Isolation and characterization of cold responsive NAC gene from Lepidium latifolium

Molecular Biology Reports

Volumn 39, Issue 10, 2012, Pages 9629-9638

  Aslam, Mohammad ^a,b   Grover, Atul ^a   Sinha, Vimlendu Bhushan ^a,c   Fakher, Beenish ^d   Pande, Veena ^e   Yadav, Patade Vikas ^a   Gupta, Sanjay Mohan ^a   Anandhan, Sivalingam ^a,f   Ahmed, Zakwan ^a  

^a Defence Institute of Bio Energy Research   (India)

^b INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

^c GURU GOBIND SINGH INDRAPRASTHA UNIVERSITY   (India)

^d G B PANT UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (India)

^e KUMAUN UNIVERSITY   (India)

^f National Research Centre for Onion and Garlic   (India)

Author keywords

Cold stress; Lepidium latifolium; NAC; RACE; Real time PCR

Indexed keywords

ABSCISIC ACID; CALCIUM CHLORIDE; COMPLEMENTARY DNA; ETHYLENE; GENOMIC DNA; LEPIDIUM LATIFOLIUM TRANSCRIPTION FACTOR NAC; SALICYLIC ACID; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; COLD STRESS; COMPUTER MODEL; CONTROLLED STUDY; DOWN REGULATION; GENE AMPLIFICATION; GENE EXPRESSION REGULATION; GENE ISOLATION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; INTRON; LEPIDIUM; LEPIDIUM LATIFOLIUM; LEPIDIUM LATIFOLIUM NAC GENE; MICROARRAY ANALYSIS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PLANT GENE; QUANTITATIVE ANALYSIS; RAPID AMPLIFICATION OF CDNA END; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; UPREGULATION;

AMINO ACID SEQUENCE; ARABIDOPSIS; BASE SEQUENCE; COLD SHOCK PROTEINS AND PEPTIDES; COLD-SHOCK RESPONSE; CONSENSUS SEQUENCE; DNA, PLANT; GENE EXPRESSION REGULATION, PLANT; LEPIDIUM; MOLECULAR SEQUENCE DATA; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PHYLOGENY; PLANT LEAVES; PLANT PROTEINS; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

ARABIDOPSIS THALIANA; LEPIDIUM LATIFOLIUM;

EID: 84868551121     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-012-1828-0     Document Type: Article

References (46)

1. Thomashow MF (1999) Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Ann Rev Plant Physiol Plant Mol Biol 50:571-599. doi:10.1146/annurev. arplant.50. 1.571
2. Fowler S, Thomashow MF (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14(8):1675-1690. doi:10.1105/tpc.003483
3. Lee BH, Henderson DA et al (2005) The Arabidopsis coldresponsive transcriptome and its regulation by ICE1. Plant Cell 17(11):3155-3175. doi:10.1105/tpc.105.035568
4. Hewezi T, Leger M et al (2006) Transcriptional profiling of sunflower plants growing under low temperatures reveals an extensive down-regulation of gene expression associated with chilling sensitivity. J Exp Bot 57(12):3109-3122. doi:10.1093/jxb/erl080
5. Nakashima K, Tran LSP et al (2007) Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J 51(4):617-630. doi:10.1111/j.1365-313X.2007. 03168.x
6. Aslam M, Sinha VB et al (2010) Isolation of cold stressresponsive genes from Lepidium latifolium by suppressive subtraction hybridization. Acta Physiol Plant 32(1):205-210. doi:10.1007/s11738-009-0382-4
7. Monroy AF, Dryanova A et al (2007) Regulatory gene candidates and gene expression analysis of cold acclimation in winter and spring wheat. Plant Mol Biol 64(4):409-423. doi:10.1007/s11103-007-9161-z
8. Kim SG, Kim SY et al (2007) A membrane-associated NAC transcription factor regulates salt-responsive flowering via FLOWERING LOCUS T in Arabidopsis. Planta 226(3):647-654. doi:10.1007/s00425-007-0513-3
9. Hu HH, You J et al (2008) Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice. Plant Mol Biol 67(1-2):169-181. doi:10.1007/s11103-008-9309-5
10. Ooka H, Satoh K et al (2003) Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res 10(6):239-247. doi:10.1093/dnares/10.6.239
11. Xiong YQ, Liu TY et al (2005) Transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots. Plant Mol Biol 59(1):191-203. doi:10.1007/s11103-005-6503-6
12. Kim SY, Kim SG et al (2007) Exploring membrane-associated NAC transcription factors in Arabidopsis: implications for membrane biology in genome regulation. Nucleic Acids Res 35(1):203-213. doi:10.1093/nar/gkl1068
13. Fujita M, Fujita Y et al (2004) A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stresssignaling pathway. Plant J 39(6):863-876. doi:10.1111/j.1365-313X.2004.02171.x
14. Tran LSP, Nakashima K et al (2004) Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell 16(9):2481-2498. doi:10.1105/tpc.104.022699
15. Uauy C, Distelfeld A et al (2006) A NAC gene regulating senescence improves grain protein, zinc, and iron content in wheat. Science 314(5803):1298-1301. doi:10.1126/science. 1133649
16. Hao YJ, Wei W, Song QX et al (2011) Soybean NAC transcription factors promote abiotic stress tolerance and lateral root formation in transgenic plants. Plant J 68:302-313. doi:10.1111/j.1365-313X.2011.04687.x
17. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols in the series methods in molecular biology. Humana, Totowa, pp 365-386
18. Guo A, He K, Liu D, Bai S, Gu S, Wei L, Luo J (2005) DATF: a database of Arabidopsis transcription factors. Bioinformatics 21(10):2568-2569
19. Riano-Pachon DM, Ruzicic S et al (2007) PlnTFDB: an integrative plant transcription factor database. Bmc Bioinform 8. doi:10.1186/1471-2105-8-42
20. Altschul SF, Madden TL et al (1997) Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389-3402. doi:10.1093/nar/25.17.3389
21. Stormo GD (2000) Gene-Finding Approaches for Eukaryotes. Genome Res 10:394-397
22. Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10(4):516-522. doi:10.1101/gr.10.4.516
23. Finn RD, Mistry J et al (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34:D247-D251. doi:10.1093/nar/gkj149
24. de Castro E, Sigrist CJA et al (2006) ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res 34:W362-W365. doi:10.1093/nar/gkl124
25. Quevillon E, Silventoinen V et al (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33:W116-W120. doi:10.1093/nar/gki442
26. Thompson JD, Higgins DG et al (1994) CLUSTAL-W-Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673-4680. doi:10.1093/nar/22.22.4673
27. Tamura K, Dudley J et al (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24(8):1596-1599. doi:10.1093/molbev/msm092
28. Bailey TL, Williams N et al (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34:W369-W373. doi:10.1093/nar/gkl198
29. Higo K, Ugawa Y et al (1999) Plant cis-acting regulatory DNA elements (PLACE) database 1999. Nucleic Acids Res 27(1):297-300. doi:10.1093/nar/27.1.297
30. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13-15
31. Sambrook J, Russell DW (2008) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York
32. Ooka H, Satoh K, Doi K, Nagata T, Otomo Y, Murakami K, Matsubara K, Osato N, Kawai J, Carninci P, Hayashizaki Y, Suzuki K, Kojima K, Takahara Y, Yamamoto K, Kikuchi S (2003) Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res 10:239-247
33. Kikuchi K, Ueguchi-Tanaka M et al (2000) Molecular analysis of the NAC gene family in rice. Mol Gen Genet 262(6):1047-1051. doi:10.1007/pl00008647
34. He XJ, Mu RL et al (2005) AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant J 44(6):903-916. doi:10.1111/j.1365-313X.2005. 02575.x
35. Souer E, van Houwelingen A et al (1996) The no apical meristem gene of petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries. Cell 85(2):159-170. doi:10.1016/s0092-8674 (00) 81093-4
36. Xie Q, Frugis G et al (2000) Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. Gene Dev 14(23):3024-3036. doi:10.1101/gad.852200
37. Duval M, Hsieh TF et al (2002) Molecular characterization of AtNAM: a member of the Arabidopsis NAC domain superfamily. Plant Mol Biol 50(2):237-248. doi:10.1023/a:1016028530943
38. Greve K, La Cour T et al (2003) Interactions between plant RING-H2 and plant-specific NAC (NAM/ATAF1/2/CUC2) proteins: rING-H2 molecular specificity and cellular localization. Biochem J 371:97-108. doi:10.1042/bj20021123
39. Narusaka Y, Nakashima K et al (2003) Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J 34(2):137-148. doi:10.1046/j.1365-313X.2003.01708.x
40. Finkelstein RR, Gampala SSL et al (2002) Abscisic acid signaling in seeds and seedlings. Plant Cell 14:S15-S45. doi:10.1105/tpc.010441
41. Ohnishi T, Sugahara S et al (2005) OsNAC6, a member of the NAC gene family, is induced by various stresses in rice. Genes Genet Syst 80(2):135-139. doi:10.1266/ggs.80.135
42. Seki M, Narusaka M et al (2001) Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell 13(1):61-72. doi:10.2307/3871153
43. Xiong LM, Schumaker KS et al (2002) Cell signaling during cold, drought, and salt stress. Plant Cell 14:S165-S183. doi:10.1105/tpc.000596
44. Zhu JK (2003) Regulation of ion homeostasis under salt stress. Curr Opin Plant Biol 6(5):441-445. doi:10.1016/s1369-5266 (03) 00085-2
45. Han Q, Zhang J et al (2012) Identification and expression pattern of one stress-responsive NAC gene from Solanum lycopersicum. Mol Biol Rep 39(2):1713-1720. doi:10.1007/s11033-011-0911-2
46. Wu A, Allu AD et al (2012) JUNGBRUNNEN1, a reactive oxygen species responsive NAC transcription factor, regulates longevity in arabidopsis. Plant Cell. doi:10.1105/tpc.111.090894