Effect of salt stress on genes encoding translation-associated proteins in Arabidopsis thaliana

Plant Signaling and Behavior

Volumn 7, Issue 9, 2012, Pages 1095-1102

  Omidbakhshfard, Mohammad Amin ^a,b,c   Omranian, Nooshin ^a,b   Ahmadi, Farajollah Shahriari ^c   Nikoloski, Zoran ^b   Mueller Roeber, Bernd ^a,b  

^a UNIVERSITY OF POTSDAM   (Germany)

^b MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^c FERDOWSI UNIVERSITY OF MASHHAD   (Iran)

Author keywords

Arabidopsis thaliana; Clustering; Dynamic time warping; Gene expression; Ribosomal protein; Salt stress; Translation; Variation of information

Indexed keywords

ARABIDOPSIS PROTEIN; CHLOROPLAST PROTEIN; SODIUM CHLORIDE;

ARABIDOPSIS; ARTICLE; CHLOROPLAST; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGICAL STRESS; PLANT GENE; PROTEIN SYNTHESIS; REAL TIME POLYMERASE CHAIN REACTION; SALT TOLERANCE;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHLOROPLAST PROTEINS; CHLOROPLASTS; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; PROTEIN BIOSYNTHESIS; REAL-TIME POLYMERASE CHAIN REACTION; SALT-TOLERANCE; SODIUM CHLORIDE; STRESS, PHYSIOLOGICAL;

ARABIDOPSIS THALIANA;

EID: 84866458417     PISSN: 15592316     EISSN: 15592324     Source Type: Journal    
DOI: 10.4161/psb.21218     Document Type: Article

References (50)

1. Chaves MM, Flexas J, Pinheiro C. Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell. Ann Bot 2009; 103:551-60; PMID:18662937; http://dx.doi.org/10.1093/aob/mcn125.
2. Munns R, Tester M. Mechanisms of salinity tolerance. Annu Rev Plant Biol 2008; 59:651-81; PMID:18444910; http://dx.doi.org/10.1146/annurev.arplant.59.032607.092911.
3. Parida AK, Das AB. Salt tolerance and salinity effects on plants: a review. Ecotoxicol Environ Saf 2005; 60:324-49; PMID:15590011; http://dx.doi.org/10.1016/j.ecoenv.2004.06.010.
4. Liu X, Ribaut J. Plant Gene Regulatory Network System Under Abiotic Stress. Acta Biologica Szegediensis 2006; 50:9.
5. Mehta P, Kraslavsky V, Bharti S, Allakhverdiev SI, Jajoo A. Analysis of salt stress induced changes in Photosystem II heterogeneity by prompt fluorescence and delayed fluorescence in wheat (Triticum aestivum) leaves. J Photochem Photobiol B 2011; 104:308-13; PMID:21414797; http://dx.doi.org/10.1016/j.jphotobiol.2011.02.016.
6. Fujita M, Fujita Y, Noutoshi Y, Takahashi F, Narusaka Y, Yamaguchi-Shinozaki K, et al. Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Curr Opin Plant Biol 2006; 9:436-42; PMID:16759898; http://dx.doi.org/10.1016/j.pbi.2006.05.014.
7. Shinozaki K, Yamaguchi-Shinozaki K. Gene networks involved in drought stress response and tolerance. J Exp Bot 2007; 58:221-7; PMID:17075077; http://dx.doi.org/10.1093/jxb/erl164.
8. Rausell A, Kanhonou R, Yenush L, Serrano R, Ros R. The translation initiation factor eIF1A is an important determinant in the tolerance to NaCl stress in yeast and plants. Plant J 2003; 34:257-67; PMID:12713533; http://dx.doi.org/10.1046/j.1365-313X.2003.01719.x.
9. Brinker M, Brosché M, Vinocur B, Abo-Ogiala A, Fayyaz P, Janz D, et al. Linking the salt transcriptome with physiological responses of a salt-resistant Populus species as a strategy to identify genes important for stress acclimation. Plant Physiol 2010; 154:1697-709; PMID:20959419; http://dx.doi.org/10.1104/pp.110.164152.
10. Kosová K, Vítámvás P, Prášil IT, Renaut J. Plant proteome changes under abiotic stress--contribution of proteomics studies to understanding plant stress response. J Proteomics 2011; 74:1301-22; PMID:21329772; http://dx.doi.org/10.1016/j.jprot.2011.02.006.
11. Pang Q, Chen S, Dai S, Chen Y, Wang Y, Yan X. Comparative proteomics of salt tolerance in Arabidopsis thaliana and Thellungiella halophila. J Proteome Res 2010; 9:2584-99; PMID:20377188; http://dx.doi.org/10.1021/pr100034f.
12. Singh BN, Mishra RN, Agarwal PK, Goswami M, Nair S, Sopory SK, et al. A pea chloroplast translation elongation factor that is regulated by abiotic factors. Biochem Biophys Res Commun 2004; 320:523-30; PMID:15219860; http://dx.doi.org/10.1016/j.bbrc.2004.05.192.
13. Ndimba BK, Chivasa S, Simon WJ, Slabas AR. Identification of Arabidopsis salt and osmotic stress responsive proteins using two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 2005; 5:4185-96; PMID:16254930; http://dx.doi.org/10.1002/pmic.200401282.
14. Fromont-Racine M, Senger B, Saveanu C, Fasiolo F. Ribosome assembly in eukaryotes. Gene 2003; 313:17-42; PMID:12957375; http://dx.doi.org/10.1016/S0378-1119(03)00629-2.
15. Palecková KM. Activity of ribosomes and tmRNA of Streptomyces aureofaciens during development and stress conditions induced by changes in temperature and the presence of antibiotics. Communicating Current Research and Educational Topics and Trends in Applied Microbiology 2007; Formatex:11-8.
16. Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 1999; 24:437-40; PMID:10542411; http://dx.doi.org/10.1016/S0968-0004(99)01460-7.
17. Kressler D, Hurt E, Bassler J. Driving ribosome assembly. Biochim Biophys Acta 2010; 1803:673-83.
18. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002; 3
19. Mukhopadhyay P, Reddy MK, Singla-Pareek SL, Sopory SK. Transcriptional downregulation of rice rpL32 gene under abiotic stress is associated with removal of transcription factors within the promoter region. PLoS One 2011; 6:e28058; PMID:22132208; http://dx.doi.org/10.1371/journal.pone.0028058.
20. Rogalski M, Schöttler MA, Thiele W, Schulze WX, Bock R. Rpl33, a nonessential plastid-encoded ribosomal protein in tobacco, is required under cold stress conditions. Plant Cell 2008; 20:2221-37; PMID:18757552; http://dx.doi.org/10.1105/tpc.108.060392.
21. Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, et al. Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 2001; 13:889-905; PMID:11283343.
22. Zorb C, Schmitt S, Neeb A, Karl S, Linder M, Schubert S. The biochemical reaction of maize (Zeamays L.) to salt stress is characterized by a mitigation of symptoms and not by a specific adaptation. Plant Sci 2004; 167:91-100; http://dx.doi.org/10.1016/j.plantsci.2004.03.004.
23. Taji T, Seki M, Satou M, Sakurai T, Kobayashi M, Ishiyama K, et al. Comparative genomics in salt tolerance between Arabidopsis and aRabidopsis-related halophyte salt cress using Arabidopsis microarray. Plant Physiol 2004; 135:1697-709; PMID:15247402; http://dx.doi.org/10.1104/pp.104.039909.
24. Barneche F, Winter V, Crèvecoeur M, Rochaix JD. ATAB2 is a novel factor in the signalling pathway of light-controlled synthesis of photosystem proteins. EMBO J 2006; 25:5907-18; PMID:17139246; http://dx.doi.org/10.1038/sj.emboj.7601472.
25. Pinon V, Etchells JP, Rossignol P, Collier SA, Arroyo JM, Martienssen RA, et al. Three genes that specifically influence leaf patterning encode ribosomal proteins. Development 2008; 135:1315-24; PMID:18305008; http://dx.doi.org/10.1242/dev.016469.
26. Dirk LM, Williams MA, Houtz RL. Eukaryotic peptide deformylases. Nuclear-encoded and chloroplast-targeted enzymes in Arabidopsis. Plant Physiol 2001; 127:97-107; PMID:11553738; http://dx.doi.org/10.1104/pp.127.1.97.
27. Dirk LMA, Schmidt JJ, Cai Y, Barnes JC, Hanger KM, Nayak NR, et al. Insights into the substrate specificity of plant peptide deformylase, an essential enzyme with potential for the development of novel biotechnology applications in agriculture. Biochem J 2008; 413:417-27; PMID:18412546; http://dx.doi.org/10.1042/BJ20071641.
28. Giglione C, Vallon O, Meinnel T. Control of protein life-span by N-terminal methionine excision. EMBO J 2003; 22:13-23; PMID:12505980; http://dx.doi.org/10.1093/emboj/cdg007.
29. Moon S, Giglione C, Lee DY, An S, Jeong DH, Meinnel T, et al. Rice peptide deformylase PDF1B is crucial for development of chloroplasts. Plant Cell Physiol 2008; 49:1536-46; PMID:18718933; http://dx.doi.org/10.1093/pcp/pcn121.
30. Duchêne AM, Giritch A, Hoffmann B, Cognat V, Lancelin D, Peeters NM, et al. Dual targeting is the rule for organellar aminoacyl-tRNA synthetases in Arabidopsis thaliana. Proc Natl Acad Sci USA 2005; 102:16484-9; PMID:16251277; http://dx.doi.org/10.1073/pnas.0504682102.
31. Berg M, Rogers R, Muralla R, Meinke D. Requirement of aminoacyl-tRNA synthetases for gametogenesis and embryo development in Arabidopsis. Plant J 2005; 44:866-78; PMID:16297076; http://dx.doi. org/10.1111/j.1365-313X.2005.02580.x.
32. Sakoe H, Chiba S. Dynamic-Programming Algorithm Optimization for Spoken Word Recognition. Ieee T Acoust Speech 1978; 26:43-9; http://dx.doi.org/10.1109/TASSP.1978.1163055.
33. Hempel S, Koseska A, Nikoloski Z, Kurths J. Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study. BMC Bioinformatics 2011; 12; PMID:21219653.
34. Meila M. Comparing clusterings - an information based distance. J Multivariate Anal 2007; 98:873-95; http://dx.doi.org/10.1016/j.jmva.2006.11.013.
35. Du J, Huang YP, Xi J, Cao MJ, Ni WS, Chen X, et al. Functional gene-mining for salt-tolerance genes with the power of Arabidopsis. Plant J 2008; 56:653-64; PMID:18643972; http://dx.doi.org/10.1111/j.1365-313X.2008.03602.x.
36. Abbasi N, Kim HB, Park NI, Kim HS, Kim YK, Park YI, et al. APUM23, a nucleolar Puf domain protein, is involved in pre-ribosomal RNA processing and normal growth patterning in Arabidopsis. Plant J 2010; 64:960-76; PMID:21143677; http://dx.doi. org/10.1111/j.1365-313X.2010.04393.x.
37. He XJ, Mu RL, Cao WH, Zhang ZG, Zhang JS, Chen SY. AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant J 2005; 44:903-16; PMID:16359384; http://dx.doi. org/10.1111/j.1365-313X.2005.02575.x.
38. Cao WH. Ethylene receptor regulates plant response to salt stress. Institute of Genetics and Developmental Biology. Beijing: Chinese Academy of Sciences, 2004.
39. Pesaresi P, Varotto C, Meurer J, Jahns P, Salamini F, Leister D. Knock-out of the plastid ribosomal protein L11 in Arabidopsis: effects on mRNA translation and photosynthesis. Plant J 2001; 27:179-89; PMID:11532164; http://dx.doi.org/10.1046/j.1365-313x.2001.01076.x.
40. Ljung K, Bhalerao RP, Sandberg G. Sites and homeostatic control of auxin biosynthesis in Arabidopsis during vegetative growth. Plant J 2001; 28:465-74; PMID:11737783; http://dx.doi.org/10.1046/j.1365-313X.2001.01173.x.
41. Wang G, Zhu QG, Meng QW, Wu CA. Transcript profiling during salt stress of young cotton (Gossypium hirsutum) seedlings via Solexa sequencing. Acta Physiol Plant 2012; 34:107-15; http://dx.doi.org/10.1007/s11738-011-0809-6.
42. Soll J, Schleiff E. Protein import into chloroplasts. Nat Rev Mol Cell Biol 2004; 5:198-208; PMID:14991000; http://dx.doi.org/10.1038/nrm1333.
43. Richly E, Leister D. An improved prediction of chloroplast proteins reveals diversities and commonalities in the chloroplast proteomes of Arabidopsis and rice. Gene 2004; 329:11-6; PMID:15033524; http://dx.doi.org/10.1016/j.gene.2004.01.008.
44. Dvinge H, Bertone P. HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R. Bioinformatics 2009; 25:3325-6; PMID:19808880; http://dx.doi.org/10.1093/bioinformatics/btp578.
45. Smyth GK. Limma: linear models for microarray data. New York: Springer, 2005:397-420.
46. Tai YC. Timecourse: statistical analysis for developmental microarray time course data. 2007.
47. Li RTaGCaBNaJ. samr: SAM: Significance Analysis of Microarrays. 2011.
48. Giorgino T. Computing and Visualizing Dynamic Time Warping Alignments in R: The dtw Package. J Stat Softw 2009; 31:1-24.
49. Itakura F. Minimum prediction residual principle applied to speech recognition. IEEE T Acoust Speech 1975; 23:67-72.
50. Rousseeuw PJ. Silhouettes - a Graphical Aid to the Interpretation and Validation of Cluster-Analysis. J Comput Appl Math 1987; 20:53-65; http://dx.doi.org/10.1016/0377-0427(87)90125-7.