Genome-wide expression analysis of reactive oxygen species gene network in Mizuna plants grown in long-term spaceflight

BMC Plant Biology

Volumn 14, Issue 1, 2014, Pages

  Sugimoto, Manabu ^a   Oono, Youko ^b   Gusev, Oleg ^b,c,d   Matsumoto, Takashi ^b,e   Yazawa, Takayuki ^f   Levinskikh, Margarita A ^g   Sychev, Vladimir N ^g   Bingham, Gail E ^h   Wheeler, Raymond ⁱ   Hummerick, Mary ⁱ  

^a OKAYAMA UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^c KAZAN FEDERAL UNIVERSITY   (Russian Federation)

^d JAPAN AEROSPACE EXPLORATION AGENCY   (Japan)

^e Agriculture Forestry and Fisheries Research Council   (Japan)

^f HITACHI LTD   (Japan)

^g INSTITUTE OF BIOMEDICAL PROBLEMS   (Russian Federation)

^h UTAH STATE UNIVERSITY   (United States)

ⁱ KENNEDY SPACE CENTER   (United States)

Author keywords

International Space Station; Mizuna; mRNA Seq; Next generation sequencing; Reactive oxygen species; Spaceflight; Transcriptome

Indexed keywords

REACTIVE OXYGEN METABOLITE;

ARTICLE; BRASSICA RAPA; GENE EXPRESSION REGULATION; METABOLISM; SPACE FLIGHT;

BRASSICA RAPA; GENE EXPRESSION REGULATION, PLANT; REACTIVE OXYGEN SPECIES; SPACE FLIGHT;

BRASSICA RAPA SUBSP. NIPPOSINICA;

EID: 84891501877     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-14-4     Document Type: Article

References (40)

1. Ferl R, Wheeler R, Levine HG, Paul A-L. Plants in space. Curr Opin Plant Biol 2002, 5:258-263. 10.1016/S1369-5266(02)00254-6, 11960745.
2. Kanazawa S, Ishikawa Y, Tomita-Yokotani K, Hashimoto H, Kitaya Y, Yamashita M, Nagatomo M, Oshima T, Wada H. Space Agriculture Task Force. Space agriculture for habitation on Mars with hyper-thermophilic aerobic composting bacteria. Adv Space Res 2008, 41:696-700.
3. Roldán-Arjona T, Ariza RR. Repair and tolerance of oxidative DNA damage in plants. Mutat Res 2009, 681:169-179. 10.1016/j.mrrev.2008.07.003, 18707020.
4. Rizzo AM, Corsetto PA, Montorfano G, Milani S, Zava S, Tavella S, Cancedda R, Berra B. Effects of long-term space flight on erythrocytes and oxidative stress of rodents. PLoS One 2012, 7(3):e32361. 10.1371/journal.pone.0032361, 3296700, 22412864.
5. Martzivanou M, Hampp R. Hyper-gravity effects on the Arabidopsis transcriptome. Plant Physiol 2003, 118:221-231.
6. Barjaktarović Z, Nordheim A, Lamkemeyer T, Fladerer C, Madlung J, Hampp R. Time-course of changes in protein amounts of specific proteins upon exposure to hyper-g, 2-D clinorotation and random positioning of Arabidopsis cell cultures. J Exp Bot 2007, 58:4357-4363. 10.1093/jxb/erm302, 18182437.
7. Barjaktarović Z, Schütz W, Madlung J, Fladerer C, Nordheim A, Hampp R. Changes in the effective gravitational field strength affect the state of phosphorylation of stress-related proteins in callus cultures of Arabidopsis thaliana. J Exp Bot 2009, 60:779-789. 10.1093/jxb/ern324, 2652066, 19129159.
8. Paul AL, Popp MP, Gurley WB, Guy C, Norwood KL, Ferl RJ. Arabidopsis gene expression patterns are altered during spaceflight. Adv Space Res 2005, 2005(36):1175-1181.
9. Paul AL, Zupanska AK, Ostrow DT, Zhang Y, Sun Y, Li JL, Shanker S, Farmerie WG, Amalfitano CE, Ferl RJ. Spaceflight transcriptomes: unique responses to a novel environment. Astrobiology 2012, 12:40-56. 10.1089/ast.2011.0696, 3264962, 22221117.
10. Fujita M, Fujita Y, Noutoshi Y, Takahashi F, Narusaka Y, Yamaguchi-Shinozaki K, Shinozaki K. Crosstalkbetween abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling network. Curr Opin Plant Biol 2006, 9:436-442. 10.1016/j.pbi.2006.05.014, 16759898.
11. Miller G, Shulaev V, Mittler R. Reactive oxygen signaling and abiotic stress. Physiol Plant 2008, 133:481-489. 10.1111/j.1399-3054.2008.01090.x, 18346071.
12. Gostimsky SA, Levinskikh MA, Sychev VN, Kokaeva ZG, Dribnokhodova OP, Khartina GA, Bingkhem G. The study of the genetic effects in generation of pea plants cultivated during the whole cycle of ontogenesis on the board of RS ISS. Russian J Genetics 2007, 43:869-874.
13. Shagimardanova EI, Gusev OA, Sychev VN, Levinskikh MA, Sharipova MR, Il'inskaya ON, Bingham G, Sugimoto M. Expression of stress response genes in barley Hordeum vulgare in a spaceflight environment. Mol Biol 2010, 44:734-740.
14. Levinskikh MA, Sychev VN, Derendiaeva TA, Signalova OB, Podol'skii IG, Gostimskii SA, Bingham G. Growth, development and genetic status of pea plants cultivated in space greenhouse " LADA". Aviakosm Ekolog Med 2005, 39:38-43.
15. Sychev VN, Levinskikh MA, Gostimsky SA, Bingham GE, Podolskii IG. Spaceflight effects on consecutive generations of peas grown onboard the Russian segment of the International Space Station. Acta Astronaut 2007, 60:426-432.
16. Werc-Reichhart D, Hehn A, Didierjean L. Cytochromes P450 for engineering herbicide tolerance. Trends Plant Sci 2000, 5:116-123. 10.1016/S1360-1385(00)01567-3, 10707077.
17. Gadjev I, Vanderauwera S, Gechev TS, Laloi C, Minkov IN, Shulaev V, Apel K, Inze' D, Mittler R, Van Breusegem F. Transcriptomic footprints disclose specificity of reactive oxygen species signaling in Arabidopsis. Plant Physiol 2006, 141:436-445. 10.1104/pp.106.078717, 1475436, 16603662.
18. Mittler R, Vanderauwera S, Gollery M, Breusegem FV. Reactive oxygen gene network of plants. Trends in Plant Sci 2004, 9:490-498.
19. Berndt C, Lillig CH, Holmgren A. Thioredoxins and glutaredoxins as facilitators of protein folding. Biochem Biophys Acta 2008, 1783:641-650. 10.1016/j.bbamcr.2008.02.003, 18331844.
20. Vanlerberghe GC, McIntosh L. Alternative oxidase: from gene to function. Annu Rev Plant Physiol Plant Mol Biol 1997, 48:703-734. 10.1146/annurev.arplant.48.1.703, 15012279.
21. Moore AL, Albury MS, Crichton PG, Affourtic C. Function of the alternative oxidase: is it still a scavenger?. Trends Plant Sci 2002, 7:478-487. 10.1016/S1360-1385(02)02366-X, 12417142.
22. Sugie A, Murai K, Takumi S. Alteration of respiration capacity and transcript accumulation level of alternative oxidase genes in necrosis lines of common wheat. Genes Genet Syst 2007, 82:231-239. 10.1266/ggs.82.231, 17660693.
23. Pitzschke A, Djamei A, Bitton F, Hirt H. A major role of the MEKK1-MKK1/2-MPK4 pathway in ROS signalling. Mol Plant 2009, 2:120-137. 10.1093/mp/ssn079, 2639734, 19529823.
24. Teige M, Scheikl E, Eulgem T, Doczi R, Ichimura K, Shinozaki K, Dangl JL, Hirt H. The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis. Mol Cell 2004, 15:141-152. 10.1016/j.molcel.2004.06.023, 15225555.
25. Ichimura K, Mizoguchi T, Yoshida R, Yuasa T, Shinozaki K. Various abiotic stresses rapidly activate Arabidopsis MAP kinases ATMPK4 and ATMPK6. Plant J 2000, 24:655-665. 10.1046/j.1365-313x.2000.00913.x, 11123804.
26. Asai T, Tena G, Plotnikova J, Willmann MR, Chiu WL, Gomez-Gomez L, Boller T, Ausubel FM, Sheen J. MAP kinase signalling cascade in Arabidopsis innate immunity. Nature 2002, 415:977-983. 10.1038/415977a, 11875555.
27. Kim SH, Woo DH, Kim JM, Lee SY, Chung WS, Moon YH. Arabidopsis MKK4 mediates osmotic-stress response via its regulation of MPK3 activity. Biochem Bioph Res Commun 2011, 412:150-154.
28. Ren DT, Yang HP, Zhang SQ. Cell death mediated by MAPK is associated with hydrogen peroxide production in Arabidopsis. J Biol Chem 2002, 277:559-565.
29. Rentel MC, Lecourieux D, Ouaked F, Usher SL, Petersen L, Okamoto H, Knight H, Peck SC, Grierson CS, Hirt H, Knight MR. OXI1 kinase is necessary for oxidative burst-mediated signalling in Arabidopsis. Nature 2004, 427:858-861. 10.1038/nature02353, 14985766.
30. Moon H, Lee B, Choi G, Shin S, Prasad DT, Lee O, Kwak SS, Kim DH, Nam J, Bahk J, Hong JC, Lee SY, Cho MJ, Lim CO, Yun DJ. NDP kinase 2 interacts with two oxidative stress-activated MAPKs to regulate cellular redox state and enhances multiple stress tolerance in transgenic plants. Proc Natl Acad Sci U S A 2003, 100:358-363. 10.1073/pnas.252641899, 140977, 12506203.
31. Li SJ, Fu QT, Huang WD, Yu DQ. Functional analysis of an Arabidopsis transcription factor WRKY25 in heat stress. Plant Cell Rep 2009, 28:683-693. 10.1007/s00299-008-0666-y, 19125253.
32. Ciftci-Yilmaz S, Morsy MR, Song L, Coutu A, Krizek BA, Lewis MW, Warren D, Cushman J, Connolly EL, Mittler R. The ear-motif of the C2H2 zinc-finger protein ZAT7 plays a key role in the defense response of Arabidopsis to salinity stress. J Biol Chem 2007, 282:9260-9268. 10.1074/jbc.M611093200, 17259181.
33. Torres MA, Dangl JL, Jones JD. Arabidopsis gp91phox homologues AtrbohD and AtrbohF are required for accumulation of reactive oxygen intermediates in the plant defense response. Proc Natl Acad Sci USA 2002, 99:517-522. 10.1073/pnas.012452499, 117592, 11756663.
34. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. Journal 2011, 17:10-12.
35. Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9:357-359. 10.1038/nmeth.1923, 3322381, 22388286.
36. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
37. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28:511-515. 10.1038/nbt.1621, 3146043, 20436464.
38. Cheng F, Liu S, Wu J, Fang L, Sun S, Liu B, Hua W, Wang X. BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol 2011, 11:136. 10.1186/1471-2229-11-136, 3213011, 21995777.
39. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:1-8.
40. Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, Castro E, Coggill P, Crbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Oivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJA, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY. InterPro in 2011: new developments in the family and domain prediction database. Nucl Acids Res 2012, 40:D306-D312. 10.1093/nar/gkr948, 3245097, 22096229.