Isolation of genomic DNAs from plants, fungi and bacteria using benzyl chloride

Zhu, Heng; Qu, Feng; Zhu, Lian

doi:10.1093/nar/21.22.5279

Cited by 407 publications

(214 citation statements)

References 4 publications

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“…The DNA of the parents and 190 F 2 plants was extracted from 3 g of fresh leaf tissue using the benzyl chloride method (Zhu et al, 1993). For restriction fragment length polymorphism (RFLP) analysis, DNA was digested with six restriction enzymes: BamHI, BglII, DraI, EcoRI, EcoRV and HindIII.…”

Section: Dna Analysismentioning

confidence: 99%

Quantitative Trait Loci for Rice Phyllochron in Lemont × IR36 Cross

Morita

Tang

Miyamoto

et al. 2005

Plant Production Science

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Section: Dna Analysismentioning

confidence: 99%

Quantitative Trait Loci for Rice Phyllochron in Lemont × IR36 Cross

Morita

Tang

Miyamoto

et al. 2005

Plant Production Science

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“…DNA was extracted by using benzyl chloride methodology (Zhu et al, 1993). The DNA G+C composition of strain CSK1 T was determined by HPLC (Mesbah et al, 1989).…”

mentioning

confidence: 99%

Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant and cellulolytic bacterium isolated from a cellulose-degrading bacterial community

Kato

Haruta

Cui

et al. 2004

International Journal of Systematic and Evolutionary Microbiology

115

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A novel anaerobic, thermophilic and cellulolytic bacterium (strain CSK1 T ) was isolated from a cellulose-degrading bacterial community. On the basis of 16S rRNA gene sequence similarity, strain CSK1 T was mapped to cluster III of the genus Clostridium. Strain CSK1 T is closely related to Clostridium thermocellum (96?2 %) and Clostridium aldrichii (95?1 %). Strain CSK1 T is a non-motile, spore-forming, straight or slightly curved rod. The optimum temperature and initial pH for its growth and cellulose degradation are 50-55 6C and pH 7?5. Strain CSK1 T grew under a gas phase containing up to 4 % O 2 . Phylogenetic and phenotypic analyses support the differentiation of strain CSK1 T from its closest relatives. Strain CSK1 T therefore represents a novel species, for which the name Clostridium straminisolvens sp. nov. is proposed, with CSK1 T (=DSM 16021 T =IAM 15070 T ) as the type strain.

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“…essentially as described previously (10,11). The leaf was immersed in a solution containing 1 N NaOH and 0.5 N Na 2 CO 3 for 15 min to remove the silicon-containing cuticle, rinsed with water, and dried on paper.…”

Section: Methodsmentioning

confidence: 99%

Characterization of Genomic Sequence Coding for Bromelain Inhibitors in Pineapple and Expression of Its Recombinant Isoform

Sawano¹,

Muramatsu²,

Hatano³

et al. 2002

Journal of Biological Chemistry

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Bromelain inhibitor (BI) is a cysteine proteinase inhibitor isolated from pineapple stem (Reddy, M. N., Keim, P. S., Heinrikson, R. L., and Ké zdy, F. J. (1975) J. Biol. Chem. 250, 1741-1750). It consists of eight isoinhibitors, and each isoinhibitor has a two-chain structure. In this study, the genomic DNA has been cloned and found to encode a precursor protein with 246 amino acids (M r ‫؍‬ ϳ27,500) containing three isoinhibitor domains (BI-III, -VI, and -VII) that are 93% identical to one another in amino acid sequences. The gene structure indicated that these isoinhibitors are produced by removal of the N-terminal pre-peptide (19 residues), 3 interchain peptides (each 5 residues), 2 interdomain peptides (each 19 residues), and the C-terminal pro-peptide (18 residues). Moreover, all the amino acid sequences of bromelain isoinhibitors could be explained by removal of one or two amino acids from BI-III, -VI, and -VII with exopeptidases. A recombinant single-chain BI-VI with and without the interchain peptide showed the same and no bromelain inhibitory activity as compared with the native BI-VI, respectively. These results indicate that the interchain peptide plays an important role of the folding process of the mature isoinhibitors.Most cysteine proteinase inhibitors obtained from plants so far have been identified as cystatins including inhibitors from rice, corn, soybean, and tomato (1). Their properties have been extensively studied, including their nucleotide and amino acid sequences and three-dimensional structures. Reddy et al. (2) have isolated a novel and microheterogeneous inhibitor toward bromelain (BI) 1 from pineapple (Ananas comosus) stem (2). Each isoform of BI consists of a light chain (10 or 11 residues) and a heavy chain (40 or 41 residues) that are cross-linked with disulfide bonds (2-4). The three-dimensional solution structure of the sixth isoinhibitor (BI-VI N ) has two distinct domains named A and B domains, each of which is formed by a threestranded antiparallel ␤-sheet (5, 6). The B domain consists of the light chain and part of the heavy chain (Glu 1H -Asp 9H and Leu 31H -Lys 41H ) 2 and was indicated to involve the major bromelain inhibitory site, possessing a more flexible structure that seems to allow the inhibitor to fit well into the catalytic site region of a target proteinase (4, 6). On the other hand, the structure of the A domain (Thr 10H -Ile 29H ) was well converged and, thus, thought to contribute greatly to the conformational stability of the B domain (6).BI has no similarity to the cystatin superfamily inhibitors in the primary structure (1) and has no Gln-X-Val-X-Gly sequence that is essential for activity against papain and other cysteine proteinases (7). For example, the structure of BI-VI N shows no homology with that of rice cystatin that consists of an ␣-helix and a five-stranded antiparallel ␤-sheet (8). Interestingly, BI-VI N shared the same folding and disulfide bond connectivities with Bowman-Birk serine proteinase inhibitor (BBI) from soybean (6), a 71-residue in...

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Isolation of genomic DNAs from plants, fungi and bacteria using benzyl chloride

Cited by 407 publications

References 4 publications

Quantitative Trait Loci for Rice Phyllochron in Lemont × IR36 Cross

Quantitative Trait Loci for Rice Phyllochron in Lemont × IR36 Cross

Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant and cellulolytic bacterium isolated from a cellulose-degrading bacterial community

Characterization of Genomic Sequence Coding for Bromelain Inhibitors in Pineapple and Expression of Its Recombinant Isoform

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