• Journal of the Korean Magnetic Resonance Society
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• v.16 no.2
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• pp.162-171
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• 2012

SAV2228 has an OB (Oligomer-Binding)-motif which is frequently used for nucleic acid recognition. To characterize the activity of translation initiation factor-1 (IF-1) from Staphylococcus aureus, SAV2228 was expressed and purified in Escherichia coli. We acquired 3D NMR spectra showing well dispersed and homogeneous signals which allow us to assign 94.4% of all $^1HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$ and $^{13}CO$ resonances. We could predict a secondary structure of SAV2228 using TALOS and CSI from NMR data. SAV2228 was consisted of one ${\alpha}$-helix and five ${\beta}$-sheets. The predicted secondary structure, ${\beta}-{\beta}-{\beta}-{\alpha}-{\beta}-{\beta}$, was similar to other bacterial IF-1, but it was not completely same to the eukaryotic one. Assigned NMR peaks and secondary structre prediction can be used for the study on interaction with nucleic acid in the future.

• The Plant Pathology Journal
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• v.38 no.2
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• pp.102-114
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• 2022

Pectobacterium carotovorum subsp. carotovorum (Pcc) is a gram-negative, broad host range bacterial pathogen which causes soft rot disease in potatoes as well as other vegetables worldwide. While Pectobacterium infection relies on the production of major cell wall degrading enzymes, other virulence factors and the mechanism of genetic adaptation of this pathogen is not yet clear. In the present study, we have performed an in-depth genome-wide characterization of Pcc strain ICMP5702 isolated from potato and compared it with other pathogenic bacteria from the Pectobacterium genus to identify key virulent determinants. The draft genome of Pcc ICMP5702 contains 4,774,457 bp with a G + C content of 51.90% and 4,520 open reading frames. Genome annotation revealed prominent genes encoding key virulence factors such as plant cell wall degrading enzymes, flagella-based motility, phage proteins, cell membrane structures, and secretion systems. Whereas, a majority of determinants were conserved among the Pectobacterium strains, few notable genes encoding AvrE-family type III secretion system effectors, pectate lyase and metalloprotease in addition to the CRISPR-Cas based adaptive immune system were uniquely represented. Overall, the information generated through this study will contribute to decipher the mechanism of infection and adaptive immunity in Pcc.

• Journal of Gastric Cancer
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• v.24 no.1
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• pp.89-98
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• 2024

This review delved into the intricate relationship between the gastrointestinal microbiome and gastric cancer, particularly focusing on post-treatment alterations, notably following gastrectomy, and the effects of anticancer therapies. Following gastrectomy, analysis of fecal samples revealed an increased presence of oral cavity aerotolerant and bile acid-transforming bacteria in the intestine. Similar changes were observed in the gastric microbiome, highlighting significant alterations in taxon abundance and emphasizing the reciprocal interaction between the oral and gastric microbiomes. In contrast, the impact of chemotherapy and immunotherapy on the gut microbiome was subtle, although discernible differences were noted between treatment responders and non-responders. Certain bacterial taxa showed promise as potential prognostic markers. Notably, probiotics emerged as a promising approach for postgastrectomy recovery, displaying the capacity to alleviate inflammation, bolster immune responses, and maintain a healthy gut microbiome. Several strains, including Bifidobacterium, Lactobacillus, and Clostridium butyricum, exhibited favorable outcomes in postoperative patients, suggesting their potential roles in comprehensive patient care. In conclusion, understanding the intricate interplay between the gastrointestinal microbiome and gastric cancer treatment offers prospects for predicting responses and enhancing postoperative recovery. Probiotics, with their positive impact on inflammation and immunity, have emerged as potential adjuncts in patient care. Continued research is imperative to fully harness the potential of microbiome-based interventions in the management of gastric cancer.

• Journal of Microbiology and Biotechnology
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• v.34 no.4
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• pp.795-803
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• 2024

Microorganisms usually coexist as a multifaceted polymicrobial community in the natural habitats and at mucosal sites of the human body. Two opportunistic human pathogens, Pseudomonas aeruginosa and Staphylococcus aureus commonly coexist in the bacterial infections for hospitalized and/or immunocompromised patients. Here, we observed that autolysis of the P. aeruginosa quorum-sensing (QS) mutant (lasRmvfR) was suppressed by the presence of the S. aureus cells in vitro. The QS mutant still displayed killing against S. aureus cells, suggesting the link between the S. aureus-killing activity and the autolysis suppression. Independent screens of the P. aeruginosa transposon mutants defective in the S. aureus-killing and the S. aureus transposon mutants devoid of the autolysis suppression revealed the genetic link between both phenotypes, suggesting that the iron-dependent metabolism involving S. aureus exoproteins might be central to both phenotypes. The autolysis was suppressed by iron treatment as well. These results suggest that the interaction between P. aeruginosa and S. aureus might be governed by mechanisms that necessitate the QS circuitry as well as the metabolism involving the extracellular iron resources during the polymicrobial infections in the human airway.

• Journal of Microbiology and Biotechnology
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• v.34 no.6
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• pp.1348-1355
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• 2024

The eukaryotic translation initiation factor eIF5B is a bacterial IF2 ortholog that plays an important role in ribosome joining and stabilization of the initiator tRNA on the AUG start codon during the initiation of translation. We identified the fluorophenyl oxazole derivative 2,2-dibromo-1-(2-(4-fluorophenyl)benzo[d]oxazol-5-yl)ethanone quinolinol as an inhibitor of fungal protein synthesis using an in vitro translation assay in a fungal system. Mutants resistant to this compound were isolated in Saccharomyces cerevisiae and were demonstrated to contain amino acid substitutions in eIF5B that conferred the resistance. These results suggest that eIF5B is a target of potential antifungal compound and that mutation of eIF5B can confer resistance. Subsequent identification of 16 other mutants revealed that primary mutations clustered mainly on domain 2 of eIF5B and secondarily mainly on domain 4. Domain 2 has been implicated in the interaction with the small ribosomal subunit during initiation of translation. The tested translation inhibitor could act by weakening the functional contact between eIF5B and the ribosome complex. This data provides the basis for the development of a new family of antifungals.

• Interdisciplinary Bio Central
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• v.1 no.1
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• pp.3.1-3.6
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• 2009

Introduction: GTPases known as translation factor play a vital role as ribosomal subunit assembly chaperone. The bacterial Obg proteins ($Spo{\underline{0B}}$-associated ${\underline{G}}TP$-binding protein) belong to the subfamily of P-loop GTPase proteins and now it is considered as one of the new target for antibacterial drug. The majority of bacterial Obgs have been commonly found to be associated with ribosome, implying that these proteins may play a fundamental role in ribosome assembly or maturation. In addition, one of the experimental evidences suggested that Bacillus subtilis Obg (BsObg) protein binds to the L13 ribosomal protein (BsL13) which is known to be one of the early assembly proteins of the 50S ribosomal subunit in Escherichia coli. In order to investigate binding mode between the BsObg and the BsL13, protein-protein docking simulation was carried out after generating 3D structure of the BsL13 structure using homology modeling method. Materials and Methods: Homology model structure of BsL13 was generated using the EcL13 crystal structure as a template. Protein-protein docking of BsObg protein with ribosomal protein BsL13 was performed by DOT, a macro-molecular docking software, in order to predict a reasonable binding mode. The solvated energy minimization calculation of the docked conformation was carried out to refine the structure. Results and Discussion: The possible binding conformation of BsL13 along with activated Obg fold in BsObg was predicted by computational docking study. The final structure is obtained from the solvated energy minimization. From the analysis, three important H-bond interactions between the Obg fold and the L13 were detected: Obg:Tyr27-L13:Glu32, Obg:Asn76-L13:Glu139, and Obg:Ala136-L13:Glu142. The interaction between the BsObg and BsL13 structures were also analyzed by electrostatic potential calculations to examine the interface surfaces. From the results, the key residues for hydrogen bonding and hydrophobic interaction between the two proteins were predicted. Conclusion and Prospects: In this study, we have focused on the binding mode of the BsObg protein with the ribosomal BsL13 protein. The interaction between the activated Obg and target protein was investigated with protein-protein docking calculations. The binding pattern can be further used as a base for structure-based drug design to find a novel antibacterial drug.

• Microbiology and Biotechnology Letters
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• v.46 no.1
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• pp.77-84
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• 2018

An increase in $CO_2$ will affect plant pathogenic microorganisms, the resistance of host plants, and host-pathogen interactions. This study used Capsicum annuum and Xanthomonas euvesicatoria, a pathogenic bacterium of pepper, to investigate the interactions between hosts and pathogens in conditions of increased $CO_2$ concentrations. Our analysis of disease resistance genes under 800 ppm $CO_2$ using quantitative RT-PCR showed that the expression of CaLRR1, CaPIK1, and PR10 decreased, but that of negative regulator WRKY1 increased. Additionally, the disease progress and severity was higher at 800 ppm than 400 ppm $CO_2$. These results will aid in understanding the interaction between red pepper and X. euvesicatoria under increased $CO_2$ concentrations in the future.

• Korean Journal of Microbiology
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• v.48 no.2
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• pp.125-133
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• 2012

Anaerobic digestion is an alternative method to digest food wastes and to produce methane that can be used as a renewable energy source. We investigated bacterial and archaeal community structures in a three-stage methane production process using food wastes with concomitant wastewater treatment. The three-stage methane process is composed of semianaerobic hydrolysis/acidogenic, anaerobic acidogenic, and strictly anaerobic methane production steps in which food wastes are converted methane and carbon dioxide. The microbial diversity was determined by the nucleotide sequences of 16S rRNA gene library and quantitative real-time PCR. The major eubacterial population of the three-stage methane process was belonging to VFA-oxidizing bacteria. The archaeal community consisted mainly of two species of hydrogenotrophic methanogen (Methanoculleus). Family Picrophilaceae (Order Thermoplasmatales) was also observed as a minor population. The predominance of hydrogenotrophic methanogen suggests that the main degradation pathway of this process is different from the classical methane production systems that have the pathway based on acetogenesis. The domination of hydrogenotrophic methanogen (Methanoculleus) may be caused by mesophilic digestion, neutral pH, high concentration of ammonia, short HRT, and interaction with VFA-oxidizing bacteria (Tepidanaerobacter etc.).

• Asian-Australasian Journal of Animal Sciences
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• v.12 no.7
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• pp.1104-1110
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• 1999

We condicted two experiments to evaluate the interaction among fumaric acid (FA), protected acids (PA), or no additional acid (NO) and two different levels of acid buffering capacity (BC) in diets for 14-d-old weaned pigs. BC was varied substituting mono-calcium phosphate and calcium sulfate for dicalcium phosphate and calcium carbonate. In the high BC diet plus PA, FA was also added. In Exp. 1, 48 gilts were raised for 31 days on the six diets, evaluating growth performance and fecal digestibility. In Exp. 2, 42 gilts were raised. With each diet three subjects were sacrificed after 19 days and four after 38 days. In addition, six subjects were sacrificed at weaning. Growth and carcass performance, ileal digestibility, bacterial populations and pH in the gut were assessed. The piglet performance and stomach, ileal and cecal pH, and empty body composition were not affected by the diets. Empty body composition other than ash content was affected by piglet age (p<0.01). The BC did not influence digestibility. The dietary inclusion of PA improved fecal digestibility of protein (p<0.05) compared to the addition of FA and NO. Ileal digestibility slightly increased with both acid additions (p<0.10), the groups receiving PA showing the higher values. Piglets fed diets with low BC had lower Lactobacillus and E. coli counts in the ileum (p=0.07) and higher Lactobacillus in the colon (p=0.08). Acidified diets tended to reduce E. coli counts in the ileum (p=0.10) and increased Lactobacillus in the colon (p=0.09). The addition in the diet of PA increased Lactobacillus in the ileum compared to the sole addition of free fumaric acid (p=0.07). The addition of protected acids, combined with free fumaric acid in the case of high BC diets, increased protein digestibility and Lactobacillus counts and reduced E.coli counts. Only some changes in the concentration of bacterial population can be expected with a diet of low BC.

• Korean Journal of Environmental Biology
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• v.21 no.2
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• pp.194-202
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• 2003

To isolate alga-lytic bacteria, a number of samples were collected from Lake of Sukchon and Pal'tang reservoir where cyanobacteria blooming occurred. HY0210-AK1, which exhibited high alga-lytic activity, was isolated using Anabaena cylindrica lawn. The morphological and biochemical characteristics of the isolate HY0210-AK1 were very similar to that of the genus Rhizobium. Taxonomic identification including 16S rDNA base sequencing and phylogenetic analysis indicated that the isolate Hy0210-AK1 had a 99.1% homology in its 16S rDNA babe sequence with Sphingobium herbicidovorans. A. cylindrica NIES-19 was susceptible to the alga-lytic bacterial attack. The growth-inhibiting offset of the bacterium was not different on A. cylindrica NIES-19 when Sphingobium herbicidovorans HY0210-AK1 was in the lag, exponential, and stationary growth phase, although the alga-Iytic effect of S. herbici-dovorans HY0210-AK1 that in stationary growth phase was somewhat pronounced at the first time of inoculation. When S. herbicidovorans HY0210-AK1 was inoculated was inoculated with $1\times 10^{8}$ CFU $ml^{-1}$ together with A cylindrica NIES-19, the bacterium proliferated and caused algal lysis. A. cylindrica NIES-19 died when S. herbicidovorans HY0210 AKl was added to the algal culture but not when duly the filtrates from the bacterial culture was added. This suggests that extracellular substances are not responsible for inhibition of A. cylindrica NIES-19 and that algal Iysis largely attributed to direct interaction between S. herbicidovorans HY0210-AK1 and A. cylindrica NIES-19. The alga-lytic bacterium HY0210-AK1 caused cell lysis and death of three strain of Micro-cystis aeruginosa, but revealed no alga-Iytic effects on the Stephanodiscus hantzschii.