• Journal of Microbiology and Biotechnology
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• v.17 no.7
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• pp.1204-1207
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• 2007

Structural analyses have shown that nucleotides at the positions 770 and 771 of Escherichia coli 16S rRNA are implicated in forming one of highly conserved intersubunit bridges of the ribosome, B2c. To examine a functional role of these residues, base substitutions were introduced at these positions and mutant ribosomes were analyzed for their protein synthesis ability using a specialized ribosome system. The results showed requirement of a pyrimidine at the position 770 for ribosome function regardless of the nucleotide identity at the position 771. Sucrose gradient profiles of ribosomes revealed that the loss of protein-synthesis ability of mutant ribosome bearing a base substitution from C to G at the position 770 stems from its inability to form 70S ribosomes. These findings indicate involvement of nucleotide at the position 770, not 771, in ribosomal subunit association and provide a useful rRNA mutation that can be used as a target to investigate the physical interaction between 16S and 23S rRNA.

• Mycobiology
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• v.32 no.3
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• pp.119-122
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• 2004

The intergenic spacer(IGS) sequence of Fusarium oxysporum have been reported to provide reliable information concerning intraspecific variation and phylogeny of fungal species. The eleven strains of Fusarium oxysporum and its formae speciales belonging to section Elegans were compared with sequencing analysis. The direct sequencing of partial IGS was carried out using PCR with primer NIGS1(5'-CTTCGCCTCGATTTCCCCAA-3')/NIGS2(5'-TCGTCGCCGACAGTTTTCTG-3') and internal primer NIGS3(5'-TCGAGGATCGATTCGAGG-3')/NIGS4(5'-CCTCGAATCGATCCTCGA-3'). A single PCR product was found for each strain. The PCR fragments were sequenced and revealed a few within species polymorphisms at the sequence level. The size of partial IGS sequencing of F. oxysporum was divided into three groups; $526{\sim}527$ bp including F. o. f. sp. chrysanthemi, cucumerinum, cyclaminis, lycopersici, and fragariae; $514{\sim}516$ bp including F. o. f. sp. lilii, conglutinans, and raphani; 435 bp for F. o. f. sp. cucumerinum from Korea. Sequence analysis of PCR products showed that transitions were more frequent than transversions as well as the average numbers of substitution per site were range 0.41% to 3.54%.

• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.426-433
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• 2018

Plant tissue culture is a technique that has invariably been used for various purposes such as obtaining transgenic plants for crop improvement or functional analysis of genes. However, this process can be associated with a variety of genetic and epigenetic instabilities in regenerated plants, termed as somaclonal variation. In this study, we investigated mutation spectrum, chromosomal distributions of nucleotide substitution types of single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) by whole genome re-sequencing between Dongjin and Nipponbare along with regenerated plants of Dongjin from different induction periods. Results indicated that molecular spectrum of mutations in regenerated rice against Dongjin genome ranged from $9.14{\times}10^{-5}$ to $1.37{\times}10^{-4}$ during one- to three-month callus inductions, while natural mutation rate between Dongjin and Nipponbare genomes was $6.97{\times}10^{-4}$. Non-random chromosome distribution of SNP and InDel was observed in both regenerants and Dongjin genomes, with the highest densities on chromosome 11. The transition to transversion ratio was 2.25 in common SNPs of regenerants against Dongjin genome with the highest C/T transition frequency, which was similar to that of Dongjin against Nipponbare genome.

• Journal of Microbiology and Biotechnology
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• v.12 no.4
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• pp.622-627
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• 2002

Diphtheria toxin repressor (DtxR) binds to approximately 30 to 35-bp regions containing an interrupted 9-bp inverted repeat within a 19-bp core sequence. The core sequence is fairly conserved and critical for DtxR binding. The flanking regions that are consisted of 5 to 8 more of nucleotides from the core are also required for DtxR binding. The nucleotides in both flanking regions are A-T rich. To examine whether the A-T nucleotides in both flanking regions from the core have significant roles for DtxR binding, a DNA fragment was constructed based on the diphtheria tox promoter/operator, and DNA fragments with substitution of A and T nucleotides In the flanking regions to G and C were also constructed. To assess the effect of these substitutions on binding of DtxR and repressibility by DtxR, $\beta$-galactosidase activity from lacZ fused to the region was assessed. Gel mobility shift of the region by purified DtxR was also examined. The DNA fragments containing the mutations in the flanking regions still exhibited repression and mobility shift with DtxR. The core segment with the mutation is still, therefore, recognized by DtxR. Nonetheless, the results from the assays indicated that the substitution significantly decreased repression of the operator by DtxR in vivo under high-iron condition and decreased binding of DtxR to the operator. These results suggest that A and T nucleotides fur both flanking regions are preferred for the binding of DtxR.

• Journal of Animal Science and Technology
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• v.45 no.6
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• pp.933-938
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• 2003

This study was performed to analyse the sequences of variations of mtDNA D-loop and their effects on carcass traits in Hnawoo(Korean cattle). The resulting sequences were compared with previously published sequences for other cattle breeds(GenBank J01394). The PCR was used to amplify a total of 964 bp between nucleotide 15758 and 383 within D-loop region of mtDNA using specific primers. Twenty five polymorphic sites by nucleotide substitution were found in mtDNA of Hanwoo. The frequencies of positions at 169, 16042, 16093, 16119, 16255 and 16302 nt with high levels of sequence polymorphism were 0.891, 0.117, 0.109, 0.182, 0.197 and 0.117, respectively. The substitution effect at 169 and 16119 nt was found significant on marbling score. Also substitution effect at 169 and 16042 nt was highly significant(p〈0.01) on backfat. thickness. Polymorphism of mtDNA sequence in D-loop region could be useful for the analysis of cytoplasmic genetic variation and associations with the other economically important traits and maternal lineage analysis in Hanwoo.

• Reproductive and Developmental Biology
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• v.29 no.1
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• pp.9-13
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• 2005

This study was performed to analyze the sequence variation in mtDNA D-loop and their effects on milk and milk fat production in Holstein cows. The analyzed sequences were compared with previously published sequences from other cattle breeds (GenBank J01394). PCR was performed to amplify a total of 964 bp between nucleotide 15758 and 383 within D-loop region of mtDNA using specific primers. Thirty five polymorphic sites by nucleotide substitution were found in mtDNA. The frequencies of positions at 106, 169, 16057, 16231 and 16255 nt with high levels of sequence polymorphism were 0.090, 0.555, 0.055, 0.090 and 0.050, respectively. The substitution effect at 169 nt was found significant on milk production, and substitution effect at 16118, 16139 and 16302 nt was highly significant (p<0.1) on milk fat production. Polymorphism of mtDNA sequence in D-loop region might be useful for the analysis of cytoplasmic genetic variation and associations with the other economically important traits and maternal lineage analysis in Holstein cows.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.9
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• pp.4315-4320
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• 2012

Background: The P53 tumor suppressor gene plays a pivotal role in maintaining cellular homeostasis by preventing the propagation of genome mutations. P53 in its transcriptionally active form is capable of activating distinct target genes that contribute to either apoptosis or growth arrest, like P21. However, the MDM2 gene is a major negative regulator of P53. Single nucleotide polymorphisms (SNP) in codon Arg72Pro of P53 results in impairment of the tumor suppressor activity of the gene. A similar effect is caused by a SNP in codon 31 of P21. In contrast, a SNP in position 309 of MDM2 results in increased expression due to substitution of thymine by guanine. All three polymorphisms have been associated with increased risk of tumorigenesis. Aim of the study: We aimed to study the prevalence of SNPs in the P53 pathway involving the three genes, P53, P21 and MDM2, among acute myeloid leukemia (AML) patients and to compare it to apparently normal healthy controls for assessment of impact on risk. Results: We found that the P21 ser31arg heterozygous polymorphism increases the risk of AML (P value=0.017, OR=2.946, 95% CI=1.216-7.134). Although the MDM2 309G allele was itself without affect, it showed a synergistic effect with P21 ser/arg polymorphism (P value=0.003, OR=6.807, 95% CI=1.909-24.629). However, the MDM2 309T allele abolish risk effect of the P21 polymorphic allele (P value=0.71). There is no significant association of P53 arg72pro polymorphism on the risk of AML. Conclusion: We suggest that SNPs in the P53 pathway, especially the P21 ser31arg polymorphism and combined polymorphisms especially the P21/MDM2 might be genetic susceptibility factors in the pathogenesis of AML.

• Journal of Life Science
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• v.9 no.2
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• pp.9-14
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• 1999

Pseudomonas iodinum IFO 3558 adenosine deaminase(ADA) gene was cloned by the polymerase chain reaction and deduced the amino acid sequence of the enzyme. DNA sequence homology of Pseudomonas iodinum IFO 3558 ADA gene was compared to those of E. coli, human and mouse ADA genes. Unambiguous sequence from both strands of pM21 was obtained for the region believed to encode ADA. The sequence included a 804-nucleotide open reading frame, bounded on one end by sense primer and on the other end by two antisense primer. This open reading frame encodes a protein of 268 amino acids having a molecular weight of 29,448. The deduced amino acid sequence shows considerable similarity to those of E. coli, mouse and human ADA. Pseudomonas iodinum IFO 3558 nucleotide sequence shows 98.5% homology with that of the E. coli ADA sequence and 51.7% homology with that of the mouse ADA sequence and 52.5% homology with that of the human ADA sequence. The ADA protein sequence of Pseudomonas iodinum IFO 3558 shows 96.9% homology with that of the E. coli and 40.7% homology with that of the mouse and 41.8% homology with that of the human. The distance between two of the conserved elements, TVHAGE and SL(1)NTDDP has veen exactly conserved at 76 amino acids for all four ADAs. Two of the four conserved sequence elements shared among the four ADAs are also present in the yeast, rat, human (M), and Human(L) AMP deaminase. The SLSTDDP sequence differs only in the conservative substitution of a serine for an asparagine. A conserved cysteine with conserved spacing between these two regions is also found. Thus, sequence analysis of four ADAs and four AMP deaminases revealed the presence of a highly conserved sequence motif, SLN(S)TDDP, a conserved dipeptide, HA, and a conserved cysteine residue.

• Korean Journal of Breeding Science
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• v.42 no.1
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• pp.1-10
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• 2010

Five mutants were investigated at the molecular level to determine the factors responsible for mutated endosperm types. They were classified as high (HA) or low amylose (LA) phenotypes based on the amylose content in endosperm. The five were previously produced from Ilpum and Shindongjin cultivar treated with N-methyl-N-nitrosourea and gamma-ray irradiation, respectively. Analysis of the genomic structure and expression of Granule-bounded Starch Synthase I (GBSSI) genes revealed that mutants generally showed a higher incidence of nucleotide transition than transversion, and the $A:T{\rightarrow}G:C$ transition was particularly prevalent. The rates of nucleotide substitution in HA mutants were generally higher than those in the LA mutants, leading to higher substitutions of amino acid in the HA mutants. Neither nucleotide substitutions interfering with intron splicing or causing early termination of protein translation were found, nor any large-sized deletions or additions were found in all the mutants. In principle, amylose content can be regulated by three factors: internal alterations of GBSSI protein, the strength of gene expression, and other unknown external factors. Our results indicate that the endosperm mutants from Shindongjin arose from internal alterations of GBSSI proteins, which may be the result of amino acid substitutions. On the other hand, the Ilpum mutants might be principally caused by the alteration of gene expression level. Analysis of another three glutinous cultivars revealed that the major factor leading to glutinous phenotypes is the 23-bp duplicative motif (5'-ACGGGTTCCAGGGCCTCAAGCCC-3') commonly found in exon 2, which results in the premature termination of protein translation leading to the production of a non-functional GBSSI enzyme.

• Genomics & Informatics
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• v.6 no.4
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• pp.166-172
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• 2008

A multitude of protein-coding sequence variations (CVs) in the human genome have been revealed as a result of major initiatives, including the Human Variome Project, the 1000 Genomes Project, and the International Cancer Genome Consortium. This naturally has led to debate over how to accurately assess the functional consequences of CVs, because predicting the functional effects of CVs and their relevance to disease phenotypes is becoming increasingly important. This article surveys and compares variation databases and in silico prediction programs that assess the effects of CVs on protein function. We also introduce a combinatorial approach that uses machine learning algorithms to improve prediction performance.