小立碗藓对重金属镉胁迫的应答特征

doi:10.3724/SP.J.1259.2015.00171

植物学报 ›› 2015, Vol. 50 ›› Issue (2): 171-179.DOI: 10.3724/SP.J.1259.2015.00171

小立碗藓对重金属镉胁迫的应答特征

伍自力^1,², 余孟瑶², 陈露², 魏静², 王晓琴³, 胡勇², 闫妍², 万平^2,^*()

¹宜宾学院生命科学与食品工程学院, 香料植物资源开发与利用四川省高校重点实验室, 宜宾 644000
²首都师范大学植物资源与低碳环境北京市重点实验室, 北京 100048
³北京农学院农业部都市农业(北方)重点实验室, 北京 102206

收稿日期:2014-10-27 接受日期:2015-02-02 出版日期:2015-03-01 发布日期:2015-04-10
通讯作者: 万平
作者简介:? 共同第一作者
基金资助:
转基因生物新品种培育重大专项(No.2013ZX08001003-008)和首都师范大学植物学国家重点学科

Transcriptome Analysis of Physcomitrella patens Response to Cadmium Stress by Bayesian Network

Zili Wu^{1, 2}, Mengyao Yu², Lu Chen², Jing Wei², Xiaoqin Wang³, Yong Hu², Yan Yan², Ping Wan^{2, *}

¹Key Laboratory of Aromatic Plant Resources Exploitation and Utilization in Sichuan Higher Education, College of Life Sciences and Food Engineering, Yibin University, Yibin 644000, China
²Beijing Key Laboratory of Plant Gene Resource and Low-carbon Environmental Biotechnology, Capital Normal University, Beijing 100048, China
³Key Laboratory of Urban Agriculture (North) Ministry of Agriculture, Beijing University of Agriculture, Beijing 102206, China

Received:2014-10-27 Accepted:2015-02-02 Online:2015-03-01 Published:2015-04-10
Contact: Wan Ping
About author:? These authors contributed equally to this paper

摘要/Abstract

摘要： 镉是植物非必需的微量重金属元素, 镉胁迫引起植物细胞的代谢紊乱, 甚至导致细胞死亡。为了探索苔藓植物对镉胁迫的应答机制, 采用高通量测序及生物信息学技术分析了藓类模式植物——小立碗藓(Physcomitrella patens)在镉胁迫下的基因表达特征。结果表明, 在镉胁迫下, 小立碗藓细胞骨架组织、微管运动、DNA修复系统、端粒维护、配子体形成与有性生殖以及与氮代谢等相关基因的表达具有明显的镉胁迫应答特征, 暗示了这些基因可能共同参与小立碗藓对镉胁迫的调控反应。该研究结果为阐明植物对镉胁迫的应答机制提供了新的线索。

关键词: 贝叶斯网络, 镉胁迫, 高通量测序, 小立碗藓, 调控机制

Abstract: Cadmium is a non-essential heavy metal for plant growth. Cadmium stress causes cell metabolism disturbance or death in plant. Here, we performed transcriptome analysis of Physcomitrella patens during cadmium stress by RNA-Seq. We revealed a new transcriptional network of cadmium stress in plants. The functions of genes that were upregulated or downregulated under cadmium stress included microtubule-based movement, microtubule-based processing, cytoskeleton organization, DNA replication, DNA metabolic process, telomere maintenance and organization, sexual reproduction, urea metabolic process, and nitrogen cycle metabolic process. These proteins may play roles in P. patens under cadmium stress. Our study provides new information for the further research of the molecular mechanisms of plant adaptation to cadmium stress.

Key words: Bayesian network, cadmium stress, high-throughput sequencing, Physcomitrella patens, regulatory mechanism

伍自力, 余孟瑶, 陈露, 魏静, 王晓琴, 胡勇, 闫妍, 万平. 小立碗藓对重金属镉胁迫的应答特征. 植物学报, 2015, 50(2): 171-179.

Zili Wu, Mengyao Yu, Lu Chen, Jing Wei, Xiaoqin Wang, Yong Hu, Yan Yan, Ping Wan. Transcriptome Analysis of Physcomitrella patens Response to Cadmium Stress by Bayesian Network. Chinese Bulletin of Botany, 2015, 50(2): 171-179.

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链接本文: https://www.chinbullbotany.com/CN/10.3724/SP.J.1259.2015.00171

https://www.chinbullbotany.com/CN/Y2015/V50/I2/171

图/表 7

参考文献 36

1	Cabot C, Gallego B, Martos S, Barceló J, Poschenrieder C (2013). Signal cross talk in Arabidopsis exposed to cadmium, silicon, and Botrytis cinerea.Planta 237, 337-349.
2	Chen YH, Yang XY, He K, Liu MH, Li JG, Gao ZF, Lin ZQ, Zhang YF, Wang XX, Qiu XM, Shen YP, Zhang L, Deng XH, Luo JC, Deng XW, Chen ZL, Gu HY, Qu LJ (2006). The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family.Plant Mol Biol 60, 107-124.
3	Chmielowska-Bak J, Deckert J (2012). A common res- ponse to common danger? Comparison of animal and plant signaling pathways involved in cadmium sensing.J Cell Commun Signal 6, 191-204.
4	Chmielowska-Bak J, Deckert J (2013). Nitric oxide med- iates Cd-dependent induction of signaling-associated genes.Plant Signal Behav 8, e26664.
5	Chmielowska-Bak J, Gzyl J, Rucińska-Sobkowiak R, Arasimowicz-Jelonek M, Deckert J (2014). The new insights into cadmium sensing.Front Plant Sci 5, 245.
6	Corradi MG, Gorbi G, Ricci A, Torelli A, Bassi M (1995). Chromium-induced sexual reproduction gives rise to a Cr-tolerant progeny in Scenedesmus acutus.Ecotoxicol Environ Saf 32, 12-18.
7	DalCorso G, Farinati S, Furini A (2010). Regulatory networks of cadmium stress in plants.Plant Signal Behav 5, 663-667.
8	Dovgalyuk A, Kalynyak T, Blume YB (2003). Heavy metals have a different action from aluminium in disrupting microtubules in Allium cepa meristematic cells.Cell Biol Int 27, 193-195.
9	Ercal N, Gurer-Orhan H, Aykin-Burns N (2001). Toxic metals and oxidative stress part I: mechanisms involved in metal-induced oxidative damage.Curr Top Med Chem 1, 529-539.
10	Farinati S, DalCorso G, Varotto S, Furini A (2010). The Brassica juncea BjCdR15, an ortholog of Arabidopsis TGA3, is a regulator of cadmium uptake, transport and accumulation in shoots and confers cadmium tolerance in transgenic plants.New Phytol 185, 964-978.
11	Fojtová M, Fulnečková J, Fajkus J, Kovařík A (2002). Recovery of tobacco cells from cadmium stress is accompanied by DNA repair and increased telomerase activity.J Exp Bot 53, 2151-2158.
12	Hart JJ, Welch RM, Norvell WA, Sullivan LA, Kochian LV (1998). Characterization of cadmium binding, uptake, and translocation in intact seedlings of bread and durum wheat cultivars.Plant Physiol 116, 1413-1420.
13	Hartwig A, Schwerdtle T (2002). Interactions by carcinogenic metal compounds with DNA repair processes: toxicological implications.Toxicol Lett 127, 47-54.
14	Hepler PK, Hush JM (1996). Behavior of microtubules in living plant cells.Plant Physiol 112, 455-461.
15	Herbette S, Taconnat L, Hugouvieux V, Piette L, Magniette MLM, Cuine S, Auroy P, Richaud P, Forestier C, Bourguignon J, Renou JP, Vavasseur A, Leonhardt N (2006). Genome-wide transcriptome profiling of the early cadmium response of Arabidopsis roots and shoots. Biochimie 88, 1751-1765.
16	Hsu YT, Kao CH (2003). Role of abscisic acid in cadmium tolerance of rice (Oryza sativa L.) seedlings.Plant Cell Environ 26, 867-874.
17	Huang JJ, Okuka M, Lu WS, Tsibris JCM, McLean MP, Keefe DL, Liu L (2013). Telomere shortening and DNA damage of embryonic stem cells induced by cigarette smoke.Reprod Toxicol 35, 89-95.
18	Liu DH, Xue P, Meng QM, Zou J, Gu JG, Jiang WS (2009). Pb/Cu effects on the organization of microtubule cyto- skeleton in interphase and mitotic cells of Allium sativum L.Plant Cell Rep 28, 695-702.
19	Liu XM, Kim KE, Kim KC, Nguyen XC, Han HJ, Jung MS, Kim HS, Kim SH, Park HC, Yun DJ, Chung WS (2010). Cadmium activates Arabidopsis MPK3 and MPK6 via accumulation of reactive oxygen species.Phytochemistry 71, 614-618.
20	Ma WW, Xu WZ, Xu H, Chen YS, He ZY, Ma M (2010). Nitric oxide modulates cadmium influx during cadmium- induced programmed cell death in tobacco BY-2 cells.Planta 232, 325-335.
21	Nzengue Y, Steiman R, Garrel C, Lefèbvre E, Guiraud P (2008). Oxidative stress and DNA damage induced by cadmium in the human keratinocyte HaCaT cell line: role of glutathione in the resistance to cadmium.Toxicology 243, 193-206.
22	Oono Y, Yazawa T, Kawahara Y, Kanamori H, Kobayashi F, Sasaki H, Mori S, Wu J, Handa H, Itoh T, Matsumoto T (2014). Genome-wide transcriptome analysis reveals that cadmium stress signaling controls the expression of genes in drought stress signal pathways in rice. PLoS One 9, e96946.
23	Přibyl P, Cepák V, Zachleder V (2008). Cytoskeletal alterations in interphase cells of the green alga Spirogyra decimina in response to heavy metals exposure: II. The effect of aluminium, nickel and copper.Toxicol In Vitro 22, 1160-1168.
24	Qi XT, Zhang YX, Chai TY (2007). Characterization of a novel plant promoter specifically induced by heavy metal and identification of the promoter regions conferring he- avy metal responsiveness.Plant Physiol 143, 50-59.
25	Rai V, Vajpayee P, Singh SN, Mehrotra S (2004). Effect of chromium accumulation on photosynthetic pigments, oxidative stress defense system, nitrate reduction, proline level and eugenol content of Ocimum tenuiflorum L.Plant Sci 167, 1159-1169.
26	Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin IT, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL (2008). The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.Science 319, 64-69.
27	Roth U, von Roepenack-Lahaye E, Clemens S (2006). Proteome changes in Arabidopsis thaliana roots upon exposure to Cd2+.J Exp Bot 57, 4003-4013.
28	Rother M, Krauss GJ, Grass G, Wesenberg D (2006). Sulphate assimilation under Cd2+ stress in Physcomitrella patens—combined transcript, enzyme and metabolite profiling. Plant Cell Environ 29, 1801-1811.
29	Singh I, Shah K (2014). Evidences for structural basis of altered ascorbate peroxidase activity in cadmium- stressed rice plants exposed to jasmonate.Biometals 27, 247-263.
30	van de Mortel JE, Schat H, Moerland PD, Ver Loren van Themaat E, van der Ent S, Blankestijn H, Ghandilyan A, Tsiatsiani S, Aarts MG (2008). Expression differences for genes involved in lignin, glutathione and sulphate metabolism in response to cadmium in Arabidopsis thaliana and the related Zn/Cd-hyperaccumulator Thlaspi caerulescens.Plant Cell Environ 31, 301-324.
31	Wang YC, Gao CQ, Liang YN, Wang C, Yang CP, Liu GF (2010). A novel bZIP gene from Tamarix hispida mediates physiological responses to salt stress in tobacco plants.J Plant Physiol 167, 222-230.
32	Weber M, Trampczynska A, Clemens S (2006). Compara- tive transcriptome analysis of toxic metal responses in Arabidopsis thaliana and the Cd2+-hypertolerant facultative metallophyte Arabidopsis halleri.Plant Cell Environ 29, 950-963.
33	Xiong J, Fu G, Tao L, Zhu C (2010). Roles of nitric oxide in alleviating heavy metal toxicity in plants.Arch Biochem Biophys 497, 13-20.
34	Xiong J, Lu H, Lu KX, Duan YX, An LY, Zhu C (2009). Cadmium decreases crown root number by decreasing endogenous nitric oxide, which is indispensable for crown root primordia initiation in rice seedlings.Planta 230, 599-610.
35	Ye Y, Li Z, Xing D (2013). Nitric oxide promotes MPK6-mediated caspase-3-like activation in cadmium- induced Arabidopsis thaliana programmed cell death.Plant Cell Environ 36, 1-15.
36	Yourtchi MS, Bayat H (2013). Effect of cadmium toxicity on growth, cadmium accumulation and macronutrient content of durum wheat (Dena CV.).Int J Agri Crop Sci 6, 1099-1103.

Type	GO number	Biological processes	P value
1	GO:0007018	Microtubule-based movement	2.80E-06
	GO:0007017	Microtubule-based process	6.90E-05
	GO:0007010	Cytoskeleton organization	0.018 8
2	GO:0006260	DNA replication	0.001 7
	GO:0006259	DNA metabolic process	0.002 5
	GO:0006302	Double-strand break repair	0.015 3
	GO:0000723	Telomere maintenance	0.033 4
	GO:0032200	Telomere organization	0.033 4
3	GO:0007276	Gamete generation	0.033 4
	GO:0007292	Female gamete generation	0.033 4
	GO:0019953	Sexual reproduction	0.033 4
4	GO:0019627	Urea metabolic process	0.033 4
4	GO:0071941	Nitrogen cycle metabolic process	0.033 4

Type	GO number	Biological processes	P value
1	GO:0007018	Microtubule-based movement	2.80E-06
	GO:0007017	Microtubule-based process	6.90E-05
	GO:0007010	Cytoskeleton organization	0.018 8
2	GO:0006260	DNA replication	0.001 7
	GO:0006259	DNA metabolic process	0.002 5
	GO:0006302	Double-strand break repair	0.015 3
	GO:0000723	Telomere maintenance	0.033 4
	GO:0032200	Telomere organization	0.033 4
3	GO:0007276	Gamete generation	0.033 4
	GO:0007292	Female gamete generation	0.033 4
	GO:0019953	Sexual reproduction	0.033 4
4	GO:0019627	Urea metabolic process	0.033 4
4	GO:0071941	Nitrogen cycle metabolic process	0.033 4

Gene identification number	The homologous gene in Arabidopsis thaliana	Function
Pp1s34_49V6	AT2G27290.1	Protein of unknown function (DUF1279)
Pp1s352_53V6	AT3G57060.2	Chromosome condensation
Pp1s59_160V6	AT3G44750.1	Histone deacetylase 3
Pp1s57_179V6	AT5G18140.1	Chaperone DnaJ-domain superfamily protein
Pp1s204_5V6	AT5G20935.1	Protein of unknown function
Pp1s68_291V6	AT5G57590.1	Adenosylmethionine-8-amino-7-oxononanoate transaminases
Pp1s13_454V6	AT5G54910.1	DEA (D/H)-box RNA helicase family protein
Pp1s133_35V6.1	AT1G08260.1	DNA polymerase epsilon catalytic subunit
Pp1s259_32V6.1	AT1G79690.1	Dipeptidyl-peptidase activity, hydrolase activity
Pp1s175_94V6.1	AT4G01130.1	GDSL-like Lipase/Acylhydrolase superfamily protein involved in lipid metabolic process

Gene identification number	The homologous gene in Arabidopsis thaliana	Function
Pp1s34_49V6	AT2G27290.1	Protein of unknown function (DUF1279)
Pp1s352_53V6	AT3G57060.2	Chromosome condensation
Pp1s59_160V6	AT3G44750.1	Histone deacetylase 3
Pp1s57_179V6	AT5G18140.1	Chaperone DnaJ-domain superfamily protein
Pp1s204_5V6	AT5G20935.1	Protein of unknown function
Pp1s68_291V6	AT5G57590.1	Adenosylmethionine-8-amino-7-oxononanoate transaminases
Pp1s13_454V6	AT5G54910.1	DEA (D/H)-box RNA helicase family protein
Pp1s133_35V6.1	AT1G08260.1	DNA polymerase epsilon catalytic subunit
Pp1s259_32V6.1	AT1G79690.1	Dipeptidyl-peptidase activity, hydrolase activity
Pp1s175_94V6.1	AT4G01130.1	GDSL-like Lipase/Acylhydrolase superfamily protein involved in lipid metabolic process

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小立碗藓对重金属镉胁迫的应答特征

Transcriptome Analysis of Physcomitrella patens Response to Cadmium Stress by Bayesian Network

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