Isolation of pigeon pea (Cajanus cajan L.) legumin gene promoter and identification of conserved regulatory elements using tools of bioinformatics

Indian Journal of Biotechnology

Volumn 6, Issue 4, 2007, Pages 495-503

  Jaiswal, Rajani ^a   Nain, Vikrant ^a   Abdin, M Z ^b   Kumar, P A ^a  

^a INDIAN AGRICULTURAL RESEARCH INSTITUTE   (India)

^b HAMDARD UNIVERSITY   (India)

Author keywords

glucuronidase (GUS); Legumin gene; Nucleosome positioning; Phylogenetic footprinting

Indexed keywords

AVENIN; BETA GLUCURONIDASE; CIS ACTING ELEMENT;

ARTICLE; BIOINFORMATICS; CHICKPEA; CONTROLLED STUDY; GENE EXPRESSION; GENE ISOLATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PEA; PEANUT; PHYLOGENY; PIGEONPEA; POLYMERASE CHAIN REACTION; PROMOTER REGION; SOYBEAN; TRANSCRIPTION INITIATION; VICIA FABA;

ARACHIS HYPOGAEA; CAJANUS CAJAN; CICER ARIETINUM; GLYCINE MAX; NICOTIANA OBTUSIFOLIA; PISUM SATIVUM; VICIA FABA;

EID: 39349113590     PISSN: 09725849     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (39)

1. Evans I M, Gatehouse J A, Croy R D & Boulter D, Regulation of the transcription of storage protein mRNA in nuclei isolated from developing pea (Pisum sativum) cotyledons, Planta, 160 (1984) 559-568.
2. Gatehouse J A, Evans I M, Croy R R D & Boulter D, Differential expression of genes during legume seed development, Philos Trans R Soc Lond (B) Biol Sci, 314 (1986) 367-384.
3. Shasany A K & Koundal K R, Isolation and characterization of legumin promoter sequence from chickpea (Cicer arietinum L.), Indian J Exp Biol, 38 (2000) 363-372.
4. Ellis J R, Shirhat A J, Hepher A, Yarwood J N, Gatehouse J A et al, Tissue specific expression of a pea legumin gene in seeds of Nicotiana plumbaginifolia, Plant Mol Biol, 10 (1988) 203-214.
5. Lycett G W, Croy R R, Shirsat A H, Richards D M & Boulter D, The 5′ flanking regions of three pea legumin genes: Comparison of the DNA sequences, Nucleic Acids Res, 13 (1985) 6733-6743.
6. Lida A, Nagasawa A & Oeda K, Positive and negative cis-regulatory regions in the soybean glycinin promoter identified by quantitative transient gene expression, Plant Cell Rep, 14 (1995) 539-544.
7. Itoh Y, Kitamura Y & Fukazawa C, The glycinin box: A soybean embryo factor binding motif within the quantitative regulatory region of the 11S seed storage globulin promoter, Mol Gen Genet, 243 (1994) 353-357.
8. Baumlein H, Wobus U, Pustell J & Kafatos F C, The legumin gene family: Structure of a B type gene of Vicia faba and a possible legumin gene specific regulatory element, Nucleic Acids Res, 14 (1986) 2707-2720.
9. Baumlein H, Nagy I, Villarroel R, Inze D & Wobus U, Cis-analysis of a seed protein gene promoter: The conservative RY repeat CATGCATG within the legumin box is essential for tissue-specific expression of a legumin gene, Plant J, 24 (1992) 233-239.
10. Blanchette M & Tompa M, Discovery of regulatory elements by a computational method for phylogenetic footprinting, Genome Res, 12 (2002) 739-748.
11. Wasserman W W & Sandelin A, Applied bioinformatics for the identification of regulatory elements, Nat Rev Genet, 5 (2004) 276-287.
12. Forde B G, Heyworth A, Pywell J & Kreis M, Nucleotide sequence of a 131 hordein gene and the identification of possible upstream regulatory elements in endosperm storage protein genes from barley, wheat and maize, Nucleic Acids Res, 13 (1985) 7327-7339.
13. Donald R G K & Cashmore A R, Mutation of either G or I box sequences profoundly affects expression from the Arabidopsis rbcS-IA promoter, EMBO J, 9 (1990) 1717-1735.
14. Mason H S, DeWald D B & Mullet J E, Identification of methyl jasmonate responsive domain in soybean vspB promoter, Plant Cell, 5 (1993) 241-251.
15. Schulze-Lefert P, Becker-Andre M, Schulz W, Hahlbrock K & Dangl J L, Functional architecture of light responsive chalcone synthase promoter from parsley, Plant Cell, 1 (1989) 707-714.
16. Eulgem T, Rushton P J, Robatzek S & Somssich I E, The WRKY super family of plant transcription factors, Trends Plant Sci, 5 (2000) 199-205.
17. Kornberg R D & Lorch Y, Twenty-five years of the nucleosome, fundamental particle of the eukaryotic chromosome, Cell, 98 (1999) 285-294.
18. Svejstrup J Q, Transcription: Histones face the FACT, Science, 301 (2003) 1053-1055.
19. Hehl R & Wingender E, Database-assisted promoter analysis, Trends Plant Sci, 6 (2001 ) 251-255.
20. Mandaokar A D, Clonining and characterization of storage protein genes in chickpea (Cicer arietinum L.). Ph D Thesis, Indian Agricultural Research Institute, New Delhi, 1994.
21. Doyle J J & Doyle J L, Isolation of plant DNA from fresh tissue, Focus, 12 (1990) 13-15.
22. Bailey T L & Elkan C, Unsupervised learning of multiple motifs in biopolymers using expectation maximization, Machine Learning, 21 (1995) 51-80.
23. Perier R C, Praz V, Junier T, Bonnard C & Bucher P, The eukaryotic promoter database (EPD): Recent developments, Nucleic Acids Res, 28 (2000) 302-303.
24. Aiyar A, The use of CLUSTAL W and CLUSTAL X for multiple sequence alignment, Methods Mol Biol, 132 (2000) 221-241.
25. Crooks G E, Hon G, Chandonia J M & Brenner S E, WebLogo: A sequence logo generator, Genome Res, 14 (2004) 1188-1190.
26. Higo K, Ugawa Y, Iwamoto M & Korenaga T, Plant cis-acting regulatory DNA elements (PLACE) database, Nucleic Acids Res, 27 (1999) 297-300.
27. Rombauts S, Dehais P, Van Montagu M & Rouze P, Plant CARE, a plant cis-acting regulatory element database, Nucleic Acids Res, 27 (1999) 295-297.
28. Kolchanov N A, Ignatieva E V, Ananko E A, Podkolodnaya O A, Stepanenko I L et al, Transcription regulatory regions database (TRRD): Its status in 2002, Nucleic Acids Res, 30 (2002) 312-317.
29. Quandt K, Frech K, Karas H, Wingender E & Werner T, Matlnd and Matlnspector - New fast and versatile tools for detection of consensus matches in nucleotide sequence data, Nucleic Acids Res, 23 (1995) 4878-4884.
30. Hofgen R & Willmitzer L, Storage of competent cells of Agrobacterium transformation, Nucleic Acids Res, 16 (1988) 9877.
31. Horsch R B, Fry J E, Ho Inan N L, Eichholtz D, Rogers S G et al, A simple method for transferring genes into plants, Science, 227 (1985) 1229-1231.
32. Jefferson R A, Assaying chimeric genes in plants: The GUS gene fusion system, Plant Mol Biol Rep, 5 (1987) 387-405.
33. Lycett G W, Croy R R, Shirsat A H & Boulter D, The complete nucleotide sequence of a legumin gene from pea (Pisum sativum L.), Nucleic Acids Res, 12 (1984) 4493-4506.
34. Vincentz M, Leite A, Neshich G, Vriend G, Matter C et al, ACGT and vicilin core sequences in a promoter domain required for seed-specific expression of a 2S storage protein gene are recognized by the opaque-2 regulatory protein, Plant Mol Biol, 34 (1997) 879-889.
35. Wu C Y, Suzuki A, Washida H & Takaiwa F, The GCN4 motif in a rice glutelin gene is essential for endosperm specific gene expression and is activated by Opaque-2 in transgenic rice plants, Plant J, 14 (1998) 673-683.
36. Shen Q & Ho T H D, Functional dissection of an abscisic acid (ABA) inducible gene reveal two independent ABA-responsive complexes each containing G Box and a novel cis-acting element, Plant Cell, 7 (1995) 295-307.
37. Hasan S, Prediction and analysis of nucleosome positioning in genomic sequences. Ph D Dissertation, Wolfson College, University of Cambridge, Cambridge, UK, 2003.
38. Levitsky V G, RECON: A program for prediction of nucleosome formation potential, Nucleic Acids Res, 32 (2004) W346-W349.
39. Levitsky V G, Podkolodnaya O A, Kolchanov N A & Podkolodny N L, Nucleosome formation of eukaryotic DNA: Calculation and promoters analysis, Bioinformatics, 17 (2001) 998-1010.