• Journal of Life Science
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• v.9 no.1
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• pp.5-8
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• 1999

Helicobacter pylori is the etiologic agent of human gastritis and peptic ulceration and produces urease as the major protein component on its surface. H. pylori urease is known to serve as a major virulence factor and a potent immunogen. Deletion mutageneses were performed in the H. pylori urease accessory genes by using combinations of restriction enzymes and other DNA modifying enzymes in order to assess the function of these accessory gene products in the expression of the active urease. Selective disruptions in the accessory gene regions resulted in complete abolishment of the urease activity, which is consistent with other bacterial ureases. Interestingly, deletions in ureE-containing regions caused reduced expression of the structural enzyme subunits.

• Archives of Pharmacal Research
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• v.22 no.3
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• pp.274-278
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• 1999

Expression of the active urease of the enterobacterium, Klebsiella aerogens, requires the presence of the accessory genes (ureD, ureE, ureF, and ureG) in addition to the three structural genes (ureA, ureB, and ureC). These accessory genes are involved in functional assembly of the nickel-metallocenter for the enzyme. Characterization of ureF gene has been hindered, however, since the UreF protein is produced in only minute amount compared to other urease gene products. In order to overexpress the ureF gene, a recombinant pMAL-UreF plasmid was constructed from which the UreF was produced as a fusion with maltose-binding protein. The MBP-UreF fusion protein was purified by using an amylose-affinity column chromatography followed by an anion exchange column chromatography. Polyclonal antibodies raised against the fusion protein were purified and shown to specifically recognize both MBP and UreF peptides. The UreF protein was shown to be unstable when separated from MBP by digestion with factor Xa.

• Molecules and Cells
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• v.20 no.3
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• pp.371-377
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• 2005

The roles that accessory gene products play in activating the Helicobacter pylori urease apoprotein were examined. The activity of the urease apoprotein increased in the following order when it was expressed with the accessory genes: ureG < ureGH < ureFGH < ureEFGH < ureIEFGH. Moreover, stepwise additions of ureE and ureI to ureFGH significantly increased urease activity. Urease apoproteins coexpressed with ureFGH, ureEFGH, and ureIEFGH had similar low chymotrypsin susceptibilities. In vivo and in vitro activation studies showed that the cooperative effect of the accessory proteins involved processes in which the UreFGH complex, UreE, and UreI were implicated. Thus, the UreFGH complex may serve to alter the conformation of the apoprotein into one that is more competent to assemble a stable metallocenter, and that facilitates cooperative effects.

• The Journal of the Korean Society for Microbiology
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• v.34 no.6
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• pp.533-542
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• 1999

H. pylori produces urease abundantly amounting to 6% of total protein of bacterial mass. Urease genes are composed of a cluster of 9 genes of ureC, ureD, ureA, ureB, ureI, ureE, ureF, ureG, ureH. Production of H. pylori urease in E. coli was studied with genetic cotransformation. Structural genes ureA and ureB produce urease apoprotein in E. coli but the apoprotein has no enzymatic activity. ureC and ureD do not affect urease production nor enzyme activity ureF, ureG, and ureH are essential to produce the catalytically active H. pylori urease of structural genes (ureA and ureB) in E.coli. The kinetics of activation of H. pylori urease apoprotein were examined to understand the production of active H. pylori urease. Activation of H. pylori urease apoprotein, pH dependency, reversibility of $CO_2$ binding, irreversibility of $CO_2$ and $Ni^{2+}$ incorporation, and $CO_2$ dependency of initial rate of urease activity have been observed in vitro. The intrinsic reactivity (ko) for carbamylation of urease apoprotein co expressed with accessory genes was 17-fold greater than that of urease apoprotein expressed without accessory genes. It is concluded that accessory genes function in maximizing the carbamylating deprotonated ${\varepsilon}$-amino group of Lys 219 of urease B subunit and metallocenter of urease apoprotein is supposed to be assembled by reaction of a deprotonated protein side chain with an activating $CO_2$ molecule to generate ligands that facilitate productive nickel binding.

• Clinical and Experimental Reproductive Medicine
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• v.26 no.2
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• pp.157-161
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• 1999

Recent studies clearly demonstrated that the novel expression of LH gene in the rat testis, and suggested the local action of the LH-like molecule. The present study was performed to analyze the expression of LH genes in the rat accessory reproductive organs. Expression of LH subunit genes in the rat uterus and epididymis was demonstrated by reverse transcription-polymerase chain reaction (RT-PCR) and specific LH radioimmunoassay (RIA). The $LH_{beta}$ transcripts in these organs contained the published cDNA structure, the pituitary type exons 1-3, which encoded the entire $LH_{beta}$ polypeptide. Presence of the transcripts for the ${\alpha}$-subunit in the rat reproductive tissues were also confirmed by RT-PCR. In the LH RIA, significant levels of LH were detected in crude extracts from the rat ovary, uterus and epididymis. The competition curves with increasing amount of tissue extracts were parallel with those of standard peptide, indicating that the immunoreactive LH-like materials in these tissues are similar to authentic pituitary LH molecule. In rat epididymis, the highest amount of immunoreactive LH was detected in corpus area. Our findings demonstrated that the genes for LH subunits are expressed in the rat accessory reproductive organs, and suggested that these extrapituitary LH may act as a local regulator with auto and/or paracrine manner.

• Journal of Microbiology and Biotechnology
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• v.18 no.1
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• pp.28-34
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• 2008

Biofilm formation in association with the intercellular adhesion (icaADBC) gene cluster is a serious problem in nosocomial infections of Staphylococcus aureus. In all 112 S. aureus strains tested, the ica genes were present, and none of these strains formed biofilms. The biofilm formation is known to be changeable by environmental factors. We have found about 30% of phase variation in these strains with treatment of tetracycline, pristinamycin, and natrium chloride. However, this phenotype disappeared without these substances. Therefore, we have constructed stable biofilm-producing variants through a passage culture method. To explain the mechanism of this variation, nucleotide changes of ica genes were tested in strain S. aureus 483 and the biofilm-producing variants. No differences of DNA sequence in ica genes were found between the strains. Additionally, molecular analysis of three regulatory genes, the accessory gene regulator (agr) and the staphylococcal accessory regulator (sarA), and in addition, alternative transcription factor ${\sigma}^B$ (sigB), was performed. The data of Northern blot and complementation showed that SigB plays an important role for this biofilm variation in S. aureus 483 and the biofilm-producing variants. Sequence analysis of the sigB operon indicated three point mutations in the rsbU gene, especially in the stop codon, and two point mutations in the rsbW gene. This study shows that this variation of biofilm formation in S. aureus is deduced by the role of sigB, not agr and sarA.

• Mycobiology
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• v.48 no.2
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• pp.104-114
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• 2020

The carbohydrate-active enzyme (CAZyme) genes of Trametes contribute to polysaccharide degradation. However, the comprehensive analysis of the composition of CAZymes and the biosynthetic gene clusters (BGCs) of Trametes remain unclear. Here, we conducted comparative analysis, detected the CAZyme genes, and predicted the BGCs for nine Trametes strains. Among the 82,053 homologous clusters obtained for Trametes, we identified 8518 core genes, 60,441 accessory genes, and 13,094 specific genes. A large proportion of CAZyme genes were cataloged into glycoside hydrolases, glycosyltransferases, and carbohydrate esterases. The predicted BGCs of Trametes were divided into six strategies, and the nine Trametes strains harbored 47.78 BGCs on average. Our study revealed that Trametes exhibits an open pan-genome structure. These findings provide insights into the genetic diversity and explored the synthetic biology of secondary metabolite production for Trametes.

• Korean Journal of Plant Resources
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• v.19 no.1
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• pp.174-179
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• 2006

A cDNA library was constructed from leaf samples of 4-year-old Panax ginseng cultured in a field. 3,000 EST from a size selected leaf cDNA library were analyzed. The 349 of 2,896 cDNA clones has related with energy metabolism genes. The 349 known genes were categorized into nine groups according to their functional classification, aerobic respiration(48.4%), accessory proteins of electron transport and membrane associated energy conservation(17.2%), glycolysis and gluconeogenesis(3.4%), electron transport and membrane associated energy conservation(2.9%), respiration(2.0%), glycolysis methylglyoxal bypass(1.7%), metabolism of energy reserves(0.6%) and alcohol fermentation(0.3%).

• Animal Bioscience
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• v.34 no.9
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• pp.1439-1450
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• 2021

Objective: With the rapid development of proteomics sequencing and RNA sequencing technology, multi-omics analysis has become a current research hotspot. Our previous study indicated that Xinjiang brown cattle have better meat quality than Kazakh cattle. In this study, Xinjiang brown cattle and Kazakh cattle were used as the research objects. Methods: Proteome sequencing and RNA sequencing technology were used to analyze the proteome and transcriptome of the longissimus dorsi muscle of the two breeds of adult steers (n = 3). Results: In this project, 22,677 transcripts and 1,874 proteins were identified through quantitative analysis of the transcriptome and proteome. By comparing the identified transcriptome and proteome, we found that 1,737 genes were identified at both the transcriptome and proteome levels. The results of the study revealed 12 differentially expressed genes and proteins: troponin I1, crystallin alpha B, cysteine, and glycine rich protein 3, phosphotriesterase-related, myosin-binding protein H, glutathione s-transferase mu 3, myosin light chain 3, nidogen 2, dihydropyrimidinase like 2, glutamate-oxaloacetic transaminase 1, receptor accessory protein 5, and aspartoacylase. We performed functional enrichment of these differentially expressed genes and proteins. The Kyoto encyclopedia of genes and genomes results showed that these differentially expressed genes and proteins are enriched in the fatty acid degradation and histidine metabolism signaling pathways. We performed parallel reaction monitoring (PRM) verification of the differentially expressed proteins, and the PRM results were consistent with the sequencing results. Conclusion: Our study provided and identified the differentially expressed genes and proteins. In addition, identifying functional genes and proteins with important breeding value will provide genetic resources and technical support for the breeding and industrialization of new genetically modified beef cattle breeds.

• Journal of Microbiology and Biotechnology
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• v.25 no.10
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• pp.1599-1605
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• 2015

The development of rapid and efficient genome sequencing methods has enabled us to study the evolutionary background of bacterial genetic information. Here, we present comparative genomic analysis of 17 Streptomyces species, for which the genome has been completely sequenced, using the pan-genome approach. The analysis revealed that 34,592 ortholog clusters constituted the pan-genome of these Streptomyces species, including 2,018 in the core genome, 11,743 in the dispensable genome, and 20,831 in the unique genome. The core genome was converged to a smaller number of genes than reported previously, with 3,096 gene families. Functional enrichment analysis showed that genes involved in transcription were most abundant in the Streptomyces pan-genome. Finally, we investigated core genes for the sigma factors, mycothiol biosynthesis pathway, and secondary metabolism pathways; our data showed that many genes involved in stress response and morphological differentiation were commonly expressed in Streptomyces species. Elucidation of the core genome offers a basis for understanding the functional evolution of Streptomyces species and provides insights into target selection for the construction of industrial strains.