Transcriptome profiling of the UV-B stress response in the desert shrub Lycium ruthenicum

详细信息    查看全文

• 作者：Haikui Chen (1) (2)
  Yang Feng (2)
  Lina Wang (2)
  Takahiro Yonezawa (2)
  M. James C. Crabbe (3) (4)
  Xiu Zhang (1)
  Yang Zhong (2) (5)
  
  1. Department of Life Science ; Beifang University of Nationalities ; Yinchuan ; 750021 ; China
  2. School of Life Sciences ; Fudan University ; Shanghai ; 200433 ; China
  3. Department of Zoology ; Tinbergen Building ; University of Oxford ; South Parks Road ; Oxford ; OX1 3PS ; UK
  4. Institute of Biomedical and Environmental Science & Technology ; Faculty of Creative Arts ; Technologies and Science ; University of Bedfordshire ; Park Square ; Luton ; LU1 3JU ; UK
  5. Institute of Biodiversity Science and Geobiology ; Tibet University ; Lhasa ; 850000 ; China
  
• 关键词：Ultraviolet ; Lycium ruthenicum ; Stress response ; Transcriptome ; RNA ; seq
• 刊名：Molecular Biology Reports
• 出版年：2015
• 出版时间：March 2015
• 年：2015
• 卷：42
• 期：3
• 页码：639-649
• 全文大小：856 KB
• 参考文献：1. Hideg E, Jansen MA, Strid A (2013) UV-B exposure, ROS, and stress: inseparable companions or loosely linked associates? Trends Plant Sci 18:107鈥?15 CrossRef
  2. Cechin I, Corniani N, de Fatima Fumis T, Cataneo AC (2008) Ultraviolet-B and water stress effects on growth, gas exchange and oxidative stress in sunflower plants. Radiat Environ Biophys 47:405鈥?13 CrossRef
  3. Wang Y, Wang XA, Wang RJ, Qiu NW, Ma ZQ et al (2012) Effects of UV-B radiation on the growth and reproduction of / Vicia angustifolia. Ying Yong Sheng Tai Xue Bao 23:1333鈥?338
  4. Mark U, SaileMark M, Tevini M (1996) Effects of solar UVB radiation on growth, flowering and yield of central and southern European maize cultivars (Zea mays L). Photochem Photobiol 64:457鈥?63 CrossRef
  5. Kataria S, Guruprasad KN, Ahuja S, Singh B (2013) Enhancement of growth, photosynthetic performance and yield by exclusion of ambient UV components in C3 and C4 plants. J Photochem Photobiol B 127:140鈥?52 CrossRef
  6. Robson TM, Aphalo PJ (2012) Species-specific effect of UV-B radiation on the temporal pattern of leaf growth. Physiol Plant 144:146鈥?60 CrossRef
  7. Frohnmeyer H, Staiger D (2003) Ultraviolet-B radiation-mediated responses in plants. Balancing damage and protection. Plant Physiol 133:1420鈥?428 CrossRef
  8. Britt AB, May GD (2003) Re-engineering plant gene targeting. Trends Plant Sci 8:90鈥?5 CrossRef
  9. Jordan BR, Hopley JG, Thompson WF (1989) Chloroplast gene expression in lettuce grown under different irradiances. Planta 178:69鈥?5 CrossRef
  10. Strid A (1993) Alteration in expression of defense genes in / Pisum sativum after exposure to supplementary ultraviolet-B radiation. Plant Cell Physiol 34:949鈥?53
  11. Ulm R, Baumann A, Oravecz A, Mate Z, Adam E et al (2004) Genome-wide analysis of gene expression reveals function of the bZIP transcription factor HY5 in the UV-B response of / Arabidopsis. Proc Natl Acad Sci USA 101:1397鈥?402 CrossRef
  12. Brosche M, Schuler MA, Kalbina I, Connor L, Strid A (2002) Gene regulation by low level UV-B radiation: identification by DNA array analysis. Photochem Photobiol Sci 1:656鈥?64 CrossRef
  13. Casati P, Walbot V (2003) Gene expression profiling in response to ultraviolet radiation in maize genotypes with varying flavonoid content. Plant Physiol 132:1739鈥?754 CrossRef
  14. Casati P, Stapleton AE, Blum JE, Walbot V (2006) Genome-wide analysis of high-altitude maize and gene knockdown stocks implicates chromatin remodeling proteins in response to UV-B. Plant J 46:613鈥?27 CrossRef
  15. Pontin MA, Piccoli PN, Francisco R, Bottini R, Martinez-Zapater JM et al (2010) Transcriptome changes in grapevine ( / Vitis vinifera L.) cv. Malbec leaves induced by ultraviolet-B radiation. BMC Plant Biol 10:224 CrossRef
  16. Liu ZG, Shu QY, Wang L, Yu MF, Hu YP et al (2012) Genetic diversity of the endangered and medically important / Lycium ruthenicum Murr. revealed by sequence-related amplified polymorphism (SRAP) markers. Biochem Syst Ecol 45:86鈥?7 CrossRef
  17. Liu Z, Dang J, Wang Q, Yu M, Jiang L et al (2013) Optimization of polysaccharides from / Lycium ruthenicum fruit using RSM and its anti-oxidant activity. Int J Biol Macromol 61:127鈥?34 CrossRef
  18. Fa OY, Ji TF, Su YL, Li J, Liu H (2012) Chemical constituents of the fruits of / Lycium ruthenicum. Zhong Yao Cai 35:1599鈥?601
  19. Blake JA, Dolan M, Drabkin H, Hill DP, Li N et al (2013) Gene ontology annotations and resources. Nucleic Acids Res 41:D530鈥揇535 CrossRef
  20. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M et al (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480鈥揇484 CrossRef
  21. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389鈥?402 CrossRef
  22. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25 CrossRef
  23. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G et al (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511鈥?15 CrossRef
  24. Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform 12:323 CrossRef
  25. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139鈥?40 CrossRef
  26. Wu J, Mao X, Cai T, Luo J, Wei L (2006) KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res 34:W720鈥揥724 CrossRef
  27. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644鈥?52 CrossRef
  28. Conesa A, Gotz S (2008) Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008:619832 CrossRef
  29. Ban Y, Kondo S, Ubi BE, Honda C, Bessho H et al (2009) UDP-sugar biosynthetic pathway: contribution to cyanidin 3-galactoside biosynthesis in apple skin. Planta 230:871鈥?81 CrossRef
  30. Lange A, Mills RE, Lange CJ, Stewart M, Devine SE et al (2007) Classical nuclear localization signals: definition, function, and interaction with importin alpha. J Biol Chem 282:5101鈥?105 CrossRef
  31. Wang S, Xie B, Yin L, Duan L, Li Z et al (2010) Increased UV-B radiation affects the viability, reactive oxygen species accumulation and antioxidant enzyme activities in maize ( / Zea mays L.) pollen. Photochem Photobiol 86:110鈥?16 CrossRef
  32. Nakano H, Kimura J, Kumano T, Hanada K, Satoh K et al (1997) Decrease in class pi glutathione transferase mRNA levels by ultraviolet irradiation of cultured rat keratinocytes. Jpn J Cancer Res 88:1063鈥?069 CrossRef
  33. Kim J, Park Y, Choi K (2009) Phototoxicity and oxidative stress responses in / Daphnia magna under exposure to sulfathiazole and environmental level ultraviolet B irradiation. Aquat Toxicol 91:87鈥?4 CrossRef
  34. Takshak S, Agrawal SB (2014) Secondary metabolites and phenylpropanoid pathway enzymes as influenced under supplemental ultraviolet-B radiation in / Withania somnifera Dunal, an indigenous medicinal plant. J Photochem Photobiol B 140C:332鈥?43 CrossRef
  35. Deckmyn G, Impens I (1999) Seasonal responses of six Poaceae to differential levels of solar UV-B radiation. Environ Exp Bot 41:177鈥?84 CrossRef
  36. Kreuzaler F, Ragg H, Fautz E, Kuhn DN, Hahlbrock K (1983) UV-induction of chalcone synthase mRNA in cell suspension cultures of / Petroselinum hortense. Proc Natl Acad Sci USA 80:2591鈥?593 CrossRef
  37. Lipton SA, Choi YB, Pan ZH, Lei SZ, Chen HS et al (1993) A redox-based mechanism for the neuroprotective and neurodestructive effects of nitric oxide and related nitroso-compounds. Nature 364:626鈥?32 CrossRef
  38. Sedoud A, Lopez-Igual R, Ur Rehman A, Wilson A, Perreau F et al (2014) The cyanobacterial photoactive orange carotenoid protein is an excellent singlet oxygen quencher. Plant Cell 26:1781鈥?791 CrossRef
  39. Meissner D, Albert A, Bottcher C, Strack D, Milkowski C (2008) The role of UDP-glucose: hydroxycinnamate glycosyltransferases in phenylpropanoid metabolism and the response to UV-B radiation in / Arabidopsis thaliana. Planta 228:663鈥?74 CrossRef
  40. Ballare CL, Caldwell MM, Flint SD, Robinson SA, Bornman JF (2011) Effects of solar ultraviolet radiation on terrestrial ecosystems. Patterns, mechanisms, and interactions with climate change. Photochem Photobiol Sci 10:226鈥?41 CrossRef
  41. Kumari R, Singh S, Agrawal SB (2010) Response of ultraviolet-B induced antioxidant defense system in a medicinal plant, / Acorus calamus. J Environ Biol 31:907鈥?11
  42. Zhao H, Xu X, Na J, Hao L, Huang L et al (2008) Protective effects of salicylic acid and vitamin C on sulfur dioxide-induced lipid peroxidation in mice. Inhal Toxicol 20:865鈥?71 CrossRef
  43. Rao MV, Paliyath G, Ormrod DP (1996) Ultraviolet-B- and ozone-induced biochemical changes in antioxidant enzymes of / Arabidopsis thaliana. Plant Physiol 110:125鈥?36 CrossRef
  44. Nyman PJ, Wamer WG, Begley TH, Diachenko GW, Perfetti GA (2010) Evaluation of accelerated UV and thermal testing for benzene formation in beverages containing benzoate and ascorbic acid. J Food Sci 75:C263鈥揅267 CrossRef
  45. Sinha M, Singh RP, Kushwaha GS, Iqbal N, Singh A et al (2014) Current overview of allergens of plant pathogenesis related protein families. Sci World J 2014:543195
  46. Balasubramanian V, Vashisht D, Cletus J, Sakthivel N (2012) Plant beta-1,3-glucanases: their biological functions and transgenic expression against phytopathogenic fungi. Biotechnol Lett 34:1983鈥?990 CrossRef
  47. Leimu R, Kloss L, Fischer M (2012) Inbreeding alters activities of the stress-related enzymes chitinases and beta-1,3-glucanases. PLoS ONE 7:e42326 CrossRef
  48. Banerjee J, Das N, Dey P, Maiti MK (2010) Transgenically expressed rice germin-like protein1 in tobacco causes hyper-accumulation of H2O2 and reinforcement of the cell wall components. Biochem Biophys Res Commun 402:637鈥?43 CrossRef
  49. Lashbrook CC, Tieman DM, Klee HJ (1998) Differential regulation of the tomato ETR gene family throughout plant development. Plant J 15:243鈥?52 CrossRef
  50. Martinez-Luscher J, Morales F, Delrot S, Sanchez-Diaz M, Gomes E et al (2013) Short- and long-term physiological responses of grapevine leaves to UV-B radiation. Plant Sci 213:114鈥?22 CrossRef
  51. Lidon FC, Ramalho JC (2011) Impact of UV-B irradiation on photosynthetic performance and chloroplast membrane components in / Oryza sativa L. J Photochem Photobiol B 104:457鈥?66 CrossRef
  52. Adamska I, Funk C, Renger G, Andersson B (1996) Developmental regulation of the PsbS gene expression in spinach seedlings: the role of phytochrome. Plant Mol Biol 31:793鈥?02 CrossRef
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Animal Anatomy, Morphology and Histology
  Animal Biochemistry
  
• 出版者：Springer Netherlands
• ISSN：1573-4978

文摘

Ultraviolet-B (UV-B) is a natural component of the solar radiation. Due to its high energy, low dosages of UV-B can bring huge potential damage effect to organisms. Despite much research that has analyzed the gene expression changes of plants that under UV-B radiation, the transcriptome response of Lycium ruthenicum under the UV-B induction is still un-available. The aim of our study was to identify UV-B responsive genes and gain an insight into the underlying genetic basis of the pathobiology of UV-B related damage. We collected leaf samples from L. ruthenicum with and without UV-B exposure, and then performed a transcriptome profiling to comprehensively investigate their expression signatures. By employing the high throughput RNA-sequencing analysis of samples with and without UV-B exposure, we identified 1,913 up-regulated and 536 down-regulated genes at least by twofold changes. The activity of antioxidant enzyme related genes, including the superoxide dismutase, was decreased, genes related to the synthesis of secondary metabolites and defense responses, such as cinnamyl alcohol dehydrogenase, chalcone-flavanone isomerase and dihydroflavonol reductase were also downregulated. The expression patterns of 14 randomly selected genes resulted from quantitative real-time PCR were basically consistent with their transcript abundance changes identified by RNA-sequencing. We found that several biological pathways related to biotic and abiotic stresses, including cell defense, photosynthesis processes, energy metabolism, were involved in the process of UV-B stress response. A genome-wide screening of gene deregulation under UV-B induction would provide an insight into the understanding of the molecular bases and pathogenesis of UV-B responses.