植物冷驯化转录调控的影响因素
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摘要
植物在冷驯化过程中通过转录调控发生大量生理生化上的变化,遗传物质、光照、温度等是影响转录调控的关键因素。本文从遗传物质及环境因子方面对植物冷驯化转录调控的影响进行了概述,希望人们在设计实验时能对其重要性予以重视。
In the process of plants cold acclimation,a lot of physiological and biochemical changes occurred through transcriptional regulation.Genetic material,light,temperature,etc.are the key factors influence transcriptional regulation.In this paper,we summarized the factors of transcriptional regulation during plants cold acclimatization from the genetic and environmental aspects,hoping the importance of factors attracts more attention when designing experiments.
In the process of plants cold acclimation,a lot of physiological and biochemical changes occurred through transcriptional regulation.Genetic material,light,temperature,etc.are the key factors influence transcriptional regulation.In this paper,we summarized the factors of transcriptional regulation during plants cold acclimatization from the genetic and environmental aspects,hoping the importance of factors attracts more attention when designing experiments.
引文
[1] Thomashow M F.Plant cold acclimation: Freezing tolerance genes and regulatory mechanisms[J].Annual Review of Plant Physiology and Plant Molecular Biology,1999,50(1): 571-599.
[2] Perea-Resa C,Rodríguez-Milla M A,Iniesto E,et al.Prefoldins negatively regulate cold acclimation in Arabidopsis thaliana by promoting nuclear proteasome-mediated HY5 degradation[J].Molecular Plant,2017,10(6): 791-804.
[3] Makarevitch I,Waters A J,West P T,et al.Transposable elements contribute to activation of maize genes in response to abiotic stress[J].PLoS Genetics,2015,11(1):E1004915.
[4] Lee B H.The Arabidopsis cold-responsive transcriptome and its regulation by ICE1[J].The Plant Cell Online,2005,17(11): 3155-3175.
[5] Waters A J,Makarevitch I,Noshay J,et al.Natural variation for gene expression responses to abiotic stress in maize[J].Plant Journal,2017,89(4): 706-717.
[6] Lister R,Gregory B D,Ecker J R.Next is now: new technologies for sequencing of genomes,transcriptomes,and beyond[J].Current Opinion in Plant Biology,2009,12(2):107-118.
[7] Cushman J C,Bohnert H J.Genomic approaches to plant stress tolerance[J].Current Opinion in Plant Biology,2000,3(2):117-124.
[8] Fowler D B,Limin A E,Ritchie J T.Low-temperature tolerance in cereals: Model and genetic interpretation[J].Crop Science,1999,39(3):626-633.
[9] Torres-Oliva M,Almudi I,McGregor A P,et al.A robust(re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species[J].BMC Genomics,2016,17(1): 1-20.
[10] Chen H,Chen X,Chen D,et al.A comparison of the low temperature transcriptomes of two tomato genotypes that differ in freezing tolerance: Solanum lycopersicum and Solanum habrochaites[J].BMC Plant Biology,2015,15(1):1-16.
[11] Kou S,Chen L,Tu W,et al.The arginine decarboxylase gene ADC1,associated to the putrescine pathway,plays an important role in potato cold-acclimated freezing tolerance as revealed by transcriptome and metabolome analyses[J/OL].The Plant Journal,2018,DOI: 10.1111/TPJ.14126.
[12] Abeynayake S W,Byrne S,Nagy I,et al.Changes in Lolium perenne transcriptome during cold acclimation in two genotypes adapted to different climatic conditions[J].BMC Plant Biology,2015,15(1): 1-15.
[13] Barah P,Jayavelu N D,Rasmussen S,et al.Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes[J].BMC Genomics,2013,14(1):722.
[14] Barrios A,Caminero C,García P,et al.Deep super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.)[J].BMC Plant Biology,2017,17(1): 1-16.
[15] Davidson R M,Gowda M,Moghe G,et al.Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution[J].Plant Journal,2012,71(3): 492-502.
[16] Zhang Y,Ngu D W,Carvalho D,et al.Differentially regulated orthologs in sorghum and the subgenomes of maize[J].The Plant Cell,2017,29(8): 1938-1951.
[17] Swigoňová Z,Lai J,Ma J,et al.Close split of sorghum and maize genome progenitors[J].Genome Research,2004,14(10A):1916-1923.
[18] de Wet J M J.Systematics and evolution of sorghum sect.sorghum(Gramineae)[J].American Journal of Botany,1978,65(8): 477-484.
[19] Hetherington S E,He J,Smillie R M.Photoinhibition at low temperature in chilling-sensitive and -resistant plants[J].Plant physiology,1989,90(4): 1609-1615.
[20] Chinnusamy V,Zhu J,Zhu J K.Cold stress regulation of gene expression in plants[J].Trends in Plant Science,2007,12(10): 444-451.
[21] Freeling M,Rapaka L,Lyons E,et al.G-boxes,bigfoot genes,and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis[J].The Plant Cell Online,2007,19(5): 1441-1457.
[22] Kovi M R,Ergon ?,Rognli O A.Freezing tolerance revisited—effects of variable temperatures on gene regulation in temperate grasses and legumes[J].Current Opinion in Plant Biology,2016,33: 140-146.
[23] Kidokoro S,Yoneda K,Takasaki H,et al.Different cold-signaling pathways function in the responses to rapid and gradual decreases in temperature[J].The Plant Cell,2017,29(4): 760-774.
[24] Yang T,Huang X S.Deep sequencing-based characterization of transcriptome of Pyrus ussuriensis in response to cold stress[J].Gene,2018,661: 109-118.
[25] Wang M,Zhang X,Liu J H.Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress[J].BMC Genomics,2015,16(1): 1-20.
[26] Gray G R,Chauvin L P,Sarhan F,et al.Cold acclimation and freezing tolerance (a complex interaction of light and temperature)[J].Plant Physiology,1997,114(2): 467-474.
[27] Zheng C,Zhao L,Wang Y,et al.Integrated RNA-Seq and sRNA-Seq analysis identifies chilling and freezing responsive key molecular players and pathways in tea plant (Camellia sinensis)[J].PLoS ONE,2015,10(4): 1-29.
[28] Hao X,Wang B,Wang L,et al.Comprehensive transcriptome analysis reveals common and specific genes and pathways involved in cold acclimation and cold stress in tea plant leaves[J].Scientia Horticulturae,2018,240: 354-368.
[29] Franklin K A,Toledo-Ortiz G,Pyott D E,et al.Interaction of light and temperature signalling[J].Journal of Experimental Botany,2014,65(11): 2859-2871.
[30] Gierczik K,Novák A,Ahres M,et al.Circadian and light regulated expression of CBFs and their upstream signalling genes in barley[J].International Journal of Molecular Sciences,2017,18(8):E1828.
[31] Fowler D B,Limin A E,Wang S,et al.Relationship between low-temperature tolerance and verndlization response in wheat and rye[J].Canadian Journal of Plant Science,1996,76: 37-42.
[32] Kippes N,Debernardi J M,Vasquez-Gross H A,et al.Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia[J].Proceedings of the National Academy of Sciences,2015,112(39): E5401-E5410.
[33] Fjellheim S,Boden S,Trevaskis B.The role of seasonal flowering responses in adaptation of grasses to temperate climates[J].Frontiers in Plant Science,2014,5(8): 1-15.
[34] Sasani S,Hemming M N,Oliver S N,et al.The influence of vernalization and daylength on expression of flowering-time genes in the shoot apex and leaves of barley (Hordeum vulgare)[J].Journal of Experimental Botany,2009,60(7): 2169-2178.
[35] Huan Q,Mao Z,Chong K,et al.Global analysis of H3K4me3/H3K27me3 in Brachypodium distachyon reveals VRN3 as critical epigenetic regulation point in vernalization and provides insights into epigenetic memory[J].New Phytologist,2018,219(4):1373-1387.
[36] Bieniawska Z,Espinoza C,Schlereth A,et al.Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome[J].Plant Physiology,2008,147(1): 263-279.
[37] Janmohammadi M.Cold acclimation and vegetative/reproductive transition in winter cereals[J].Albanian Journal of Agricultural Sciences,2012,11(4):199-205.
[38] Dhillon T,Pearce S P,Stockinger E J,et al.Regulation of freezing tolerance and flowering in temperate cereals: The VRN-1 connection[J].Plant Physiology,2010,153(4):1846-1858.
[39] Cuesta-Marcos A,Mun?z-Amatriaín M,Filichkin T,et al.The relationships between development and low temperature tolerance in barley near isogenic lines differing for flowering behavior[J].Plant and Cell Physiology,2015,56(12):2312-2324.
[40] Deng W,Casao M C,Wang P,et al.Nature Publishing Group,2015.Direct links between the vernalization response and other key traits of cereal crops[J].Nature Communications,2015,6(3):1-8.
[41] Mahfoozi S,Limin A E,Hayes P M,et al.Influence of photoperiod response on the expression of cold hardiness in wheat and barley[J].Canadian Journal of Plant Science,2000,80(4): 721-724.
[42] Ergon ?,Melby T I,H?glind M,et al.Vernalization requirement and the chromosomal VRN1-region can affect freezing tolerance and expression of cold-regulated genes in Festuca pratensis[J].Frontiers in Plant Science,2016,7: 1-15.
[43] Janmohammadi M,Enayati V,Sabaghnia N.Impact of cold acclimation,de-acclimation and re-acclimation on carbohydrate content and antioxidant enzyme activities in spring and winter wheat[J].Icelandic Agricultural Sciences,2012,25(1): 3-11.
[44] Skinner D Z,Bellinger B,Hiscox W,et al.Evidence of cyclical light/dark-regulated expression of freezing tolerance in young winter wheat plants[J].PLoS ONE,2018,13(6):1-18.
[45] Kenchanmane Raju S K,Barnes A C,Schnable J C,et al.Low-temperature tolerance in land plants: Are transcript and membrane responses conserved?[J].Plant Science,2018,276(8): 73-86.
[2] Perea-Resa C,Rodríguez-Milla M A,Iniesto E,et al.Prefoldins negatively regulate cold acclimation in Arabidopsis thaliana by promoting nuclear proteasome-mediated HY5 degradation[J].Molecular Plant,2017,10(6): 791-804.
[3] Makarevitch I,Waters A J,West P T,et al.Transposable elements contribute to activation of maize genes in response to abiotic stress[J].PLoS Genetics,2015,11(1):E1004915.
[4] Lee B H.The Arabidopsis cold-responsive transcriptome and its regulation by ICE1[J].The Plant Cell Online,2005,17(11): 3155-3175.
[5] Waters A J,Makarevitch I,Noshay J,et al.Natural variation for gene expression responses to abiotic stress in maize[J].Plant Journal,2017,89(4): 706-717.
[6] Lister R,Gregory B D,Ecker J R.Next is now: new technologies for sequencing of genomes,transcriptomes,and beyond[J].Current Opinion in Plant Biology,2009,12(2):107-118.
[7] Cushman J C,Bohnert H J.Genomic approaches to plant stress tolerance[J].Current Opinion in Plant Biology,2000,3(2):117-124.
[8] Fowler D B,Limin A E,Ritchie J T.Low-temperature tolerance in cereals: Model and genetic interpretation[J].Crop Science,1999,39(3):626-633.
[9] Torres-Oliva M,Almudi I,McGregor A P,et al.A robust(re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species[J].BMC Genomics,2016,17(1): 1-20.
[10] Chen H,Chen X,Chen D,et al.A comparison of the low temperature transcriptomes of two tomato genotypes that differ in freezing tolerance: Solanum lycopersicum and Solanum habrochaites[J].BMC Plant Biology,2015,15(1):1-16.
[11] Kou S,Chen L,Tu W,et al.The arginine decarboxylase gene ADC1,associated to the putrescine pathway,plays an important role in potato cold-acclimated freezing tolerance as revealed by transcriptome and metabolome analyses[J/OL].The Plant Journal,2018,DOI: 10.1111/TPJ.14126.
[12] Abeynayake S W,Byrne S,Nagy I,et al.Changes in Lolium perenne transcriptome during cold acclimation in two genotypes adapted to different climatic conditions[J].BMC Plant Biology,2015,15(1): 1-15.
[13] Barah P,Jayavelu N D,Rasmussen S,et al.Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes[J].BMC Genomics,2013,14(1):722.
[14] Barrios A,Caminero C,García P,et al.Deep super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.)[J].BMC Plant Biology,2017,17(1): 1-16.
[15] Davidson R M,Gowda M,Moghe G,et al.Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution[J].Plant Journal,2012,71(3): 492-502.
[16] Zhang Y,Ngu D W,Carvalho D,et al.Differentially regulated orthologs in sorghum and the subgenomes of maize[J].The Plant Cell,2017,29(8): 1938-1951.
[17] Swigoňová Z,Lai J,Ma J,et al.Close split of sorghum and maize genome progenitors[J].Genome Research,2004,14(10A):1916-1923.
[18] de Wet J M J.Systematics and evolution of sorghum sect.sorghum(Gramineae)[J].American Journal of Botany,1978,65(8): 477-484.
[19] Hetherington S E,He J,Smillie R M.Photoinhibition at low temperature in chilling-sensitive and -resistant plants[J].Plant physiology,1989,90(4): 1609-1615.
[20] Chinnusamy V,Zhu J,Zhu J K.Cold stress regulation of gene expression in plants[J].Trends in Plant Science,2007,12(10): 444-451.
[21] Freeling M,Rapaka L,Lyons E,et al.G-boxes,bigfoot genes,and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis[J].The Plant Cell Online,2007,19(5): 1441-1457.
[22] Kovi M R,Ergon ?,Rognli O A.Freezing tolerance revisited—effects of variable temperatures on gene regulation in temperate grasses and legumes[J].Current Opinion in Plant Biology,2016,33: 140-146.
[23] Kidokoro S,Yoneda K,Takasaki H,et al.Different cold-signaling pathways function in the responses to rapid and gradual decreases in temperature[J].The Plant Cell,2017,29(4): 760-774.
[24] Yang T,Huang X S.Deep sequencing-based characterization of transcriptome of Pyrus ussuriensis in response to cold stress[J].Gene,2018,661: 109-118.
[25] Wang M,Zhang X,Liu J H.Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress[J].BMC Genomics,2015,16(1): 1-20.
[26] Gray G R,Chauvin L P,Sarhan F,et al.Cold acclimation and freezing tolerance (a complex interaction of light and temperature)[J].Plant Physiology,1997,114(2): 467-474.
[27] Zheng C,Zhao L,Wang Y,et al.Integrated RNA-Seq and sRNA-Seq analysis identifies chilling and freezing responsive key molecular players and pathways in tea plant (Camellia sinensis)[J].PLoS ONE,2015,10(4): 1-29.
[28] Hao X,Wang B,Wang L,et al.Comprehensive transcriptome analysis reveals common and specific genes and pathways involved in cold acclimation and cold stress in tea plant leaves[J].Scientia Horticulturae,2018,240: 354-368.
[29] Franklin K A,Toledo-Ortiz G,Pyott D E,et al.Interaction of light and temperature signalling[J].Journal of Experimental Botany,2014,65(11): 2859-2871.
[30] Gierczik K,Novák A,Ahres M,et al.Circadian and light regulated expression of CBFs and their upstream signalling genes in barley[J].International Journal of Molecular Sciences,2017,18(8):E1828.
[31] Fowler D B,Limin A E,Wang S,et al.Relationship between low-temperature tolerance and verndlization response in wheat and rye[J].Canadian Journal of Plant Science,1996,76: 37-42.
[32] Kippes N,Debernardi J M,Vasquez-Gross H A,et al.Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia[J].Proceedings of the National Academy of Sciences,2015,112(39): E5401-E5410.
[33] Fjellheim S,Boden S,Trevaskis B.The role of seasonal flowering responses in adaptation of grasses to temperate climates[J].Frontiers in Plant Science,2014,5(8): 1-15.
[34] Sasani S,Hemming M N,Oliver S N,et al.The influence of vernalization and daylength on expression of flowering-time genes in the shoot apex and leaves of barley (Hordeum vulgare)[J].Journal of Experimental Botany,2009,60(7): 2169-2178.
[35] Huan Q,Mao Z,Chong K,et al.Global analysis of H3K4me3/H3K27me3 in Brachypodium distachyon reveals VRN3 as critical epigenetic regulation point in vernalization and provides insights into epigenetic memory[J].New Phytologist,2018,219(4):1373-1387.
[36] Bieniawska Z,Espinoza C,Schlereth A,et al.Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome[J].Plant Physiology,2008,147(1): 263-279.
[37] Janmohammadi M.Cold acclimation and vegetative/reproductive transition in winter cereals[J].Albanian Journal of Agricultural Sciences,2012,11(4):199-205.
[38] Dhillon T,Pearce S P,Stockinger E J,et al.Regulation of freezing tolerance and flowering in temperate cereals: The VRN-1 connection[J].Plant Physiology,2010,153(4):1846-1858.
[39] Cuesta-Marcos A,Mun?z-Amatriaín M,Filichkin T,et al.The relationships between development and low temperature tolerance in barley near isogenic lines differing for flowering behavior[J].Plant and Cell Physiology,2015,56(12):2312-2324.
[40] Deng W,Casao M C,Wang P,et al.Nature Publishing Group,2015.Direct links between the vernalization response and other key traits of cereal crops[J].Nature Communications,2015,6(3):1-8.
[41] Mahfoozi S,Limin A E,Hayes P M,et al.Influence of photoperiod response on the expression of cold hardiness in wheat and barley[J].Canadian Journal of Plant Science,2000,80(4): 721-724.
[42] Ergon ?,Melby T I,H?glind M,et al.Vernalization requirement and the chromosomal VRN1-region can affect freezing tolerance and expression of cold-regulated genes in Festuca pratensis[J].Frontiers in Plant Science,2016,7: 1-15.
[43] Janmohammadi M,Enayati V,Sabaghnia N.Impact of cold acclimation,de-acclimation and re-acclimation on carbohydrate content and antioxidant enzyme activities in spring and winter wheat[J].Icelandic Agricultural Sciences,2012,25(1): 3-11.
[44] Skinner D Z,Bellinger B,Hiscox W,et al.Evidence of cyclical light/dark-regulated expression of freezing tolerance in young winter wheat plants[J].PLoS ONE,2018,13(6):1-18.
[45] Kenchanmane Raju S K,Barnes A C,Schnable J C,et al.Low-temperature tolerance in land plants: Are transcript and membrane responses conserved?[J].Plant Science,2018,276(8): 73-86.