Bioinformatics and Expression Analysis of Circadian Related Gene BpLHY、BpTOC1 and BpGI in Betula platyphylla Suk.

SUN Feng-kun; ZHOU Shan; LI Lei-lei; ZHAN Ya-guang; ZENG Fan-suo

Volume 29 Issue 5

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Bioinformatics and Expression Analysis of Circadian Related Gene BpLHY、BpTOC1 and BpGI in Betula platyphylla Suk.

1.
College of Life Science, Northeast Forestry University, Harbin 150040, Heilongjiang, China
2.
Key Laboratory of Forest Tree Genetic Improvement and Biotechnology, Northeast Forestry University, Harbin 150040, Heilongjiang, China

Received Date: 2015-08-09

Abstract

[Objective] To clarify the mechanism and functions in regulating plant growth and stress response of circadian clock genes in Betula platyphylla Suk. [Method] The sequences of BpLHY, BpTOC1 and BpGI were analyzed, and the structure and functions of coding proteins were predicted by bioinformatics method. The expression levels of BpLHY, BpTOC1 and BpGI were quantified using qRT-PCR. [Result] BpLHY, BpTOC1 and BpGI genes in B. platyphylla were 2 283bp, 1 623bp, and 3 507bp, encoding 760, 540, and 1 168 amino acids, respectively. The proteins encoded by these genes were hydrophobic, non-secreted transmembrane protein.BpTOC1 and BpLHY transcript levels were low during the daytime, but high at night. In contrast, BpGI expression was low during the daytime, and high at night and its highest expression levels increased by 29.28 times at 9:00 am. The expressions of BpLHY, BpTOC1 and BpGI increased by 105% to 2 390% in the abiotic stress of heavy metal cadmium, low temperature (4℃), salt (NaCl); SA and SNP induced the transcription levels of BpLHY, BpTOC1 genes reducing by 70.1% to 97.75% while the expression of BpGI increasing by 150% to 280%. [Conclusion] This study may provide some references for further study of BpLHY, BpTOC1 and BpGI function in regulation of plant growth and stress response and the mechanism of circadian clock in B. platyphylla.
- Betula platyphylla,
- circadian gene,
- bioinformatics,
- abiotic stress

References

[1]	门中华, 李生秀. 植物生物节律性研究进展[J]. 生物学杂志, 2009, 26(5):53-55.
[2]	徐小冬, 谢启光. 植物生物钟研究的历史回顾与最新进展[J]. 自然杂志, 2013, 35(2):118-126.
[3]	Casal J J, Luccioni L G, Oliverio K A, et al. Light, phytochrome signalling and photomorphogenesis in Arabidopsis[J]. Photochemical & Photobiological Sciences, 2003, 2(6):625-636.
[4]	Kim J Y, Song H R, Taylor B L, et al. Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY[J]. The EMBO Journal, 2003, 22:935-944.
[5]	陈晓, 李思远, 吴连成,等. 光周期影响植物花时的分子机制. 西北植物学报[J], 2006. 26(7):1490-1499.
[6]	Dong M A, Farré E M, Thomashow M F. CIRCADIAN CLOCK-ASSOCIATED 1 and LATE ELONGATED HYPOCOTYL regulate expression of the C-REPEAT BINDING FACTOR (CBF) pathway in Arabidopsis[J]. Proceedings of the National Academy of Science, 2011, 108(17):7241-7246.
[7]	王璇, 曾凡锁, 詹亚光,等. 水曲柳节律基因LHY启动子的克隆和功能分析[J]. 植物生理学报, 2014,11:1675-1682.
[8]	John M W. The Proteomics Protocols Handbook[M]. Humana Press 2005:571-607.
[9]	Kyte J,Doolittle R F,A simple method for displaying the hydropathic character of a protein[J]. Journal of Molecular Biology, 1982, 157(06):105-132.
[10]	Thomas N P, Soren B,Gunnar H. SignalP 4.0:discriminating signal peptides from transmembrane regions[J]. Nature Methods,2011, 785-786.
[11]	Hofmann K, Stoffel W. TMbase-A database of membrane spanning proteins segments[M]. Biol Chem Hoppe-Seyler,1993, 374:166.
[12]	Peitsch M C. Protein modeling by E-mail:from amino acid sequence to protein structure:a free one-hour service[J]. Nature Biotechnology, 1995.
[13]	Skolnick J, Fetrow J S. From genes to protein structure and function:novel applications of computational approaches in the genomic era[J]. Trends in Biotechnology, 2000, 18(1):34-39.
[14]	Sen T Z, Jernigan R L, Garnier J, et al. GOR V server for protein secondary structure prediction[J]. Bioinformatics, 2005, (21)2787-2788.
[15]	Tamura K, Dudley J, Nei M. MEGA4:Molecular evolutionary genetics analysis (MEGA) software version 4.0[M]. Molecular Biology and Evolution, 2007:1596-1599.
[16]	Covington M F, Maloof J N, Straume M, et al. Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development[J].Genome Biology, 2008, 9(8):R130.
[17]	Kreps J A, Wu Y, Chang H S, et al. Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress[J]. Plant Physiology, 2002, 130(4):2129-2141.
[18]	Lai A G,Doherty C J, Mueller-Roeber B, et al. CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses[J]. Proceedings of the National Academy of Sciences, 2012, 109(42):17129-17134.
[19]	Legnaioli T, Cuevas J, Mas P. TOC1 functions as a molecular switch connecting the circadian clock with plant responses to drought[J]. The EMBO Journal, 2009, 28(23):3745-3757.
[20]	Sarah F, Thomashow M F. Arabidopsis Transcriptome Profiling Indicates That Multiple Regulatory Pathways Are Activated during Cold Acclimation in Addition to the CBF Cold Response Pathway[J]. Plant Cell, 2002, 14(8):1675-1690.
[21]	Shuqing C, Ming Y, Shaotong J. Involvement of GIGANTEA gene in the regulation of the cold stress response in Arabidopsis.[J]. Plant Cell Reports, 2005, 24(11):683-690.
[22]	Paltiel J, Amin R, Gover A, et al. Novel roles for GIGANTEA revealed under environmental conditions that modify its expression in Arabidopsis and Medicago truncatula[J]. Planta, 2006, 224(6):1255-1268.

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通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

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Bioinformatics and Expression Analysis of Circadian Related Gene BpLHY、BpTOC1 and BpGI in Betula platyphylla Suk.

1. College of Life Science, Northeast Forestry University, Harbin 150040, Heilongjiang, China

2. Key Laboratory of Forest Tree Genetic Improvement and Biotechnology, Northeast Forestry University, Harbin 150040, Heilongjiang, China

Received Date: 2015-08-09

Abstract: [Objective] To clarify the mechanism and functions in regulating plant growth and stress response of circadian clock genes in Betula platyphylla Suk. [Method] The sequences of BpLHY, BpTOC1 and BpGI were analyzed, and the structure and functions of coding proteins were predicted by bioinformatics method. The expression levels of BpLHY, BpTOC1 and BpGI were quantified using qRT-PCR. [Result] BpLHY, BpTOC1 and BpGI genes in B. platyphylla were 2 283bp, 1 623bp, and 3 507bp, encoding 760, 540, and 1 168 amino acids, respectively. The proteins encoded by these genes were hydrophobic, non-secreted transmembrane protein.BpTOC1 and BpLHY transcript levels were low during the daytime, but high at night. In contrast, BpGI expression was low during the daytime, and high at night and its highest expression levels increased by 29.28 times at 9:00 am. The expressions of BpLHY, BpTOC1 and BpGI increased by 105% to 2 390% in the abiotic stress of heavy metal cadmium, low temperature (4℃), salt (NaCl); SA and SNP induced the transcription levels of BpLHY, BpTOC1 genes reducing by 70.1% to 97.75% while the expression of BpGI increasing by 150% to 280%. [Conclusion] This study may provide some references for further study of BpLHY, BpTOC1 and BpGI function in regulation of plant growth and stress response and the mechanism of circadian clock in B. platyphylla.

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[1]	门中华, 李生秀. 植物生物节律性研究进展[J]. 生物学杂志, 2009, 26(5):53-55.
[2]	徐小冬, 谢启光. 植物生物钟研究的历史回顾与最新进展[J]. 自然杂志, 2013, 35(2):118-126.
[3]	Casal J J, Luccioni L G, Oliverio K A, et al. Light, phytochrome signalling and photomorphogenesis in Arabidopsis[J]. Photochemical & Photobiological Sciences, 2003, 2(6):625-636.
[4]	Kim J Y, Song H R, Taylor B L, et al. Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY[J]. The EMBO Journal, 2003, 22:935-944.
[5]	陈晓, 李思远, 吴连成,等. 光周期影响植物花时的分子机制. 西北植物学报[J], 2006. 26(7):1490-1499.
[6]	Dong M A, Farré E M, Thomashow M F. CIRCADIAN CLOCK-ASSOCIATED 1 and LATE ELONGATED HYPOCOTYL regulate expression of the C-REPEAT BINDING FACTOR (CBF) pathway in Arabidopsis[J]. Proceedings of the National Academy of Science, 2011, 108(17):7241-7246.
[7]	王璇, 曾凡锁, 詹亚光,等. 水曲柳节律基因LHY启动子的克隆和功能分析[J]. 植物生理学报, 2014,11:1675-1682.
[8]	John M W. The Proteomics Protocols Handbook[M]. Humana Press 2005:571-607.
[9]	Kyte J,Doolittle R F,A simple method for displaying the hydropathic character of a protein[J]. Journal of Molecular Biology, 1982, 157(06):105-132.
[10]	Thomas N P, Soren B,Gunnar H. SignalP 4.0:discriminating signal peptides from transmembrane regions[J]. Nature Methods,2011, 785-786.
[11]	Hofmann K, Stoffel W. TMbase-A database of membrane spanning proteins segments[M]. Biol Chem Hoppe-Seyler,1993, 374:166.
[12]	Peitsch M C. Protein modeling by E-mail:from amino acid sequence to protein structure:a free one-hour service[J]. Nature Biotechnology, 1995.
[13]	Skolnick J, Fetrow J S. From genes to protein structure and function:novel applications of computational approaches in the genomic era[J]. Trends in Biotechnology, 2000, 18(1):34-39.
[14]	Sen T Z, Jernigan R L, Garnier J, et al. GOR V server for protein secondary structure prediction[J]. Bioinformatics, 2005, (21)2787-2788.
[15]	Tamura K, Dudley J, Nei M. MEGA4:Molecular evolutionary genetics analysis (MEGA) software version 4.0[M]. Molecular Biology and Evolution, 2007:1596-1599.
[16]	Covington M F, Maloof J N, Straume M, et al. Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development[J].Genome Biology, 2008, 9(8):R130.
[17]	Kreps J A, Wu Y, Chang H S, et al. Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress[J]. Plant Physiology, 2002, 130(4):2129-2141.
[18]	Lai A G,Doherty C J, Mueller-Roeber B, et al. CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses[J]. Proceedings of the National Academy of Sciences, 2012, 109(42):17129-17134.
[19]	Legnaioli T, Cuevas J, Mas P. TOC1 functions as a molecular switch connecting the circadian clock with plant responses to drought[J]. The EMBO Journal, 2009, 28(23):3745-3757.
[20]	Sarah F, Thomashow M F. Arabidopsis Transcriptome Profiling Indicates That Multiple Regulatory Pathways Are Activated during Cold Acclimation in Addition to the CBF Cold Response Pathway[J]. Plant Cell, 2002, 14(8):1675-1690.
[21]	Shuqing C, Ming Y, Shaotong J. Involvement of GIGANTEA gene in the regulation of the cold stress response in Arabidopsis.[J]. Plant Cell Reports, 2005, 24(11):683-690.
[22]	Paltiel J, Amin R, Gover A, et al. Novel roles for GIGANTEA revealed under environmental conditions that modify its expression in Arabidopsis and Medicago truncatula[J]. Planta, 2006, 224(6):1255-1268.

Bioinformatics and Expression Analysis of Circadian Related Gene BpLHY、BpTOC1 and BpGI in Betula platyphylla Suk.

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通讯作者: 陈斌, bchen63@163.com

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Bioinformatics and Expression Analysis of Circadian Related Gene BpLHY、BpTOC1 and BpGI in Betula platyphylla Suk.

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