Gene expression analysis in cadmium-stressed roots of a low cadmium-accumulating solanaceous plant, Solanum torvum

Journal of Experimental Botany

Volumn 61, Issue 2, 2010, Pages 423-437

  Yamaguchi, Hirotaka ^a   Fukuoka, Hiroyuki ^a   Arao, Tomohito ^b   Ohyama, Akio ^a   Nunome, Tsukasa ^a   Miyatake, Koji ^a   Negoro, Satomi ^a  

^a NATIONAL INSTITUTE OF VEGETABLE AND TEA SCIENCE   (Japan)

^b NATIONAL INSTITUTE FOR AGRO ENVIRONMENTAL SCIENCES   (Japan)

Author keywords

Cadmium; Gene expression; Illumina sequencing; SAGE; Solanum torvum; Solexa sequencing; Transcriptome

Indexed keywords

CADMIUM; VEGETABLE PROTEIN;

ARTICLE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PLANT ROOT; TOMATO;

CADMIUM; GENE EXPRESSION REGULATION, PLANT; LYCOPERSICON ESCULENTUM; PLANT PROTEINS; PLANT ROOTS;

LYCOPERSICON ESCULENTUM; SOLANUM; SOLANUM MELONGENA; SOLANUM TORVUM;

EID: 74249114406     PISSN: 00220957     EISSN: 14602431     Source Type: Journal    
DOI: 10.1093/jxb/erp313     Document Type: Article

References (47)

1. Alexandersson E, Fraysse L, Sjövall-Larsen S, Gustavsson S, Fellert M, Karlsson M, Johanson U, Kjellbom P. 2005. Whole gene family expression and drought stress regulation of aquaporins. Plant Molecular Biology 59, 469-484.
2. Arao T, Takeda H, Nishihara E. 2008. Reduction of cadmium translocation from roots to shoots in eggplant (Solanum melongena) by grafting onto Solanum torvum rootstock. Soil Science and Plant Nutrition 54, 555-559.
3. Baxter I, Tchieu J, Sussman MR, Boutry M, Palmgren MG, Gribskov M, Harper JF, Axelsen KB. 2003. Genomic comparison of P-type ATPase ion pumps in Arabidopsis and rice. Plant Physiology 132, 618-628.
4. Boursiac Y, Chen S, Luu DT, Sorieul M, van den Dries N, Maurel C. 2005. Early effects of salinity on water transport in Arabidopsis roots. Molecular and cellular features of aquaporin expression. Plant Physiology 139, 790-805.
5. Courbot M, Willems G, Motte P, Arvidsson S. 2007. A major quantitative trait locus for cadmium tolerance in Arabidopsis halleri colocalizes with HMA4, a gene encoding a heavy metal ATPase. Plant Physiology 144, 1052-1065.
6. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Research 8, 186-194. (Pubitemid 28177230)
7. Ewing B, Hillier LD, Wendl MC, Green P. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Research 8, 175-185. (Pubitemid 28177229)
8. Gao W, Xiao S, Li H, Tsao S, Chye M. 2009. Arabidopsis thaliana acyl-CoA-binding protein ACBP2 interacts with heavy-metal-binding farnesylated protein AtFP6. New Phytologist 181, 89-102.
9. Hall JL, Williams LE. 2003. Transition metal transporters in plants. Journal of Experimental Botany 54, 2601-2613.
10. Herbette S, Taconnat L, Hugouvieux V, et al. 2006. Genome-wide transcriptome profiling of the early cadmium response of Arabidopsis roots and shoots. Biochimie 88, 1751-1765.
11. Hoen PAC't, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RHAM, de Menezes RX, Boer JM, van Ommen GB, den Dunnen JT. 2008. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Research 36, e141.
12. Hussain D, Haydon MJ, Wang Y, Wong E, Sherson SM, Young J, Camakaris J, Harper JF, Cobbett CS. 2004. P-type ATPase heavy metal transporters with roles in essential zinc homeostasis in Arabidopsis. The Plant Cell 16, 1327-1339.
13. Kaldenhoff R, Fischer M. 2006. Functional aquaporin diversity in plants. Biochimica et Biophysica Acta 1758, 1134-1141
14. Mäser P, Thomine S, Schroeder JI, et al. 2001. Phylogenetic relationships within cation transporter families of Arabidopsis. Plant Physiology 126, 1646-1667.
15. Matsumura H, Krüger D, Kahl G, Terauchi R. 2008. SuperSAGE: a modern platform for genome-wide quantitative transcript profiling. Current Pharmaceutical Biotechnology 9, 368-374.
16. Matsumura H, Reich S, Ito A, Saitoh H, Kamoun S, Winter P, Kahl G, Reuter M, Krüger D, Terauchi R. 2003. Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Procedings of the National Academy of Sciences, USA 100, 15718-15723.
17. 1B-type ATPase of the Zn/Co/ Cd/Pb subclass. The Plant Journal 35, 164-176.
18. Mori S, Uraguchi S, Ishikawa S, Arao T. 2009. Xylem loading process is a critical factor in determining Cd accumulation in the shoots of Solanum melongena and Solanum torvum. Environmental and Experimental Botany 67, 127-132.
19. Nakano T, Suzuki K, Fujimura T, Shinshi H. 2006. Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiology 140, 411-432.
20. Nakashima K, Yamaguchi-Shinozaki K. 2006. Regulons involved in osmotic stress-responsive and cold stress-responsive gene expression in plants. Physiologia Plantarum 126, 62-71.
21. Osato N, Itoh M, Konno H, et al. 2002. A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs. Genome Research 12, 1127-1134.
22. Perfus-Barbeoch L, Leonhardt N, Vavasseur A, Forestier C. 2002. Heavy metal toxicity: cadmium permeates through calcium channels and disturbs the plant water status. The Plant Journal 32, 539-548.
23. Poole RL, Barker GLA, Werner K, Biggi GF, Coghill J, Gibbings JG, Berry S, Dunwell JM, Edwards KJ. 2008. Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription. BMC Genomics 9, 475-491.
24. Poschenrieder C, Gunsé B, Barceló J. 1989. Influence of cadmium on water relations, stomatal resistance, and abscisic acid content in expanding bean leaves. Plant Physiology 90, 1365-1371.
25. Pruitt KD, Tatusova T, Maglott DR. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research 35, D61-D65.
26. Puig S, Mira H, Dorcey E, et al. 2007. Higher plants possess two different types of ATX1-like copper chaperones. Biochemical and Biophysical Research Communications 354, 385-390.
27. Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J. 2001. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Research 29, 159-164.
28. Rodríguez L, Ruiz E, Alonso-Azcarate J, Rincon J. 2009. Heavy metal distribution and chemical speciation in tailings and soils aroung a Pb-Zn mine in Spain. Journal of Environmental Management 90, 1106-1116.
29. Rogers EE, Guerinot ML. 2002. FRD3, a member of the multidrug and toxin efflux family, controls iron deficiency responses in Arabidopsis. The Plant Cell 14, 1787-1799.
30. Romero-Puertas MC, Corpas FJ, Rodríguez-Serrano M, Gomez M, del Río LA, Sandalio LM. 2007. Differential expression and regulation of antioxidative enzymes by cadmium in pea plants. Journal of Plant Physiology 164, 1346-1357.
31. Rudd S. 2003. Expressed sequence tags: alternative or complement to whole genome sequences? Trends in Plant Science 8, 321-329.
32. Sancenon V, Puig S, Mira H, Thiele DJ, Penarrubia L. 2003. Identification of a copper transporter family in Arabidopsis thaliana. Plant Molecular Biology 51, 577-587.
33. Senden MHMN, Meer AJGMvd, Verburg TG, Wolterbeek HT. 1995. Citric acid in tomato plant roots and its effect on cadmium uptake and distribution. Plant and Soil 171, 333-339.
34. Smeets K, Ruytinx J, Semane B, Van Belleghem F, Remans T, Van Sanden S, Vangronsveld J, Cuypers A. 2008. Cadmium-induced transcriptional and enzymatic alterations related to oxidative stress. Environmental and Experimental Botany 63, 1-8.
35. Suzuki N, Yamaguchi Y, Koizumi N, Sano H. 2002. Functional characterization of a heavy metal binding protein CdI19 from Arabidopsis. The Plant Journal 32, 165-173.
36. Takeda H, Sato A, Nishihara E, Arao T. 2007. Reduction of cadmium concentration in eggplant (Solanum melongena) fruits by grafting onto Solanum torvum rootstock. Japanese Journal of Soil Science and Plant Nutrition 78, 581-586 (in Japanese with English summary).
37. Talke IN, Hanikenne M, Kramer U. 2006. Zinc-dependent global transcriptional control, transcriptional deregulation, and higher gene copy number for genes in metal homeostasis of the hyperaccumulator Arabidopsis halleri. Plant Physiology 142, 148-167.
38. Tamas L, Dudikova J, Durcekova K, Haluskova L, Huttova J, Mistrík I, Olle M. 2008. Alterations of the gene expression, lipid peroxidation, proline and thiol content along the barley root exposed to cadmium. Journal of Plant Physiology 165, 1193-1203.
39. Tatusov RL, Fedorova ND, Jackson JD, et al. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41.
40. Uetani M, Kobayashi E, Suwazono Y, Honda R, Nishijo M, Nakagawa H, Kido T, Nogawa K. 2006. Tissue cadmium (Cd) concentrations of people living in a Cd polluted area, Japan. BioMetals 19, 521-525.
41. Uraguchi S, Mori S, Kuramata M, Kawasaki A, Arao T, Ishikawa S. 2009. Root-to-shoot Cd translocation via the xylem is the major process determining shoot and grain cadmium accumulation in rice. Journal of Experimental Botany 60, 2677-2688.
42. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. 1995. Serial analysis of gene expression. Science 274, 484-487.
43. Vencio RZN, Brentani H, Patrao DFC, Pereira CAB. 2004. Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE). BMC Bioinformatics 5, 119-131.
44. Verdoucq L, Grondin A, Maurel C. 2008. Structure-function analysis of plant aquaporin AtPIP2;1 gating by divalent cations and protons. Biochemical Journal 415, 409-416.
45. 2+-hypertolerant facultative metallophyte Arabidopsis halleri. Plant, Cell and Environment 29, 950-963.
46. 1B-ATPases\-an ancient family of transition metal pumps with diverse functions in plants. Trends in Plant Science 10, 491-502.
47. Wintz H, Vulpe C. 2002. Plant copper chaperones. Biochemical Society Transactions 30, 732-735.