Acetobacterstrains contain DNA modified at GAATTC and GANTC

1997 ◽  
Vol 43 (5) ◽  
pp. 456-460 ◽  
Author(s):  
Dag H. Coucheron
Keyword(s):  
Data Base ◽  
Restriction Enzyme ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Dna Methyltransferase ◽  
Acetobacter Xylinum ◽  
Acetobacter Aceti ◽  
Acetobacter Pasteurianus ◽  
Specific Modification ◽  
Dna Modifications

Total DNAs from nine strains of Acetobacter xylinum, two strains of Acetobacter aceti, and one Acetobacter pasteurianus strain were examined for the extent of digestion by various restriction endonucleases. The majority of the endonucleases cleaved the total DNAs with a frequency expected from the number of sites present in DNA sequences deposited in the GenBank data base. However, the restriction enzyme digestions identified two different genomic DNA modifications in Acetobacter. One sequence-specific modification protected total DNAs from seven of the A. xylinum strains against cleavage by EcoRI (GAATTC). Digestion of total DNAs from A. xylinum ATCC 10245 (DNA not cut by EcoRI) and the closely related A. xylinum NRCC 17005 (DNA cut by EcoRI) with Tsp509I (AATT) revealed differences in restriction frequencies that indicated methylation of the first or second adenine within GAATTC. Another sequence-specific modification rendered total DNAs from all the 12 strains recalcitrant to digestion by HinfI. The latter modification indicated that species of the genus Acetobacter contain a solitary DNA methyltransferase that probably methylates adenine in GANTC.Key words: Acetobacter, genomic DNA, modifications, EcoRI, HinfI.

Evidence for genetic diversity in Trypanosoma (Nannomonas) congolense

Parasitology ◽  
1986 ◽  
Vol 93 (2) ◽  
pp. 291-304 ◽  
Author(s):  
P. A. O. Majiva ◽  
R. Hamers ◽  
N. Van Meirvenne ◽  
G. Matthyssens
Keyword(s):  
Genetic Diversity ◽  
Trypanosoma Brucei ◽  
Restriction Enzyme ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Trypanosoma Congolense ◽  
Synthetic Oligonucleotide ◽  
Hybridization Probes ◽  
Conserved Genes ◽  
Variant Antigen

SUMMARYGenetic proximity between two karyotypic groups of Trypanosoma congolense was investigated using as hybridization probes: (i) total genomic DNA, (ii) a 35 nucleotide long synthetic oligonucleotide, and (iii) non-variant antigen type (non-VAT) specific complementary DNAs. The phylogenetic relationship between Trypanosoma brucei and T. evansi, both of which are accepted species in the subgenus Trypanozoon, was used as a reference to assess the phylogenetic proximity of the two groups of T. congolense. Results indicate that some morphologically indistinguishable T. congolense populations differ in a variety of molecular and genetic properties: molecular karyotypes, majority of the DNA sequences, and the restriction enzyme sites in the genomic environments of various conserved genes. The implications of these findings for trypanosome evolution and T. congolense epidemiology are discussed.

scholarly journals Characterization of squalene synthase gene from Gymnema sylvestre R. Br.

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Kuldeepsingh A. Kalariya ◽  
Ram Prasnna Meena ◽  
Lipi Poojara ◽  
Deepa Shahi ◽  
Sandip Patel
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Competitive Inhibition ◽  
Sequence Data ◽  
Homology Model ◽  
Squalene Synthase ◽  
Gymnema Sylvestre ◽  
Gardenia Jasminoides ◽  
Ramachandran Plots ◽  
Flanking Regions

Abstract Background Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant. Results Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br. Conclusion This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.

Rapid Amplification of Uncharacterized Transposon-tagged DNA Sequences from Genomic DNA

Yeast ◽  
1997 ◽  
Vol 13 (3) ◽  
pp. 233-240 ◽  
Author(s):  
KRISTIN T. CHUN ◽  
HOWARD J. EDENBERG ◽  
MARK R. KELLEY ◽  
MARK G. GOEBL
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Rapid Amplification

scholarly journals Distribution of sequence-dependent curvature in genomic DNA sequences

FEBS Letters ◽  
1997 ◽  
Vol 406 (1-2) ◽  
pp. 69-74 ◽  
Author(s):  
Andrei Gabrielian ◽  
Kristian Vlahovicek ◽  
Sándor Pongor
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Sequence Dependent

scholarly journals Thermodynamic Model for B-Z Transition of DNA Induced by Z-DNA Binding Proteins

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2748 ◽  
Author(s):  
Ae-Ree Lee ◽  
Na-Hyun Kim ◽  
Yeo-Jin Seo ◽  
Seo-Ree Choi ◽  
Joon-Hwa Lee
Keyword(s):  
Dna Binding ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Multiple Sequence ◽  
Left Handed ◽  
Transition Mechanism ◽  
Dna Strands ◽  
Z Dna

Z-DNA is stabilized by various Z-DNA binding proteins (ZBPs) that play important roles in RNA editing, innate immune response, and viral infection. In this review, the structural and dynamics of various ZBPs complexed with Z-DNA are summarized to better understand the mechanisms by which ZBPs selectively recognize d(CG)-repeat DNA sequences in genomic DNA and efficiently convert them to left-handed Z-DNA to achieve their biological function. The intermolecular interaction of ZBPs with Z-DNA strands is mediated through a single continuous recognition surface which consists of an α3 helix and a β-hairpin. In the ZBP-Z-DNA complexes, three identical, conserved residues (N173, Y177, and W195 in the Zα domain of human ADAR1) play central roles in the interaction with Z-DNA. ZBPs convert a 6-base DNA pair to a Z-form helix via the B-Z transition mechanism in which the ZBP first binds to B-DNA and then shifts the equilibrium from B-DNA to Z-DNA, a conformation that is then selectively stabilized by the additional binding of a second ZBP molecule. During B-Z transition, ZBPs selectively recognize the alternating d(CG)n sequence and convert it to a Z-form helix in long genomic DNA through multiple sequence discrimination steps. In addition, the intermediate complex formed by ZBPs and B-DNA, which is modulated by varying conditions, determines the degree of B-Z transition.

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