The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis)
Abstract Background Trihelix transcription factors (TTFs) are photoresponsive proteins that have a representative three-helix structure (helix-loop-helix-loop-helix). Members of this gene family have been reported to play roles in many plant processes. Results In this study, we performed a functiona...
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BMC
2019-04-01
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| Series: | BMC Plant Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12870-019-1744-8 |
| _version_ | 1819017216797966336 |
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| author | Xinran Cheng Rui Xiong Hanwei Yan Yameng Gao Huanlong Liu Min Wu Yan Xiang |
| author_facet | Xinran Cheng Rui Xiong Hanwei Yan Yameng Gao Huanlong Liu Min Wu Yan Xiang |
| author_sort | Xinran Cheng |
| collection | DOAJ |
| description | Abstract Background Trihelix transcription factors (TTFs) are photoresponsive proteins that have a representative three-helix structure (helix-loop-helix-loop-helix). Members of this gene family have been reported to play roles in many plant processes. Results In this study, we performed a functional and evolutionary analysis of the TTFs in Moso bamboo (Phyllostachys edulis). A total of 35 genes were identified and grouped into five subfamilies (GT-1, GT-γ, GT-2, SIP1 and SH4) according to their structural properties. Gene structure analysis showed that most genes in the PeTTF family had fewer introns. A unique motif (Motif 16) to the GT-γ subfamily was identified by conserved motif analysis. Promoter analysis revealed various cis-acting elements related to plant growth and development, abiotic and biotic stresses, and phytohormone responses. Data for the 35 Moso bamboo TTF genes were used to generate heat maps, which indicated that these genes were expressed in different tissues or developmental stages. Most of the TTF genes identified here had high expression in leaves and panicles according to the expression profile analysis. The expression levels of the TTF members in young leaves were studied using quantitative real-time PCR to determine their tissue specificity and stress-related expression patterns to help functionally characterize individual members. Conclusions The results indicated that members of the TTF gene family may be involved in plant responses to stress conditions. Additionally, PeTTF29 was shown to be located in the nucleus by subcellular localization analysis and to have transcriptional activity in a transcriptional activity assay. Our research provides a comprehensive summary of the PeTTF gene family, including functional and evolutionary perspectives, and provides a basis for functionally characterizing these genes. |
| first_indexed | 2024-12-21T03:00:00Z |
| format | Article |
| id | doaj.art-e5909b9c84c64dc69a8f21746fc8321a |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-21T03:00:00Z |
| publishDate | 2019-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-e5909b9c84c64dc69a8f21746fc8321a2022-12-21T19:18:12ZengBMCBMC Plant Biology1471-22292019-04-0119112010.1186/s12870-019-1744-8The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis)Xinran Cheng0Rui Xiong1Hanwei Yan2Yameng Gao3Huanlong Liu4Min Wu5Yan Xiang6Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural UniversityLaboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural UniversityLaboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural UniversityNational Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural UniversityNational Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural UniversityNational Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural UniversityLaboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural UniversityAbstract Background Trihelix transcription factors (TTFs) are photoresponsive proteins that have a representative three-helix structure (helix-loop-helix-loop-helix). Members of this gene family have been reported to play roles in many plant processes. Results In this study, we performed a functional and evolutionary analysis of the TTFs in Moso bamboo (Phyllostachys edulis). A total of 35 genes were identified and grouped into five subfamilies (GT-1, GT-γ, GT-2, SIP1 and SH4) according to their structural properties. Gene structure analysis showed that most genes in the PeTTF family had fewer introns. A unique motif (Motif 16) to the GT-γ subfamily was identified by conserved motif analysis. Promoter analysis revealed various cis-acting elements related to plant growth and development, abiotic and biotic stresses, and phytohormone responses. Data for the 35 Moso bamboo TTF genes were used to generate heat maps, which indicated that these genes were expressed in different tissues or developmental stages. Most of the TTF genes identified here had high expression in leaves and panicles according to the expression profile analysis. The expression levels of the TTF members in young leaves were studied using quantitative real-time PCR to determine their tissue specificity and stress-related expression patterns to help functionally characterize individual members. Conclusions The results indicated that members of the TTF gene family may be involved in plant responses to stress conditions. Additionally, PeTTF29 was shown to be located in the nucleus by subcellular localization analysis and to have transcriptional activity in a transcriptional activity assay. Our research provides a comprehensive summary of the PeTTF gene family, including functional and evolutionary perspectives, and provides a basis for functionally characterizing these genes.http://link.springer.com/article/10.1186/s12870-019-1744-8Trihelix transcription factorsGene ontologyPhylogenetic analysisExpression profilingMoso bambooSubcellular localization |
| spellingShingle | Xinran Cheng Rui Xiong Hanwei Yan Yameng Gao Huanlong Liu Min Wu Yan Xiang The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis) BMC Plant Biology Trihelix transcription factors Gene ontology Phylogenetic analysis Expression profiling Moso bamboo Subcellular localization |
| title | The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis) |
| title_full | The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis) |
| title_fullStr | The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis) |
| title_full_unstemmed | The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis) |
| title_short | The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis) |
| title_sort | trihelix family of transcription factors functional and evolutionary analysis in moso bamboo phyllostachys edulis |
| topic | Trihelix transcription factors Gene ontology Phylogenetic analysis Expression profiling Moso bamboo Subcellular localization |
| url | http://link.springer.com/article/10.1186/s12870-019-1744-8 |
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