracy and error analysis of all genes with single AP2 domain in tomato by comparing sequences of DNA, CDS, cDNA, and protein among genome sequencing version 2.0, 3.0, and 4.0.
- TableS1.docx
Table S1. Accuracy and error analysis of all genes with single AP2 domain in tomato by comparing sequences of DNA, CDS, cDNA, and protein among genome sequencing version 2.0, 3.0, and 4.0.
- TableS2.docx
Table S2. Protein sequences of all ERF and DREB subfamily members in tomato.
- TableS2.docx
Table S2. Protein sequences of all ERF and DREB subfamily members in tomato.
- TableS3.docx
Table S3. CDS sequences of all ERF and DREB subfamily members in tomato.
- TableS3.docx
Table S3. CDS sequences of all ERF and DREB subfamily members in tomato.
- TableS4.docx
Table S4. The 14th and 19th amino acids and EAR motif statistic of 60 DREB genes in tomato.
- TableS4.docx
Table S4. The 14th and 19th amino acids and EAR motif statistic of 60 DREB genes in tomato.
- TableS5.docx
Table S5. The 14th and 19th amino acids and EAR motif statistic of 80 ERF genes in tomato.
- TableS5.docx
Table S5. The 14th and 19th amino acids and EAR motif statistic of 80 ERF genes in tomato.
- DataS1.xlsx
Data S1. The TPM mean value of 60 DREB and 80 ERF genes in tomato 30 organs.
- DataS1.xlsx
Data S1. The TPM mean value of 60 DREB and 80 ERF genes in tomato 30 organs.
- DataS2.xlsx
Data S2. The TPM mean value of 60 DREB and 80 ERF genes in tomato leaves under different abiotic stresses.
- DataS2.xlsx
Data S2. The TPM mean value of 60 DREB and 80 ERF genes in tomato leaves under different abiotic stresses.
- DataS3.xlsx
Data S3. The TPM mean value of 60 DREB and 80 ERF genes in tomato leaves and roots under different biotic stresses.
- DataS3.xlsx
Data S3. The TPM mean value of 60 DREB and 80 ERF genes in tomato leaves and roots under different biotic stresses.
- FigureS1.jpg
Figure S1. Number and TPM ratio analysis of repressor and activator ERF genes in tomato.
- FigureS1.jpg
Figure S1. Number and TPM ratio analysis of repressor and activator ERF genes in tomato.
- FigureS2.jpg
Figure S2. AP2 domain and expression analysis of activators with EDLL motif in tomato.
- FigureS2.jpg
Figure S2. AP2 domain and expression analysis of activators with EDLL motif in tomato.
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