• Research in Plant Disease
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• v.17 no.2
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• pp.111-120
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• 2011

A bacterial artificial chromosome library of Pectobacterium carotovorum 35 was constructed to characterize the genome and to sequence its hrp region. The hrp cluster of P. carotovorum 35 consisted of 26 open reading frames in five operons. A promoter-based green fluorescent protein technology was used to identify the genes regulated by the alternative sigma factor, HrpL, in P. carotovorum 35. The majority of the selected clones contained the hrpJ operon promoter sequence, which harbors a hrp box, but no putative hrp boxes were detected within the promoter sequences of two other hrpL-regulated genes encoding for pectate lyase and large repetitive protein. Although the promoters of five other hrp operons also contained hrp boxes, their expression was not HrpL-dependent in the promoter-based selection in E. coli. However, transcriptional analysis showed that expression from all operons harboring hrp boxes, except for the hrpN operon, was reduced significantly in the hrpL mutant. The severity of soft-rot symptoms when the hrpL mutant was applied to the surface of tobacco leaves, mimicking natural infection, was greatly attenuated. These results indicate that the hrpL gene of P. carotovorum 35 may be involved in the development of soft-rot symptoms.

• Journal of Plant Biology
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• v.35 no.2
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• pp.155-163
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• 1992

To elucidate the regulatory mechanism of virE operon in Agrobacterium tumefaciens pTiA6 plasmid at the molecular level, the regulatory site of virE promoter was determined using truncated virE recombinant plasmids obtained by 5' deletion analysis of virE promoter. The size of deleted nucleotides of p]S201, a functional recombinant plasmid, was found to be about 130 nucleotides from 5'-end of virE promoter. On the other hand the size of deleted nucleotides of p]S301, nonfunctional recombinant plasmid, was identified 263 nucleotides by DNA sequencing. Hence it was thought that the essential site of virE promoter was located between about 130th nucleotide and 263th nucleotide. Since the inverted repeat sequence (AACTTTGCGCTATAGGCAMGTT) is included in this essential site of virE promoter, it could be the first recognition site of the RNA polymerase in virE promoter.omoter.

• Parasites, Hosts and Diseases
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• v.35 no.4
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• pp.295-298
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• 1997

Genonlic DNA from Metagonimn vokogawci and Metagonimw Miyata type was amplified by polymerase chain reaction based on the random amplification of polymorphic DNA (RAPDI technique. Eight random 10-mer oligonucleotide primers (OPA-02, 5-TGCCGAGCTG-3; OPA-09, 5-GGGTAACGCC-3; OPA-17, 5-GTGATCGCAG-3; OPA-11, 5-CAATCGCCGT-3; OPA-13, 5-CAGCACCCAC-3; OPA-17. 5-GACCGCTrGT-3; OPA-19, 5-CAAACGTCGG-3; OPA-20, 5-GTTGCGATCC-3) WITH A G+C CONTENT FO 60-70% (Kit A. Operon Technologies Inc., California, USAI could produce distinguishable banding patterns between the two Metngonimus species. From the results of this study, it was suggested that Metcsonimus Miyata type has a different DNA sequence from M. WOkQgGUIGi. Key words: Metcgonimw vokognwai, MetnBonimw Miyata type, random amplification of polymorphic DNA (RAPD)

• ALGAE
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• v.17 no.1
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• pp.53-58
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• 2002

The transition of plant life from aquatic algae to land to land plants was one of the major events in the history of life. However, in hypothesizing the exact evolutionary path of the transition, limited shared phenotypic characters in aquatic algae and land plants (embryophytes) have been a major hinderance. Chloroplast genomes contain characters useful in tracing evolutionary histories. Embryophyte chloroplast genomes are distinguished from algal cpDNAs by having over 20 group Ⅱ introns, some of which were gained during the transition from algae to embryophytes (Manhart and Palmer 1990; Lew and Manhart 1993;Lee and Manhart 2002). Here we examine a gene cluster that, in land plants, contains psbB, psbT, psbH, petB and petD with introns found in petB and petD (petB.i and petD.i). In addition the presence/absence of introns in trnA and trnI (trnA.i and trnI.i) were determined in all five major lineages of charophytes. We found that the psbB gene cluster occurs in most surveyed charophytes and embryophytes except Spirogyra (Zygnematales) which lacks it due to intra-genomic rearrangement. All four introns are absent in Chlorokybus but present in some or all of the other four charophyte lineages (Klebsormidiales, Zygnematales, Coleochaetales, and Charales). In addition, Chlorokybus is distinguished from other charophytes and embryophytes by having an unusually long spacer (over 2 kb) between psbH-petB. The results indicate that Chlorokybus diverged before the intron gains but after psbB gene cluster formation, placing the other charophyte lineages closer to embryophytes.

• Journal of Microbiology and Biotechnology
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• v.9 no.5
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• pp.637-645
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• 1999

Two putative regulator genes, mocR and mocS, of the moc (mannityl opine catabolism) operons in pTi15955 of the octopine-/mannityl opine-type Agrobacterium tumefaciens strain 15955, were tested for their possible roles as repressors in the moc operons. The regions upstream of macC and mocD, the first structural genes in the two divergently oriented moc operons, were transcriptionally fused into the promoterless lacZ reporter gene. Each of the lacZ-fusions was introduced into Agrobacterium strain UIA5, a Ti plasmid-cured derivative, harboring either a mocR or a mocS clone. The resulting strains were grown in media containing various sugar sources, and the $\beta$-galactosidase activities were quantitatively measured. The results suggested that MocR repressed the expression of macC and macD. The expression of the fused $\beta$-galactosidase was not induced by mannopine (MOP) or possible catabolic intermediates of the opine, e.g. santhopine (SOP), glucose, mannose, or glutamine. However, the repression was significantly relieved by the supplementation of MOP and the concomitant introduction of the agcA gene encoding MOP cyclase that catalyzes the lactonization of MOP to agropine (AGR). These results suggested that AGR, rather than MOP or the other catabolic intermediates, is the inducer for the expression of the operon. On the contrary to previous report showing that the induction levels of macC and macD were lowered by the supplementation of inorganic nitrogen in media, the expression of these genes was not affected by the level of nitrogen in our reporter system. MocS did not strongly repress the expressions of macC and mocD. It is possible that MocS may be involved in the regulation of the operons present downstream of the moc operon, which are responsible for the utilization of mannopinic acid and agropinic acid.

• Journal of Microbiology and Biotechnology
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• v.23 no.6
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• pp.739-749
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• 2013

The seasonal and spatial diversity of picocyanobacteria (Pcy) in lakes of the Great Mazurian Lakes (GLM) system was examined by DGGE analysis of molecular markers derived from the 16S-23S internal transcribed spacer (ITS) of the ribosomal operon and the phycocyanin operon (cpcBA-IGS). The study of nine lakes, ranging from mesotrophy to hypereutrophy, demonstrated seasonal variance of Pcy. The richness and Shannon diversity index calculated on the basis of both markers were higher in spring and lower in early and late summer. No statistically significant relationships were found between the markers and trophic status of the studied lakes or Pcy abundance. There were, however, statistically significant relationships between the diversity indices and sampling time. The analysis pointed to a different distribution of the two markers. The ITS marker exhibited more unique sequences in time and space, whereas a greater role for common and ubiquitous sequences was indicated by the cpcBA-IGS data. Examination of the Pcy community structure demonstrated that communities were grouped in highly similar clusters according to sampling season/time rather than to the trophic status of the lake. Our results suggest that time is more important than trophic status in shaping the diversity and structure of Pcy communities. The seasonal changes in picocyanobacteria and differences in diversity and community structures are discussed in the context of well-established ecological hypotheses: the PEG model, intermediate disturbance hypothesis (IDH), and horizontal gene transfer (HGT).

• Journal of Life Science
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• v.14 no.1
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• pp.110-114
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• 2004

The optimized RAPD-PCR conditions, that can be utilized as a basic information for analysis of the gelletic characteristics were developed for genetic analysis of four mulberry varieties, named Milsung, Chungil, Suil, and Hansung using a primer, OPY15 (5'-AGTCGCCCTT-3') from Operon company. We tested several different factors for best PCR condition including concentrations of DNA, primer, Mgclu annealing temperature, number of PCR cycle, and prosence/absence of pre-heating time at the begining of PCR reaction in the $25 \mul$volume. The best RAPD profiles were obtained using 50 ng of DNA, 1 $\mu$M of primer, $1 \mum$of $MgCl_2\;,45^{\circ}C$ of annealing temperature and an absence of pre-heating time. An establishment of the stable and reproducible RAPD-PCR conditions are expected to be useful for the subsequent RAPD-related investigation, such as genetic characterization of the mulberry varieties, re-establishment of phylogenetic relationships and development of new varieties.

• Journal of fish pathology
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• v.17 no.2
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• pp.91-98
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• 2004

This study was performed for the identification of Streptococcus sp. from cultured flounders (Paralichthys olivaceus) showing streptococcosis in the Jeju island. We isolated 10 strains of Streptococcus iniae from the cultured olive flounders with streptococcosis. Isolated strains were identified in S. iniae since they have formed the expected band through performing PCR assay using specific primers, Sin-1 (5'-CTAGAGTACACATGTACT(AGCT)AAG-3') and Sin-2 (5'-GGATTTTCCACTCCCATTAC-3'). In addition to 16S-23S rRNA intergenic spacers (ISR), operon structure of isolated strains showed that all strains had three 16S-23S rRNA ISR band patterns. The 16S-23S rRNA ISR sequence of isolated strains showed 96% sequence identity with S. iniae (GenBank accession number AF 048773). This paper is the first report that S. iniae is associated with streptococcosis of Olive flounder in Korea.

• Korean Journal of Microbiology
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• v.39 no.3
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• pp.123-127
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• 2003

Sphingomonas chungbukensis DJ77 is able to metabolize phenanthrene as the sole carbon and energy source. The plasmid pUPX5 includes phnS gene encoding 2-hydroxychromene-2-carboxylate (HCCA) isomerase, which is needed for phenanthrene and naphthanene degradation. We determined the nucleotide sequence of DNA fragment of 3271 bp which included the phnS gene. The fragment included an open reading frame of 594 bp which has ATG initiation codon and TAA termination codon and GGAA ribosomal binding site. The predicted amino acid sequence of the enzyme consists of 198 amino acids. The deduced amino acid sequence of the phnS enzyme exhibited 94％ identity with that of the corresponding enzyme in Sphingomonas aromaticivorans F199. The phnS gene is located downstream and in the same operon as phnQ and phnR, encoding a 2,3-dihydroxybiphenyl 1,2-dioxygenase and a ferredoxin component of biphenyl dioxygenase, respectively.

• Journal of Microbiology and Biotechnology
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• v.11 no.5
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• pp.825-830
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• 2001

Escherichia coli, which harbored the ars operon from a plasmid pMH12 of Klebsiella oxytoca D12, showed filamentation due to the expression of ars genes in the presence of arsenite. The continued DNA replication in the absence of cell division was revealed, since nucleoids abound with DAPI appeared to be arranged in chains. In contrast to overexpression of arsA, its frame-shift mutant and knock-out mutant lost filamentation in the presence of arsenite, which suggested that ars-induced division block was dependent on expression of arsA. ArsA-induced division inhibition was not a consequence of an inhibition of DNA replication, and the inability of arsenite to induce an SOS response indicated that arsA-mediated division inhibition was dependent on the expression of the gene product encoded by the minB operon. ArsA is a peripheral membrane protein with an ATP-binding domain, which is homologous to MinD that requires ATP-dependent efflux. These results suggested that ArsA could possibly recruit MinC to the membrane and modulate cytoplasmic FtsZ to block assembly at the middle of the cell.