生菜LsPHYB可变剪接体的克隆与高温诱导表达模式

doi:10.3864/j.issn.0578-1752.2022.09.011

Abstract

Abstract:

【Objective】Phytochrome B (PHYB) is a receptor for both light and temperature. In this study, the biological functions of alternative splice variants of LsPHYB in lettuce in response to high environmental temperatures were investigated through cloning them and analyzing their expression patterns, so as to provide a theoretical basis for breeding heat-tolerant lettuce.【Method】The cDNA sequences of LsPHYB were searched from the genomic database of lettuce by bioinformatics method. The cloned LsPHYB1, LsPHYB2 and LsPHYB3 were subjected to multi-sequence alignment, alternative splice variants form analysis and phylogenetic analysis. Protein properties, such as molecular weight, theoretical isoelectric point, hydrophilicity and hydrophobicity, were predicted by online software. Secondary structure, tertiary structure and conserved domains were analyzed by bioinformatics software. Three alternative splice variants were characterized for expression after high temperature treatment by RT-PCR. 【Result】There were three alternative splice variants of LsPHYB obtained by cloning, namely LsPHYB1, LsPHYB2 and LsPHYB3, with their CDS lengths of 3 509, 3 877 and 2 690 bp, which encoded 1 094, 960 and 853 amino acids, respectively. Alternative splice forms of LsPHYB1 were alternative 3′ splice site and skipped exon. Alternative splice forms of LsPHYB2 were alternative polyA and retain intron. An alternative splice form of LsPHYB3 was skipped exon. Conserved structural domain analysis showed that the N-terminal of PHYB2 lacked the PAS and PHY domains. The N-terminal of PHYB3 lacked the PAS and PHY domains, and its C-terminal lacked the HisKA domain. Phylogenetic analysis showed that three alternative splice variants were clustered into a clade. qRT-PCR analysis showed that the expression of LsPHYB3 was the highest at the first day of high temperature treatment; LsPHYB2 had higher expression than LsPHYB1 and LsPHYB3 at days 5-9 of high temperature treatment; at day 11 of high temperature treatment, the expression of LsPHYB1 was higher than that of LsPHYB2 and LsPHYB3. The three alternative splice variants peaked at different times during the 11 days of high temperature treatment. 【Conclusion】There were three alternative transcript variants of LsPHYB, named LsPHYB1, LsPHYB2 and LsPHYB3. LsPHYB3 expression was the highest in the early stage of high temperature treatment, LsPHYB2 in the middle stage, and LsPHYB1 in the late stage, suggesting that the three alternative splice variants were functionally differentiated in response to high temperature stress.

Key words: lettuce, LsPHYB, alternative splice variants, heat stress, response

SUI XinYi,ZHAO XiaoGang,CHEN PengYu,LI YaLing,WEN XiangZhen. Cloning of Alternative Splice Variants of LsPHYB in Lettuce and Its Expression Patterns Under Heat Stress[J].Scientia Agricultura Sinica, 2022, 55(9): 1822-1830.

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References 41

[1]	LIPPMANN R, BABBEN S, MENGER A, DELKER C, QUINT M. Development of wild and cultivated plants under global warming conditions. Current Biology, 2019, 29(24): R1326-R1338. doi: 10.1016/j.cub.2019.10.016. doi: 10.1016/j.cub.2019.10.016
[2]	HAO J H, ZHANG L L, LI P P, SUN Y C, LI J K, QIN X X, WANG L, QI Z Y, XIAO S, HAN Y Y, LIU C J, FAN S X. Quantitative proteomics analysis of lettuce (Lactuca sativa L.) reveals molecular basis-associated auxin and photosynthesis with bolting induced by high temperature. International Journal of Molecular Sciences, 2018, 19(10): 2967. doi: 10.3390/ijms19102967
[3]	HALLIDAY K J, DAVIS S J. Light-sensing phytochromes feel the heat. Science, 2016, 354(6314): 832-833. doi: 10.1126/science.aaj1918. doi: 10.1126/science.aaj1918
[4]	LIN J Y, ZHU Z Q. Plant responses to high temperature: A view from pre-mRNA alternative splicing. Plant Molecular Biology, 2021, 105(6): 575-583. doi: 10.1007/s11103-021-01117-z. doi: 10.1007/s11103-021-01117-z
[5]	CAPOVILLA G, PAJORO A, IMMINK R G, SCHMID M. Role of alternative pre-mRNA splicing in temperature signaling. Current Opinion in Plant Biology, 2015, 27: 97-103. doi: 10.1016/j.pbi.2015.06.016. doi: 10.1016/j.pbi.2015.06.016
[6]	STAIGER D, BROWN J W S. Alternative splicing at the intersection of biological timing, development, and stress responses. The Plant Cell, 2013, 25(10): 3640-3656. doi: 10.1105/tpc.113.113803 doi: 10.1105/tpc.113.113803
[7]	曾纪晴, 张明永. 选择性剪接在植物逆境相关基因表达调控中的作用. 植物生理学通讯, 2006, 42(6): 1005-1014.
	ZENG J Q, ZHANG M Y. The role of alternative splicing in the regulation of plant stress-associated gene expression. Plant Physiology Communications, 2006, 42(6): 1005-1014. (in Chinese)
[8]	GILBERT W. Why genes in pieces? Nature, 1978, 271(5645): 501. doi: 10.1038/271501a0
[9]	KEREN H, LEV-MAOR G, AST G. Alternative splicing and evolution: diversification, exon definition and function. Nature Reviews Genetics, 2010, 11(5): 345-355. doi: 10.1038/nrg2776. doi: 10.1038/nrg2776
[10]	KANNAN S, HALTER G, RENNER T, WATERS E R. Patterns of alternative splicing vary between species during heat stress. AoB PLANTS, 2018, 10(2): ply013. doi: 10.1093/aobpla/ply013. doi: 10.1093/aobpla/ply013
[11]	CHANG C Y, LIN W D, TU S L. Genome-wide analysis of heat-sensitive alternative splicing in Physcomitrella patens. Plant Physiology, 2014, 165(2): 826-840. doi: 10.1104/pp.113.230540. doi: 10.1104/pp.113.230540
[12]	HAYNES J G, HARTUNG A J, HENDERSHOT J D, PASSINGHAM R S, RUNDLE S J. Molecular characterization of the B' regulatory subunit gene family of Arabidopsis protein phosphatase 2A. European Journal of Biochemistry, 1999, 260(1): 127-136. doi: 10.1046/j.1432-1327.1999.00154.x. doi: 10.1046/j.1432-1327.1999.00154.x.
[13]	KINOSHITA S, KANEKO G, LEE J H, KIKUCHI K, YAMADA H, HARA T, ITOH Y, WATABE S. A novel heat stress-responsive gene in the marine diatom Chaetoceros compressum encoding two types of transcripts, a trypsin-like protease and its related protein, by alternative RNA splicing. European Journal of Biochemistry, 2001, 268(17): 4599-4609. doi: 10.1046/j.1432-1327.2001.02360.x
[14]	KELLER M, HU Y J, MESIHOVIC A, FRAGKOSTEFANAKIS S, SCHLEIFF E, SIMM S. Alternative splicing in tomato pollen in response to heat stress. DNA Research, 2016, 24(2): 205-217. doi: 10.1093/dnares/dsw051. doi: 10.1093/dnares/dsw051
[15]	MATSUKURA S, MIZOI J, YOSHIDA T, TODAKA D, ITO Y, MARUYAMA K, SHINOZAKI K, YAMAGUCHI-SHINOZAKI K. Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress- responsive genes. Molecular Genetics and Genomics, 2010, 283(2): 185-196. doi: 10.1007/s00438-009-0506-y. doi: 10.1007/s00438-009-0506-y
[16]	LEE S S, JUNG W Y, PARK H J, LEE A, KWON S Y, KIM H S, CHO H S. Genome-wide analysis of alternative splicing in an inbred cabbage (Brassica oleracea L.) line ‘HO’ in response to heat stress. Current Genomics, 2018, 19(1): 12-20.
[17]	AIROLDI C A, MARY M, BRENDAN D. MAF₂ is regulated by temperature-dependent splicing and represses flowering at low temperatures in parallel with FLM. PLoS ONE, 2015, 10(5): e0126516. doi: 10.1371/journal.pone.0126516. doi: 10.1371/journal.pone.0126516
[18]	POSE D, VERHAGE L, OTT F, YANT L, MATHIEU J, ANGENENT G C, IMMINK R, SCHMID M. Temperature-dependent regulation of flowering by antagonistic FLM variants. Nature, 2013, 503(7476): 414-417. doi: 10.1038/nature12633. doi: 10.1038/nature12633
[19]	YAN K, LIU P, WU C G, YANG G D, XU R, GUO Q H, HUANG J G, ZHENG C C. Stress-induced alternative splicing provides a mechanism for the regulation of microRNA processing in Arabidopsis thaliana. Molecular Cell, 2012, 48(4): 521-531. doi: 10.1016/j.molcel.2012.08.032. doi: 10.1016/j.molcel.2012.08.032
[20]	LEGRIS M, KLOSE C, BURGIE E S, ROJAS C C R, NEME M, HILTBRUNNER A, WIGGE P A, SCHÄFER E, VIERSTRA R D, CASAL J J. Phytochrome B integrates light and temperature signals in Arabidopsis. Science, 2016, 354(6314): 897-900. doi: 10.1126/science.aaf5656. doi: 10.1126/science.aaf5656
[21]	JAEHOON J, MIRELA D, CORNELIA K, SUROJIT B, DAPHNE E, GAO M J, KHAN K A, BOX M S, VARODOM C, SANDRA C, MANOJ K, ALASTAIR G, LOCKE J C W, EBERHARD S, JAEGER K E, WIGGE P A. Phytochromes function as thermosensors in Arabidopsis. Science, 2016, 354(6314): 886-889. doi: 10.1126/science.aaf6005. doi: 10.1126/science.aaf6005
[22]	LIVAK K J, SCHMITTGEN T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2^-∆∆Ct method. Methods, 2001, 25(4): 402-408. doi: 10.1006/meth.2001.1262
[23]	冯雅岚, 熊瑛, 张均, 原佳乐, 蔡艾杉, 马超. 可变剪切在植物发育和非生物胁迫响应中的作用. 核农学报, 2020, 34(1): 62-70. doi: 10.11869/j.issn.100-8551.2020.01.0062. doi: 10.11869/j.issn.100-8551.2020.01.0062
	FENG Y L, XIONG Y, ZHANG J, YUAN J L, CAI A S, MA C. Role of alternative splicing in plant development and abiotic stress responses. Journal of Nuclear Agricultural Sciences, 2020, 34(1): 62-70. doi: 10.11869/j.issn.100-8551.2020.01.0062. (in Chinese) doi: 10.11869/j.issn.100-8551.2020.01.0062
[24]	卢欢欢, 邓琴霖, 吴梦丹, 王志敏, 魏大勇, 王鹤冰, 向华丰, 张洪成, 汤青林. 可变剪接调控植物开花的作用机制进展. 生物工程学报, 2021, 37(9): 2991-3004. doi: 10.13345/j.cjb.200628. doi: 10.13345/j.cjb.200628
	LU H H, DENG Q L, WU M D, WANG Z M, WEI D Y, WANG H B, XIANG H F, ZHANG H C, TANG Q L. Mechanisms of alternative splicing in regulating plant flowering: A review. Chinese Journal of Biotechnology, 2021, 37(9): 2991-3004. doi: 10.13345/j.cjb.200628. (in Chinese) doi: 10.13345/j.cjb.200628
[25]	石国良, 武强, 杨念婉, 黄聪, 刘万学, 钱万强, 万方浩. 苹果蠹蛾几丁质脱乙酰基酶2的基因克隆、表达模式和分子特性. 中国农业科学, 2021, 54(10): 2105-2117. doi: 10.3864/j.issn.0578-1752.2021.10.007. doi: 10.3864/j.issn.0578-1752.2021.10.007
	SHI G L, WU Q, YANG N W, HUANG C, LIU W X, QIAN W Q, WAN F H. Gene cloning, expression pattern and molecular characterization of chitin deacetylase 2 in Cydia pomonella. Scientia Agricultura Sinica, 2021, 54(10): 2105-2117. doi: 10.3864/j.issn.0578-1752.2021.10.007. (in Chinese) doi: 10.3864/j.issn.0578-1752.2021.10.007
[26]	FANKHAUSER C. The phytochromes, a family of red/far-red absorbing photoreceptors. Journal of Biological Chemistry, 2001, 276(15): 11453-11456. doi: 10.1074/jbc.R100006200
[27]	BAE G, CHOI G. Decoding of light signals by plant phytochromes and their interacting proteins. Annual Review of Plant Biology, 2008, 59: 281-311. doi: 10.1146/annurev.arplant.59.032607.092859. doi: 10.1146/annurev.arplant.59.032607.092859
[28]	张媛媛. 光敏色素的结构及其信号调控机制. 湖北农业科学, 2020, 59(4): 5-10. doi: 10.14088/j.cnki.issn0439-8114.2020.04.001. doi: 10.14088/j.cnki.issn0439-8114.2020.04.001
	ZHANG Y Y. Structure and signal regulation mechanism of phytochrome. Hubei Agricultural Sciences, 2020, 59(4): 5-10. doi: 10.14088/j.cnki.issn0439-8114.2020.04.001. (in Chinese) doi: 10.14088/j.cnki.issn0439-8114.2020.04.001
[29]	KLOSE C, VICZIÁN A, KIRCHER S, SCHÄFER E, NAGY F. Molecular mechanisms for mediating light-dependent nucleo/cytoplasmic partitioning of phytochrome photoreceptors. The New Phytologist, 2015, 206(3): 965-971. doi: 10.1111/nph.13207
[30]	BURGIE E S, BUSSELL A N, WALKER J M, DUBIEL K, VIERSTRA R D. Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111(28): 10179-10184.
[31]	BURGIE E S, BUSSELL A N, LYE S H, WANG T, HU W M, MCLOUGHLIN K E, WEBER E L, LI H L, VIERSTRA R D. Photosensing and thermosensing by phytochrome B require both proximal and distal allosteric features within the dimeric photoreceptor. Scientific Reports, 2017, 7(1): 13648. doi: 10.1038/s41598-017-14037-0. doi: 10.1038/s41598-017-14037-0
[32]	BURGIE E S, ZHANG J R, VIERSTRA R D. Crystal structure of Deinococcus phytochrome in the photoactivated state reveals a cascade of structural rearrangements during photoconversion. Structure, 2016, 24(3): 448-457. doi: 10.1016/j.str.2016.01.001. doi: 10.1016/j.str.2016.01.001
[33]	XU D Q. Multifaceted roles of PIF4 in plants. Trends in Plant Science, 2018, 23(9): 749-751. doi: 10.1016/j.tplants.2018.07.003. doi: 10.1016/j.tplants.2018.07.003
[34]	吴发强. 大豆光敏色素基因的克隆和功能研究[D]. 北京: 中国农业科学院, 2011.
	WU F Q. Cloning and functional study of soybean phytochrome genes[D]. Beijing: Chinese Academy of Agricultural Sciences, 2011. (in Chinese)
[35]	LIU B, ZHAO S, LI P L, YIN Y L, NIU Q L, YAN J Q, HUANG D F. Plant buffering against the high-light stress-induced accumulation of CsGA2ox8 transcripts via alternative splicing to finely tune gibberellin levels and maintain hypocotyl elongation. Horticulture Research, 2021, 8(1): 170-180. doi: 10.1038/s41438-021-00606-y
[36]	WU Z, LIANG J H, WANG C P, DING L P, ZHAO X, CAO X, XU S J, TENG N J, YI M F. Alternative splicing provides a mechanism to regulate LlHSFA3 function in response to heat stress in lily. Plant Physiology, 2019, 181(4): 1651-1667. doi: 10.1104/pp.19.00839. doi: 10.1104/pp.19.00839
[37]	CHEN M, TAO Y, LIM J, SHAW A, CHORY J. Regulation of phytochrome B nuclear localization through light-dependent unmasking of nuclear-localization signals. Current Biology, 2005, 15(7): 637-642. doi: 10.1016/j.cub.2005.02.028. doi: 10.1016/j.cub.2005.02.028
[38]	MATSUSHITA T, MOCHIZUKI N, NAGATANI A. Dimers of the N-terminal domain of phytochrome B are functional in the nucleus. Nature, 2003, 424(6948): 571-574. doi: 10.1038/nature01837
[39]	HUQ E, AL-SADY B, QUAIL P H. Nuclear translocation of the photoreceptor phytochrome B is necessary for its biological function in seedling photomorphogenesis. The Plant Journal, 2003, 35(5): 660-664. doi: 10.1046/j.1365-313X.2003.01836.x
[40]	KOO S C, YOON H W, KIM C Y, MOON B C, CHEONG Y H, HAN H J, LEE S M, KANG K Y, KIM M C, LEE S Y, CHUNG W S, CHO M J. Alternative splicing of the OsBWMK1 gene generates three transcript variants showing differential subcellular localizations. Biochemical and Biophysical Research Communications, 2007, 360(1): 188-193. doi: 10.1016/j.bbrc.2007.06.052. doi: 10.1016/j.bbrc.2007.06.052
[41]	HE Z S, XIE R, ZOU H S, WANG Y Z, ZHU J B, YU G Q. Structure and alternative splicing of a heat shock transcription factor gene, MsHSF1, in Medicago sativa. Biochemical and Biophysical Research Communications, 2007, 364(4): 1056-1061. doi: 10.1016/j.bbrc.2007.10.131

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Cloning of Alternative Splice Variants of LsPHYB in Lettuce and Its Expression Patterns Under Heat Stress

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