Using the presence or absence of 63 variable restriction endonuclease (RE) sites selected from 225 sites with six REs, genomic polymorphism of 242 herpes simplex virus type 1 (HSV-1) strains from six countries (Japan, Korea, China, Sweden, U.S.A. and Kenya) was quantitatively analysed. Twenty-five of the 63 sites were found to differ between Korean and Kenyan strains. In contrast, only three and six sites were found to differ between isolates from Sweden and the U.S.A. and between those from Korea and China, respectively, suggesting that they are closely related to each other. In this way, characterization of 63 sites enabled us to categorize 186 distinct HSV-1 genotypes from 242 individuals. Some strains from Japan, Korea and China shared the same genotypes, indicating that they are phylogenetically closely related. Many significant correlation coefficients (] r ] > 0.42; P < 0.01) between pairs of sites were found in isolates from the three Asian countries (Japan, Korea and China) as well as in those from Sweden and the U.S.A., suggesting that HSV-1 strains from within the same ethnic groups are evolutionarily closer. The average number of nucleotide substitutions per nucleotide, as defined by nucleotide diversity (~), was estimated for HSV-1 genomes within (~x or ~y) and between (~xY) countries. On the basis of 225 sites, nucleotide diversity for Kenyan isolates was 0-0056, almost three times higher than that for Korean isolates, implying that Kenyan HSV-1 genomes are much more diverse than those from Korea. In addition, the diversity between HSV-1 isolates from different countries (~xY) was highest between isolates from the three Asian countries and Kenya (0.0075 to 0.0081) and lowest among those from the three Asian countries (0.0032 to 0.0040). The mutation rate (k) for HSV-1 was estimated to be 3-5 x 10 S/site/year. All these findings show that the evolution of HSV-1 may be host-dependent and very slow.
The ferritin-encoding gene (cft) of Campylobacter jejuni was cloned and sequenced. The nucleotide sequence of cft had a 501 bp open reading frame for a protein with 167 amino acids and a predicted molecular mass of 19 180 Da, and showed a high similarity to that of Helicobacter pylori and Escherichia coli ferritin genes. To determine the biological function of ferritin in C. jejuni, a ferritin-deficient mutant was constructed. The growth of ferritin-deficient strain SNA 1 was clearly inhibited under iron deprivation. The ferritin-deficient mutant was more sensitive to killing by H2O2 and paraquat than the isogenic parent strain. These findings demonstrate that ferritin in C. jejuni makes a significant contribution to both iron storage and protection from intracellular iron overload, and resulting iron-mediated oxidative stress.
Genomic profiles of 66 strains of herpes simplex virus type 1 (HSV-1) isolated in Japan were investigated with regard to restriction fragment length polymorphism (RFLP) and length variation of fragments containing reiterations. There were two predominant genotypes of F1 and F35, and the genomic characteristics of each were studied. The nucleotide change between F1 and F35 was estimated to be 1.5%. An RFLP marker (VR23) peculiar to genotype F35 was identified as the first case of genomic marker specific to a predominant genotype of HSV-1, and is the diagnostic marker of F35. The a sequences (repeating in an HSV-1 genome and containing reiterations) of F35 were cleaved by SacII on the DR4 (direct repeat 4) stretch, while a sequences of F1 had a rearranged DR4 and were resistant to SacII digestion. Thus, analyses of fragments containing reiterations, such as a sequences, can serve to classify HSV-1 strains as well as for purpose of differentiation. The proportion of strains derived from primary infection to those from recurrent infection was higher in strains of F35 than in those of F1, and this genotypic difference within HSV-1 may possibly influence clinical manifestations.
Regions of herpes simplex virus type 1 (HSV-1) DNA with variation in the size of restriction endonuclease fragments were identified by comparison of the BamHI, KpnI or SalI restriction endonuclease digestion patterns among 15 HSV-1 isolates after hybridization with specific 32P-labeled cloned HSV-1 DNA fragments. Of the types of restriction fragment polymorphism identified, one was a strain with a distinctly different restriction fragment than the prototype (loss or gain of restriction sites). Another type, the specific fragment varied only in size among strains. Thirteen distinct variations were identified. Ten were mapped to the unique sequence of the L component; two to the inverted repeat of the L component and one to the inverted repeat of the S component. The presence of a common ancestor from which some isolates of HSV-1 might derive was deduced from an analysis of the distribution of the thirteen variations among the 15 HSV-1 isolates.
Variation of restriction endonuclease cleavage patterns between herpes simplex virus type 1 (HSV-1) strains was investigated using restriction endonucleases recognizing DNA sequences of four base pairs (4-bp enzymes) (HaeIII, HhaI, Sau3AI). The analysis made feasible identification of variations not heretofore detectable, using enzymes recognizing DNA sequences of six base pairs (BamHI, KpnI, SalI), and proved to be most useful for distinction and classification of HSV-1 strains. Ten of the fifteen strains analysed using 4-bp enzymes were closely related, and were put into group 1, and the other five not so related strains were classed into the non-group 1. The observations suggested a possible common ancestor from which group 1 strains had derived.
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